diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 2c53b698663..49debe090ff 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -216,11 +216,10 @@ jobs:
- name: Install Qt (Windows)
if: startsWith(matrix.os, 'windows')
- uses: jurplel/install-qt-action@v3
+ uses: jurplel/install-qt-action@v4
with:
- version: '5.15.2' # 5.12.7 is broken https://bugreports.qt.io/browse/QTBUG-81715, > 5.15.2 is not available on official archives (https://github.com/miurahr/aqtinstall/issues/636)
+ version: '6.7.2'
cache: 'false'
- aqtversion: '==3.1.*'
archives: 'qtsvg qtimageformats qtbase'
- name: Setup build tools (and system contrib on Linux and Mac)
@@ -234,7 +233,7 @@ jobs:
sudo add-apt-repository universe
sudo apt update
sudo apt-get -qq install -y build-essential cmake autoconf patch libtool git automake ninja-build xvfb ccache
- sudo apt-get -qq install -y qtbase5-dev libqt5svg5-dev libqt5opengl5-dev
+ sudo apt-get -qq install -y qt6-base-dev libqt6svg6-dev libqt6opengl6-dev libqt6openglwidgets6 libgl-dev
sudo apt-get -qq install -y libeigen3-dev libboost-random-dev libboost-regex-dev libboost-iostreams-dev \
libboost-date-time-dev libboost-math-dev libxerces-c-dev zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev
@@ -246,8 +245,8 @@ jobs:
fi
if [[ "${{ matrix.os }}" == windows-* ]]; then
- # Qt5_DIR set by Install Qt5 step
- echo "cmake_prefix=$Qt5_DIR/lib/cmake;$Qt5_DIR" >> $GITHUB_OUTPUT
+ # QT_ROOT_DIR set by Install Qt step
+ echo "cmake_prefix=$QT_ROOT_DIR/lib/cmake;$QT_ROOT_DIR" >> $GITHUB_OUTPUT
choco install ccache ninja cmake -y --no-progress
## GH CLI "SHOULD BE" installed. Sometimes I had to manually install nonetheless. Super weird.
# https://github.com/actions/runner-images/blob/main/images/win/scripts/Installers/Install-GitHub-CLI.ps1
@@ -255,9 +254,9 @@ jobs:
# Install eigen from choco
choco install eigen -y --no-progress
echo "eigen_choco=C:\ProgramData\chocolatey\lib\eigen\share\cmake" >> $GITHUB_OUTPUT
-
+ choco install doxygen.portable ghostscript graphviz -y --no-progress
+
if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
- choco install doxygen.portable ghostscript graphviz -y --no-progress
# uses a custom NSIS, which provides 8-k string support and has UltraModernUI integrated already
curl --no-progress-meter -L -o NSIS.tar.gz https://github.com/OpenMS/NSIS/raw/main/NSIS.tar.gz
## overwrite existing NSIS (which has only 1k-string support)
@@ -269,12 +268,9 @@ jobs:
## Needed for Qt. Install before to overwrite the default softlinks on the GH runners
brew install python3 --force --overwrite
brew install --quiet ccache autoconf automake libtool ninja && brew link --overwrite ccache
- brew install libsvm xerces-c boost eigen sqlite coinutils cbc cgl clp qt@5
- echo "cmake_prefix=$(brew --prefix qt@5)/lib/cmake;$(brew --prefix qt@5)" >> $GITHUB_OUTPUT
- echo "Qt5_DIR=$(brew --prefix qt@5)/lib/cmake/Qt5" >> $GITHUB_ENV
- if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
- brew install --quiet doxygen ghostscript graphviz
- fi
+ brew install libsvm xerces-c boost eigen sqlite coinutils cbc cgl clp qt
+ echo "cmake_prefix=$(brew --prefix qt)/lib/cmake;$(brew --prefix qt)" >> $GITHUB_OUTPUT
+ brew install --quiet doxygen ghostscript graphviz
fi
- name: Cache contrib (Windows)
@@ -458,8 +454,8 @@ jobs:
type: 'tar'
directory: ${{ github.workspace }}
path: OpenMS
- exclusions: 'bld/* ./source.tar.gz THIRDPARTY/* .git/*'
- filename: 'source.tar.gz'
+ exclusions: 'bld/* ./OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz THIRDPARTY/* .git/*'
+ filename: 'OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz'
@@ -468,9 +464,9 @@ jobs:
if: steps.set-vars.outputs.pkg_type != 'none' && startsWith(matrix.os, 'ubuntu')
uses: actions/upload-artifact@v4
with:
- name: source.tar.gz
+ name: OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz
path: |
- ${{ github.workspace }}/source.tar.gz
+ ${{ github.workspace }}/OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz
# Only upload docs when we are building the package, use the ubuntu build simply 'cause its fast
@@ -539,7 +535,7 @@ jobs:
- name: Download source archive as artifact
uses: actions/download-artifact@v4
with:
- name: source.tar.gz
+ name: OpenMS-${{ steps.create_changelog.outputs.version_number }}.tar.gz
- name: Download changelog as artifact
if: inputs.do_release
diff --git a/.github/workflows/pyopenms-wheels.yml b/.github/workflows/pyopenms-wheels.yml
index 0aa828a1ea8..244b4ab1de1 100644
--- a/.github/workflows/pyopenms-wheels.yml
+++ b/.github/workflows/pyopenms-wheels.yml
@@ -7,6 +7,11 @@ name: pyopenms-wheels-and-packages
# events but only for the master branch
on:
workflow_dispatch:
+ inputs:
+ upload-to-pypi:
+ type: boolean
+ description: actually upload the release package to pypi.org
+ default: false
push:
tags:
- 'Release*'
@@ -26,8 +31,12 @@ jobs:
with:
cmake-version: '3.25.x'
- - name: Reduce PATH
- run: echo "PATH=C:\hostedtoolcache\windows\Python\3.7.9\x64\Scripts;C:\hostedtoolcache\windows\Python\3.7.9\x64;C:\hostedtoolcache\windows\Ruby\2.5.8\x64\bin;C:\Program Files\Java\jdk8u265-b01\bin;C:\ProgramData\kind;C:\vcpkg;C:\cf-cli;C:\Program Files (x86)\NSIS;C:\windows\system32;C:\windows;C:\windows\System32\Wbem;C:\windows\System32\WindowsPowerShell\v1.0;C:\windows\System32\OpenSSH;C:\ProgramData\Chocolatey\bin;C:\Program Files\Docker;C:\Program Files\PowerShell\7;C:\Program Files\OpenSSL\bin;C:\Strawberry\c\bin;C:\Strawberry\perl\site\bin;C:\Strawberry\perl\bin;C:\Program Files\Git\cmd;C:\Program Files\Git\mingw64\bin;C:\Program Files\Git\usr\bin;C:\Program Files (x86)\Microsoft Visual Studio\2019\\Enterprise\Common7\IDE\CommonExtensions\Microsoft\CMake\CMake\bin" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+ - name: Reduce PATH # This fixes a bug described in https://github.com/facebook/watchman/commit/59bcfbf91d2a24ab580b8a78e384f133cc202383
+ run: echo "DISTUTILS_USE_SDK=1"
+
+ - name: Get number of CPU cores
+ uses: SimenB/github-actions-cpu-cores@v2
+ id: cpu-cores
- name: Install Qt
uses: jurplel/install-qt-action@v3
@@ -46,20 +55,26 @@ jobs:
curl -o $MINICONDA_FILENAME "https://repo.anaconda.com/miniconda/$MINICONDA_FILENAME"
./Miniconda3-latest-Windows-x86_64.exe //InstallationType=JustMe //RegisterPython=0 //S //D=$HOME/miniconda3
+
+ - name: Download contrib build from archive (Windows)
+ shell: bash
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ run: |
+ cd OpenMS/contrib
+ # Download the file using the URL fetched from GitHub
+ gh release download -R OpenMS/contrib --pattern 'contrib_build-Windows.tar.gz'
+ # Extract the archive
+ 7z x -so contrib_build-Windows.tar.gz | 7z x -si -ttar
+ rm contrib_build-Windows.tar.gz
+ ls -la
+
# https://github.com/marketplace/actions/visual-studio-shell
- name: Set up Visual Studio shell
uses: egor-tensin/vs-shell@v2
with:
arch: x64
- - name: Load contrib build
- run: |
- mkdir contribbld
- cd contribbld
- curl -o contribbld.tar.gz https://abibuilder.cs.uni-tuebingen.de/archive/openms/contrib/windows/x64/msvc-14.2/contrib_build.tar.gz
- tar -xzf contribbld.tar.gz
- rm contribbld.tar.gz
-
- name: Setup conda paths
shell: bash
run: |
@@ -74,7 +89,7 @@ jobs:
pushd bld
# TODO: set generator via variable, then we can share this step
cmake --version
- cmake -G "Visual Studio 17 2022" -A x64 -DOPENMS_CONTRIB_LIBS="$GITHUB_WORKSPACE/contribbld" -DCMAKE_PREFIX_PATH="$(echo $Qt5_Dir)/lib/cmake;${Qt5_Dir}" ../OpenMS
+ cmake -G "Visual Studio 17 2022" -A x64 -DOPENMS_CONTRIB_LIBS="$GITHUB_WORKSPACE/OpenMS/contrib" -DCMAKE_PREFIX_PATH="$(echo $Qt5_Dir)/lib/cmake;${Qt5_Dir}" ../OpenMS
# Note: multiple --targets only supported by CMake 3.15+
cmake --build . --config Release --target OpenMS
@@ -103,14 +118,14 @@ jobs:
pip install -U pip
pip install -U autowrap
pip install -U pytest
- pip install -U numpy
+ pip install 'numpy<=1.26.4'
pip install -U wheel
echo $CURRENT_PYTHON_EXECUTABLE
# build pyopenms distribution
cmake --version
- cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON -DPY_NUM_THREADS=4 .
+ cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON -DPY_NUM_THREADS=${{ steps.cpu-cores.outputs.count }} .
cmake --build . --config Release --target pyopenms
# copy to directory
@@ -139,6 +154,10 @@ jobs:
with:
path: OpenMS
+ - name: Get number of CPU cores
+ uses: SimenB/github-actions-cpu-cores@v2
+ id: cpu-cores
+
- name: Setup cmake
uses: jwlawson/actions-setup-cmake@v2
with:
@@ -187,7 +206,7 @@ jobs:
pushd bld
# Use -DCMAKE_FIND_DEBUG_MODE=ON for debug
cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_PREFIX_PATH="$(brew --prefix libomp);$(echo $Qt5_Dir)/lib/cmake;${Qt5_Dir}" -DCMAKE_OSX_DEPLOYMENT_TARGET=12 -DBOOST_USE_STATIC=OFF ../OpenMS
- make -j4 OpenMS
+ make -j${{ steps.cpu-cores.outputs.count }} OpenMS
mkdir pyopenms_whls
@@ -205,13 +224,13 @@ jobs:
pip install -U pip
pip install -U autowrap
pip install -U pytest
- pip install -U numpy
+ pip install 'numpy<=1.26.4'
pip install -U wheel
pip install -U pandas
# build pyopenms distribution (macOS)
- cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON -DPY_NUM_THREADS=4 .
- make -j4 pyopenms
+ cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON -DPY_NUM_THREADS=${{ steps.cpu-cores.outputs.count }} .
+ make -j${{ steps.cpu-cores.outputs.count }} pyopenms
# copy to directory
cp pyOpenMS/dist/*.whl pyopenms_whls/
@@ -249,6 +268,10 @@ jobs:
with:
path: OpenMS
+ - name: Get number of CPU cores
+ uses: SimenB/github-actions-cpu-cores@v2
+ id: cpu-cores
+
- name: Setup cmake
uses: jwlawson/actions-setup-cmake@v2
with:
@@ -297,7 +320,7 @@ jobs:
pushd bld
# Use -DCMAKE_FIND_DEBUG_MODE=ON for debug
cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_PREFIX_PATH="$(brew --prefix libomp);$(echo $Qt5_Dir)/lib/cmake;${Qt5_Dir}" -DCMAKE_OSX_DEPLOYMENT_TARGET=12 -DBOOST_USE_STATIC=OFF ../OpenMS
- make -j4 OpenMS
+ make -j${{ steps.cpu-cores.outputs.count }} OpenMS
mkdir pyopenms_whls
@@ -315,13 +338,13 @@ jobs:
pip install -U pip
pip install -U autowrap
pip install -U pytest
- pip install -U numpy
+ pip install 'numpy<=1.26.4'
pip install -U wheel
pip install -U pandas
# build pyopenms distribution (macOS)
- cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON -DPY_NUM_THREADS=4 .
- make -j4 pyopenms
+ cmake -DPYTHON_EXECUTABLE:FILEPATH=$CURRENT_PYTHON_EXECUTABLE -DPYOPENMS=ON -DPY_NUM_THREADS=${{ steps.cpu-cores.outputs.count }} .
+ make -j${{ steps.cpu-cores.outputs.count }} pyopenms
# copy to directory
cp pyOpenMS/dist/*.whl pyopenms_whls/
@@ -357,6 +380,10 @@ jobs:
with:
path: OpenMS
+ - name: Get number of CPU cores
+ uses: SimenB/github-actions-cpu-cores@v2
+ id: cpu-cores
+
- name: Setup cmake
uses: jwlawson/actions-setup-cmake@v2
with:
@@ -377,7 +404,7 @@ jobs:
mkdir openms-build
cd openms-build
cmake -DCMAKE_BUILD_TYPE="Release" -DOPENMS_CONTRIB_LIBS="/contrib-build/" -DCMAKE_PREFIX_PATH="/contrib-build/" $GITHUB_WORKSPACE/OpenMS
- make -j4 OpenMS
+ make -j${{ steps.cpu-cores.outputs.count }} OpenMS
# compile and configure OpenMS
for py in $(echo "${PYTHON_VERSIONS}" | jq -r '.[]'); do
@@ -393,13 +420,13 @@ jobs:
"$PYBIN/bin/pip" install -U Cython
"$PYBIN/bin/pip" install -U setuptools
"$PYBIN/bin/pip" install -U wheel
- "$PYBIN/bin/pip" install -U numpy
+ "$PYBIN/bin/pip" install 'numpy<=1.26.4'
"$PYBIN/bin/pip" install -U pytest
"$PYBIN/bin/pip" install -U autowrap
# configure (don't copy deps since we use auditwheel)
- cmake -DNO_DEPENDENCIES=ON -DOPENMS_CONTRIB_LIBS="/contrib-build/" -DCMAKE_PREFIX_PATH="/contrib-build/" -DPYOPENMS=On -DPython_ROOT_DIR=$PYBIN -DPython_FIND_STRATEGY="LOCATION" -DPY_NUM_THREADS=4 $GITHUB_WORKSPACE/OpenMS
- make -j4 pyopenms
+ cmake -DNO_DEPENDENCIES=ON -DOPENMS_CONTRIB_LIBS="/contrib-build/" -DCMAKE_PREFIX_PATH="/contrib-build/" -DPYOPENMS=On -DPython_ROOT_DIR=$PYBIN -DPython_FIND_STRATEGY="LOCATION" -DPY_NUM_THREADS=${{ steps.cpu-cores.outputs.count }} $GITHUB_WORKSPACE/OpenMS
+ make -j${{ steps.cpu-cores.outputs.count }} pyopenms
# ensure auditwheel can find the libraries
export LD_LIBRARY_PATH=$LD_OLD_LIBRARY_PATH:`pwd`/lib
@@ -551,18 +578,20 @@ jobs:
ls -la wheels/
- name: Publish package to nightly PyPI
- if: "contains(github.ref, 'develop') || contains(github.ref, 'nightly')"
+ # Upload the wheels to our pypi server for develop, nightly and release branches (unless it's explictly stated to upload it to pypi.org)
+ if: contains(github.ref, 'develop') || contains(github.ref, 'nightly') || (contains(github.ref, 'Release') && inputs.upload-to-pypi == 'false')
uses: pypa/gh-action-pypi-publish@release/v1
with:
- repository_url: https://pypi.cs.uni-tuebingen.de/
+ repository-url: https://pypi.cs.uni-tuebingen.de/
user: openms
password: ${{ secrets.abiservices_pypi_pw }}
packages-dir: ${{ github.workspace }}/wheels
- name: Publish package to PyPI
- if: "contains(github.ref, 'Release')"
+ if: contains(github.ref, 'Release') && inputs.upload-to-pypi
uses: pypa/gh-action-pypi-publish@release/v1
with:
user: __token__
+ repository-url: https://test.pypi.org/
password: ${{ secrets.pypi_api_token_release }}
packages-dir: ${{ github.workspace }}/wheels
diff --git a/.github/workflows/test_pyopenms.yml b/.github/workflows/test_pyopenms.yml
index 9fd76237428..bd19260cc8f 100644
--- a/.github/workflows/test_pyopenms.yml
+++ b/.github/workflows/test_pyopenms.yml
@@ -1,9 +1,9 @@
-name: Test nightly pyOpenMS on different platforms
+name: Test pyOpenMS on different platforms
on:
workflow_dispatch: # Trigger manually
- workflow_run:
- workflows: [ pyopenms-wheels ]
+ workflow_run: # Trigger on pyopenms-wheels
+ workflows: ["pyopenms-wheels-and-packages"]
types:
- completed
@@ -15,11 +15,11 @@ jobs:
matrix: ${{ steps.python_versions.outputs.content }}
steps:
- name: Checkout repository
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
- name: Read python_versions.json
id: python_versions
- uses: juliangruber/read-file-action@v1
+ uses: juliangruber/read-file-action@v1.1.7
with:
path: .github/workflows/python_versions.json
@@ -35,7 +35,7 @@ jobs:
python-version: ${{ fromJson(needs.read-python-versions.outputs.matrix) }}
steps:
- name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v2
+ uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
diff --git a/.github/workflows/update_nightly.yml b/.github/workflows/update_nightly.yml
index 40463609db9..4ea9446a899 100644
--- a/.github/workflows/update_nightly.yml
+++ b/.github/workflows/update_nightly.yml
@@ -69,3 +69,10 @@ jobs:
gh workflow run openms-ci-full --ref develop
env:
GH_TOKEN: ${{ github.token }}
+
+ - name: Build wheels
+ if: steps.compare_branches.outputs.behind == 'true' || inputs.force
+ run: |
+ gh workflow run pyopenms-wheels-and-packages --ref nightly
+ env:
+ GH_TOKEN: ${{ github.token }}
diff --git a/CHANGELOG b/CHANGELOG
index 9fdf4a3a7d2..9647706d07e 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -87,6 +87,8 @@ Cleanup/Removal:
- PeakPickerCWT_test
- PeakShape_test
+- Deprecated (and likely removed in the next release)
+ - XTandemAdapter
------------------------------------------------------------------------------------------
---- OpenMS 3.1 (released 10/2023) ----
------------------------------------------------------------------------------------------
diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
index ca645b28a67..5108d5974eb 100644
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
@@ -122,7 +122,7 @@ if(ENABLE_DOCS)
set(DOXYGEN_MIN_REQUIRED "1.8.13")
if (DOXYGEN_VERSION VERSION_LESS DOXYGEN_MIN_REQUIRED )
- message(STATUS "Warning: Doxygen ( vers. installed = ${DOXYGEN_VERSION} < ${DOXYGEN_MIN_REQUIRED}) does not correctly process \\includedoc commands in developer's installation instructions. This will make them incomplete. Upgrade Doxygen to fix.")
+ message(STATUS "Warning: Doxygen ( vers. installed = ${DOXYGEN_VERSION} < ${DOXYGEN_MIN_REQUIRED}) does not correctly process \\include commands in developer's installation instructions. This will make them incomplete. Upgrade Doxygen to fix.")
endif()
## if not found, use empty string to avoid `warning: the dot tool could not be found as 'DOXYGEN_DOT_EXECUTABLE-NOTFOUND/dot.exe'` in doxygen-error.log
diff --git a/doc/doxygen/install/install-linux.doxygen b/doc/doxygen/install/install-linux.doxygen
index 61817b4fa62..a9be676af9f 100644
--- a/doc/doxygen/install/install-linux.doxygen
+++ b/doc/doxygen/install/install-linux.doxygen
@@ -233,7 +233,7 @@
HAS_XSERVER=Off, especially as you may not have compiled Qt with
OpenGL and you may not have an X server.
- \includedoc "../doxygen/install/common-cmake-parameters.doxygen"
+ \include "../doxygen/install/common-cmake-parameters.doxygen"
A full list of the CMake variables is shown when you execute
diff --git a/doc/doxygen/install/install-macs.doxygen b/doc/doxygen/install/install-macs.doxygen
index 8a44da1c34f..e8dd4d6d4d2 100644
--- a/doc/doxygen/install/install-macs.doxygen
+++ b/doc/doxygen/install/install-macs.doxygen
@@ -191,7 +191,7 @@
- \includedoc "../doxygen/install/common-cmake-parameters.doxygen"
+ \include "../doxygen/install/common-cmake-parameters.doxygen"
After CMake was executed, you can list the make targets by calling:
diff --git a/doc/doxygen/install/install-win.doxygen b/doc/doxygen/install/install-win.doxygen
index aef26879918..5546146b285 100644
--- a/doc/doxygen/install/install-win.doxygen
+++ b/doc/doxygen/install/install-win.doxygen
@@ -259,7 +259,7 @@
- \includedoc "../doxygen/install/common-cmake-parameters.doxygen"
+ \include "../doxygen/install/common-cmake-parameters.doxygen"
Now there should be a OpenMS_host.sln file in your build directory, which you can open using Visual Studio.
diff --git a/share/OpenMS/CV/psi-ms.obo b/share/OpenMS/CV/psi-ms.obo
index 81e59bd87fb..a31142a0fc4 100644
--- a/share/OpenMS/CV/psi-ms.obo
+++ b/share/OpenMS/CV/psi-ms.obo
@@ -1,13 +1,14 @@
format-version: 1.2
-data-version: 4.1.56
-date: 25:06:2021 00:00
-saved-by: Chris Bielow
+data-version: 4.1.155
+date: 03:06:2024 13:22
+saved-by: Eric Deutsch
auto-generated-by: OBO-Edit 2.3.1
-import: http://ontologies.berkeleybop.org/pato.obo
-import: http://ontologies.berkeleybop.org/uo.obo
+import: http://purl.obolibrary.org/obo/pato.obo
+import: http://purl.obolibrary.org/obo/stato.owl
default-namespace: MS
namespace-id-rule: * MS:$sequence(7,0,9999999)$
namespace-id-rule: * PEFF:$sequence(7,0,9999999)$
+remark: coverage of namespace-id: MS:$sequence(7,4000000,4999999)$: Mass spectrometry quality control metrics
remark: namespace: MS
remark: namespace: PEFF
remark: coverage: Mass spectrometer output files and spectra interpretation
@@ -20,10 +21,15 @@ remark: creator: Fredrik Levander immun.lth.se>
remark: creator: Pierre-Alain Binz chuv.ch>
remark: creator: Gerhard Mayer rub.de>
remark: creator: Joshua Klein bu.edu>
+remark: creator: Chris Bielow fu-berlin.de>
+remark: creator: Wout Bittremieux health.ucsd.edu>
+remark: creator: Nils Hoffmann < nils.hoffmann <-at-> cebitec.uni-bielefeld.de>
+remark: creator: Julian Uszkoreit ruhr-uni-bochum.de>
+remark: creator: Mathias Walzer ebi.ac.uk>
remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group
remark: When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page
remark: For any queries contact psidev-ms-vocab@lists.sourceforge.net
-remark: URL: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
+remark: URL: http://purl.obolibrary.org/obo/ms/psi-ms.obo
remark: This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.
remark: To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.
ontology: ms
@@ -39,6 +45,7 @@ name: has_units
[Typedef]
id: part_of
name: part_of
+xref: BFO:0000050
is_transitive: true
[Typedef]
@@ -49,6 +56,148 @@ name: has_order
id: has_domain
name: has_domain
+[Typedef]
+id: has_value_type
+name: has value type
+def: "'Entity A' has value type 'Entity B', such as xsd:float." []
+
+[Typedef]
+id: has_structured_representation_in_format
+name: has structured representation in format
+def: "The term is encoded in the structure of the named file format rather than as an explicit parameter, and should not be used as one in that format." []
+
+[Typedef]
+id: has_metric_category
+name: has_metric_category
+
+[Typedef]
+id: has_value_concept
+name: has_value_concept
+
+[Typedef]
+id: has_column
+name: has_column
+
+[Typedef]
+id: has_optional_column
+name: has_optional_column
+
+[Term]
+id: NCIT:C25330
+name: Duration
+def: "The period of time during which something continues." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
+is_a: NCIT:C21514 ! Temporal Qualifier
+
+[Term]
+id: NCIT:C45781
+name: Density
+def: "The amount of something per unit size." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
+is_a: NCIT:C25447 ! Characteristic
+
+[Term]
+id: NCIT:C68811
+name: Cover
+def: "Span a region or interval of distance, space or time." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
+is_a: NCIT:C25404 ! Action
+
+[Term]
+id: NCIT:C79083
+name: Outlier
+def: "An observation in a data set that is numerically distant from the rest of the data." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
+is_a: NCIT:C20181 ! Conceptual Entity
+
+[Term]
+id: NCIT:C21514
+name: Temporal Qualifier
+def: "Terms used to indicate units of time or other terms associated with time." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
+synonym: "Temporal Qualifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
+synonym: "Temporal Qualifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NICHD"}
+is_a: NCIT:C41009 ! Qualifier
+
+[Term]
+id: NCIT:C41009
+name: Qualifier
+def: "A term that helps define and render a concept unique." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
+synonym: "Modifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
+synonym: "Qualifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
+is_a: NCIT:C20189 ! Property or Attribute
+
+[Term]
+id: NCIT:C25447
+name: Characteristic
+def: "The distinguishing qualities or prominent aspect of a person, object, action, process, or substance." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
+synonym: "Characteristic" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
+synonym: "Characteristic" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"}
+synonym: "Characteristic" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NICHD"}
+synonym: "Characteristics" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
+synonym: "Feature" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
+synonym: "Features" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"}
+is_a: NCIT:C20189 ! Property or Attribute
+
+[Term]
+id: NCIT:C20189
+name: Property or Attribute
+def: "A distinguishing quality or prominent aspect of a person, object, action, process, or substance." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
+synonym: "Property or Attribute" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
+synonym: "Property or Attribute" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NICHD"}
+
+[Term]
+id: NCIT:C25404
+name: Action
+def: "A thing done." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
+subset: NCIT:C105763
+synonym: "Action" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
+synonym: "Action" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"}
+synonym: "Generic Action" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
+is_a: NCIT:C43431 ! Activity
+
+[Term]
+id: NCIT:C43431
+name: Activity
+def: "An active process; excludes processes and mechanisms which fulfill biological functions." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
+synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"}
+synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
+synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="BRIDG 3.0.3"}
+synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="BRIDG 5.3"}
+synonym: "General activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"}
+
+[Term]
+id: NCIT:C20181
+name: Conceptual Entity
+def: "An organizational header for concepts representing mostly abstract entities." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
+synonym: "Conceptual Entity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
+
+[Term]
+id: NCIT:C16847
+name: Technique
+def: "A practiced and regimented skill or series of actions." [] {http://purl.obolibrary.org/obo/NCIT_C16847="NCI"}
+is_a: NCIT:C43431 ! Activity
+
+[Term]
+id: NCIT:C19044
+name: Statistical Technique
+def: "A method of analyzing or representing statistical data; a procedure for calculating a statistic." [] {http://purl.obolibrary.org/obo/NCIT_C19044="NCI"}
+is_a: NCIT:C16847 ! Technique
+
+[Term]
+id: NCIT:C60694
+name: Principal Component
+def: "One of the axes representing the projection of varience resulting from principal component analysis." [] {http://purl.obolibrary.org/obo/NCIT_C60694="NCI"}
+is_a: NCIT:C19044 ! Statistical Technique
+
+[Term]
+id: NCIT:C25337
+name: Number
+def: "A numeral or string of numerals expressing value, quantity, or identification." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
+is_a: NCIT:C20189 ! Property or Attribute
+
+[Term]
+id: NCIT:C150827
+name: Number of Occurrences
+def: "The number of times something happened." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
+synonym: "Number of Occurrences" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"}
+is_a: NCIT:C25337 ! Number
+
[Term]
id: MS:0000000
name: Proteomics Standards Initiative Mass Spectrometry Vocabularies
@@ -58,15 +207,15 @@ def: "Proteomics Standards Initiative Mass Spectrometry Vocabularies." [PSI:MS]
id: MS:1000001
name: sample number
def: "A reference number relevant to the sample under study." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000002
name: sample name
def: "A reference string relevant to the sample under study." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000003
@@ -78,25 +227,25 @@ is_a: MS:1000548 ! sample attribute
id: MS:1000004
name: sample mass
def: "Total mass of sample used." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute
relationship: has_units UO:0000021 ! gram
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000005
name: sample volume
def: "Total volume of solution used." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute
relationship: has_units UO:0000098 ! milliliter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000006
name: sample concentration
def: "Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute
relationship: has_units UO:0000175 ! gram per liter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000007
@@ -128,8 +277,8 @@ is_obsolete: true
id: MS:1000011
name: mass resolution
def: "Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000012
@@ -148,28 +297,28 @@ is_obsolete: true
id: MS:1000014
name: accuracy
def: "Accuracy is the degree of conformity of a measured mass to its actual value." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000480 ! mass analyzer attribute
relationship: has_units MS:1000040 ! m/z
relationship: has_units UO:0000169 ! parts per million
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000015
name: scan rate
def: "Rate in Th/sec for scanning analyzers." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units MS:1000807 ! Th/s
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000016
name: scan start time
def: "The time that an analyzer started a scan, relative to the start of the MS run." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
is_a: MS:1002345 ! PSM-level attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000017
@@ -208,25 +357,25 @@ is_a: MS:1000480 ! mass analyzer attribute
id: MS:1000022
name: TOF Total Path Length
def: "The length of the field free drift space in a time of flight mass spectrometer." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000480 ! mass analyzer attribute
relationship: has_units UO:0000008 ! meter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000023
name: isolation width
def: "OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion." [PSI:MS]
comment: This former purgatory term was made obsolete.
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: has_units MS:1000040 ! m/z
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000024
name: final MS exponent
def: "Final MS level achieved when performing PFF with the ion trap (e.g. MS E10)." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1000480 ! mass analyzer attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1000025
@@ -234,9 +383,9 @@ name: magnetic field strength
def: "A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity." [PSI:MS]
synonym: "B" EXACT []
synonym: "Magnetic Field" RELATED []
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000480 ! mass analyzer attribute
relationship: has_units UO:0000228 ! tesla
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000026
@@ -254,17 +403,17 @@ relationship: part_of MS:1000453 ! detector
id: MS:1000028
name: detector resolution
def: "The resolving power of the detector to detect the smallest difference between two ions so that the valley between them is a specified fraction of the peak height." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000481 ! detector attribute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000029
name: sampling frequency
def: "The rate of signal sampling (measurement) with respect to time." [PSI:MS]
synonym: "ADC Sampling Frequency" NARROW []
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000481 ! detector attribute
relationship: has_units UO:0000106 ! hertz
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000030
@@ -283,13 +432,13 @@ relationship: part_of MS:1000463 ! instrument
id: MS:1000032
name: customization
def: "Free text description of a single customization made to the instrument; for several modifications, use several entries." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000496 ! instrument attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000033
name: deisotoping
-def: "The removal of isotope peaks to represent the fragment ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution." [PSI:MS]
+def: "The removal of isotope peaks to represent the ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution." [PSI:MS]
is_a: MS:1000543 ! data processing action
[Term]
@@ -346,15 +495,14 @@ id: MS:1000041
name: charge state
def: "Number of net charges, positive or negative, on an ion." [PSI:MS]
synonym: "z" EXACT []
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
is_a: MS:1000507 ! ion property
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1000042
name: peak intensity
def: "Intensity of ions as measured by the height or area of a peak in a mass spectrum." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
relationship: has_units MS:1000131 ! number of detector counts
relationship: has_units MS:1000132 ! percent of base peak
@@ -362,6 +510,7 @@ relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100
relationship: has_units UO:0000269 ! absorbance unit
relationship: part_of MS:1000231 ! peak
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000043
@@ -380,9 +529,9 @@ relationship: part_of MS:1000456 ! precursor activation
id: MS:1000045
name: collision energy
def: "Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
relationship: has_units UO:0000266 ! electronvolt
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000046
@@ -432,8 +581,8 @@ is_a: MS:1000003 ! sample state
id: MS:1000053
name: sample batch
def: "Sample batch lot identifier." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000054
@@ -953,8 +1102,8 @@ is_a: MS:1000043 ! intensity unit
id: MS:1000132
name: percent of base peak
def: "The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000043 ! intensity unit
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000133
@@ -997,9 +1146,9 @@ is_obsolete: true
id: MS:1000138
name: normalized collision energy
def: "Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
relationship: has_units UO:0000187 ! percent
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000139
@@ -1405,7 +1554,8 @@ def: "The operation of a mass spectrometer in which the intensities of several s
synonym: "MIM" RELATED []
synonym: "Multiple Ion Monitoring" EXACT []
synonym: "SIM" EXACT []
-is_a: MS:1000596 ! measurement method
+is_a: MS:1003215 ! data-independent acquisition
+is_a: MS:1003213 ! mass spectrometry acquisition method
[Term]
id: MS:1000206
@@ -1414,35 +1564,36 @@ def: "Data acquired from specific product ions corresponding to m/z selected pre
synonym: "MRM" RELATED []
synonym: "Multiple Reaction Monitoring" RELATED []
synonym: "SRM" EXACT []
-is_a: MS:1000596 ! measurement method
+is_a: MS:1003215 ! data-independent acquisition
+is_a: MS:1003213 ! mass spectrometry acquisition method
[Term]
id: MS:1000207
name: accurate mass
def: "OBSOLETE An experimentally determined mass that is can be to determine a unique elemental formula. For ions less than 200 u, a measurement with 5 ppm accuracy is sufficient to determine the elemental composition." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
comment: This child of the former purgatory term ion attribute was made obsolete.
relationship: has_units UO:0000002 ! mass unit
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000208
name: average mass
def: "OBSOLETE The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
comment: This child of the former purgatory term ion attribute was made obsolete.
relationship: has_units UO:0000002 ! mass unit
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000209
name: appearance energy
def: "OBSOLETE The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended." [PSI:MS]
synonym: "AE" EXACT []
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
comment: This child of the former purgatory term ion attribute was made obsolete.
relationship: has_units UO:0000266 ! electronvolt
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000210
@@ -1455,8 +1606,8 @@ is_a: MS:1000231 ! peak
id: MS:1000211
name: OBSOLETE charge number
def: "OBSOLETE The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_obsolete: true
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1000212
@@ -1471,8 +1622,8 @@ name: electron affinity
def: "OBSOLETE The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy." [PSI:MS]
comment: This child of the former purgatory term ion attribute was made obsolete.
synonym: "EA" EXACT []
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000214
@@ -1485,10 +1636,10 @@ is_obsolete: true
id: MS:1000215
name: exact mass
def: "OBSOLETE The calculated mass of an ion or molecule containing a single isotope of each atom." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
comment: This child of the former purgatory term ion attribute was made obsolete.
relationship: has_units UO:0000002 ! mass unit
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000216
@@ -1509,8 +1660,8 @@ id: MS:1000218
name: ionization efficiency
def: "OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS]
comment: This term was made obsolete because it was replaced by ionization efficiency (MS:1000392).
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000219
@@ -1518,9 +1669,9 @@ name: ionization energy
def: "OBSOLETE The minimum energy required to remove an electron from an atom or molecule to produce a positive ion." [PSI:MS]
synonym: "IE" EXACT []
comment: This child of the former purgatory term ion attribute was made obsolete.
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: has_units UO:0000266 ! electronvolt
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000220
@@ -1540,35 +1691,35 @@ is_a: MS:1000597 ! ion optics type
id: MS:1000222
name: mass defect
def: "OBSOLETE The difference between the monoisotopic and nominal mass of a molecule or atom." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
comment: This child of the former purgatory term ion attribute was made obsolete.
relationship: has_units UO:0000002 ! mass unit
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000223
name: mass number
def: "OBSOLETE The sum of the protons and neutrons in an atom, molecule or ion." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
comment: This child of the former purgatory term ion attribute was made obsolete.
is_obsolete: true
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1000224
name: molecular mass
def: "Mass of a molecule measured in unified atomic mass units (u or Da)." [https://en.wikipedia.org/wiki/Molecular_mass]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000861 ! molecular entity property
relationship: has_units UO:0000002 ! mass unit
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000225
name: monoisotopic mass
def: "OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
comment: This child of the former purgatory term ion attribute was made obsolete.
relationship: has_units UO:0000002 ! mass unit
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000226
@@ -1596,10 +1747,10 @@ is_obsolete: true
id: MS:1000229
name: nominal mass
def: "OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer value." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
comment: This child of the former purgatory term ion attribute was made obsolete.
relationship: has_units UO:0000002 ! mass unit
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000230
@@ -1627,16 +1778,16 @@ name: proton affinity
def: "OBSOLETE The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states." [PSI:MS]
synonym: "PA" EXACT [PSI:MS]
comment: This child of the former purgatory term ion attribute was made obsolete.
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000234
name: mass resolving power
def: "OBSOLETE In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported." [PSI:MS]
comment: This term was made obsolete because it was replaced by mass resolving power (MS:1000800).
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000235
@@ -1649,8 +1800,8 @@ is_a: MS:1000810 ! ion current chromatogram
id: MS:1000236
name: transmission
def: "The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000496 ! instrument attribute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000237
@@ -1842,7 +1993,7 @@ id: MS:1000262
name: infrared multiphoton dissociation
def: "Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons." [PSI:MS]
synonym: "IRMPD" EXACT []
-is_a: MS:1000044 ! dissociation method
+is_a: MS:1000435 ! photodissociation
[Term]
id: MS:1000263
@@ -2015,8 +2166,8 @@ id: MS:1000285
name: total ion current
def: "The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum." [PSI:MS]
synonym: "TIC" EXACT []
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1003058 ! spectrum property
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000286
@@ -2147,9 +2298,9 @@ is_obsolete: true
id: MS:1000304
name: accelerating voltage
def: "The electrical potential used to impart kinetic energy to ions in a mass spectrometer." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000487 ! ion optics attribute
relationship: has_units UO:0000218 ! volt
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000305
@@ -2175,9 +2326,9 @@ is_a: MS:1000597 ! ion optics type
id: MS:1000308
name: electric field strength
def: "The magnitude of the force per unit charge at a given point in space." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000487 ! ion optics attribute
relationship: has_units UO:0000268 ! volt per meter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000309
@@ -2367,9 +2518,9 @@ is_obsolete: true
[Term]
id: MS:1000336
name: neutral loss
-def: "The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID: 21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type)." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+def: "The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID:21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type)." [PSI:MS]
is_a: MS:1001055 ! modification parameters
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000337
@@ -2746,8 +2897,8 @@ is_obsolete: true
id: MS:1000392
name: ionization efficiency
def: "The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000393
@@ -2755,6 +2906,12 @@ name: laser desorption ionization
def: "The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material." [PSI:MS]
is_a: MS:1000247 ! desorption ionization
+[Term]
+id: MS:1000394
+name: no sequence database
+def: "No reference sequence database was used in the search process to determine the identified peptide sequence, for example as with de novo sequencing." [PSI:PI]
+is_a: MS:1001347 ! database file format
+
[Term]
id: MS:1000395
name: liquid secondary ionization
@@ -2866,8 +3023,8 @@ is_obsolete: true
id: MS:1000412
name: buffer gas
def: "An inert gas used for collisional deactivation of internally excited ions." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000413
@@ -2915,8 +3072,8 @@ is_obsolete: true
id: MS:1000419
name: collision gas
def: "An inert gas used for collisional excitation. The term target gas is not recommended." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000420
@@ -3359,9 +3516,9 @@ is_a: MS:1000057 ! electrospray inlet
id: MS:1000486
name: source potential
def: "Potential difference at the MS source in volts." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000218 ! volt
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000487
@@ -3450,28 +3607,28 @@ id: MS:1000500
name: scan window upper limit
def: "The lower m/z bound of a mass spectrometer scan window." [PSI:MS]
synonym: "mzRangeStop" RELATED []
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000549 ! selection window attribute
relationship: has_units MS:1000040 ! m/z
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000501
name: scan window lower limit
def: "The upper m/z bound of a mass spectrometer scan window." [PSI:MS]
synonym: "mzRangeStart" RELATED []
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000549 ! selection window attribute
relationship: has_units MS:1000040 ! m/z
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000502
name: dwell time
def: "The time spent gathering data across a peak." [PSI:MS]
synonym: "Scan Duration" RELATED []
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000503
@@ -3484,21 +3641,21 @@ relationship: part_of MS:1000441 ! scan
id: MS:1000504
name: base peak m/z
def: "M/z value of the signal of highest intensity in the mass spectrum." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1003058 ! spectrum property
relationship: has_units MS:1000040 ! m/z
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000505
name: base peak intensity
def: "The intensity of the greatest peak in the mass spectrum." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1003058 ! spectrum property
relationship: has_units MS:1000131 ! number of detector counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100
relationship: has_units UO:0000269 ! absorbance unit
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000506
@@ -3524,9 +3681,9 @@ is_obsolete: true
id: MS:1000509
name: activation energy
def: "Activation Energy." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
relationship: has_units UO:0000266 ! electronvolt
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000510
@@ -3538,15 +3695,15 @@ relationship: part_of MS:1000456 ! precursor activation
id: MS:1000511
name: ms level
def: "Stage number achieved in a multi stage mass spectrometry acquisition." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1000499 ! spectrum attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1000512
name: filter string
def: "A string unique to Thermo instrument describing instrument settings for the scan." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000513
@@ -3652,26 +3809,26 @@ is_a: MS:1000560 ! mass spectrometer file format
id: MS:1000527
name: highest observed m/z
def: "Highest m/z value observed in the m/z array." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000808 ! chromatogram attribute
is_a: MS:1003058 ! spectrum property
relationship: has_units MS:1000040 ! m/z
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000528
name: lowest observed m/z
def: "Lowest m/z value observed in the m/z array." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000808 ! chromatogram attribute
is_a: MS:1003058 ! spectrum property
relationship: has_units MS:1000040 ! m/z
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000529
name: instrument serial number
def: "Serial Number of the instrument." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000496 ! instrument attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000530
@@ -3934,15 +4091,15 @@ is_a: MS:1000560 ! mass spectrometer file format
id: MS:1000568
name: MD5
def: "MD5 (Message-Digest algorithm 5) is a (now deprecated) cryptographic hash function with a 128-bit hash value used to check the integrity of files." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000561 ! data file checksum type
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000569
name: SHA-1
def: "SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA). It is also used to verify file integrity. Since 2011 it has been deprecated by the NIST as a U. S. government standard." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000561 ! data file checksum type
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000570
@@ -4061,36 +4218,36 @@ relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrom
id: MS:1000586
name: contact name
def: "Name of the contact person or organization." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000585 ! contact attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000587
name: contact address
def: "Postal address of the contact person or organization." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000585 ! contact attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000588
name: contact URL
def: "Uniform Resource Locator related to the contact person or organization." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000585 ! contact attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000589
name: contact email
def: "Email address of the contact person or organization." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000585 ! contact attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000590
name: contact affiliation
def: "Home institution of the contact person." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000585 ! contact attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000591
@@ -4142,7 +4299,7 @@ is_a: MS:1000462 ! ion optics
[Term]
id: MS:1000598
name: electron transfer dissociation
-def: "A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons to them." [PSI:MS]
+def: "A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons from radical-anions." [DOI:10.1073/pnas.0402700101, PMID:15210983, PSI:MS]
synonym: "ETD" EXACT []
is_a: MS:1000044 ! dissociation method
@@ -4258,8 +4415,8 @@ is_a: MS:1001457 ! data processing software
id: MS:1000616
name: preset scan configuration
def: "A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo \"scan event\", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000617
@@ -4274,19 +4431,19 @@ relationship: has_units UO:0000018 ! nanometer
id: MS:1000618
name: highest observed wavelength
def: "Highest wavelength observed in an EMR spectrum." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1003058 ! spectrum property
is_a: MS:1000808 ! chromatogram attribute
relationship: has_units UO:0000018 ! nanometer
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000619
name: lowest observed wavelength
def: "Lowest wavelength observed in an EMR spectrum." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1003058 ! spectrum property
is_a: MS:1000808 ! chromatogram attribute
relationship: has_units UO:0000018 ! nanometer
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000620
@@ -4352,13 +4509,13 @@ is_a: MS:1000810 ! ion current chromatogram
id: MS:1000629
name: low intensity threshold
def: "Threshold below which some action is taken." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter
relationship: has_units MS:1000131 ! number of detector counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100
relationship: has_units UO:0000269 ! absorbance unit
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000630
@@ -4370,13 +4527,13 @@ relationship: part_of MS:1001458 ! spectrum generation information
id: MS:1000631
name: high intensity threshold
def: "Threshold above which some action is taken." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter
relationship: has_units MS:1000131 ! number of detector counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100
relationship: has_units UO:0000269 ! absorbance unit
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000632
@@ -4388,8 +4545,8 @@ is_a: MS:1000126 ! Waters instrument model
id: MS:1000633
name: possible charge state
def: "A possible charge state of the ion in a situation where the charge of an ion is known to be one of several possible values rather than a completely unknown value or determined to be a specific charge with reasonable certainty." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1000634
@@ -5134,9 +5291,9 @@ is_a: MS:1000494 ! Thermo Scientific instrument model
id: MS:1000744
name: selected ion m/z
def: "Mass-to-charge ratio of an selected ion." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
relationship: has_units MS:1000040 ! m/z
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000745
@@ -5154,8 +5311,8 @@ is_a: MS:1001486 ! data filtering
id: MS:1000747
name: completion time
def: "The time that a data processing action was finished." [PSI:MS]
-xref: value-type:xsd\:dateTime "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter
+relationship: has_value_type xsd:dateTime ! The allowed value-type for this CV term
[Term]
id: MS:1000748
@@ -5414,32 +5571,32 @@ xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000522 "64-bit integer"
xref: binary-data-type:MS\:1000523 "64-bit float"
xref: binary-data-type:MS\:1001479 "null-terminated ASCII string"
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000513 ! binary data array
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000787
name: inclusive low intensity threshold
def: "Threshold at or below which some action is taken." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter
relationship: has_units MS:1000131 ! number of detector counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100
relationship: has_units UO:0000269 ! absorbance unit
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000788
name: inclusive high intensity threshold
def: "Threshold at or above which some action is taken." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter
relationship: has_units MS:1000131 ! number of detector counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100
relationship: has_units UO:0000269 ! absorbance unit
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000789
@@ -5472,20 +5629,20 @@ id: MS:1000793
name: isolation window upper limit
def: "OBSOLETE The highest m/z being isolated in an isolation window." [PSI:MS]
comment: This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829.
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000792 ! isolation window attribute
relationship: has_units MS:1000040 ! m/z
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000794
name: isolation window lower limit
def: "OBSOLETE The lowest m/z being isolated in an isolation window." [PSI:MS]
comment: This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829.
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000792 ! isolation window attribute
relationship: has_units MS:1000040 ! m/z
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000795
@@ -5498,41 +5655,41 @@ id: MS:1000796
name: spectrum title
def: "Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file." [PSI:MS]
comment: This is the preferred storage place for the spectrum TITLE from an MGF peak list.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1000499 ! spectrum attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000797
name: peak list scans
def: "A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS]
comment: This is the preferred storage place for the spectrum SCANS attribute from an MGF peak list.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1003058 ! spectrum property
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000798
name: peak list raw scans
def: "A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS]
comment: This is the preferred storage place for the spectrum RAWSCANS attribute from an MGF peak list.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
is_a: MS:1003058 ! spectrum property
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000799
name: custom unreleased software tool
def: "A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000531 ! software
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000800
name: mass resolving power
def: "The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000801
@@ -5552,9 +5709,9 @@ is_a: MS:1000035 ! peak picking
id: MS:1000803
name: analyzer scan offset
def: "Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units MS:1000040 ! m/z
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000804
@@ -5596,8 +5753,8 @@ id: MS:1000809
name: chromatogram title
def: "A free-form text title describing a chromatogram." [PSI:MS]
comment: This is the preferred storage place for the spectrum title.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000808 ! chromatogram attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000810
@@ -5713,34 +5870,44 @@ is_a: MS:1000560 ! mass spectrometer file format
id: MS:1000826
name: elution time
def: "The time of elution from all used chromatographic columns (one or more) in the chromatographic separation step, relative to the start of the chromatography." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000827
name: isolation window target m/z
def: "The primary or reference m/z about which the isolation window is defined." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000792 ! isolation window attribute
relationship: has_units MS:1000040 ! m/z
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000828
name: isolation window lower offset
def: "The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000792 ! isolation window attribute
relationship: has_units MS:1000040 ! m/z
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000829
name: isolation window upper offset
def: "The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000792 ! isolation window attribute
relationship: has_units MS:1000040 ! m/z
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1000830
+name: precision
+def: "Precision is the degree of how close repeated measurements are to each other. This can, for example, be expressed using the standard deviation." [PSI:MS]
+comment: See MS:1000014 for the related term of accuracy.
+is_a: MS:1000480 ! mass analyzer attribute
+relationship: has_units MS:1000040 ! m/z
+relationship: has_units UO:0000169 ! parts per million
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000831
@@ -5765,16 +5932,16 @@ relationship: part_of MS:1000832 ! MALDI matrix application
id: MS:1000834
name: matrix solution
def: "Describes the chemical solution used as matrix." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000832 ! MALDI matrix application
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000835
name: matrix solution concentration
def: "Concentration of the chemical solution used as matrix." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000832 ! MALDI matrix application
relationship: has_units UO:0000175 ! gram per liter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000836
@@ -5824,58 +5991,58 @@ id: MS:1000843
name: wavelength
def: "OBSOLETE The distance between two peaks of the emitted laser beam." [PSI:MS]
comment: This term was made obsolete because it was redundant with the Pato Ontology term wavelength (UO:0001242).
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000841 ! laser attribute
relationship: has_units UO:0000018 ! nanometer
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000844
name: focus diameter x
def: "Describes the diameter of the laser beam in x direction." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000841 ! laser attribute
relationship: has_units UO:0000017 ! micrometer
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000845
name: focus diameter y
def: "Describes the diameter of the laser beam in y direction." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000841 ! laser attribute
relationship: has_units UO:0000017 ! micrometer
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000846
name: pulse energy
def: "Describes output energy of the laser system. May be attenuated by filters or other means." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000841 ! laser attribute
relationship: has_units UO:0000112 ! joule
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000847
name: pulse duration
def: "Describes how long the laser beam was emitted from the laser device." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000841 ! laser attribute
relationship: has_units UO:0000150 ! nanosecond
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000848
name: attenuation
def: "Describes the reduction of the intensity of the laser beam energy." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000841 ! laser attribute
relationship: has_units UO:0000187 ! percent
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000849
name: impact angle
def: "Describes the angle between the laser beam and the sample target." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000841 ! laser attribute
relationship: has_units UO:0000185 ! degree
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000850
@@ -5929,8 +6096,8 @@ is_a: MS:1000547 ! object attribute
id: MS:1000858
name: fraction identifier
def: "Identier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000857 ! run attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000859
@@ -5955,16 +6122,16 @@ id: MS:1000862
name: isoelectric point
def: "The pH of a solution at which a charged molecule does not migrate in an electric field." [PSI:MS]
synonym: "pI" EXACT []
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000861 ! molecular entity property
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000863
name: predicted isoelectric point
def: "The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm." [PSI:MS]
synonym: "predicted pI" EXACT []
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000862 ! isoelectric point
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000864
@@ -5976,37 +6143,37 @@ is_a: MS:1003033 ! molecular entity attribute
id: MS:1000865
name: empirical formula
def: "A chemical formula which expresses the proportions of the elements present in a substance." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000864 ! chemical formula
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000866
name: molecular formula
def: "A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000864 ! chemical formula
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000867
name: structural formula
def: "A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000864 ! chemical formula
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000868
-name: SMILES formula
+name: SMILES string
def: "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string." [EDAM:2301]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
-is_a: MS:1000864 ! chemical formula
+is_a: MS:1000867 ! structural formula
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000869
name: collision gas pressure
def: "The gas pressure of the collision gas used for collisional excitation." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
relationship: has_units UO:0000110 ! pascal
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000870
@@ -6044,25 +6211,25 @@ is_a: MS:1000873 ! peptide attribute calculation software
id: MS:1000875
name: declustering potential
def: "Potential difference between the orifice and the skimmer in volts." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000218 ! volt
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000876
name: cone voltage
def: "Potential difference between the sampling cone/orifice in volts." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000218 ! volt
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000877
name: tube lens voltage
def: "Potential difference setting of the tube lens in volts." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000218 ! volt
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000878
@@ -6074,16 +6241,16 @@ is_a: MS:1002840 ! external reference data
id: MS:1000879
name: PubMed identifier
def: "A unique identifier for a publication in the PubMed database (MIR:00000015)." [PSI:MS]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1000880
name: interchannel delay
def: "The duration of intervals between scanning, during which the instrument configuration is switched." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000881
@@ -6101,8 +6268,8 @@ is_a: MS:1000859 ! molecule
id: MS:1000883
name: protein short name
def: "A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN)." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000884 ! protein attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000884
@@ -6115,16 +6282,16 @@ is_a: MS:1001806 ! quantification object attribute
id: MS:1000885
name: protein accession
def: "Identifier for a specific protein in a database." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000884 ! protein attribute
is_a: MS:1003046 ! peptide-to-protein mapping attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000886
name: protein name
def: "A long name describing the function of the protein." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000884 ! protein attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000887
@@ -6136,16 +6303,16 @@ relationship: part_of MS:1000860 ! peptide
id: MS:1000888
name: stripped peptide sequence
def: "Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1003050 ! peptidoform attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000889
name: peptidoform sequence
def: "Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present." [PSI:MS]
comment: Make it more general as there are actually many other ways to display a modified peptide sequence.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1003050 ! peptidoform attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000890
@@ -6170,44 +6337,46 @@ is_a: MS:1000890 ! peptidoform labeling state
id: MS:1000893
name: peptidoform group label
def: "An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1003050 ! peptidoform attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000894
name: retention time
def: "A time interval from the start of chromatography when an analyte exits a chromatographic column." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1003050 ! peptidoform attribute
+is_a: MS:1003295 ! summary statistics of replicates
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000895
name: local retention time
def: "A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000894 ! retention time
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000896
name: normalized retention time
def: "A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000894 ! retention time
+is_a: MS:1003295 ! summary statistics of replicates
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000897
name: predicted retention time
def: "A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000894 ! retention time
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000898
@@ -6243,8 +6412,8 @@ is_a: MS:1000901 ! retention time normalization standard
id: MS:1000903
name: product ion series ordinal
def: "The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion)." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001221 ! product ion attribute
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1000904
@@ -6257,24 +6426,24 @@ relationship: has_units MS:1000040 ! m/z
id: MS:1000905
name: percent of base peak times 100
def: "The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000043 ! intensity unit
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000906
name: peak intensity rank
def: "Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc." [PSI:MS]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
relationship: part_of MS:1000231 ! peak
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1000907
name: peak targeting suitability rank
def: "Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitability peak is 2, etc. Suitability is algorithm and context dependant." [PSI:MS]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
relationship: part_of MS:1000231 ! peak
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1000908
@@ -6330,19 +6499,19 @@ relationship: part_of MS:1000894 ! retention time
id: MS:1000916
name: retention time window lower offset
def: "The extent of the retention time window in time units below the target retention time. The lower and upper offsets may be asymmetric about the target time." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000915 ! retention time window attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000917
name: retention time window upper offset
def: "The extent of the retention time window in time units above the target retention time. The lower and upper offsets may be asymmetric about the target time." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000915 ! retention time window attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000918
@@ -6399,16 +6568,16 @@ is_a: MS:1000871 ! SRM software
id: MS:1000926
name: product interpretation rank
def: "The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1." [PSI:MS]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001221 ! product ion attribute
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1000927
name: ion injection time
def: "The length of time spent filling an ion trapping device." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000028 ! millisecond
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1000928
@@ -6444,15 +6613,33 @@ is_a: MS:1000121 ! SCIEX instrument model
id: MS:1000933
name: protein modifications
def: "Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000884 ! protein attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1000934
name: gene name
def: "Name of the gene from which the protein is translated." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000884 ! protein attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1000935
+name: 6470A Triple Quadrupole LC/MS
+def: "The 6470A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS]
+is_a: MS:1000490 ! Agilent instrument model
+
+[Term]
+id: MS:1000936
+name: 6470B Triple Quadrupole LC/MS
+def: "The 6470B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS]
+is_a: MS:1000490 ! Agilent instrument model
+
+[Term]
+id: MS:1000937
+name: 6495C Triple Quadrupole LC/MS
+def: "The 6495C Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS]
+is_a: MS:1000490 ! Agilent instrument model
[Term]
id: MS:1001000
@@ -6463,8 +6650,8 @@ relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrom
[Term]
id: MS:1001005
name: SEQUEST:CleavesAt
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002096 ! SEQUEST input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001006
@@ -6476,15 +6663,15 @@ is_a: MS:1002096 ! SEQUEST input parameter
id: MS:1001007
name: SEQUEST:OutputLines
def: "Number of peptide results to show." [PSI:MS]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1002096 ! SEQUEST input parameter
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001009
name: SEQUEST:DescriptionLines
def: "Number of full protein descriptions to show for top N peptides." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002096 ! SEQUEST input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001010
@@ -6502,8 +6689,8 @@ is_a: MS:1001249 ! search input details
id: MS:1001012
name: database source
def: "The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other)." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001013
@@ -6522,22 +6709,24 @@ is_obsolete: true
id: MS:1001015
name: database original uri
def: "URI, from where the search database was originally downloaded." [PSI:PI]
-xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details
+relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term
[Term]
id: MS:1001016
name: database version
def: "Version of the search database. In mzIdentML use the attribute instead." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001017
-name: database release date
-def: "OBSOLETE: Use attribute in mzIdentML instead. Release date of the search database." [PSI:PI]
+name: release date
+def: "Date and time at which a product was publicly released. For mzIdentML, use the database release date XML attribute instead of this term." [PSI:PI]
is_a: MS:1001011 ! search database details
-is_obsolete: true
+is_a: MS:1003171 ! spectral library attribute
+relationship: has_value_type xsd:dateTime
+relationship: has_structured_representation_in_format MS:1002073 ! mzIdentML format
[Term]
id: MS:1001018
@@ -6585,14 +6774,14 @@ is_a: MS:1001011 ! search database details
id: MS:1001025
name: translation table
def: "The translation table used to translate the nucleotides to amino acids." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001026
name: SEQUEST:NormalizeXCorrValues
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002096 ! SEQUEST input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001027
@@ -6604,23 +6793,23 @@ is_a: MS:1001511 ! Sequence database filter types
id: MS:1001028
name: SEQUEST:SequenceHeaderFilter
def: "String in the header of a sequence entry for that entry to be searched." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002096 ! SEQUEST input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001029
name: number of sequences searched
def: "The number of sequences (proteins / nucleotides) from the database search after filtering." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001030
name: number of peptide seqs compared to each spectrum
def: "Number of peptide seqs compared to each spectrum." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details
is_a: MS:1001405 ! spectrum identification result details
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001031
@@ -6631,8 +6820,8 @@ is_a: MS:1001080 ! search type
[Term]
id: MS:1001032
name: SEQUEST:SequencePartialFilter
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002096 ! SEQUEST input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001035
@@ -6645,22 +6834,22 @@ is_obsolete: true
id: MS:1001036
name: search time taken
def: "The time taken to complete the search in seconds." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001184 ! search statistics
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001037
name: SEQUEST:ShowFragmentIons
def: "Flag indicating that fragment ions should be shown." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002096 ! SEQUEST input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001038
name: SEQUEST:Consensus
def: "Specify depth as value of the CVParam." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001006 ! SEQUEST:ViewCV
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001040
@@ -6678,8 +6867,8 @@ is_a: MS:1001006 ! SEQUEST:ViewCV
id: MS:1001042
name: SEQUEST:LimitTo
def: "Specify \"number of dtas shown\" as value of the CVParam." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1002096 ! SEQUEST input parameter
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001044
@@ -6697,57 +6886,57 @@ is_a: MS:1001044 ! cleavage agent details
id: MS:1001046
name: SEQUEST:sort by dCn
def: "Sort order of SEQUEST search results by the delta of the normalized correlation score." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! SEQUEST:sortCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001047
name: SEQUEST:sort by dM
def: "Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! SEQUEST:sortCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001048
name: SEQUEST:sort by Ions
def: "Sort order of SEQUEST search results given by the ions." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! SEQUEST:sortCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001049
name: SEQUEST:sort by MH+
def: "Sort order of SEQUEST search results given by the mass of the protonated ion." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! SEQUEST:sortCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001050
name: SEQUEST:sort by P
def: "Sort order of SEQUEST search results given by the probability." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! SEQUEST:sortCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001051
name: multiple enzyme combination rules
def: "OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001052
name: SEQUEST:sort by PreviousAminoAcid
def: "Sort order of SEQUEST search results given by the previous amino acid." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! SEQUEST:sortCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001053
name: SEQUEST:sort by Ref
def: "Sort order of SEQUEST search results given by the reference." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! SEQUEST:sortCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001055
@@ -6778,8 +6967,8 @@ is_a: MS:1001060 ! quality estimation method details
id: MS:1001059
name: SEQUEST:sort by RSp
def: "Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide)." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! SEQUEST:sortCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001060
@@ -6820,36 +7009,36 @@ is_a: MS:1001249 ! search input details
id: MS:1001068
name: SEQUEST:sort by Sp
def: "Sort order of SEQUEST search results by the Sp score." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! SEQUEST:sortCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001069
name: SEQUEST:sort by TIC
def: "Sort order of SEQUEST search results given by the total ion current." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! SEQUEST:sortCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001070
name: SEQUEST:sort by Scan
def: "Sort order of SEQUEST search results given by the scan number." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! SEQUEST:sortCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001071
name: SEQUEST:sort by Sequence
def: "Sort order of SEQUEST search results given by the sequence." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! SEQUEST:sortCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001072
name: SEQUEST:sort by Sf
def: "Sort order of SEQUEST search results given by the SEQUEST result 'Sf'." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! SEQUEST:sortCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001073
@@ -6903,8 +7092,8 @@ is_a: MS:1002694 ! single identification result attribute
id: MS:1001086
name: SEQUEST:sort by XCorr
def: "Sort order of SEQUEST search results by the correlation score." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! SEQUEST:sortCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001087
@@ -6916,18 +7105,18 @@ is_a: MS:1002096 ! SEQUEST input parameter
id: MS:1001088
name: protein description
def: "The protein description line from the sequence entry in the source database FASTA file." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein-level identification attribute
is_a: MS:1001342 ! database sequence details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001089
name: molecule taxonomy
def: "The taxonomy of the resultant molecule from the search." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein-level identification attribute
is_a: MS:1001342 ! database sequence details
is_a: MS:1001512 ! Sequence database filters
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001090
@@ -6957,56 +7146,56 @@ is_a: MS:1001105 ! peptide sequence-level identification attribute
id: MS:1001093
name: sequence coverage
def: "The percent coverage for the protein based upon the matched peptide sequences (can be calculated)." [PSI:PI]
-xref: value-type:xsd\:decimal "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein-level identification attribute
+relationship: has_value_type xsd:decimal ! The allowed value-type for this CV term
[Term]
id: MS:1001094
name: SEQUEST:sort by z
def: "Sort order of SEQUEST search results given by the charge." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! SEQUEST:sortCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001095
name: SEQUEST:ProcessAll
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001087 ! SEQUEST:ProcessCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001096
name: SEQUEST:TopPercentMostIntense
def: "Specify \"percentage\" as value of the CVParam." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001087 ! SEQUEST:ProcessCV
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001097
name: distinct peptide sequences
def: "This counts distinct sequences hitting the protein without regard to a minimal confidence threshold." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein-level identification attribute
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001098
name: confident distinct peptide sequences
def: "This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein-level identification attribute
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001099
name: confident peptide qualification
def: "The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein-level identification attribute
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001100
name: confident peptide sequence number
def: "This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein-level identification attribute
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001101
@@ -7017,14 +7206,14 @@ is_a: MS:1001085 ! protein-level identification attribute
[Term]
id: MS:1001102
name: SEQUEST:Chromatogram
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001006 ! SEQUEST:ViewCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001103
name: SEQUEST:InfoAndLog
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001006 ! SEQUEST:ViewCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001104
@@ -7042,8 +7231,8 @@ is_a: MS:1002694 ! single identification result attribute
id: MS:1001106
name: SEQUEST:TopNumber
def: "Specify \"number\" as value of the CVParam." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001087 ! SEQUEST:ProcessCV
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001107
@@ -7061,8 +7250,8 @@ is_a: MS:1002473 ! ion series considered in search
id: MS:1001109
name: SEQUEST:CullTo
def: "Specify cull string as value of the CVParam." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001087 ! SEQUEST:ProcessCV
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001110
@@ -7073,35 +7262,35 @@ is_a: MS:1002096 ! SEQUEST input parameter
[Term]
id: MS:1001111
name: SEQUEST:Full
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001110 ! SEQUEST:modeCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001112
name: n-terminal flanking residue
def: "Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1003046 ! peptide-to-protein mapping attribute
is_a: MS:1001105 ! peptide sequence-level identification attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001113
name: c-terminal flanking residue
def: "Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1003046 ! peptide-to-protein mapping attribute
is_a: MS:1001105 ! peptide sequence-level identification attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001114
name: retention time(s)
def: "OBSOLETE Retention time of the spectrum from the source file." [PSI:PI]
comment: This term was made obsolete because scan start time (MS:1000016) should be used instead.
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide sequence-level identification attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
is_obsolete: true
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001115
@@ -7119,10 +7308,10 @@ is_a: MS:1001085 ! protein-level identification attribute
[Term]
id: MS:1001117
name: theoretical mass
-def: "The theoretical mass of the molecule (e.g. the peptide sequence and its modifications)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
+def: "The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier." [PSI:PI]
is_a: MS:1001105 ! peptide sequence-level identification attribute
relationship: has_units UO:0000221 ! dalton
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001118
@@ -7139,15 +7328,15 @@ is_a: MS:1002473 ! ion series considered in search
[Term]
id: MS:1001120
name: SEQUEST:FormatAndLinks
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001110 ! SEQUEST:modeCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001121
name: number of matched peaks
def: "The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide sequence-level identification attribute
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001122
@@ -7159,29 +7348,29 @@ is_a: MS:1001105 ! peptide sequence-level identification attribute
id: MS:1001123
name: number of peaks used
def: "The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide sequence-level identification attribute
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001124
name: number of peaks submitted
def: "The number of peaks from the original peaks listed that were submitted to the search engine." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide sequence-level identification attribute
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001125
name: manual validation
def: "Result of quality estimation: decision of a manual validation." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide sequence-level identification statistic
is_a: MS:1001116 ! single protein identification statistic
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001126
name: SEQUEST:Fast
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001110 ! SEQUEST:modeCV
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001127
@@ -7206,67 +7395,67 @@ id: MS:1001130
name: peptide raw area
def: "OBSOLETE Peptide raw area." [PSI:PI]
comment: This term was made obsolete because it is replaced by 'MS1 feature area' (MS:1001844).
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
is_obsolete: true
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001131
name: error on peptide area
def: "Error on peptide area." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001132
name: peptide ratio
def: "Peptide ratio." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001133
name: error on peptide ratio
def: "Error on peptide ratio." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001134
name: protein ratio
def: "Protein ratio." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002738 ! protein-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001135
name: error on protein ratio
def: "Error on protein ratio." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002738 ! protein-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001136
name: p-value (protein diff from 1 randomly)
def: "OBSOLETE P-value (protein diff from 1 randomly)." [PSI:PI]
comment: This term was made obsolete because it is replaced by 't-test p-value' (MS:1001855).
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002738 ! protein-level quantification datatype
is_obsolete: true
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001137
name: absolute quantity
def: "Absolute quantity in terms of real concentration or molecule copy number in sample." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001138
name: error on absolute quantity
def: "Error on absolute quantity." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001139
@@ -7287,8 +7476,8 @@ is_obsolete: true
id: MS:1001141
name: intensity of precursor ion
def: "The intensity of the precursor ion." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001142
@@ -7365,150 +7554,150 @@ is_a: MS:1002694 ! single identification result attribute
id: MS:1001154
name: SEQUEST:probability
def: "The SEQUEST result 'Probability'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001155
name: SEQUEST:xcorr
def: "The SEQUEST result 'XCorr'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001156
name: SEQUEST:deltacn
def: "The SEQUEST result 'DeltaCn'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001157
name: SEQUEST:sp
def: "The SEQUEST result 'Sp' (protein)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001158
name: SEQUEST:Uniq
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001159
name: SEQUEST:expectation value
def: "The SEQUEST result 'Expectation value'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001160
name: SEQUEST:sf
def: "The SEQUEST result 'Sf'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001161
name: SEQUEST:matched ions
def: "The SEQUEST result 'Matched Ions'." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1001162
name: SEQUEST:total ions
def: "The SEQUEST result 'Total Ions'." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1001163
name: SEQUEST:consensus score
def: "The SEQUEST result 'Consensus Score'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001164
name: Paragon:unused protscore
def: "The Paragon result 'Unused ProtScore'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
is_a: MS:1002368 ! search engine specific score for protein groups
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001165
name: Paragon:total protscore
def: "The Paragon result 'Total ProtScore'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
is_a: MS:1002368 ! search engine specific score for protein groups
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001166
name: Paragon:score
def: "The Paragon result 'Score'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001167
name: Paragon:confidence
def: "The Paragon result 'Confidence'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001168
name: Paragon:expression error factor
def: "The Paragon result 'Expression Error Factor'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001169
name: Paragon:expression change p-value
def: "The Paragon result 'Expression change P-value'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001170
name: Paragon:contrib
def: "The Paragon result 'Contrib'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001171
name: Mascot:score
def: "The Mascot result 'Score'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001172
name: Mascot:expectation value
def: "The Mascot result 'expectation value'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001173
name: Mascot:matched ions
def: "The Mascot result 'Matched ions'." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001174
name: Mascot:total ions
def: "The Mascot result 'Total ions'." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001175
@@ -7526,8 +7715,8 @@ is_a: MS:1001180 ! Cleavage agent regular expression
id: MS:1001177
name: number of molecular hypothesis considered
def: "Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001184 ! search statistics
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001178
@@ -7565,33 +7754,33 @@ id: MS:1001191
name: p-value
def: "OBSOLETE Quality estimation by p-value." [PSI:PI]
comment: This term was made obsolete because now is split into peptide and protein terms.
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide sequence-level identification statistic
is_a: MS:1001198 ! protein identification confidence metric
is_obsolete: true
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001192
name: Expect value
def: "Result of quality estimation: Expect value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide sequence-level identification statistic
is_a: MS:1001116 ! single protein identification statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001193
name: confidence score
def: "Result of quality estimation: confidence score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide sequence-level identification statistic
is_a: MS:1001116 ! single protein identification statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001194
name: quality estimation with decoy database
def: "Quality estimation by decoy database." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001060 ! quality estimation method details
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001195
@@ -7633,33 +7822,33 @@ is_a: MS:1001040 ! intermediate analysis format
id: MS:1001201
name: DB MW filter maximum
def: "Maximum value of molecular weight filter." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters
relationship: has_units UO:0000221 ! dalton
relationship: has_units UO:0000222 ! kilodalton
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001202
name: DB MW filter minimum
def: "Minimum value of molecular weight filter." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters
relationship: has_units UO:0000221 ! dalton
relationship: has_units UO:0000222 ! kilodalton
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001203
name: DB PI filter maximum
def: "Maximum value of isoelectric point filter." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001204
name: DB PI filter minimum
def: "Minimum value of isoelectric point filter." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001207
@@ -7708,37 +7897,37 @@ is_obsolete: true
id: MS:1001214
name: protein-level global FDR
def: "Estimation of the global false discovery rate of proteins." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002705 ! protein-level result list statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001215
name: SEQUEST:PeptideSp
def: "The SEQUEST result 'Sp' in out file (peptide)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001217
name: SEQUEST:PeptideRankSp
def: "The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1001218
name: SEQUEST:PeptideNumber
def: "The SEQUEST result '#' in out file (peptide)." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1001219
name: SEQUEST:PeptideIdnumber
def: "The SEQUEST result 'Id#' in out file (peptide)." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1001220
@@ -7796,6 +7985,7 @@ def: "The product ion m/z error." [PSI:PI]
is_a: MS:1001221 ! product ion attribute
relationship: has_units MS:1000040 ! m/z
relationship: has_units UO:0000166 ! parts per notation unit
+relationship: has_units UO:0000169 ! parts per million
[Term]
id: MS:1001228
@@ -7921,9 +8111,9 @@ relationship: part_of MS:1001000 ! spectrum interpretation
id: MS:1001250
name: local FDR
def: "Result of quality estimation: the local FDR at the current position of a sorted list." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide sequence-level identification statistic
is_a: MS:1001116 ! single protein identification statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001251
@@ -8020,22 +8210,22 @@ is_a: MS:1001266 ! role type
id: MS:1001268
name: programmer
def: "Programmer role." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001266 ! role type
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001269
name: instrument vendor
def: "Instrument vendor role." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001266 ! role type
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001270
name: lab personnel
def: "Lab personnel role." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001266 ! role type
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001271
@@ -8077,8 +8267,8 @@ is_a: MS:1001040 ! intermediate analysis format
id: MS:1001283
name: decoy DB accession regexp
def: "Specify the regular expression for decoy accession numbers." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001450 ! decoy DB details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001284
@@ -8198,8 +8388,8 @@ is_obsolete: true
id: MS:1001301
name: protein rank
def: "The rank of the protein in a list sorted by the search engine." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein-level identification attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001302
@@ -8305,71 +8495,71 @@ relationship: has_regexp MS:1001341 ! (?<=[EZ])(?!P)
id: MS:1001316
name: Mascot:SigThreshold
def: "Significance threshold below which the p-value of a peptide match must lie to be considered statistically significant (default 0.05)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001317
name: Mascot:MaxProteinHits
def: "The number of protein hits to display in the report. If 'Auto', all protein hits that have a protein score exceeding the average peptide identity threshold are reported. Otherwise an integer at least 1." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001318
name: Mascot:ProteinScoringMethod
def: "Mascot protein scoring method; either 'Standard' or 'MudPIT'." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001319
name: Mascot:MinMSMSThreshold
def: "Mascot peptide match ion score threshold. If between 0 and 1, then peptide matches whose expect value exceeds the thresholds are suppressed; if at least 1, then peptide matches whose ion score is below the threshold are suppressed." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001320
name: Mascot:ShowHomologousProteinsWithSamePeptides
def: "If true, show (sequence or spectrum) same-set proteins. Otherwise they are suppressed." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001321
name: Mascot:ShowHomologousProteinsWithSubsetOfPeptides
def: "If true, show (sequence or spectrum) sub-set and subsumable proteins. Otherwise they are suppressed." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001322
name: Mascot:RequireBoldRed
def: "Only used in Peptide Summary and Select Summary reports. If true, a peptide match must be 'bold red' to be included in the report; bold red means the peptide is a top ranking match in a query and appears for the first time (in linear order) in the list of protein hits." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001323
name: Mascot:UseUnigeneClustering
def: "If true, then the search results are against a nucleic acid database and Unigene clustering is enabled. Otherwise UniGene clustering is not in use." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001324
name: Mascot:IncludeErrorTolerantMatches
def: "If true, then the search results are error tolerant and peptide matches from the second pass are included in search results. Otherwise no error tolerant peptide matches are included." [http://www.matrixscience.com/help/error_tolerant_help.html]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001325
name: Mascot:ShowDecoyMatches
def: "If true, then the search results are against an automatically generated decoy database and the reported peptide matches and protein hits come from the decoy database. Otherwise peptide matches and protein hits come from the original database." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001326
@@ -8378,33 +8568,40 @@ def: "OBSOLETE." [PSI:PI]
comment: This former purgatory term was made obsolete.
is_obsolete: true
+[Term]
+id: MS:1001327
+name: Spectronaut
+def: "Commercial cross-vendor software for library (peptide centric), and library-free (spectrum centric) analysis and quantification of DIA data." [https://doi.org/10.1074/mcp.M114.044305]
+is_a: MS:1001456 ! analysis software
+is_a: MS:1003207 ! library creation software
+
[Term]
id: MS:1001328
name: OMSSA:evalue
def: "OMSSA E-value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001329
name: OMSSA:pvalue
def: "OMSSA p-value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001330
name: X\!Tandem:expect
def: "The X!Tandem expectation value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001331
name: X\!Tandem:hyperscore
def: "The X!Tandem hyperscore." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001332
@@ -8566,8 +8763,8 @@ is_a: MS:1001356 ! spectrum descriptions
id: MS:1001358
name: msmsEval quality
def: "This term reports the quality of the spectrum assigned by msmsEval." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001357 ! spectrum quality descriptions
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001359
@@ -8579,23 +8776,23 @@ relationship: part_of MS:1001000 ! spectrum interpretation
id: MS:1001360
name: alternate single letter codes
def: "List of standard residue one letter codes which are used to replace a non-standard." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001359 ! ambiguous residues
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001361
name: alternate mass
def: "List of masses a non-standard letter code is replaced with." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001359 ! ambiguous residues
relationship: has_units UO:0000221 ! dalton
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001362
name: number of unmatched peaks
def: "The number of unmatched peaks." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1002345 ! PSM-level attribute
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001363
@@ -8607,9 +8804,9 @@ is_a: MS:1001127 ! peptide sharing details
id: MS:1001364
name: peptide sequence-level global FDR
def: "Estimation of the global false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002703 ! peptide sequence-level result list statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001365
@@ -8645,205 +8842,205 @@ is_a: MS:1000560 ! mass spectrometer file format
id: MS:1001370
name: Mascot:homology threshold
def: "The Mascot result 'homology threshold'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001371
name: Mascot:identity threshold
def: "The Mascot result 'identity threshold'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001372
name: SEQUEST:Sequences
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001373
name: SEQUEST:TIC
def: "SEQUEST total ion current." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001374
name: SEQUEST:Sum
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001375
name: Phenyx:Instrument Type
def: "The instrument type parameter value in Phenyx." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001376
name: Phenyx:Scoring Model
def: "The selected scoring model in Phenyx." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001377
name: Phenyx:Default Parent Charge
def: "The default parent charge value in Phenyx." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001378
name: Phenyx:Trust Parent Charge
def: "The parameter in Phenyx that specifies if the experimental charge state is to be considered as correct." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001379
name: Phenyx:Turbo
def: "The turbo mode parameter in Phenyx." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001380
name: Phenyx:Turbo:ErrorTol
def: "The maximal allowed fragment m/z error filter considered in the turbo mode of Phenyx." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001381
name: Phenyx:Turbo:Coverage
def: "The minimal peptide sequence coverage value, expressed in percent, considered in the turbo mode of Phenyx." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001382
name: Phenyx:Turbo:Series
def: "The list of ion series considered in the turbo mode of Phenyx." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001383
name: Phenyx:MinPepLength
def: "The minimal number of residues for a peptide to be considered for a valid identification in Phenyx." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001384
name: Phenyx:MinPepzscore
def: "The minimal peptide z-score for a peptide to be considered for a valid identification in Phenyx." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001385
name: Phenyx:MaxPepPvalue
def: "The maximal peptide p-value for a peptide to be considered for a valid identification in Phenyx." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001386
name: Phenyx:AC Score
def: "The minimal protein score required for a protein database entry to be displayed in the list of identified proteins in Phenyx." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001387
name: Phenyx:Conflict Resolution
def: "The parameter in Phenyx that specifies if the conflict resolution algorithm is to be used." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001388
name: Phenyx:AC
def: "The primary sequence database identifier of a protein in Phenyx." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001389
name: Phenyx:ID
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
def: "A secondary sequence database identifier of a protein in Phenyx." [PSI:PI]
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001390
name: Phenyx:Score
def: "The protein score of a protein match in Phenyx." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001391
name: Phenyx:Peptides1
def: "First number of phenyx result \"#Peptides\"." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001392
name: Phenyx:Peptides2
def: "Second number of phenyx result \"#Peptides\"." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001393
name: Phenyx:Auto
def: "The value of the automatic peptide acceptance filter in Phenyx." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001394
name: Phenyx:User
def: "The value of the user-defined peptide acceptance filter in Phenyx." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001395
name: Phenyx:Pepzscore
def: "The z-score value of a peptide sequence match in Phenyx." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001396
name: Phenyx:PepPvalue
def: "The p-value of a peptide sequence match in Phenyx." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001397
name: Phenyx:NumberOfMC
def: "The number of missed cleavages of a peptide sequence in Phenyx." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001398
name: Phenyx:Modif
def: "The expression of the nature and position(s) of modified residue(s) on a matched peptide sequence in Phenyx." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001399
@@ -8897,8 +9094,8 @@ is_a: MS:1002473 ! ion series considered in search
id: MS:1001410
name: translation start codons
def: "The translation start codons used to translate the nucleotides to amino acids." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001411
@@ -8909,77 +9106,77 @@ is_a: MS:1001249 ! search input details
[Term]
id: MS:1001412
name: search tolerance plus value
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001411 ! search tolerance specification
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000169 ! parts per million
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001413
name: search tolerance minus value
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001411 ! search tolerance specification
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000169 ! parts per million
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001414
name: MGF scans
def: "OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
is_obsolete: true
replaced_by: MS:1000797
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001415
name: MGF raw scans
def: "OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
is_obsolete: true
replaced_by: MS:1000798
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001416
name: spectrum title
def: "OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
is_obsolete: true
replaced_by: MS:1000796
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001417
name: SpectraST:dot
def: "SpectraST dot product of two spectra, measuring spectral similarity." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001418
name: SpectraST:dot_bias
def: "SpectraST measure of how much of the dot product is dominated by a few peaks." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001419
name: SpectraST:discriminant score F
def: "SpectraST spectrum score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001420
name: SpectraST:delta
def: "SpectraST normalised difference between dot product of top hit and runner-up." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001421
@@ -8997,189 +9194,189 @@ is_a: MS:1001040 ! intermediate analysis format
id: MS:1001423
name: translation table description
def: "A URL that describes the translation table used to translate the nucleotides to amino acids." [PSI:PI]
-xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details
+relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term
[Term]
id: MS:1001424
name: ProteinExtractor:Methodname
def: "Name of the used method in the ProteinExtractor algorithm." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001425
name: ProteinExtractor:GenerateNonRedundant
def: "Flag indicating if a non redundant scoring should be generated." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001426
name: ProteinExtractor:IncludeIdentified
def: "Flag indicating if identified proteins should be included." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001427
name: ProteinExtractor:MaxNumberOfProteins
def: "The maximum number of proteins to consider." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001428
name: ProteinExtractor:MaxProteinMass
def: "The maximum considered mass for a protein." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001429
name: ProteinExtractor:MinNumberOfPeptides
def: "The minimum number of proteins to consider." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001430
name: ProteinExtractor:UseMascot
def: "Flag indicating to include Mascot scoring for calculation of the ProteinExtractor meta score." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001431
name: ProteinExtractor:MascotPeptideScoreThreshold
def: "Only peptides with scores higher than that threshold are taken into account in Mascot scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001432
name: ProteinExtractor:MascotUniqueScore
def: "In the final result each protein must have at least one peptide above this Mascot score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001433
name: ProteinExtractor:MascotUseIdentityScore
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001434
name: ProteinExtractor:MascotWeighting
def: "Influence of Mascot search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001435
name: ProteinExtractor:UseSequest
def: "Flag indicating to include SEQUEST scoring for calculation of the ProteinExtractor meta score." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001436
name: ProteinExtractor:SequestPeptideScoreThreshold
def: "Only peptides with scores higher than that threshold are taken into account in SEQUEST scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001437
name: ProteinExtractor:SequestUniqueScore
def: "In the final result each protein must have at least one peptide above this SEQUEST score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001438
name: ProteinExtractor:SequestWeighting
def: "Influence of SEQUEST search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001439
name: ProteinExtractor:UseProteinSolver
def: "Flag indicating to include ProteinSolver scoring for calculation of the ProteinExtractor meta score." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001440
name: ProteinExtractor:ProteinSolverPeptideScoreThreshold
def: "Only peptides with scores higher than that threshold are taken into account in ProteinSolver scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001441
name: ProteinExtractor:ProteinSolverUniqueScore
def: "In the final result each protein must have at least one peptide above this ProteinSolver score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001442
name: ProteinExtractor:ProteinSolverWeighting
def: "Influence of ProteinSolver search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001443
name: ProteinExtractor:UsePhenyx
def: "Flag indicating to include Phenyx scoring for calculation of the ProteinExtractor meta score." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001444
name: ProteinExtractor:PhenyxPeptideScoreThreshold
def: "Only peptides with scores higher than that threshold are taken into account in Phenyx scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001445
name: ProteinExtractor:PhenyxUniqueScore
def: "In the final result each protein must have at least one peptide above this Phenyx score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001446
name: ProteinExtractor:PhenyxWeighting
def: "Influence of Phenyx search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001447
name: prot:FDR threshold
def: "False-discovery rate threshold for proteins." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002485 ! protein-level statistical threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001448
name: pep:FDR threshold
def: "False-discovery rate threshold for peptides." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002484 ! peptide-level statistical threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001449
name: OMSSA e-value threshold
def: "Threshold for OMSSA e-value for quality estimation." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002099 ! OMSSA input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001450
@@ -9191,8 +9388,8 @@ is_a: MS:1001011 ! search database details
id: MS:1001451
name: decoy DB generation algorithm
def: "Name of algorithm used for decoy generation." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001450 ! decoy DB details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001452
@@ -9283,29 +9480,29 @@ is_a: MS:1000560 ! mass spectrometer file format
id: MS:1001467
name: taxonomy: NCBI TaxID
def: "This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001089 ! molecule taxonomy
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001468
name: taxonomy: common name
def: "This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001089 ! molecule taxonomy
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001469
name: taxonomy: scientific name
def: "This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001089 ! molecule taxonomy
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001470
name: taxonomy: Swiss-Prot ID
def: "This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001089 ! molecule taxonomy
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001471
@@ -9351,8 +9548,10 @@ is_a: MS:1001456 ! analysis software
[Term]
id: MS:1001477
name: SpectraST
-def: "SpectraST was used to analyze the spectra." [PSI:PI]
+def: "Open-source software for mass spectral library creation and searching, developed at the Institute for Systems Biology and the Hong Kong University of Science and Technology. Part of the Trans-Proteomic Pipeline." [PSI:PI]
is_a: MS:1001456 ! analysis software
+is_a: MS:1003207 ! library creation software
+is_a: MS:1003406 ! spectrum clustering software
[Term]
id: MS:1001478
@@ -9441,22 +9640,22 @@ is_a: MS:1001456 ! analysis software
id: MS:1001491
name: percolator:Q value
def: "Percolator:Q value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001492
name: percolator:score
def: "Percolator:score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001493
name: percolator:PEP
def: "Posterior error probability." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001494
@@ -9468,92 +9667,92 @@ is_a: MS:1002482 ! statistical threshold
id: MS:1001495
name: ProteinScape:SearchResultId
def: "The SearchResultId of this peptide as SearchResult in the ProteinScape database." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001496
name: ProteinScape:SearchEventId
def: "The SearchEventId of the SearchEvent in the ProteinScape database." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001497
name: ProteinScape:ProfoundProbability
def: "The Profound probability score stored by ProteinScape." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001498
name: Profound:z value
def: "The Profound z value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001499
name: Profound:Cluster
def: "The Profound cluster score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001500
name: Profound:ClusterRank
def: "The Profound cluster rank." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001501
name: MSFit:Mowse score
def: "The MSFit Mowse score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001502
name: Sonar:Score
def: "The Sonar score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001503
name: ProteinScape:PFFSolverExp
def: "The ProteinSolver exp value stored by ProteinScape." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001504
name: ProteinScape:PFFSolverScore
def: "The ProteinSolver score stored by ProteinScape." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001505
name: ProteinScape:IntensityCoverage
def: "The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001506
name: ProteinScape:SequestMetaScore
def: "The SEQUEST meta score calculated by ProteinScape from the original SEQUEST scores." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001507
name: ProteinExtractor:Score
def: "The score calculated by ProteinExtractor." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001508
@@ -9589,15 +9788,15 @@ is_a: MS:1001019 ! database filtering
id: MS:1001513
name: DB sequence filter pattern
def: "DB sequence filter pattern." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001514
name: DB accession filter string
def: "DB accession filter string." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001515
@@ -9657,17 +9856,17 @@ is_a: MS:1002307 ! fragmentation ion type
id: MS:1001524
name: fragment neutral loss
def: "This term can describe a neutral loss m/z value that is lost from an ion." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details
relationship: has_units UO:0000221 ! dalton
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001525
name: precursor neutral loss
def: "This term can describe a neutral loss m/z value that is lost from an ion." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details
relationship: has_units UO:0000221 ! dalton
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001526
@@ -9924,43 +10123,43 @@ is_a: MS:1001040 ! intermediate analysis format
id: MS:1001568
name: Scaffold:Peptide Probability
def: "Scaffold peptide probability score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001569
name: IdentityE Score
def: "Waters IdentityE peptide score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001570
name: ProteinLynx:Log Likelihood
def: "ProteinLynx log likelihood score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001571
name: ProteinLynx:Ladder Score
def: "Waters ProteinLynx Ladder score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001572
name: SpectrumMill:Score
def: "Spectrum mill peptide score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001573
name: SpectrumMill:SPI
def: "SpectrumMill SPI score (%)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001574
@@ -9972,52 +10171,54 @@ is_a: MS:1001060 ! quality estimation method details
id: MS:1001575
name: Scaffold: Minimum Peptide Count
def: "Minimum number of peptides a protein must have to be accepted." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1002106 ! Scaffold input parameter
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001576
name: Scaffold: Minimum Protein Probability
def: "Minimum protein probability a protein must have to be accepted." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002106 ! Scaffold input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001577
name: Scaffold: Minimum Peptide Probability
def: "Minimum probability a peptide must have to be accepted for protein scoring." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002106 ! Scaffold input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001578
name: minimum number of enzymatic termini
def: "Minimum number of enzymatic termini a peptide must have to be accepted." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1002094 ! common search engine input parameter
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001579
name: Scaffold:Protein Probability
def: "Scaffold protein probability score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001580
name: SpectrumMill:Discriminant Score
def: "Discriminant score from Agilent SpectrumMill software." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001581
name: FAIMS compensation voltage
def: "The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
synonym: "FAIMS CV" EXACT []
is_a: MS:1002892 ! ion mobility attribute
+is_a: MS:1000455 ! ion selection attribute
+is_a: MS:1003254 ! peak attribute
relationship: has_units UO:0000218 ! volt
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001582
@@ -10083,15 +10284,15 @@ is_a: MS:1001143 ! PSM-level search engine specific statistic
id: MS:1001591
name: anchor protein
def: "A representative protein selected from a set of sequence same-set or spectrum same-set proteins." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001592
name: family member protein
def: "A protein with significant homology to another protein, but some distinguishing peptide matches." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001593
@@ -10103,1099 +10304,1099 @@ is_a: MS:1001101 ! protein group or subset relationship
id: MS:1001594
name: sequence same-set protein
def: "A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001595
name: spectrum same-set protein
def: "A protein which is indistinguishable or equivalent to another protein, having matches to a set of peptide sequences that cannot be distinguished using the evidence in the mass spectra." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001596
name: sequence sub-set protein
def: "A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001597
name: spectrum sub-set protein
def: "A protein with a sub-set of the matched spectra for another protein, where the matches cannot be distinguished using the evidence in the mass spectra, and no distinguishing peptide matches." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001598
name: sequence subsumable protein
def: "A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001599
name: spectrum subsumable protein
def: "A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001600
name: protein inference confidence category
def: "Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable)." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001601
name: ProteomeDiscoverer:Spectrum Files:Raw File names
def: "OBSOLETE Name and location of the .raw file or files." [PSI:MS]
comment: This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001602
name: ProteomeDiscoverer:SRF File Selector:SRF File Path
def: "OBSOLETE Path and name of the .srf (SEQUEST Result Format) file." [PSI:MS]
comment: This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001603
name: ProteomeDiscoverer:Spectrum Selector:Ionization Source
def: "OBSOLETE Ionization source (electro-, nano-, thermospray, electron impact, APCI, MALDI, FAB etc)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use one of the 'inlet type' (MS:1000007) or 'ionization type' (MS:1000008) terms instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001604
name: ProteomeDiscoverer:Activation Type
def: "OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use one of the 'ionization type' terms (MS:1000008) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001605
name: ProteomeDiscoverer:Spectrum Selector:Lower RT Limit
def: "Lower retention-time limit." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001606
name: ProteomeDiscoverer:Mass Analyzer
def: "OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, SectorMS)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use mass analyzer type (MS:1000443) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001607
name: ProteomeDiscoverer:Max Precursor Mass
def: "Maximum mass limit of a singly charged precursor ion." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001608
name: ProteomeDiscoverer:Min Precursor Mass
def: "Minimum mass limit of a singly charged precursor ion." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001609
name: ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count
def: "Minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001610
name: ProteomeDiscoverer:MS Order
def: "OBSOLETE Level of the mass spectrum (MS2 ... MS10)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579) or MSn spectrum (MS:1000580) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001611
name: ProteomeDiscoverer:Polarity Mode
def: "OBSOLETE Polarity mode (positive or negative)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use scan polarity (MS:1000465) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001612
name: ProteomeDiscoverer:Spectrum Selector:Precursor Selection
def: "Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3)." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001613
name: ProteomeDiscoverer:SN Threshold
def: "Signal-to-Noise ratio below which peaks are removed." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001614
name: ProteomeDiscoverer:Scan Type
def: "OBSOLETE Scan type for the precursor ion (full, Single Ion Monitoring (SIM), Single Reaction Monitoring (SRM))." [PSI:MS]
comment: This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579), MSn spectrum (MS:1000580), CRM spectrum (MS:1000581), SIM spectrum (MS:1000582) or SRM spectrum (MS:1000583) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001615
name: ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold
def: "Used to filter out tandem mass spectra that have a total intensity current(sum of the intensities of all peaks in a spectrum) below the specified value." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001616
name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements
def: "Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001617
name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements
def: "Specifies the charge state of the precursor ions, if it is not defined in the scan header." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001618
name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements
def: "Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001619
name: ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements
def: "Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001620
name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements
def: "Specifies the polarity of the ions monitored if it is not included in the scan header." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001621
name: ProteomeDiscoverer:Spectrum Selector:Upper RT Limit
def: "Upper retention-time limit." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001622
name: ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset
def: "Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001623
name: ProteomeDiscoverer:Non-Fragment Filter:Maximum Neutral Loss Mass
def: "Maximum allowed mass of a neutral loss." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001624
name: ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor
def: "Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001625
name: ProteomeDiscoverer:Non-Fragment Filter:Remove Neutral Loss Peaks
def: "Determines whether neutral loss peaks are removed from ETD and ECD spectra." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001626
name: ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses
def: "Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001627
name: ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones
def: "Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001628
name: ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak
def: "Determines whether precursor artifact peaks from the MS2 input spectra are removed." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001629
name: ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch
def: "Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001630
name: ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch
def: "Determines whether spectra from different MS order scans can be grouped together." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001631
name: ProteomeDiscoverer:Spectrum Grouper:Max RT Difference
def: "OBSOLETE Chromatographic window where precursors to be grouped must reside to be considered the same species." [PSI:MS]
comment: This term was made obsolete because it's recommended to use retention time window width (MS:1001907) instead.
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001632
name: ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion
def: "Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001633
name: ProteomeDiscoverer:Xtract:Highest Charge
def: "Highest charge state that is allowed for the deconvolution of multiply charged data." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001634
name: ProteomeDiscoverer:Xtract:Highest MZ
def: "OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract." [PSI:MS]
comment: This term was made obsolete because it's recommended to use scan window upper limit (MS:1000500) instead.
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001635
name: ProteomeDiscoverer:Xtract:Lowest Charge
def: "Lowest charge state that is allowed for the deconvolution of multiply charged data." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001636
name: ProteomeDiscoverer:Xtract:Lowest MZ
def: "OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract." [PSI:MS]
comment: This term was made obsolete because it's recommended to use scan window lower limit (MS:1000501) instead.
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001637
name: ProteomeDiscoverer:Xtract:Monoisotopic Mass Only
def: "Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001638
name: ProteomeDiscoverer:Xtract:Overlapping Remainder
def: "Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted)." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001639
name: ProteomeDiscoverer:Xtract:Required Fitting Accuracy
def: "Accuracy required for a pattern fit to be considered valid." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001640
name: ProteomeDiscoverer:Xtract:Resolution At 400
def: "Resolution at mass 400." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001641
name: ProteomeDiscoverer:Lowest Charge State
def: "Minimum charge state below which peptides are filtered out." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001642
name: ProteomeDiscoverer:Highest Charge State
def: "Maximum charge above which peptides are filtered out." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001643
name: ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores
def: "Determines whether spectra with scores above the threshold score are retained rather than filtered out." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001644
name: ProteomeDiscoverer:Dynamic Modification
def: "Determine dynamic post-translational modifications (PTMs)." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001645
name: ProteomeDiscoverer:Static Modification
def: "Static Modification to all occurrences of a named amino acid." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001646
name: ProteomeDiscoverer:Mascot:Decoy Search
def: "OBSOLETE Determines whether the Proteome Discoverer application searches an additional decoy database." [PSI:MS]
comment: This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead.
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001647
name: ProteomeDiscoverer:Mascot:Error tolerant Search
def: "Determines whether to search error-tolerant." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001648
name: ProteomeDiscoverer:Mascot:Max MGF File Size
def: "Maximum size of the .mgf (Mascot Generic Format) file in MByte." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001649
name: ProteomeDiscoverer:Mascot:Mascot Server URL
def: "URL (Uniform resource Locator) of the Mascot server." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001650
name: ProteomeDiscoverer:Mascot:Number of attempts to submit the search
def: "Number of attempts to submit the Mascot search." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001651
name: ProteomeDiscoverer:Mascot:X Static Modification
def: "Number of attempts to submit the Mascot search." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001652
name: ProteomeDiscoverer:Mascot:User Name
def: "OBSOLETE Name of the user submitting the Mascot search." [PSI:MS]
comment: This term was made obsolete because it's recommended to use researcher (MS:1001271) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001653
name: ProteomeDiscoverer:Mascot:Time interval between attempts to submit a search
def: "Time interval between attempts to submit a search in seconds." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001654
name: ProteomeDiscoverer:Enzyme Name
def: "OBSOLETE Specifies the enzyme reagent used for protein digestion." [PSI:MS]
comment: This term was made obsolete because it's recommended to use cleavage agent name (MS:1001045) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001655
name: ProteomeDiscoverer:Fragment Mass Tolerance
def: "OBSOLETE Mass tolerance used for matching fragment peaks in Da or mmu." [PSI:MS]
comment: This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead.
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001656
name: Mascot:Instrument
def: "Type of instrument used to acquire the data in the raw file." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001657
name: ProteomeDiscoverer:Maximum Missed Cleavage Sites
def: "Maximum number of missed cleavage sites to consider during the digest." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001658
name: ProteomeDiscoverer:Mascot:Peptide CutOff Score
def: "Minimum score in the IonScore column that each peptide must exceed in order to be reported." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001659
name: ProteomeDiscoverer:Precursor Mass Tolerance
def: "OBSOLETE Mass window for which precursor ions are considered to be the same species." [PSI:MS]
comment: This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead.
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001660
name: ProteomeDiscoverer:Mascot:Protein CutOff Score
def: "Minimum protein score in the IonScore column that each protein must exceed in order to be reported." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001661
name: ProteomeDiscoverer:Protein Database
def: "OBSOLETE Database to use in the search (configured on the Mascot server)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use database name (MS:1001013) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001662
name: ProteomeDiscoverer:Mascot:Protein Relevance Factor
def: "Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001663
name: ProteomeDiscoverer:Target FDR Relaxed
def: "Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001664
name: ProteomeDiscoverer:Target FDR Strict
def: "Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001665
name: ProteomeDiscoverer:Mascot:Taxonomy
def: "OBSOLETE Limits searches to entries from a particular species or group of species." [PSI:MS]
comment: This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001666
name: ProteomeDiscoverer:Use Average Precursor Mass
def: "OBSOLETE Use average mass for the precursor." [PSI:MS]
comment: This term was made obsolete because it's recommended to use parent mass type average (MS:1001212) instead.
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001667
name: Mascot:use MudPIT scoring
def: "OBSOLETE Determines whether to use MudPIT or normal scoring." [PSI:MS]
comment: This term was made obsolete because it's recommended to use Mascot:ProteinScoringMethod (MS:1001318) instead.
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
is_obsolete: true
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001668
name: ProteomeDiscoverer:Absolute XCorr Threshold
def: "Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001669
name: ProteomeDiscoverer:SEQUEST:Calculate Probability Score
def: "Determines whether to calculate a probability score for every peptide match." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001670
name: ProteomeDiscoverer:SEQUEST:CTerminal Modification
def: "Dynamic C-terminal modification that is used during the search." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001671
name: ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage
def: "Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001672
name: ProteomeDiscoverer:SEQUEST:Max Identical Modifications Per Peptide
def: "Maximum number of identical modifications that a single peptide can have." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001673
name: ProteomeDiscoverer:Max Modifications Per Peptide
def: "Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001674
name: ProteomeDiscoverer:SEQUEST:Maximum Peptides Considered
def: "Maximum number of peptides that are searched and scored per spectrum." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001675
name: ProteomeDiscoverer:Maximum Peptides Output
def: "Maximum number of peptide matches reported per spectrum." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001676
name: ProteomeDiscoverer:Maximum Protein References Per Peptide
def: "Maximum number of proteins that a single identified peptide can be associated with during protein assembly." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001677
name: ProteomeDiscoverer:SEQUEST:NTerminal Modification
def: "Dynamic N-terminal modification that is used during the search." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001678
name: ProteomeDiscoverer:Peptide CTerminus
def: "Static modification for the C terminal of the peptide used during the search." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001679
name: ProteomeDiscoverer:Peptide NTerminus
def: "Static modification for the N terminal of the peptide used during the search." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001680
name: ProteomeDiscoverer:SEQUEST:Peptide Relevance Factor
def: "Specifies a factor to apply to the protein score." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001681
name: ProteomeDiscoverer:Protein Relevance Threshold
def: "Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001682
name: ProteomeDiscoverer:Search Against Decoy Database
def: "OBSOLETE Determines whether the Proteome Discoverer application searches against a decoy database." [PSI:MS]
comment: This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead.
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001683
name: ProteomeDiscoverer:SEQUEST:Use Average Fragment Masses
def: "Use average masses for the fragments." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001684
name: ProteomeDiscoverer:Use Neutral Loss a Ions
def: "Determines whether a ions with neutral loss are used for spectrum matching." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001685
name: ProteomeDiscoverer:Use Neutral Loss b Ions
def: "Determines whether b ions with neutral loss are used for spectrum matching." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001686
name: ProteomeDiscoverer:Use Neutral Loss y Ions
def: "Determines whether y ions with neutral loss are used for spectrum matching." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001687
name: ProteomeDiscoverer:Use Neutral Loss z Ions
def: "Determines whether z ions with neutral loss are used for spectrum matching." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001688
name: ProteomeDiscoverer:SEQUEST:Weight of a Ions
def: "Uses a ions for spectrum matching with this relative factor." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001689
name: ProteomeDiscoverer:SEQUEST:Weight of b Ions
def: "Uses b ions for spectrum matching with this relative factor." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001690
name: ProteomeDiscoverer:SEQUEST:Weight of c Ions
def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001691
name: ProteomeDiscoverer:SEQUEST:Weight of d Ions
def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001692
name: ProteomeDiscoverer:SEQUEST:Weight of v Ions
def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001693
name: ProteomeDiscoverer:SEQUEST:Weight of w Ions
def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001694
name: ProteomeDiscoverer:SEQUEST:Weight of x Ions
def: "Uses x ions for spectrum matching with this relative factor." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001695
name: ProteomeDiscoverer:SEQUEST:Weight of y Ions
def: "Uses y ions for spectrum matching with this relative factor." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001696
name: ProteomeDiscoverer:SEQUEST:Weight of z Ions
def: "Uses z ions for spectrum matching with this relative factor." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001697
name: ProteomeDiscoverer:ZCore:Protein Score Cutoff
def: "Sets a minimum protein score that each protein must exceed in order to be reported." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001698
name: ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method
def: "Specifies which peak to select if more than one peak is found inside the integration window." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001699
name: ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance
def: "Specifies the mass-to-charge window that enables one to look for the reporter peaks." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001700
name: ProteomeDiscoverer:Reporter Ions Quantizer:Quantitation Method
def: "Quantitation method for isobarically labeled quantitation." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001701
name: ProteomeDiscoverer:Spectrum Exporter:Export Format
def: "OBSOLETE Format of the exported spectra (dta, mgf or mzData)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001702
name: ProteomeDiscoverer:Spectrum Exporter:File name
def: "Name of the output file that contains the exported data." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001703
name: ProteomeDiscoverer:Search Modifications Only For Identified Proteins
def: "Influences the modifications search." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001704
name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge1
def: "Standard high confidence XCorr parameter for charge = 1." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001705
name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge2
def: "Standard high confidence XCorr parameter for charge = 2." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001706
name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge3
def: "Standard high confidence XCorr parameter for charge = 3." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001707
name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge4
def: "Standard high confidence XCorr parameter for charge >= 4." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001708
name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge1
def: "Standard medium confidence XCorr parameter for charge = 1." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001709
name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge2
def: "Standard medium confidence XCorr parameter for charge = 2." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001710
name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge3
def: "Standard medium confidence XCorr parameter for charge = 3." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001711
name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge4
def: "Standard medium confidence XCorr parameter for charge >= 4." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001712
name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1
def: "FT high confidence XCorr parameter for charge = 1." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001713
name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2
def: "FT high confidence XCorr parameter for charge = 2." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001714
name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3
def: "FT high confidence XCorr parameter for charge = 3." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001715
name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4
def: "FT high confidence XCorr parameter for charge >= 4." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001716
name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1
def: "FT medium confidence XCorr parameter for charge = 1." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001717
name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2
def: "FT medium confidence XCorr parameter for charge = 2." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001718
name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3
def: "FT medium confidence XCorr parameter for charge = 3." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001719
name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4
def: "FT medium confidence XCorr parameter for charge >= 4." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001720
name: ProteomeDiscoverer:1. Dynamic Modification
def: "OBSOLETE ProteomeDiscoverer's 1st dynamic post-translational modification (PTM) input parameter." [PSI:PI]
comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001721
name: ProteomeDiscoverer:2. Dynamic Modification
def: "OBSOLETE ProteomeDiscoverer's 2nd dynamic post-translational modification (PTM) input parameter." [PSI:PI]
comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001722
name: ProteomeDiscoverer:3. Dynamic Modification
def: "OBSOLETE ProteomeDiscoverer's 3rd dynamic post-translational modification (PTM) input parameter." [PSI:PI]
comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001723
name: ProteomeDiscoverer:4. Dynamic Modification
def: "OBSOLETE ProteomeDiscoverer's 4th dynamic post-translational modification (PTM) input parameter." [PSI:PI]
comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001724
name: ProteomeDiscoverer:Static Modification for X
def: "Static Modification for X." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001725
name: ProteomeDiscoverer:Initial minimal peptide probability
def: "Minimal initial peptide probability to contribute to analysis." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001726
name: ProteomeDiscoverer:Minimal peptide probability
def: "Minimum adjusted peptide probability contributing to protein probability." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001727
name: ProteomeDiscoverer:Minimal peptide weight
def: "Minimum peptide weight contributing to protein probability." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001728
name: ProteomeDiscoverer:Number of input1 spectra
def: "Number of spectra from 1+ precursor ions." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001729
name: ProteomeDiscoverer:Number of input2 spectra
def: "Number of spectra from 2+ precursor ions." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001730
name: ProteomeDiscoverer:Number of input3 spectra
def: "Number of spectra from 3+ precursor ions." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001731
name: ProteomeDiscoverer:Number of input4 spectra
def: "Number of spectra from 4+ precursor ions." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001732
name: ProteomeDiscoverer:Number of input5 spectra
def: "Number of spectra from 5+ precursor ions." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001733
name: ProteomeDiscoverer:Number of predicted correct proteins
def: "Total number of predicted correct protein ids (sum of probabilities)." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001734
name: ProteomeDiscoverer:Organism
def: "OBSOLETE Sample organism (used for annotation purposes)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001735
name: ProteomeDiscoverer:Reference Database
def: "OBSOLETE Full path database name." [PSI:MS]
comment: This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001736
name: ProteomeDiscoverer:Residue substitution list
def: "Residues considered equivalent when comparing peptides." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001737
name: ProteomeDiscoverer:Source file extension
def: "OBSOLETE File type (if not pepXML)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use mass spectrometer file format (MS:1000560) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001738
name: ProteomeDiscoverer:Source Files
def: "OBSOLETE Input pepXML files." [PSI:MS]
comment: This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001739
name: ProteomeDiscoverer:Source Files old
def: "OBSOLETE Input pepXML files (old)." [PSI:MS]
comment: This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001740
name: ProteomeDiscoverer:WinCyg reference database
def: "Windows full path for database." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001741
name: ProteomeDiscoverer:WinCyg source files
def: "Windows pepXML file names." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001742
@@ -11207,127 +11408,127 @@ is_a: MS:1000494 ! Thermo Scientific instrument model
id: MS:1001743
name: ProteomeDiscoverer:Mascot:Weight of A Ions
def: "Determines if to use A ions for spectrum matching." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001744
name: ProteomeDiscoverer:Mascot:Weight of B Ions
def: "Determines if to use B ions for spectrum matching." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001745
name: ProteomeDiscoverer:Mascot:Weight of C Ions
def: "Determines if to use C ions for spectrum matching." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001746
name: ProteomeDiscoverer:Mascot:Weight of D Ions
def: "Determines if to use D ions for spectrum matching." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001747
name: ProteomeDiscoverer:Mascot:Weight of V Ions
def: "Determines if to use V ions for spectrum matching." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001748
name: ProteomeDiscoverer:Mascot:Weight of W Ions
def: "Determines if to use W ions for spectrum matching." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001749
name: ProteomeDiscoverer:Mascot:Weight of X Ions
def: "Determines if to use X ions for spectrum matching." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001750
name: ProteomeDiscoverer:Mascot:Weight of Y Ions
def: "Determines if to use Y ions for spectrum matching." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001751
name: ProteomeDiscoverer:Mascot:Weight of Z Ions
def: "Determines if to use z ions for spectrum matching." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001752
name: ProteomeDiscoverer:Spectrum Selector:Use New Precursor Reevaluation
def: "Determines if to use precursor reevaluation." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001753
name: ProteomeDiscoverer:Spectrum Selector:SN Threshold FTonly
def: "Signal-to-Noise ratio below which peaks are removed (in FT mode only)." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001754
name: ProteomeDiscoverer:Mascot:Please Do not Touch this
def: "Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001755
name: contact phone number
def: "Phone number of the contact person or organization." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000585 ! contact attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001756
name: contact fax number
def: "Fax number for the contact person or organization." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000585 ! contact attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001757
name: contact toll-free phone number
def: "Toll-free phone number of the contact person or organization." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000585 ! contact attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001758
name: Mascot:SigThresholdType
def: "Significance threshold type used in Mascot reporting (either 'identity' or 'homology')." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001759
name: Mascot:ProteinGrouping
def: "Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam's razor' or 'family clustering')." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001760
name: Percolator:features
def: "List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002107 ! Percolator input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001761
@@ -11525,8 +11726,8 @@ is_a: MS:1000126 ! Waters instrument model
id: MS:1001793
name: Mascot:PreferredTaxonomy
def: "NCBI TaxID taxonomy ID to prefer when two or more proteins match the same set of peptides or when protein entry in database represents multiple sequences." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001795
@@ -11619,8 +11820,8 @@ is_a: MS:1001806 ! quantification object attribute
id: MS:1001808
name: technical replicate
def: "The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001807 ! study variable attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001809
@@ -11656,22 +11857,22 @@ is_a: MS:1001807 ! study variable attribute
id: MS:1001814
name: generic experimental condition
def: "The experimental condition is given in the value of this term." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001807 ! study variable attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001815
name: time series, time point X
def: "The experimental design followed a time series design. The time point of this run is given in the value of this term." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001807 ! study variable attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001816
name: dilution series, concentration X
def: "The experimental design followed a dilution series design. The concentration of this run is given in the value of this term." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001807 ! study variable attribute
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001817
@@ -11749,8 +11950,8 @@ is_a: MS:1001806 ! quantification object attribute
id: MS:1001829
name: SRM transition ID
def: "Identifier for an SRM transition in an external document describing additional information about the transition." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001828 ! feature attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001830
@@ -11769,8 +11970,8 @@ is_a: MS:1000752 ! TOPP software
id: MS:1001832
name: quantitation software comment or customizations
def: "Quantitation software comment or any customizations to the default setup of the software." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001129 ! quantification information
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001833
@@ -11818,59 +12019,59 @@ is_a: MS:1001833 ! quantitation analysis summary
id: MS:1001840
name: LC-MS feature intensity
def: "Maximum peak intensity of the LC-MS feature." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001841
name: LC-MS feature volume
def: "Real (intensity times area) volume of the LC-MS feature." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001842
name: sequence-level spectral count
def: "The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001843
name: MS1 feature maximum intensity
def: "Maximum intensity of MS1 feature." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001844
name: MS1 feature area
def: "Area of MS1 feature." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001845
name: peak area
def: "OBSOLETE Area of MS1 peak (e.g. SILAC, 15N)." [PSI:PI]
comment: This term was made obsolete because it was a duplication of MS:1001844.
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
is_obsolete: true
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001846
name: isotopic pattern area
def: "Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001847
name: reporter ion intensity
def: "Intensity of MS2 reporter ion (e.g. iTraq)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001848
@@ -11883,86 +12084,86 @@ id: MS:1001849
name: sum of MatchedFeature values
def: "OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values." [PSI:PI]
comment: This term was made obsolete because the concept MatchedFeature was dropped.
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype
is_obsolete: true
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001850
name: normalized peptide value
def: "Normalized peptide value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001851
name: protein value: sum of peptide values
def: "Protein quantification value calculated as sum of peptide values." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002738 ! protein-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001852
name: normalized protein value
def: "Normalized protein value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002738 ! protein-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001853
name: max fold change
def: "Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001854
name: ANOVA p-value
def: "Global datatype: p-value of ANOVA of group means (e.g. Progenesis)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002072 ! p-value
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001855
name: t-test p-value
def: "P-value of t-Test of two groups." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002072 ! p-value
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001856
name: reporter ion raw value
def: "Intensity (or area) of MS2 reporter ion (e.g. iTraq)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001857
name: reporter ion normalized value
def: "Normalized value of MS2 reporter ion (e.g. iTraq)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001858
name: XIC area
def: "Area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001859
name: normalized XIC area
def: "Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001860
name: protein value: mean of peptide ratios
def: "Protein quantification value calculated as mean of peptide ratios." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002738 ! protein-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001861
@@ -12010,66 +12211,66 @@ is_a: MS:1001861 ! quantification data processing
id: MS:1001868
name: distinct peptide-level q-value
def: "Estimation of the q-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs, possibly with different mass modifications, mapping to the same sequence have been collapsed to one entry)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002484 ! peptide-level statistical threshold
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001869
name: protein-level q-value
def: "Estimation of the q-value for proteins." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001870
name: peptide sequence-level p-value
def: "Estimation of the p-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide sequence-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001871
name: protein-level p-value
def: "Estimation of the p-value for proteins." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001872
name: peptide sequence-level e-value
def: "Estimation of the e-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide sequence-level identification statistic
relationship: has_domain MS:1002306 ! value greater than zero
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001873
name: protein-level e-value
def: "Estimation of the e-value for proteins." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein identification statistic
relationship: has_domain MS:1002306 ! value greater than zero
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001874
name: FDRScore
def: "OBSOLETE A smoothing of the distribution of q-values calculated for PSMs from individual search engines, such that ordering of result quality is maintained and all FDRScore values are guaranteed to have a value > 0." [PMID:19253293]
comment: This term was made obsolete because it was split into the more specific terms for PSM-level FDRScore (1002355), distinct peptide-level FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein group-level FDRScore (MS:1002374).
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
is_obsolete: true
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001875
name: modification motif
def: "The regular expression describing the sequence motif for a modification." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001056 ! modification specificity rule
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001876
@@ -12096,9 +12297,9 @@ is_a: MS:1001558 ! MALDI Solutions
id: MS:1001879
name: offset voltage
def: "The potential difference between two adjacent interface voltages affecting in-source collision induced dissociation." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000218 ! volt
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001880
@@ -12122,22 +12323,23 @@ relationship: part_of MS:1000908 ! transition
id: MS:1001883
name: coefficient of variation
def: "Variation of a set of signal measurements calculated as the standard deviation relative to the mean." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001882 ! transition validation attribute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001884
name: signal-to-noise ratio
def: "Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001882 ! transition validation attribute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001885
name: command-line parameters
def: "Parameters string passed to a command-line interface software application, omitting the executable name." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter
+is_a: MS:1003201 ! library provenance attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001886
@@ -12168,129 +12370,129 @@ is_a: MS:1002363 ! search engine specific score for proteins
id: MS:1001890
name: Progenesis:protein normalised abundance
def: "The data type normalised abundance for proteins produced by Progenesis LC-MS." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002738 ! protein-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001891
name: Progenesis:peptide normalised abundance
def: "The data type normalised abundance for peptides produced by Progenesis LC-MS." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001892
name: Progenesis:protein raw abundance
def: "The data type raw abundance for proteins produced by Progenesis LC-MS." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002738 ! protein-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001893
name: Progenesis:peptide raw abundance
def: "The data type raw abundance for peptide produced by Progenesis LC-MS." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001894
name: Progenesis:confidence score
def: "The data type confidence score produced by Progenesis LC-MS." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001895
name: Progenesis:peptide count
def: "The data type peptide count produced by Progenesis LC-MS." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001896
name: Progenesis:feature intensity
def: "The data type feature intensity produced by Progenesis LC-MS." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001897
name: MaxQuant:peptide counts (unique)
def: "The data type peptide counts (unique) produced by MaxQuant." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001898
name: MaxQuant:peptide counts (all)
def: "The data type peptide counts (all) produced by MaxQuant." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001899
name: MaxQuant:peptide counts (razor+unique)
def: "The data type peptide counts (razor+unique) produced by MaxQuant." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001900
name: MaxQuant:sequence length
def: "The data type sequence length produced by MaxQuant." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001901
name: MaxQuant:PEP
def: "The data type PEP (posterior error probability) produced by MaxQuant." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001902
name: MaxQuant:LFQ intensity
def: "The data type LFQ intensity produced by MaxQuant." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001903
name: MaxQuant:feature intensity
def: "The data type feature intensity produced by MaxQuant." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001904
name: MaxQuant:MS/MS count
def: "The data type MS2 count produced by MaxQuant." [PSI:MS]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1001905
name: emPAI value
def: "The emPAI value of protein abundance, produced from the emPAI algorithm." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002738 ! protein-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001906
name: APEX value
def: "The APEX value of protein abundance, produced from the APEX software." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002738 ! protein-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001907
name: retention time window width
def: "The full width of a retention time window for a chromatographic peak." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000915 ! retention time window attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001908
@@ -12328,9 +12530,9 @@ is_a: MS:1001457 ! data processing software
id: MS:1001913
name: S-lens voltage
def: "Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000218 ! volt
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001914
@@ -12372,80 +12574,80 @@ relationship: has_regexp MS:1001960 ! (?<=W)
id: MS:1001919
name: ProteomeXchange accession number
def: "Main identifier of a ProteomeXchange dataset." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001921
name: ProteomeXchange accession number version number
def: "Version number of a ProteomeXchange accession number." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001922
name: Digital Object Identifier (DOI)
def: "DOI unique identifier of a publication." [PSI:PI, http://dx.doi.org]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
synonym: "doi" EXACT []
is_a: MS:1000878 ! external reference identifier
relationship: has_regexp MS:1002480 ! (10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+)
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001923
name: external reference keyword
def: "Free text attribute that can enrich the information about an entity." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002840 ! external reference data
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001924
name: journal article keyword
def: "Keyword present in a scientific publication." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001923 ! external reference keyword
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001925
name: submitter keyword
def: "Keyword assigned by the data submitter." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001923 ! external reference keyword
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001926
name: curator keyword
def: "Keyword assigned by a data curator." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001923 ! external reference keyword
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001927
name: Tranche file hash
def: "Hash assigned by the Tranche resource to an individual file." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001928
name: Tranche project hash
def: "Hash assigned by the Tranche resource to a whole project." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001929
name: PRIDE experiment URI
def: "URI that allows the access to one experiment in the PRIDE database." [PSI:PI]
-xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term
[Term]
id: MS:1001930
name: PRIDE project URI
def: "URI that allows the access to one project in the PRIDE database." [PSI:PI]
-xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term
[Term]
id: MS:1001931
@@ -12457,15 +12659,15 @@ relationship: part_of MS:1000458 ! source
id: MS:1001932
name: source interface model
def: "The source interface model." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:1001931 ! source interface
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001933
name: source sprayer
def: "The source sprayer." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:1000458 ! source
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001934
@@ -12477,15 +12679,15 @@ relationship: part_of MS:1001933 ! source sprayer
id: MS:1001935
name: source sprayer manufacturer
def: "The source sprayer manufacturer." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:1001933 ! source sprayer
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001936
name: source sprayer model
def: "The source sprayer model." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:1001933 ! source sprayer
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001937
@@ -12533,10 +12735,10 @@ is_a: MS:1001941 ! electrospray supply type
id: MS:1001944
name: Collision cell exit potential
def: "Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
relationship: has_units UO:0000218 ! volt
synonym: "CXP" EXACT []
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001945
@@ -12578,36 +12780,36 @@ is_a: MS:1000531 ! software
id: MS:1001950
name: PEAKS:peptideScore
def: "The PEAKS peptide '-10lgP Score'." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001951
name: PEAKS:proteinScore
def: "The PEAKS protein '-10lgP Score'." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001952
name: ZCore:probScore
def: "The ZCore probability score." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001953
name: source interface manufacturer
def: "The source interface manufacturer." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:1001931 ! source interface
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001954
name: acquisition parameter
def: "Parameters used in the mass spectrometry acquisition." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:1001458 ! spectrum generation information
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001955
@@ -12649,36 +12851,36 @@ is_a: MS:1001180 ! Cleavage agent regular expression
id: MS:1001961
name: peptide spectrum match scoring algorithm
def: "Algorithm used to score the match between a spectrum and a peptide ion." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:1001458 ! spectrum generation information
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001962
name: Mascot:C13 counts
def: "C13 peaks to use in peak detection." [PSI:MS]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1001963
name: ProteinExtractor:Weighting
def: "Weighting factor for protein list compilation by ProteinExtractor." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001964
name: ProteinScape:second round Mascot
def: "Flag indicating a second round search with Mascot." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002100 ! ProteinScape input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001965
name: ProteinScape:second round Phenyx
def: "Flag indicating a second round search with Phenyx." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002100 ! ProteinScape input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1001966
@@ -12690,11 +12892,11 @@ is_a: MS:1001221 ! product ion attribute
id: MS:1001967
name: product ion drift time
def: "OBSOLETE The ion drift time of an MS2 product ion." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002222 ! SRM transition attribute
relationship: has_units UO:0000028 ! millisecond
comment: This term was made obsolete because it was replaced by ion mobility drift time (MS:1002476).
is_obsolete: true
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1001968
@@ -12706,32 +12908,32 @@ is_a: MS:1002689 ! PTM localization single result statistic
id: MS:1001969
name: phosphoRS score
def: "phosphoRS score for PTM site location at the PSM-level." [DOI:10.1021/pr200611n, PMID:22073976]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001970
name: phosphoRS sequence probability
def: "Probability that the respective isoform is correct." [DOI:10.1021/pr200611n, PMID:22073976]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001971
name: phosphoRS site probability
def: "Estimate of the probability that the respective site is truly phosphorylated." [DOI:10.1021/pr200611n, PMID:22073976]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001972
name: PTM scoring algorithm version
def: "Version of the post-translational modification scoring algorithm." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001973
@@ -12743,32 +12945,34 @@ is_a: MS:1001456 ! analysis software
id: MS:1001974
name: DeBunker:score
def: "Score specific to DeBunker." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001975
name: delta m/z
def: "The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value." [PSI:MS]
synonym: "m/z difference" EXACT []
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
relationship: has_units UO:0000166 ! parts per notation unit
+relationship: has_units UO:0000169 ! parts per million
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001976
name: delta M
def: "The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value." [PSI:MS]
synonym: "mass difference" EXACT []
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
relationship: has_units UO:0000166 ! parts per notation unit
+relationship: has_units UO:0000169 ! parts per million
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1001977
@@ -12780,48 +12984,48 @@ is_a: MS:1001456 ! analysis software
id: MS:1001978
name: MSQuant:PTM-score
def: "The PTM score from MSQuant software." [DOI:10.1021/pr900721e, PMID:19888749]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001979
name: MaxQuant:PTM Score
def: "The PTM score from MaxQuant software." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001980
name: MaxQuant:Phospho (STY) Probabilities
def: "The Phospho (STY) Probabilities from MaxQuant software." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001981
name: MaxQuant:Phospho (STY) Score Diffs
def: "The Phospho (STY) Score Diffs from MaxQuant software." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001982
name: MaxQuant:P-site localization probability
def: "The P-site localization probability value from MaxQuant software." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001983
name: MaxQuant:PTM Delta Score
def: "The PTM Delta Score value from MaxQuant software (Difference between highest scoring site and second highest)." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001984
@@ -12833,17 +13037,17 @@ is_a: MS:1001456 ! analysis software
id: MS:1001985
name: Ascore
def: "A-score for PTM site location at the PSM-level." [DOI:10.1038/nbt1240, PMID:16964243]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001986
name: H-Score
def: "H-Score for peptide phosphorylation site location." [DOI:10.1021/pr1006813, PMID:20836569]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1001987
@@ -12934,29 +13138,29 @@ is_a: MS:1000044 ! dissociation method
id: MS:1002001
name: MS1 label-based raw feature quantitation
def: "MS1 label-based raw feature quantitation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002018 ! MS1 label-based analysis
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002002
name: MS1 label-based peptide level quantitation
def: "MS1 label-based peptide level quantitation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002018 ! MS1 label-based analysis
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002003
name: MS1 label-based protein level quantitation
def: "MS1 label-based protein level quantitation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002018 ! MS1 label-based analysis
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002004
name: MS1 label-based proteingroup level quantitation
def: "MS1 label-based proteingroup level quantitation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002018 ! MS1 label-based analysis
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002005
@@ -13008,46 +13212,46 @@ is_a: MS:1000240 ! atmospheric pressure ionization
id: MS:1002012
name: Mascot:PTM site assignment confidence
def: "Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score)." [http://www.matrixscience.com/help/pt_mods_help.html#SITE]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_units UO:0000187 ! percent
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002013
name: collision energy ramp start
def: "Collision energy at the start of the collision energy ramp." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000045 ! collision energy
relationship: has_units UO:0000266 ! electronvolt
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002014
name: collision energy ramp end
def: "Collision energy at the end of the collision energy ramp." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000045 ! collision energy
relationship: has_units UO:0000266 ! electronvolt
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002015
name: spectral count peptide level quantitation
def: "Spectral count peptide level quantitation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001836 ! spectral counting quantitation analysis
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002016
name: spectral count protein level quantitation
def: "Spectral count protein level quantitation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001836 ! spectral counting quantitation analysis
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002017
name: spectral count proteingroup level quantitation
def: "Spectral count proteingroup level quantitation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001836 ! spectral counting quantitation analysis
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002018
@@ -13059,29 +13263,29 @@ is_a: MS:1001833 ! quantitation analysis summary
id: MS:1002019
name: label-free raw feature quantitation
def: "Label-free raw feature quantitation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001834 ! LC-MS label-free quantitation analysis
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002020
name: label-free peptide level quantitation
def: "Label-free peptide level quantitation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001834 ! LC-MS label-free quantitation analysis
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002021
name: label-free protein level quantitation
def: "Label-free protein level quantitation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001834 ! LC-MS label-free quantitation analysis
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002022
name: label-free proteingroup level quantitation
def: "Label-free proteingroup level quantitation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001834 ! LC-MS label-free quantitation analysis
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002023
@@ -13093,64 +13297,64 @@ is_a: MS:1001833 ! quantitation analysis summary
id: MS:1002024
name: MS2 tag-based feature level quantitation
def: "MS2 tag-based feature level quantitation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002023 ! MS2 tag-based analysis
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002025
name: MS2 tag-based peptide level quantitation
def: "MS2 tag-based peptide level quantitation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002023 ! MS2 tag-based analysis
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002026
name: MS2 tag-based protein level quantitation
def: "MS2 tag-based protein level quantitation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002023 ! MS2 tag-based analysis
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002027
name: MS2 tag-based proteingroup level quantitation
def: "MS2 tag-based proteingroup level quantitation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002023 ! MS2 tag-based analysis
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002028
name: nucleic acid base modification
def: "Nucleic acid base modification (substitution, insertion or deletion)." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002029
name: original nucleic acid sequence
def: "Specification of the original nucleic acid sequence, prior to a modification. The value slot should hold the DNA or RNA sequence." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002030
name: modified nucleic acid sequence
def: "Specification of the modified nucleic acid sequence. The value slot should hold the DNA or RNA sequence." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002031
name: PASSEL transition group browser URI
def: "URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment." [PSI:PI]
-xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term
[Term]
id: MS:1002032
name: PeptideAtlas dataset URI
def: "URI that allows access to a PeptideAtlas dataset." [PSI:PI]
-xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term
[Term]
id: MS:1002033
@@ -13200,29 +13404,29 @@ relationship: part_of MS:1000458 ! source
id: MS:1002040
name: inlet temperature
def: "The temperature of the inlet of a mass spectrometer." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
is_a: MS:1002039 ! inlet attribute
relationship: has_units UO:0000012 ! kelvin
relationship: has_units UO:0000027 ! degree Celsius
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002041
name: source temperature
def: "The temperature of the source of a mass spectrometer." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000012 ! kelvin
relationship: has_units UO:0000027 ! degree Celsius
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002042
name: modulation time
def: "The duration of a complete cycle of modulation in a comprehensive two-dimensional separation system, equals the length of a second dimension chromatogram, i.e., the time between two successive injections into the second column." [http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000857 ! run attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002043
@@ -13234,22 +13438,22 @@ is_a: MS:1001456 ! analysis software
id: MS:1002044
name: ProteinProspector:score
def: "The ProteinProspector result 'Score'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002045
name: ProteinProspector:expectation value
def: "The ProteinProspector result 'Expectation value'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002046
name: native source path
def: "The original source path used for directory-based sources." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001458 ! spectrum generation information
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002047
@@ -13268,62 +13472,62 @@ is_a: MS:1001456 ! analysis software
id: MS:1002049
name: MS-GF:RawScore
def: "MS-GF raw score." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002050
name: MS-GF:DeNovoScore
def: "MS-GF de novo score." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002051
name: MS-GF:Energy
def: "MS-GF energy score." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1002052
name: MS-GF:SpecEValue
def: "MS-GF spectral E-value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002353 ! PSM-level e-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002053
name: MS-GF:EValue
def: "MS-GF E-value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002353 ! PSM-level e-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002054
name: MS-GF:QValue
def: "MS-GF Q-value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002354 ! PSM-level q-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002055
name: MS-GF:PepQValue
def: "MS-GF peptide-level Q-value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002056
name: MS-GF:PEP
def: "MS-GF posterior error probability." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002057
@@ -13372,29 +13576,29 @@ is_a: MS:1001139 ! quantitation software name
id: MS:1002064
name: peptide consensus RT
def: "Peptide consensus retention time." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002065
name: peptide consensus m/z
def: "Peptide consensus mass/charge ratio." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002066
name: ratio calculation method
def: "Method used to calculate the ratio." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002067
name: protein value: median of peptide ratios
def: "Protein quantification value calculated as median of peptide ratios." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002738 ! protein-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002068
@@ -13406,30 +13610,30 @@ is_a: MS:1001055 ! modification parameters
id: MS:1002069
name: metabolic labelling purity
def: "Metabolic labelling: Description of labelling purity. Usually the purity of feeding material (e.g. 95%), or the inclusion rate derived from isotopic peak pattern shape." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001055 ! modification parameters
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002070
name: t-test
def: "Perform a t-test (two groups). Specify in string value, whether paired / unpaired, variance equal / different, one- / two-sided version is performed." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001861 ! quantification data processing
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002071
name: ANOVA-test
def: "Perform an ANOVA-test (more than two groups). Specify in string value, which version is performed." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001861 ! quantification data processing
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002072
name: p-value
def: "P-value as result of one of the processing steps described. Specify in the description, which processing step it was." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002073
@@ -13466,52 +13670,52 @@ id: MS:1002078
name: ProteomeDiscoverer:1. Static Modification
def: "OBSOLETE ProteomeDiscoverer's 1st static post-translational modification (PTM) input parameter." [PSI:PI]
comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002079
name: ProteomeDiscoverer:2. Static Modification
def: "OBSOLETE ProteomeDiscoverer's 2nd static post-translational modification (PTM) input parameter." [PSI:PI]
comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002080
name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before
def: "Precursor clipping range before." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
relationship: has_units UO:0000221 ! dalton
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002081
name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After
def: "Precursor clipping range after." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
relationship: has_units UO:0000221 ! dalton
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002082
name: first column elution time
def: "The time of elution from the first chromatographic column in the chromatographic separation step, relative to the start of chromatography on the first column." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002083
name: second column elution time
def: "The time of elution from the second chromatographic column in the chromatographic separation step, relative to the start of the chromatography on the second column." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002084
@@ -13547,29 +13751,29 @@ is_a: MS:1002084 ! multidimensional chromatography modulation description
id: MS:1002089
name: ProteomeDiscoverer:Peptide Without Protein XCorr Threshold
def: "XCorr threshold for storing peptides that do not belong to a protein." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002090
name: Calculate Probability Scores
def: "Flag indicating that a probability score for the assessment that a reported peptide match is a random occurrence is calculated." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002094 ! common search engine input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002091
name: ProteomeDiscoverer:Maximum Delta Cn
def: "Delta Cn threshold for filtering out PSM's." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002092
name: Percolator:Validation based on
def: "Algorithm (e.g. q-value or PEP) used for calculation of the validation score using Percolator." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002107 ! Percolator input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002093
@@ -13762,10 +13966,10 @@ id: MS:1002125
name: combined FDRScore
def: "OBSOLETE FDRScore values specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PMID:19253293]
comment: This term was made obsolete because it was split into the more specific terms for PSM-level combined FDRScore (MS:1002356), distinct peptide-level combined FDRScore (MS:1002361), protein-level combined FDRScore (MS:1002366) and protein group-level combined FDRScore (MS:1002375).
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
is_obsolete: true
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002126
@@ -13934,8 +14138,8 @@ is_a: MS:1001806 ! quantification object attribute
id: MS:1002153
name: protein level PSM counts
def: "The number of spectra identified for this protein in spectral counting." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002738 ! protein-level quantification datatype
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002154
@@ -14296,52 +14500,52 @@ is_a: MS:1002009 ! isobaric label quantitation analysis
id: MS:1002213
name: PAnalyzer:conclusive protein
def: "A protein identified by at least one unique (distinct, discrete) peptide (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002214
name: PAnalyzer:indistinguishable protein
def: "A member of a group of proteins sharing all peptides that are exclusive to the group (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002215
name: PAnalyzer:non-conclusive protein
def: "A protein sharing all its matched peptides with either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002216
name: PAnalyzer:ambiguous group member
def: "A protein sharing at least one peptide not matched to either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001600 ! protein inference confidence category
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002217
name: decoy peptide
def: "A putative identified peptide issued from a decoy sequence database." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide sequence-level identification attribute
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002218
name: percent collision energy ramp start
def: "Collision energy at the start of the collision energy ramp in percent, normalized to the mass of the ion." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! normalized collision energy
relationship: has_units UO:0000187 ! percent
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002219
name: percent collision energy ramp end
def: "Collision energy at the end of the collision energy ramp in percent, normalized to the mass of the ion." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! normalized collision energy
relationship: has_units UO:0000187 ! percent
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002220
@@ -14367,15 +14571,15 @@ relationship: part_of MS:1000908 ! transition
id: MS:1002223
name: precursor ion detection probability
def: "Probability of detecting precursor when parent protein is present." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002222 ! SRM transition attribute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002224
name: product ion detection probability
def: "Probability of detecting product ion when precursor ion is present." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002222 ! SRM transition attribute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002225
@@ -14401,29 +14605,29 @@ relationship: has_units MS:1000905 ! percent of base peak times 100
id: MS:1002227
name: number of product ion observations
def: "The number of times the specific product ion has been observed in a series of SRM experiments." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002222 ! SRM transition attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002228
name: number of precursor ion observations
def: "The number of times the specific precursor ion has been observed in a series of SRM experiments." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002222 ! SRM transition attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002229
name: ProteomeDiscoverer:Mascot:Significance Middle
def: "Calculated relaxed significance when performing a decoy search for high-confidence peptides." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002230
name: ProteomeDiscoverer:Mascot:Significance High
def: "Calculated relaxed significance when performing a decoy search for medium-confidence peptides." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002231
@@ -14442,31 +14646,31 @@ relationship: has_regexp MS:1002231 ! regular expressions for a GUID
id: MS:1002233
name: ProteomeDiscoverer:SEQUEST:Low resolution spectra contained
def: "Flag indicating if low-resolution spectra are taken into consideration." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002234
name: selected precursor m/z
def: "Mass-to-charge ratio of a precursor ion selected for fragmentation." [PSI:PI]
synonym: "selected ion m/z" RELATED []
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
relationship: has_units MS:1000040 ! m/z
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002235
name: ProteoGrouper:PDH score
def: "A score assigned to a single protein accession (modelled as ProteinDetectionHypothesis in mzIdentML), based on summed peptide level scores." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002236
name: ProteoGrouper:PAG score
def: "A score assigned to a protein group (modelled as ProteinAmbiguityGroup in mzIdentML), based on all summed peptide level scores that have been assigned to the group as unique or razor peptides." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002368 ! search engine specific score for protein groups
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002237
@@ -14538,22 +14742,22 @@ is_a: MS:1002237 ! mzidLib
id: MS:1002248
name: SEQUEST:spscore
def: "The SEQUEST result 'SpScore'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002249
name: SEQUEST:sprank
def: "The SEQUEST result 'SpRank'." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002250
name: SEQUEST:deltacnstar
def: "The SEQUEST result 'DeltaCnStar'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002251
@@ -14565,65 +14769,65 @@ is_a: MS:1001456 ! analysis software
id: MS:1002252
name: Comet:xcorr
def: "The Comet result 'XCorr'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002253
name: Comet:deltacn
def: "The Comet result 'DeltaCn'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002254
name: Comet:deltacnstar
def: "The Comet result 'DeltaCnStar'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002255
name: Comet:spscore
def: "The Comet result 'SpScore'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002256
name: Comet:sprank
def: "The Comet result 'SpRank'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002257
name: Comet:expectation value
def: "The Comet result 'Expectation value'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002258
name: Comet:matched ions
def: "The Comet result 'Matched Ions'." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002259
name: Comet:total ions
def: "The Comet result 'Total Ions'." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002260
name: PSM:FDR threshold
def: "False-discovery rate threshold for peptide-spectrum matches." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002483 ! PSM-level statistical threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002261
@@ -14635,67 +14839,67 @@ is_a: MS:1001456 ! analysis software
id: MS:1002262
name: Byonic:Score
def: "The Byonic score is the primary indicator of PSM correctness. The Byonic score reflects the absolute quality of the peptide-spectrum match, not the relative quality compared to other candidate peptides. Byonic scores range from 0 to about 1000, with 300 a good score, 400 a very good score, and PSMs with scores over 500 almost sure to be correct." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002263
name: Byonic:Delta Score
def: "The drop in Byonic score from the top-scoring peptide to the next peptide with distinct sequence. In this computation, the same peptide with different modifications is not considered distinct." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002264
name: Byonic:DeltaMod Score
def: "The drop in Byonic score from the top-scoring peptide to the next peptide different in any way, including placement of modifications. DeltaMod gives an indication of whether modifications are confidently localized; DeltaMod over 10.0 means that there is high likelihood that all modification placements are correct." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002265
name: Byonic:PEP
def: "Byonic posterior error probability." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002266
name: Byonic:Peptide LogProb
def: "The log p-value of the PSM. This is the log of the probability that the PSM with such a score and delta would arise by chance in a search of this size (the size of the protein database, as expanded by the modification rules). A log p-value of -3.0 should happen by chance on only one of a thousand spectra. Caveat: it is very hard to compute a p-value that works for all searches and all spectra, so read Byonic p-values with a certain amount of skepticism." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002267
name: Byonic:Protein LogProb
def: "The log p-value of the protein." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
is_a: MS:1002363 ! search engine specific score for proteins
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002268
name: Byonic:Best LogProb
def: "Best (most negative) log p-value of an individual PSM." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein identification statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002269
name: Byonic:Best Score
def: "Best (largest) Byonic score of a PSM." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002270
@@ -14719,9 +14923,9 @@ is_a: MS:1002270 ! chromatography separation
id: MS:1002273
name: detector potential
def: "Detector potential difference in volts." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000481 ! detector attribute
relationship: has_units UO:0000218 ! volt
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002274
@@ -14904,8 +15108,8 @@ is_a: MS:1000560 ! mass spectrometer file format
id: MS:1002303
name: Bruker Container nativeID format
def: "Native identifier (UUID)." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000767 ! native spectrum identifier format
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002304
@@ -14941,25 +15145,25 @@ is_a: MS:1000026 ! detector type
id: MS:1002309
name: Byonic: Peptide AbsLogProb
def: "The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the PSM." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002310
name: Byonic: Protein AbsLogProb
def: "The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the protein." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002311
name: Byonic: Peptide AbsLogProb2D
def: "The absolute value of the log-base10 Byonic two-dimensional posterior error probability (PEP) of the PSM. The two-dimensional PEP takes into account protein ranking information as well as PSM information." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002312
@@ -14989,117 +15193,117 @@ is_a: MS:1001405 ! spectrum identification result details
id: MS:1002316
name: ProteomeDiscoverer:Amanda:high confidence threshold
def: "Strict confidence probability score." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002317
name: ProteomeDiscoverer:Amanda:middle confidence threshold
def: "Relaxed confidence probability score." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002318
name: ProteomeDiscoverer:automatic workload
def: "Flag indicating automatic estimation of the workload level." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002319
name: Amanda:AmandaScore
def: "The Amanda score of the scoring function for a PSM." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002320
name: ProteomeDiscoverer:max differential modifications
def: "Maximum dynamic modifications per PSM." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002321
name: ProteomeDiscoverer:max equal modifications
def: "Maximum equal modifications per PSM." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002322
name: ProteomeDiscoverer:min peptide length
def: "Minimum peptide length." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002323
name: ProteomeDiscoverer:max peptide length
def: "Maximum peptide length." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002324
name: ProteomeDiscoverer:max number neutral loss
def: "Maximum number of same neutral losses." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002325
name: ProteomeDiscoverer:max number neutral loss modifications
def: "Max number of same neutral losses of modifications." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002326
name: ProteomeDiscoverer:use flanking ions
def: "Flag for usage of flanking ions." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002327
name: ProteomeDiscoverer:max number of same modifs
def: "The maximum number of possible equal modifications per PSM." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002328
name: ProteomeDiscoverer:perform deisotoping
def: "Defines whether a simple deisotoping shall be performed." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002329
name: ProteomeDiscoverer:ion settings
def: "Specifies the fragment ions and neutral losses that are calculated." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002330
name: ProteomeDiscoverer:3. Static Modification
def: "OBSOLETE ProteomeDiscoverer's 3rd static post-translational modification (PTM) input parameter." [PSI:PI]
comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002331
name: ProteomeDiscoverer:5. Dynamic Modification
def: "OBSOLETE ProteomeDiscoverer's 5th dynamic post-translational modification (PTM) input parameter." [PSI:PI]
comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002332
@@ -15141,30 +15345,30 @@ is_a: MS:1001456 ! analysis software
id: MS:1002338
name: Andromeda:score
def: "The probability based score of the Andromeda search engine." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002339
name: site:global FDR
def: "Estimation of global false discovery rate of peptides with a post-translational modification." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002340
name: ProteomeXchange project tag
def: "Tag that can be added to a ProteomeXchange dataset, to enable the grouping of datasets. One tag can be used for indicating that a given dataset is part of a bigger project, like e.g. the Human Proteome Project." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002341
name: second-pass peptide identification
def: "A putative identified peptide found in a second-pass search of protein sequences selected from a first-pass search." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide sequence-level identification attribute
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002342
@@ -15192,6 +15396,7 @@ id: MS:1002345
name: PSM-level attribute
def: "Attribute of a single peptide-spectrum match." [PSI:PI]
is_a: MS:1002694 ! single identification result attribute
+relationship: part_of MS:1003301 ! peptide-spectrum match
[Term]
id: MS:1002346
@@ -15221,67 +15426,67 @@ is_a: MS:1002304 ! domain range
id: MS:1002350
name: PSM-level global FDR
def: "Estimation of the global false discovery rate of peptide spectrum matches." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002701 ! PSM-level result list statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002351
name: PSM-level local FDR
def: "Estimation of the local false discovery rate of peptide spectrum matches." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002347 ! PSM-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002352
name: PSM-level p-value
def: "Estimation of the p-value for peptide spectrum matches." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002347 ! PSM-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002353
name: PSM-level e-value
def: "Estimation of the e-value for peptide spectrum matches." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002347 ! PSM-level identification statistic
relationship: has_domain MS:1002306 ! value greater than zero
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002354
name: PSM-level q-value
def: "Estimation of the q-value for peptide spectrum matches." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002347 ! PSM-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002355
name: PSM-level FDRScore
def: "mzidLibrary FDRScore for peptide spectrum matches." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1002363 ! search engine specific score for proteins
relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to 1
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002356
name: PSM-level combined FDRScore
def: "mzidLibrary Combined FDRScore for peptide spectrum matches specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1002363 ! search engine specific score for proteins
relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to 1
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002357
name: PSM-level probability
def: "Probability that the reported peptide ion is truly responsible for some or all of the components of the specified mass spectrum." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002347 ! PSM-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002358
@@ -15293,35 +15498,35 @@ is_a: MS:1001092 ! peptide sequence-level identification statistic
id: MS:1002359
name: peptide sequence-level local FDR
def: "Estimation of the local false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide sequence-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002360
name: distinct peptide-level FDRScore
def: "MzidLibrary FDRScore for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic
is_a: MS:1002363 ! search engine specific score for proteins
relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002361
name: distinct peptide-level combined FDRScore
def: "Combined FDRScore for peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry) specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given peptide, used for integrating results from these distinct pools." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic
is_a: MS:1002363 ! search engine specific score for proteins
relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002362
name: peptide sequence-level probability
def: "Probability that the reported distinct peptide sequence (irrespective of mass modifications) has been correctly identified via the referenced PSMs." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide sequence-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002363
@@ -15333,32 +15538,32 @@ is_a: MS:1001116 ! single protein identification statistic
id: MS:1002364
name: protein-level local FDR
def: "Estimation of the local false discovery rate of proteins." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein identification statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002365
name: FDRScore for proteins
def: "MzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002366
name: combined FDRScore for proteins
def: "MzidLibrary Combined FDRScore for proteins." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002367
name: probability for proteins
def: "Probability that a specific protein sequence has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002368
@@ -15370,91 +15575,91 @@ is_a: MS:1002348 ! protein group-level identification statistic
id: MS:1002369
name: protein group-level global FDR
def: "Estimation of the global false discovery rate of protein groups." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002706 ! protein group-level result list statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002370
name: protein group-level local FDR
def: "Estimation of the local false discovery rate of protein groups." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002348 ! protein group-level identification statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002371
name: protein group-level p-value
def: "Estimation of the p-value for protein groups." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002348 ! protein group-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002372
name: protein group-level e-value
def: "Estimation of the e-value for protein groups." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002348 ! protein group-level identification statistic
relationship: has_domain MS:1002306 ! value greater than zero
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002373
name: protein group-level q-value
def: "Estimation of the q-value for protein groups." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002348 ! protein group-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002374
name: protein group-level FDRScore
def: "mzidLibrary FDRScore for protein groups." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002368 ! search engine specific score for protein groups
relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002375
name: protein group-level combined FDRScore
def: "mzidLibrary Combined FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PMID:19253293]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002368 ! search engine specific score for protein groups
relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002376
name: protein group-level probability
def: "Probability that at least one of the members of a group of protein sequences has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002348 ! protein group-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002377
name: ProteomeDiscoverer:Relaxed Score Threshold
def: "Specifies the threshold value for relaxed scoring." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002378
name: ProteomeDiscoverer:Strict Score Threshold
def: "Specifies the threshold value for strict scoring." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002379
name: ProteomeDiscoverer:Peptide Without Protein Cut Off Score
def: "Cut off score for storing peptides that do not belong to a protein." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002380
name: false localization rate
def: "Estimation of the false localization rate for modification site assignment." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002381
@@ -15521,79 +15726,79 @@ is_a: MS:1001302 ! search engine specific input parameter
id: MS:1002390
name: PIA:FDRScore calculated
def: "Indicates whether the FDR score was calculated for the input file." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002391
name: PIA:Combined FDRScore calculated
def: "Indicates whether the combined FDR score was calculated for the PIA compilation." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002392
name: PIA:PSM sets created
def: "Indicates whether PSM sets were created." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002393
name: PIA:used top identifications for FDR
def: "The number of top identifications per spectrum used for the FDR calculation, 0 means all." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1002394
name: PIA:protein score
def: "The score given to a protein by any protein inference." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002395
name: PIA:protein inference
def: "The used algorithm for the protein inference using PIA." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002396
name: PIA:protein inference filter
def: "A filter used by PIA for the protein inference." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002397
name: PIA:protein inference scoring
def: "The used scoring method for the protein inference using PIA." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002398
name: PIA:protein inference used score
def: "The used base score for the protein inference using PIA." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002399
name: PIA:protein inference used PSMs
def: "The method to determine the PSMs used for scoring by the protein inference." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002400
name: PIA:filter
def: "A filter used for the report generation." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002389 ! PIA workflow parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002401
@@ -15617,8 +15822,10 @@ is_a: MS:1001101 ! protein group or subset relationship
id: MS:1002404
name: count of identified proteins
def: "The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002704 ! protein-level result list attribute
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002405
@@ -15630,22 +15837,22 @@ is_a: MS:1002699 ! result list attribute
id: MS:1002406
name: count of identified clusters
def: "The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file." [DOI:10.1002/pmic.201400080, PMID:25092112]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002405 ! protein group-level result list attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002407
name: cluster identifier
def: "An identifier applied to protein groups to indicate that they are linked by shared peptides." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002698 ! protein cluster identification attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002408
name: number of distinct protein sequences
def: "The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002405 ! protein group-level result list attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002409
@@ -15670,15 +15877,15 @@ is_a: MS:1002128 ! method file format
id: MS:1002412
name: total XIC area
def: "Summed area of all the extracted ion chromatogram for the peptide (e.g. of all the transitions in SRM)." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002413
name: product background
def: "The background area for the quantified transition." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002414
@@ -15690,8 +15897,8 @@ is_a: MS:1001457 ! data processing software
id: MS:1002415
name: protein group passes threshold
def: "A Boolean attribute to determine whether the protein group has passed the threshold indicated in the file." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002346 ! protein group-level identification attribute
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002416
@@ -15721,8 +15928,8 @@ is_a: MS:1000494 ! Thermo Scientific instrument model
id: MS:1002420
name: PASSEL experiment URI
def: "URI that allows access to a PASSEL experiment." [PSI:PI]
-xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term
[Term]
id: MS:1002421
@@ -15734,71 +15941,71 @@ is_a: MS:1001302 ! search engine specific input parameter
id: MS:1002422
name: Paragon: sample type
def: "The Paragon method setting indicating the type of sample at the high level, generally meaning the type of quantitation labelling or lack thereof. 'Identification' is indicated for samples without any labels for quantitation." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002423
name: Paragon: cysteine alkylation
def: "The Paragon method setting indicating the actual cysteine alkylation agent; 'None' is indicated if there was no cysteine alkylation." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002424
name: Paragon: instrument setting
def: "The Paragon method setting (translating to a large number of lower level settings) indicating the instrument used or a category of instrument." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002425
name: Paragon: search effort
def: "The Paragon method setting that controls the two major modes of search effort of the Paragon algorithm: the Rapid mode uses a conventional database search, while the Thorough mode uses a hybrid search, starting with the same approach as the Rapid mode but then follows it with a separate tag-based approach enabling a more extensive search." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002426
name: Paragon: ID focus
def: "A Paragon method setting that allows the inclusion of large sets of features such as biological modification or substitutions." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002427
name: Paragon: FDR analysis
def: "The Paragon method setting that controls whether FDR analysis is conducted." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002428
name: Paragon: quantitation
def: "The Paragon method setting that controls whether quantitation analysis is conducted." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002429
name: Paragon: background correction
def: "The Paragon method setting that controls whether the 'Background Correction' analysis is conducted; this processing estimates a correction to the attenuation in extremity ratios that can occur in isobaric quantatitation workflows on complex samples." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002430
name: Paragon: bias correction
def: "The Paragon method setting that controls whether 'Bias Correction' is invoked in quantitation analysis; this correction is a normalization to set the central tendency of protein ratios to unity." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002431
name: Paragon: channel to use as denominator in ratios
def: "The Paragon method setting that controls which label channel is used as the denominator in calculating relative expression ratios." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002432
@@ -15810,36 +16017,36 @@ is_a: MS:1001249 ! search input details
id: MS:1002433
name: Paragon: modified data dictionary or parameter translation
def: "This metric detects if any changes have been made to the originally installed key control files for the software; if no changes have been made, then the software version and settings are sufficient to enable exact reproduction; if changes have been made, then the modified ParameterTranslation- and ProteinPilot DataDictionary-XML files much also be provided in order to exactly reproduce a result." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002432 ! search engine specific input metadata
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002434
name: number of spectra searched
def: "Number of spectra in a search." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001249 ! search input details
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002435
name: data processing start time
def: "The time that a data processing action was started." [PSI:MS]
-xref: value-type:xsd\:dateTime "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter
+relationship: has_value_type xsd:dateTime ! The allowed value-type for this CV term
[Term]
id: MS:1002436
name: Paragon: digestion
def: "The Paragon method setting indicating the actual digestion agent - unlike other search tools, this setting does not include options that control partial specificity like 'semitrypsin'; if trypsin is used, trypsin is set, and partially conforming peptides are found in the Thorough mode of search; 'None' should be indicated only if there was really no digestion done." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001249 ! search input details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002437
name: number of decoy sequences
def: "The number of decoy sequences, if the concatenated target-decoy approach is used." [PSI:PI]
-xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1002438
@@ -15899,22 +16106,22 @@ is_a: MS:1000490 ! Agilent instrument model
id: MS:1002447
name: Paragon:special factor
def: "The Paragon method setting indicating a list of one or more 'special factors', which generally capture secondary effects (relative to other settings) as a set of probabilities of modification features that override the assumed levels. For example the 'gel-based ID' special factor causes an increase probability of oxidation on several resides because of the air exposure impact on a gel, in addition to other effects." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002448
name: PEAKS:inChorusPeptideScore
def: "The PEAKS inChorus peptide score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002449
name: PEAKS:inChorusProteinScore
def: "The PEAKS inChorus protein score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002450
@@ -16029,51 +16236,51 @@ is_a: MS:1002701 ! PSM-level result list statistic
id: MS:1002466
name: PeptideShaker PSM score
def: "The probability based PeptideShaker PSM score." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002467
name: PeptideShaker PSM confidence
def: "The probability based PeptideShaker PSM confidence." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002468
name: PeptideShaker peptide score
def: "The probability based PeptideShaker peptide score." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic
is_a: MS:1002363 ! search engine specific score for proteins
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002469
name: PeptideShaker peptide confidence
def: "The probability based PeptideShaker peptide confidence." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002470
name: PeptideShaker protein group score
def: "The probability based PeptideShaker protein group score." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
is_a: MS:1002368 ! search engine specific score for protein groups
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002471
name: PeptideShaker protein group confidence
def: "The probability based PeptideShaker protein group confidence." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002472
@@ -16091,34 +16298,35 @@ is_a: MS:1001249 ! search input details
id: MS:1002474
name: ProteoAnnotator:non-canonical gene model score
def: "The sum of peptide-level scores for peptides mapped only to non-canonical gene models within the group." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002368 ! search engine specific score for protein groups
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002475
name: ProteoAnnotator:count alternative peptides
def: "The count of the number of peptide sequences mapped to non-canonical gene models only within the group." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002368 ! search engine specific score for protein groups
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002476
name: ion mobility drift time
def: "Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
is_a: MS:1002892 ! ion mobility attribute
+is_a: MS:1003254 ! peak attribute
relationship: has_units UO:0000028 ! millisecond
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002477
name: mean ion mobility drift time array
def: "Array of population mean ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002478
@@ -16179,15 +16387,15 @@ is_a: MS:1002572 ! protein detection statistical threshold
id: MS:1002487
name: MassIVE dataset identifier
def: "Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002488
name: MassIVE dataset URI
def: "URI that allows the access to one dataset in the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
-xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term
[Term]
id: MS:1002489
@@ -16222,8 +16430,9 @@ is_a: MS:1002489 ! special processing
[Term]
id: MS:1002494
-name: cross-linking search
-def: "Cross-linking search performed." [PSI:PI]
+name: crosslinking search
+def: "Crosslinking search performed." [PSI:PI]
+synonym: "cross-linking search" EXACT []
is_a: MS:1002489 ! special processing
[Term]
@@ -16262,8 +16471,8 @@ is_obsolete: true
id: MS:1002500
name: peptide passes threshold
def: "A Boolean attribute to determine whether the peptide has passed the threshold indicated in the file." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide sequence-level identification attribute
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002501
@@ -16287,13 +16496,13 @@ is_a: MS:1001105 ! peptide sequence-level identification attribute
id: MS:1002504
name: modification index
def: "The order of modifications to be referenced elsewhere in the document." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1001055 ! modification parameters
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002505
name: regular expression for modification localization scoring
-def: "([:digit:]+:[0|1]\{1\}.[:digit:]+[Ee]{0,1}[+-]{0,1}[:digit:]*:[:digit:]+[|]\{1\}[:digit:]+:(true|false)\{1\})." [PSI:PI]
+def: "(?[0-9]+):(?[01][.][0-9]+(?:[Ee][+\-]?[0-9]+)?):(?[0-9]+(?:[|][0-9]+)*):(?true|false)" [PSI:PI]
is_a: MS:1002479 ! regular expression
[Term]
@@ -16306,50 +16515,55 @@ is_a: MS:1001055 ! modification parameters
id: MS:1002507
name: modification rescoring:false localization rate
def: "Mod position score: false localization rate." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002506 ! modification position score
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002508
-name: cross-linking attribute
-def: "Cross-linking attribute." [PSI:PI]
+name: crosslinking attribute
+def: "Crosslinking attribute." [PSI:PI]
+synonym: "cross-linking attribute" EXACT []
is_a: MS:1002694 ! single identification result attribute
[Term]
id: MS:1002509
-name: cross-link donor
-def: "The Cross-linking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
-is_a: MS:1002508 ! cross-linking attribute
+name: crosslink donor
+def: "The crosslinking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the crosslink donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI]
+synonym: "cross-link donor" EXACT []
+is_a: MS:1002508 ! crosslinking attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002510
-name: cross-link acceptor
-def: "Cross-linking acceptor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
-is_a: MS:1002508 ! cross-linking attribute
+name: crosslink acceptor
+def: "Crosslinking acceptor, assigned according to the following rules: the export software SHOULD use the following rules to choose the crosslink donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI]
+synonym: "cross-link acceptor" EXACT []
+is_a: MS:1002508 ! crosslinking attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002511
-name: cross-link spectrum identification item
-def: "Cross-linked spectrum identification item." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
-is_a: MS:1002508 ! cross-linking attribute
+name: crosslink spectrum identification item
+def: "Crosslinked spectrum identification item." [PSI:PI]
+synonym: "cross-link spectrum identification item" EXACT []
+is_a: MS:1002508 ! crosslinking attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002512
-name: cross-linking score
-def: "Cross-linking scoring value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
+name: crosslinking score
+def: "Crosslinking scoring value." [PSI:PI]
+synonym: "cross-linking score" EXACT []
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002513
name: molecules per cell
def: "The absolute abundance of protein in a cell." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002514
@@ -16361,43 +16575,43 @@ is_a: MS:1001833 ! quantitation analysis summary
id: MS:1002515
name: internal peptide reference used
def: "States whether an internal peptide reference is used or not in absolute quantitation analysis." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001832 ! quantitation software comment or customizations
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002516
name: internal protein reference used
def: "States whether an internal protein reference is used or not in absolute quantitation analysis." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001832 ! quantitation software comment or customizations
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002517
name: internal reference abundance
def: "The absolute abundance of the spiked in reference peptide or protein used for absolute quantitation analysis." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002518
name: Progenesis:protein group normalised abundance
def: "The data type normalised abundance for protein groups produced by Progenesis LC-MS." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002739 ! protein group-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002519
name: Progenesis:protein group raw abundance
def: "The data type raw abundance for protein groups produced by Progenesis LC-MS." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002739 ! protein group-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002520
name: peptide group ID
def: "Peptide group identifier for peptide-level stats." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide sequence-level identification attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002521
@@ -16409,8 +16623,8 @@ is_a: MS:1000857 ! run attribute
id: MS:1002522
name: ProteomeDiscoverer:1. Static Terminal Modification
def: "Determine 1st static terminal post-translational modifications (PTMs)." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002523
@@ -16487,87 +16701,87 @@ is_a: MS:1000121 ! SCIEX instrument model
id: MS:1002534
name: ProLuCID:xcorr
def: "The ProLuCID result 'XCorr'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002535
name: ProLuCID:deltacn
def: "The ProLuCID result 'DeltaCn'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002536
name: D-Score
def: "D-Score for PTM site location at the PSM-level." [PMID:23307401]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002537
name: MD-Score
def: "MD-Score for PTM site location at the PSM-level." [PMID:21057138]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002538
name: PTM localization confidence metric
def: "Localization confidence metric for a post translational modification (PTM)." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002539
name: PeptideShaker PTM confidence type
def: "PeptideShaker quality criteria for the confidence of PTM localizations." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002538 ! PTM localization confidence metric
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002540
name: PeptideShaker PSM confidence type
def: "PeptideShaker quality criteria for the confidence of PSM's." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002347 ! PSM-level identification statistic
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002541
name: PeptideShaker peptide confidence type
def: "PeptideShaker quality criteria for the confidence of peptide identifications." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002542
name: PeptideShaker protein confidence type
def: "PeptideShaker quality criteria for the confidence of protein identifications." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein identification statistic
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002543
name: xiFDR
-def: "Target/Decoy based FDR estimation for cross-linking peptide-identifications." [PSI:PI]
+def: "Target/Decoy based FDR estimation for crosslinking peptide-identifications." [PSI:PI]
is_a: MS:1001456 ! analysis software
[Term]
id: MS:1002544
name: xi
-def: "Search engine for cross-linked peptides." [PSI:PI]
+def: "Search engine for crosslinked peptides." [PSI:PI]
is_a: MS:1001456 ! analysis software
[Term]
id: MS:1002545
name: xi:score
def: "The xi result 'Score'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002546
@@ -16598,41 +16812,41 @@ is_a: MS:1002689 ! PTM localization single result statistic
id: MS:1002550
name: peptide:phosphoRS score
def: "phosphoRS score for PTM site location at the peptide-level." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! PTM localization distinct peptide-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002551
name: peptide:Ascore
def: "A-score for PTM site location at the peptide-level." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! PTM localization distinct peptide-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002552
name: peptide:H-Score
def: "H-Score for peptide phosphorylation site location at the peptide-level." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! PTM localization distinct peptide-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002553
name: peptide:D-Score
def: "D-Score for PTM site location at the peptide-level." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! PTM localization distinct peptide-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002554
name: peptide:MD-Score
def: "MD-Score for PTM site location at the peptide-level." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! PTM localization distinct peptide-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002555
@@ -16644,113 +16858,113 @@ is_a: MS:1001405 ! spectrum identification result details
id: MS:1002556
name: Ascore threshold
def: "Threshold for Ascore PTM site location score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002557
name: D-Score threshold
def: "Threshold for D-score PTM site location score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002558
name: MD-Score threshold
def: "Threshold for MD-score PTM site location score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002559
name: H-Score threshold
def: "Threshold for H-score PTM site location score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002560
name: DeBunker:score threshold
def: "Threshold for DeBunker PTM site location score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002561
name: Mascot:PTM site assignment confidence threshold
def: "Threshold for Mascot PTM site assignment confidence." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002562
name: MSQuant:PTM-score threshold
def: "Threshold for MSQuant:PTM-score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002563
name: MaxQuant:PTM Score threshold
def: "Threshold for MaxQuant:PTM Score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002564
name: MaxQuant:P-site localization probability threshold
def: "Threshold for MaxQuant:P-site localization probability." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002565
name: MaxQuant:PTM Delta Score threshold
def: "Threshold for MaxQuant:PTM Delta Score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002566
name: MaxQuant:Phospho (STY) Probabilities threshold
def: "Threshold for MaxQuant:Phospho (STY) Probabilities." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002567
name: phosphoRS score threshold
def: "Threshold for phosphoRS score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002568
name: phosphoRS site probability threshold
def: "Threshold for phosphoRS site probability." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002569
name: ProteomeDiscoverer:Number of Spectra Processed At Once
def: "Number of spectra processed at once in a ProteomeDiscoverer search." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002570
name: sequence multiply subsumable protein
def: "A protein for which the matched peptide sequences are the same, or a subset of, the matched peptide sequences for two or more other proteins combined. These other proteins need not all be in the same group." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002571
name: spectrum multiply subsumable protein
def: "A protein for which the matched spectra are the same, or a subset of, the matched spectra for two or more other proteins combined. These other proteins need not all be in the same group." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001101 ! protein group or subset relationship
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002572
@@ -16918,8 +17132,8 @@ is_a: MS:1001456 ! analysis software
id: MS:1002599
name: splash key
def: "Spectral Hash key, an unique identifier for spectra." [PMID:27824832]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002600
@@ -17111,24 +17325,24 @@ is_a: MS:1002622 ! iTRAQ reagent
[Term]
id: MS:1002631
-name: Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)
-def: "A dissociation process combining electron-transfer and higher-energy collision dissociation (EThcD). It combines ETD (reaction time) followed by HCD (activation energy)." [PSI:PI]
+name: electron-transfer/higher-energy collision dissociation
+def: "Dissociation process combining electron-transfer dissociation and higher-energy collision dissociation. It combines ETD (reaction time) followed by HCD (activation energy)." [PSI:PI]
synonym: "EThcD" EXACT []
-is_a: MS:1000044 ! dissociation method
+is_a: MS:1003181 ! combined dissociation method
[Term]
id: MS:1002632
name: jPOST dataset identifier
def: "Dataset identifier issued by the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002633
name: jPOST dataset URI
def: "URI that allows the access to one dataset in the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
-xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term
[Term]
id: MS:1002634
@@ -17152,59 +17366,59 @@ is_a: MS:1001105 ! peptide sequence-level identification attribute
id: MS:1002637
name: chromosome name
def: "The name or number of the chromosome to which a given peptide has been mapped." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002638
name: chromosome strand
def: "The strand (+ or -) to which the peptide has been mapped." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002639
name: peptide start on chromosome
def: "OBSOLETE The overall start position on the chromosome to which a peptide has been mapped i.e. the position of the first base of the first codon, using a zero-based counting system." [PSI:PI]
comment: This term was obsoleted because it contains redundant info contained in term MS:1002643 - peptide start positions on chromosome.
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute
is_obsolete: true
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002640
name: peptide end on chromosome
def: "The overall end position on the chromosome to which a peptide has been mapped i.e. the position of the third base of the last codon, using a zero-based counting system." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002641
name: peptide exon count
def: "The number of exons to which the peptide has been mapped." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002642
name: peptide exon nucleotide sizes
def: "A comma separated list of the number of DNA bases within each exon to which a peptide has been mapped. Assuming standard operation of a search engine, the peptide exon sizes should sum to exactly three times the peptide length." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002643
name: peptide start positions on chromosome
def: "A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002644
name: genome reference version
def: "The reference genome and versioning string as used for mapping. All coordinates are within this frame of reference." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002636 ! proteogenomics attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002645
@@ -17224,84 +17438,84 @@ relationship: part_of MS:1000577 ! source data file
id: MS:1002647
name: Thermo nativeID format, combined spectra
def: "Thermo comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002646 ! native spectrum identifier format, combined spectra
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002648
name: Waters nativeID format, combined spectra
def: "Waters comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002646 ! native spectrum identifier format, combined spectra
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002649
name: WIFF nativeID format, combined spectra
def: "WIFF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002646 ! native spectrum identifier format, combined spectra
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002650
name: Bruker/Agilent YEP nativeID format, combined spectra
def: "Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002646 ! native spectrum identifier format, combined spectra
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002651
name: Bruker BAF nativeID format, combined spectra
def: "Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002646 ! native spectrum identifier format, combined spectra
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002652
name: Bruker FID nativeID format, combined spectra
def: "Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002646 ! native spectrum identifier format, combined spectra
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002653
name: multiple peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002646 ! native spectrum identifier format, combined spectra
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002654
name: single peak list nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002646 ! native spectrum identifier format, combined spectra
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002655
name: scan number only nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002646 ! native spectrum identifier format, combined spectra
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002656
name: spectrum identifier nativeID format, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: Used for conversion from mzData. The spectrum id attribute is referenced.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002646 ! native spectrum identifier format, combined spectra
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002657
name: mzML unique identifier, combined spectra
def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
comment: A unique identifier of a spectrum stored in an mzML file.
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002646 ! native spectrum identifier format, combined spectra
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002658
@@ -17313,7 +17527,6 @@ relationship: part_of MS:1001000 ! spectrum interpretation
id: MS:1002659
name: UniProtKB text sequence format
def: "Text-based format used by UniProtKB for sequence entries." [PSI:PI]
-xref: SWO:http://edamontology.org/format_2187
is_a: MS:1001347 ! database file formats
[Term]
@@ -17332,30 +17545,32 @@ is_a: MS:1001456 ! analysis software
id: MS:1002662
name: Morpheus:Morpheus score
def: "Morpheus score for PSMs." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002663
name: Morpheus:summed Morpheus score
def: "Summed Morpheus score for protein groups." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002368 ! search engine specific score for protein groups
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002664
-name: interaction score derived from cross-linking
-def: "Parent term for interaction scores derived from cross-linking." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
-is_a: MS:1002675 ! cross-linking result details
-relationship: has_regexp MS:1002665 ! ([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\}))
+name: interaction score derived from crosslinking
+def: "Parent term for interaction scores derived from crosslinking." [PSI:PI]
+synonym: "interaction score derived from cross-linking" EXACT []
+is_a: MS:1002675 ! crosslinking result details
+relationship: has_regexp MS:1002665 ! regular expression for interaction scores derived from crosslinking
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002665
-name: regular expression for interaction scores derived from cross-linking
-def: "([:digit:]+[.][a|b]:([:digit:]+|null):[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\}))." [PSI:PI]
+name: regular expression for interaction scores derived from crosslinking
+def: "((?[0-9]+)[.](?[a|b]):(?[0-9]+|null):(?[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+)?):(?true|false))|(?[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+)?)" [PSI:PI]
+synonym: "regular expression for interaction scores derived from cross-linking" EXACT []
is_a: MS:1002479 ! regular expression
[Term]
@@ -17374,29 +17589,29 @@ is_a: MS:1001536 ! Bruker Daltonics micrOTOF series
id: MS:1002668
name: frag: iTRAQ 4plex reporter ion
def: "Standard reporter ion for iTRAQ 4Plex. The value slot holds the integer mass of the iTRAQ 4Plex reporter ion, e.g. 114." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002669
name: frag: iTRAQ 8plex reporter ion
def: "Standard reporter ion for iTRAQ 8Plex. The value slot holds the integer mass of the iTRAQ 8Plex reporter ion, e.g. 113." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002670
name: frag: TMT reporter ion
def: "Standard reporter ion for TMT. The value slot holds the integer mass of the TMT reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127N." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002671
name: frag: TMT ETD reporter ion
def: "Standard reporter ion for TMT with ETD fragmentation. The value slot holds the integer mass of the TMT ETD reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127C." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002307 ! fragmentation ion type
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002672
@@ -17418,27 +17633,28 @@ is_a: MS:1000121 ! SCIEX instrument model
[Term]
id: MS:1002675
-name: cross-linking result details
-def: "This subsection describes terms which can describe details of cross-linking results." [PSI:PI]
+name: crosslinking result details
+def: "This subsection describes terms which can describe details of crosslinking results." [PSI:PI]
+synonym: "cross-linking result details" EXACT []
relationship: part_of MS:1001000 ! spectrum interpretation
[Term]
id: MS:1002676
name: protein-pair-level global FDR
-def: "Estimation of the global false discovery rate of proteins-pairs in cross-linking experiments." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
-is_a: MS:1002664 ! interaction score derived from cross-linking
-relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
-relationship: has_regexp MS:1002665 ! ([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\}))
+def: "Estimation of the global false discovery rate of proteins-pairs in crosslinking experiments." [PSI:PI]
+is_a: MS:1002664 ! interaction score derived from crosslinking
+relationship: has_domain MS:1003277 ! value between -1 and 1 inclusive
+relationship: has_regexp MS:1002665 ! regular expression for interaction scores derived from crosslinking
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002677
name: residue-pair-level global FDR
-def: "Estimation of the global false discovery rate of residue-pairs in cross-linking experiments." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
-is_a: MS:1002664 ! interaction score derived from cross-linking
-relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
-relationship: has_regexp MS:1002665 ! ([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\}))
+def: "Estimation of the global false discovery rate of residue-pairs in crosslinking experiments." [PSI:PI]
+is_a: MS:1002664 ! interaction score derived from crosslinking
+relationship: has_domain MS:1003277 ! value between -1 and 1 inclusive
+relationship: has_regexp MS:1002665 ! regular expression for interaction scores derived from crosslinking
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002678
@@ -17456,66 +17672,66 @@ is_a: MS:1000133 ! collision-induced dissociation
id: MS:1002680
name: supplemental collision energy
def: "Energy for an ion experiencing supplemental collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
relationship: has_units UO:0000266 ! electronvolt
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002681
name: OpenXQuest:combined score
-def: "OpenXQuest's combined score for a cross-link spectrum match." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
+def: "OpenXQuest's combined score for a crosslink spectrum match." [PSI:PI]
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002682
name: OpenXQuest:xcorr xlink
-def: "OpenXQuest's cross-correlation of cross-linked ions subscore." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
+def: "OpenXQuest's cross-correlation of crosslinked ions subscore." [PSI:PI]
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002683
name: OpenXQuest:xcorr common
def: "OpenXQuest's cross-correlation of unlinked ions subscore." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002684
name: OpenXQuest:match-odds
def: "OpenXQuest's match-odds subscore." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002306 ! value greater than zero
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002685
name: OpenXQuest:intsum
def: "OpenXQuest's sum of matched peak intensity subscore." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002306 ! value greater than zero
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002686
name: OpenXQuest:wTIC
def: "OpenXQuest's weighted percent of total ion current subscore." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002687
@@ -17645,6 +17861,45 @@ synonym: "Tryp-N" EXACT []
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1002707 ! (?=[KR])
+[Term]
+id: MS:1002709
+name: compound data type
+def: "A data type representing more than a single value." []
+
+[Term]
+id: MS:1002710
+name: list of type
+def: "A data type defining a list of values of a single type." []
+is_a: MS:1002709 ! compound data type
+
+[Term]
+id: MS:1002711
+name: list of strings
+def: "A list of xsd:string." []
+is_a: MS:1002710 ! list of type
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1002712
+name: list of integers
+def: "A list of xsd:integer." []
+is_a: MS:1002710 ! list of type
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1002713
+name: list of floats
+def: "A list of xsd:float." []
+is_a: MS:1002710 ! list of type
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1002714
+name: FLASHDeconv
+def: "Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics." [DOI:10.1016/j.cels.2020.01.003]
+is_a: MS:1001456 ! analysis software
+is_a: MS:1001457 ! data processing software
+
[Term]
id: MS:1002719
name: Pegasus BT
@@ -17661,41 +17916,41 @@ is_a: MS:1001456 ! analysis software
id: MS:1002721
name: MSPathFinder:SpecEValue
def: "MSPathFinder spectral E-value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002353 ! PSM-level e-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002722
name: MSPathFinder:EValue
def: "MSPathFinder E-value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002353 ! PSM-level e-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002723
name: MSPathFinder:QValue
def: "MSPathFinder Q-value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002354 ! PSM-level q-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002724
name: MSPathFinder:PepQValue
def: "MSPathFinder peptide-level Q-value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002725
name: MSPathFinder:RawScore
def: "MSPathFinder raw score." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002726
@@ -17717,7 +17972,7 @@ is_a: MS:1000126 ! Waters instrument model
[Term]
id: MS:1002729
-name: Xevo G2 XS Tof
+name: Xevo G2-XS Tof
def: "Waters Corporation Xevo G2 XS Tof orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI]
is_a: MS:1000126 ! Waters instrument model
@@ -17743,15 +17998,15 @@ is_a: MS:1000494 ! Thermo Scientific instrument model
id: MS:1002733
name: peptide-level spectral count
def: "The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002734
name: peptide ion-level spectral count
def: "The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting." [PSI:PI]
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002737 ! peptide-level quantification datatype
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
[Term]
id: MS:1002735
@@ -17851,8 +18106,8 @@ is_a: MS:1000572 ! binary data compression type
id: MS:1002749
name: Mascot:IntegratedSpectralLibrarySearch
def: "Means that Mascot has integrated the search results of database and spectral library search into a single data set." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002750
@@ -18219,16 +18474,17 @@ relationship: part_of MS:1000353 ! adduct ion
[Term]
id: MS:1002810
name: adduct ion X m/z
-def: "Theoretical m/z of the X component in the adduct M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+def: "Theoretical m/z of the X component in the adduct (addition product) M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator." [PSI:MS]
is_a: MS:1003056 ! adduct ion property
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units MS:1000040 ! m/z
[Term]
id: MS:1002811
name: adduct ion isotope
def: "Isotope of the matrix molecule M of an adduct formation." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1003056 ! adduct ion property
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002812
@@ -18240,9 +18496,9 @@ is_a: MS:1002479 ! regular expression
id: MS:1002813
name: adduct ion formula
def: "Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002809 ! adduct ion attribute
relationship: has_regexp MS:1002812 ! (\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-])
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002814
@@ -18255,19 +18511,20 @@ is_a: UO:0000000 ! unit
id: MS:1002815
name: inverse reduced ion mobility
def: "Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
is_a: MS:1002892 ! ion mobility attribute
+is_a: MS:1003254 ! peak attribute
relationship: has_units MS:1002814 ! volt-second per square centimeter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002816
name: mean ion mobility array
def: "Array of population mean ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002817
@@ -18285,8 +18542,8 @@ is_a: MS:1000767 ! native spectrum identifier format
id: MS:1002819
name: Bruker TDF nativeID format, combined spectra
def: "Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002646 ! native spectrum identifier format, combined spectra
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002820
@@ -18336,45 +18593,45 @@ is_a: MS:1001456 ! analysis software
id: MS:1002827
name: MetaMorpheus:score
def: "MetaMorpheus score for PSMs." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002828
name: MetaMorpheus:protein score
def: "MetaMorpheus score for protein groups." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002368 ! search engine specific score for protein groups
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002829
name: XCMS:into
def: "Feature intensity produced by XCMS findPeaks() from integrated peak intensity." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002830
name: XCMS:intf
def: "Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002831
name: XCMS:maxo
def: "Feature intensity produced by XCMS findPeaks() from maximum peak intensity." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002832
name: XCMS:area
def: "Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002833
@@ -18386,8 +18643,8 @@ is_a: MS:1000857 ! run attribute
id: MS:1002834
name: ProteomeDiscoverer:Delta Score
def: "The Delta Score reported by Proteome Discoverer version 2." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002835
@@ -18399,15 +18656,15 @@ is_a: MS:1000494 ! Thermo Scientific instrument model
id: MS:1002836
name: iProX dataset identifier
def: "Dataset identifier issued by the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002837
name: iProX dataset URI
def: "URI that allows the access to one dataset in the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
-xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term
[Term]
id: MS:1002838
@@ -18431,24 +18688,24 @@ relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrom
id: MS:1002841
name: external HDF5 dataset
def: "The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the section of the BinaryDataArray." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002840 ! external reference data
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002842
name: external offset
def: "The position in the external data where the array begins." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: has_units UO:0000189 ! Count
is_a: MS:1002840 ! external reference data
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1002843
name: external array length
def: "Describes how many fields an array contains." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: has_units UO:0000189 ! Count
is_a: MS:1002840 ! external reference data
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1002844
@@ -18460,57 +18717,57 @@ is_a: MS:1001458 ! spectrum generation information
id: MS:1002845
name: Associated file URI
def: "URI of one external file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002844 ! Experiment additional parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002846
name: Associated raw file URI
def: "URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002845 ! Associated file URI
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002847
name: ProteomeCentral dataset URI
def: "URI associated to one PX submission in ProteomeCentral." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002844 ! Experiment additional parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002848
name: Result file URI
def: "URI of one file labeled as 'Result', associated to one PX submission." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002845 ! Associated file URI
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002849
name: Search engine output file URI
def: "URI of one search engine output file associated to one PX submission." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002845 ! Associated file URI
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002850
name: Peak list file URI
def: "URI of one of one search engine output file associated to one PX submission." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002845 ! Associated file URI
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002851
name: Other type file URI
def: "URI of one file labeled as 'Other', associated to one PX submission." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002845 ! Associated file URI
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002852
name: Dataset FTP location
def: "FTP location of one entire PX data set." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002844 ! Experiment additional parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002853
@@ -18552,29 +18809,29 @@ is_a: MS:1002844 ! Experiment additional parameter
id: MS:1002859
name: Additional associated raw file URI
def: "Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002845 ! Associated file URI
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002860
name: Gel image file URI
def: "URI of one gel image file associated to one PX submission." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002845 ! Associated file URI
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002861
name: Reprocessed complete dataset
def: "All the raw files included in the original dataset (or group of original datasets) have been reanalysed." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002844 ! Experiment additional parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002862
name: Reprocessed subset dataset
def: "A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002844 ! Experiment additional parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002863
@@ -18598,8 +18855,8 @@ is_a: MS:1002844 ! Experiment additional parameter
id: MS:1002866
name: Reference
def: "Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002844 ! Experiment additional parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002867
@@ -18638,15 +18895,15 @@ is_a: MS:1001457 ! data processing software
id: MS:1002872
name: Panorama Public dataset identifier
def: "Dataset identifier issued by the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002873
name: Panorama Public dataset URI
def: "URI that allows the access to one dataset in the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
-xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term
[Term]
id: MS:1002874
@@ -18730,8 +18987,8 @@ is_a: MS:1001805 ! quantification datatype
id: MS:1002887
name: Progenesis QI normalised abundance
def: "The normalised abundance produced by Progenesis QI LC-MS." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002886 ! small molecule quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002888
@@ -18743,22 +19000,22 @@ is_a: MS:1002694 ! single identification result attribute
id: MS:1002889
name: Progenesis MetaScope score
def: "The confidence score produced by Progenesis QI." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002888 ! small molecule confidence measure
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002890
name: fragmentation score
def: "The fragmentation confidence score." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002888 ! small molecule confidence measure
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002891
name: isotopic fit score
def: "The isotopic fit confidence score." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002888 ! small molecule confidence measure
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1002892
@@ -18777,8 +19034,8 @@ is_a: MS:1000513 ! binary data array
id: MS:1002894
name: InChIKey
def: "Unique chemical structure identifier for chemical compounds." [PMID:273343401]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002895
@@ -18790,17 +19047,17 @@ is_a: MS:1002694 ! single identification result attribute
id: MS:1002896
name: compound identification confidence level
def: "Confidence level for annotation of identified compounds as defined by the Metabolomics Standards Initiative (MSI). The value slot can have the values 'Level 0' until 'Level 4'." [PMID:29748461]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002895 ! small molecule identification attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002897
name: isotopomer peak
def: "OBSOLETE Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'." [PSI:PI]
comment: This term was obsoleted because it was replaced by the more exact terms MS:1002956 'isotopic ion MS peak', MS:1002957 'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead.
-xref: value-type:xsd:string "The allowed value-type for this CV term."
is_a: MS:1000231 ! peak
is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002898
@@ -18860,17 +19117,17 @@ is_a: MS:1002905 ! proteoform-level identification statistic
id: MS:1002907
name: proteoform-level global FDR
def: "Estimation of the global false discovery rate of proteoforms." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002905 ! proteoform-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002908
name: proteoform-level local FDR
def: "Estimation of the local false discovery rate of proteoforms." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002905 ! proteoform-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002909
@@ -18882,15 +19139,15 @@ is_a: MS:1002573 ! spectrum identification statistical threshold
id: MS:1002910
name: proteoform-level global FDR threshold
def: "Threshold for the global false discovery rate of proteoforms." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002909 ! proteoform-level statistical threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002911
name: proteoform-level local FDR threshold
def: "Threshold for the local false discovery rate of proteoforms." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002909 ! proteoform-level statistical threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002912
@@ -18914,71 +19171,71 @@ is_a: MS:1002912 ! TopPIC input parameter
id: MS:1002915
name: TopPIC:error tolerance
def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1002916
name: TopPIC:max shift
def: "Maximum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1002917
name: TopPIC:min shift
def: "Minimum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1002918
name: TopPIC:shift num
def: "Maximum number of unexpected modifications in a proteoform spectrum match." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1002919
name: TopPIC:spectral cutoff type
def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002920
name: TopPIC:spectral cutoff value
def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002921
name: TopPIC:proteoform-level cutoff type
def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002922
name: TopPIC:proteoform-level cutoff value
def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002923
name: TopPIC:generating function
def: "P-value and E-value estimation using generating function." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002924
name: TopPIC:combined spectrum number
def: "Number of combined spectra." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1002925
@@ -18990,62 +19247,62 @@ is_a: MS:1002912 ! TopPIC input parameter
id: MS:1002926
name: TopPIC:thread number
def: "Number of threads used in TopPIC." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1002927
name: TopPIC:use TopFD feature
def: "Proteoform identification using TopFD feature file." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002928
name: TopPIC:spectral E-value
def: "TopPIC spectrum-level E-value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1002353 ! PSM-level e-value
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002929
name: TopPIC:spectral FDR
def: "TopPIC spectrum-level FDR." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1002351 ! PSM-level local FDR
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002930
name: TopPIC:proteoform-level FDR
def: "TopPIC proteoform-level FDR." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002908 ! proteoform-level local FDR
is_a: MS:1002906 ! search engine specific score for proteoforms
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002931
name: TopPIC:spectral p-value
def: "TopPIC spectrum-level p-value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1002352 ! PSM-level p-value
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002932
name: TopPIC:MIScore
def: "Modification identification score." [PMID:27291504]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002933
name: TopPIC:MIScore threshold
def: "TopPIC:MIScore threshold." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002934
@@ -19069,43 +19326,43 @@ is_a: MS:1002934 ! TopMG input parameter
id: MS:1002937
name: TopMG:error tolerance
def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1002938
name: TopMG:max shift
def: "Maximum value of the mass shift (in Dalton)." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1002939
name: TopMG:spectral cutoff type
def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002940
name: TopMG:spectral cutoff value
def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002941
name: TopMG:proteoform-level cutoff type
def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002942
name: TopMG:proteoform-level cutoff value
def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002943
@@ -19117,133 +19374,134 @@ is_a: MS:1002934 ! TopMG input parameter
id: MS:1002944
name: TopMG:thread number
def: "Number of threads used in TopMG." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1002945
name: TopMG:use TopFD feature
def: "Proteoform identification using TopFD feature file." [PSI:PI]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002946
name: TopMG:proteoform graph gap size
def: "Gap size in constructing proteoform graph." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1002947
name: TopMG:variable PTM number
def: "Maximum number of variable PTMs." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1002948
name: TopMG:variable PTM number in proteoform graph gap
def: "Maximum number of variable PTMs in a proteoform graph gap." [PSI:PI]
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1002949
name: TopMG:use ASF-DIAGONAL
def: "Protein filtering using ASF-DIAGONAL method." [PMID:29327814]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1002950
name: TopMG:spectral E-value
def: "TopMG spectrum-level E-value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002353 ! PSM-level e-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002951
name: TopMG:spectral FDR
def: "TopMG spectrum-level FDR." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002351 ! PSM-level local FDR
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002952
name: TopMG:proteoform-level FDR
def: "TopMG proteoform-level FDR." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002908 ! proteoform-level local FDR
is_a: MS:1002906 ! search engine specific score for proteoforms
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002953
name: TopMG:spectral p-value
def: "TopMG spectrum-level p-value." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002352 ! PSM-level p-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002954
name: collisional cross sectional area
def: "Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1000861 ! molecular entity property
+is_a: MS:1000455 ! ion selection attribute
relationship: has_units UO:0000324 ! square angstrom
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002955
name: hr-ms compound identification confidence level
def: "Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'." [PMID:24476540]
-xref: value-type:xsd:string "The allowed value-type for this CV term."
is_a: MS:1002895 ! small molecule identification attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002956
name: isotopic ion MS peak
def: "A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000231 ! peak
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002957
name: isotopomer MS peak
def: "The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002956 ! isotopic ion MS peak
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002958
name: isotopologue MS peak
def: "The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002956 ! isotopic ion MS peak
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002959
name: isomer
def: "One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae." [https://goldbook.iupac.org/html/I/I03289.html]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000859 ! molecule
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002960
name: isotopomer
def: "An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms." [https://goldbook.iupac.org/html/I/I03352.html]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002959 ! isomer
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002961
name: isotopologue
def: "A molecular entity that differs only in isotopic composition (number of isotopic substitutions)." [https://goldbook.iupac.org/html/I/I03351.html]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002959 ! isomer
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1002962
@@ -19420,17 +19678,17 @@ is_a: MS:1001456 ! analysis software
id: MS:1002988
name: IdentiPy:RHNS
def: "The IdentiPy result 'RHNS'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002989
name: IdentiPy:hyperscore
def: "The IdentiPy result 'hyperscore'." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002990
@@ -19448,10 +19706,10 @@ is_a: MS:1002333 ! conversion software
id: MS:1002995
name: Andromeda:PEP
def: "Posterior error probability of the best identified peptide of the Andromeda search engine." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1002996
@@ -19463,8 +19721,8 @@ is_a: MS:1000560 ! mass spectrometer file format
id: MS:1002997
name: ProteomeXchange dataset identifier reanalysis number
def: "Index number of a reanalysis within a ProteomeXchange reprocessed dataset identifier container (RPXD)." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1002998
@@ -19518,26 +19776,26 @@ is_a: MS:1003123 ! Bruker Daltonics timsTOF series
id: MS:1003006
name: mean inverse reduced ion mobility array
def: "Array of population mean ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units MS:1002814 ! volt-second per square centimeter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003007
name: raw ion mobility array
def: "Array of raw ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003008
name: raw inverse reduced ion mobility array
def: "Array of raw ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units MS:1002814 ! volt-second per square centimeter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003009
@@ -19587,21 +19845,21 @@ is_a: MS:1000860 ! peptide
id: MS:1003016
name: ProteinProphet:peptide weight
def: "Fraction of peptide evidence attributable to a protein or a set of indistinguishable proteins." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002490 ! peptide-level scoring
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003017
name: ProteinProphet:peptide group weight
def: "Fraction of peptide evidence attributable to a group of proteins." [PSI:PI]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002490 ! peptide-level scoring
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003018
@@ -19644,11 +19902,11 @@ is_a: MS:1000752 ! TOPP software
[Term]
id: MS:1003024
name: OpenPepXL:score
-def: "The OpenPepXL score for a cross-link spectrum match." [PSI:PI]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
+def: "The OpenPepXL score for a crosslink spectrum match." [PSI:PI]
is_a: MS:1001143 ! PSM-level search engine specific statistic
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003025
@@ -19684,22 +19942,22 @@ is_a: MS:1000494 ! Thermo Scientific instrument model
id: MS:1003030
name: Mascot:MinNumSigUniqueSeqs
def: "Minimum number of significant unique sequences required in a protein hit. The setting is only relevant if the protein grouping strategy is 'family clustering'." [PSI:PI]
-xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter
+relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term
[Term]
id: MS:1003031
name: CPTAC accession number
def: "Main identifier of a CPTAC dataset." [PSI:PI]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1003032
name: compound identification confidence code in MS-DIAL
def: "The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program." [PMID:25938372, http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002895 ! small molecule identification attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1003033
@@ -19766,12 +20024,14 @@ id: MS:1003043
name: number of residues
def: "Number of amino acid residues in a peptide, commonly referred to as the peptide length." [PSI:PI]
is_a: MS:1000887 ! peptide attribute
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1003044
name: number of missed cleavages
def: "Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not." [PSI:PI]
is_a: MS:1000887 ! peptide attribute
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1003045
@@ -19790,12 +20050,14 @@ id: MS:1003047
name: protein sequence offset
def: "Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence." [PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1003048
name: number of enzymatic termini
def: "Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules." [PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1003049
@@ -19829,12 +20091,14 @@ id: MS:1003053
name: theoretical monoisotopic m/z
def: "Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003054
name: theoretical average m/z
def: "Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003055
@@ -19853,6 +20117,7 @@ id: MS:1003057
name: scan number
def: "Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run." [PSI:PI]
is_a: MS:1000503 ! scan attribute
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1003058
@@ -19865,30 +20130,37 @@ id: MS:1003059
name: number of peaks
def: "Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points." [PSI:PI]
is_a: MS:1003058 ! spectrum property
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1003060
name: number of data points
def: "Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks." [PSI:PI]
is_a: MS:1003058 ! spectrum property
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1003061
-name: spectrum name
+name: library spectrum name
def: "Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+synonym: "spectrum name" EXACT []
[Term]
id: MS:1003062
-name: spectrum index
-def: "Integer index value associated with a spectrum within a collection of spectra, often in a spectral library. By custom, index counters should begin with 0." [PSI:PI]
-is_a: MS:1000499 ! spectrum attribute
+name: library spectrum index
+def: "Integer index value that indicates the spectrum's ordered position within a spectral library. By custom, index counters should begin with 0." [PSI:PI]
+is_a: MS:1003234 ! library spectrum attribute
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1003063
name: universal spectrum identifier
def: "PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+synonym: "USI" EXACT []
[Term]
id: MS:1003064
@@ -19925,12 +20197,14 @@ id: MS:1003069
name: number of replicate spectra available
def: "Number of replicate spectra available for use during the aggregation process." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1003070
name: number of replicate spectra used
def: "Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
[Term]
id: MS:1003071
@@ -19985,20 +20259,22 @@ id: MS:1003079
name: total unassigned intensity fraction
def: "Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum." [PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003080
name: top 20 peak unassigned intensity fraction
def: "Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum." [PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003081
name: unidentified modification monoisotopic mass delta
def: "Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the element in mzIdentML." [PSI:PI]
is_a: MS:1001471 ! peptide modification details
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
relationship: has_units UO:0000221 ! dalton
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003082
@@ -20017,24 +20293,24 @@ is_a: MS:1000577 ! source data file
id: MS:1003084
name: processed data file
def: "File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000577 ! source data file
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1003085
name: previous MSn-1 scan precursor intensity
def: "Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001141 ! intensity of precursor ion
is_a: MS:1000499 ! spectrum attribute
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003086
name: precursor apex intensity
def: "Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001141 ! intensity of precursor ion
is_a: MS:1000499 ! spectrum attribute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003087
@@ -20071,8 +20347,8 @@ relationship: part_of MS:1000625 ! chromatogram
id: MS:1003092
name: number of mantissa bits truncated
def: "Number of extraneous mantissa bits truncated to improve subsequent compression." [PSI:MS]
-xref: value-type:xsd\:positiveInteger "Number of mantissa bits truncated."
is_a: MS:1003091 ! binary data compression parameter
+relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term
[Term]
id: MS:1003093
@@ -20103,73 +20379,75 @@ is_a: MS:1000494 ! Thermo Scientific instrument model
id: MS:1003097
name: MaxQuant protein group-level score
def: "The probability based MaxQuant protein group score." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002368 ! search engine specific score for protein groups
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003098
name: Andromeda peptide PEP
def: "Peptide probability from Andromeda." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003099
name: MaxQuant-DIA peptide PEP
def: "Peptide probability from MaxQuant-DIA algorithm." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003100
name: MaxQuant-DIA score
def: "PSM evidence score from MaxQuant-DIA algorithm." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003101
name: MaxQuant-DIA PEP
def: "PSM evidence PEP probability from MaxQuant-DIA algorithm." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003102
name: NIST msp comment
def: "Term for a comment field withing the NIST msp file format" [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000499 ! spectrum attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1003103
-name: ion interpretation format
-def: "Interpretation format used for annotating individual spectrum ion peaks." [PSI:MS]
+name: ion annotation format
+def: "Annotation format used for annotating individual spectrum ion peaks." [PSI:MS]
is_a: MS:1003078 ! interpreted spectrum attribute
[Term]
id: MS:1003104
-name: peptide ion interpretation format
-def: "Interpretation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions." [PSI:MS]
-is_a: MS:1003103 ! ion interpretation format
+name: mzPAF peptide ion annotation format
+def: "Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions." [PSI:MS]
+is_a: MS:1003103 ! ion annotation format
+synonym: "peptide ion annotation format" EXACT []
[Term]
id: MS:1003105
-name: cross-linked peptide ion interpretation format
-def: "Interpretation format designed specifically for cross-linked peptide ion peaks." [PSI:MS]
-is_a: MS:1003103 ! ion interpretation format
+name: crosslinked peptide ion annotation format
+def: "Annotation format designed specifically for crosslinked peptide ion peaks." [PSI:MS]
+synonym: "cross-linked peptide ion annotation format" EXACT []
+is_a: MS:1003103 ! ion annotation format
[Term]
id: MS:1003106
-name: glycan ion interpretation format
-def: "Interpretation format designed specifically for glycan ion peaks." [PSI:MS]
-is_a: MS:1003103 ! ion interpretation format
+name: glycan ion annotation format
+def: "Annotation format designed specifically for glycan ion peaks." [PSI:MS]
+is_a: MS:1003103 ! ion annotation format
[Term]
id: MS:1003107
-name: lipid ion interpretation format
-def: "Interpretation format designed specifically for lipid ion peaks." [PSI:MS]
-is_a: MS:1003103 ! ion interpretation format
+name: lipid ion annotation format
+def: "Annotation format designed specifically for lipid ion peaks." [PSI:MS]
+is_a: MS:1003103 ! ion annotation format
[Term]
id: MS:1003108
@@ -20181,21 +20459,21 @@ is_a: MS:1001456 ! analysis software
[Term]
id: MS:1003109
name: SIM-XL
-def: "Identifying cross-linked peptides in complex protein mixtures" [PSI:MS]
+def: "Identifying crosslinked peptides in complex protein mixtures" [PSI:MS]
is_a: MS:1001456 ! analysis software
[Term]
id: MS:1003110
name: SIM-XL score
def: "SIM-XL identification search engine score" [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003111
name: QUIN-XL
-def: "Quantification of cross-linked peptides in complex protein mixtures" [PSI:MS]
+def: "Quantification of crosslinked peptides in complex protein mixtures" [PSI:MS]
is_a: MS:1001139 ! quantitation software name
[Term]
@@ -20208,36 +20486,36 @@ is_a: MS:1000494 ! Thermo Scientific instrument model
id: MS:1003113
name: OpenMS:ConsensusID PEP
def: "The OpenMS ConsesusID tool posterior error probability" [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003114
name: OpenMS:Best PSM Score
def: "The score of the best PSM selected by the underlying identification tool" [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003115
name: OpenMS:Target-decoy PSM q-value
def: "The OpenMS Target-decoy q-values at PSM level" [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003116
name: OpenMS:Target-decoy peptide q-value
def: "The OpenMS Target-decoy q-values at peptide sequence level" [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003117
name: OpenMS:Target-decoy protein q-value
def: "The OpenMS Target-decoy q-values at protein level" [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003118
@@ -20250,22 +20528,22 @@ is_a: MS:1000752 ! TOPP software
id: MS:1003119
name: EPIFANY:Protein posterior probability
def: "Protein Posterior probability calculated by EPIFANY protein inference algorithm" [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002363 ! search engine specific score for proteins
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003120
name: OpenMS:LFQ intensity
def: "The data type LFQ intensity produced by OpenMS." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003121
name: OpenMS:LFQ spectral count
def: "The data type LFQ spectral count produced by OpenMS." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003122
@@ -20289,52 +20567,52 @@ is_a: MS:1003123 ! Bruker Daltonics timsTOF series
id: MS:1003125
name: ProSight:spectral Q-value
def: "ProSight spectrum-level Q-value." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002354 ! PSM-level q-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003126
name: ProSight:spectral P-score
def: "ProSight spectrum-level P-score." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003127
name: ProSight:spectral E-value
def: "ProSight spectrum-level E-value." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002353 ! PSM-level e-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003128
name: ProSight:spectral C-score
def: "ProSight spectrum-level C-score." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003129
name: proteoform-level Q-value
def: "Estimation of the Q-value for proteoforms." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002905 ! proteoform-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003130
name: ProSight:proteoform Q-value
def: "ProSight proteoform-level Q-value." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1003129 ! proteoform-level Q-value
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003131
@@ -20352,25 +20630,25 @@ is_a: MS:1003131 ! isoform-level identification attribute
id: MS:1003133
name: isoform-level Q-value
def: "Estimation of the Q-value for isoforms." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1003132 ! isoform-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003134
name: ProSight:isoform Q-value
def: "ProSight isoform-level Q-value." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1003133 ! isoform-level Q-value
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003135
name: ProSight:protein Q-value
def: "ProSight protein-level Q-value." [PSI:MS]
-xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001869 ! protein-level q-value
relationship: has_order MS:1002109 ! lower score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
[Term]
id: MS:1003136
@@ -20388,25 +20666,25 @@ is_a: MS:1001302 ! search engine specific input parameter
id: MS:1003138
name: ProSight:Run delta m mode
def: "If true, runs delta m mode in ProSight." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1003136 ! ProSight input parameter
is_a: MS:1003137 ! TDPortal input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1003139
name: ProSight:Run Subsequence Search mode
def: "If true, runs Subsequence Search mode in ProSight." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1003136 ! ProSight input parameter
is_a: MS:1003137 ! TDPortal input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1003140
name: ProSight:Run Annotated Proteoform Search mode
def: "If true, runs Annotated Proteoform Search mode in ProSight." [PSI:MS]
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1003136 ! ProSight input parameter
is_a: MS:1003137 ! TDPortal input parameter
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
[Term]
id: MS:1003141
@@ -20464,15 +20742,14 @@ relationship: has_regexp MS:1002505 ! regular expression for modification locali
[Term]
id: MS:1003149
name: PTMProphet normalized information content
-def: "PTMProphet-computed PSM-specific normalized (0.0 - 1.0) measure of information content across all modifications of a specific type." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668]
+def: " PTMProphet-computed PSM-specific normalized (0.0 - 1.0) measure of information content across all modifications of a specific type." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668]
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
-
[Term]
id: MS:1003150
name: PTMProphet information content
-def: "PTMProphet-computed PSM-specific measure of information content per modification type ranging from 0 to m, where m is the number of modifications of a specific type." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668]
+def: " PTMProphet-computed PSM-specific measure of information content per modification type ranging from 0 to m, where m is the number of modifications of a specific type." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668]
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
@@ -20480,8 +20757,8 @@ relationship: has_regexp MS:1002505 ! regular expression for modification locali
id: MS:1003151
name: SHA-256
def: "SHA-256 (member of Secure Hash Algorithm-2 family) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity." [PSI:MS]
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000561 ! data file checksum type
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: MS:1003152
@@ -20493,52 +20770,52 @@ is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model
id: MS:1003153
name: raw ion mobility drift time array
def: "Array of raw ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003154
name: deconvoluted ion mobility array
def: "Array of ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003155
name: deconvoluted inverse reduced ion mobility array
def: "Array of ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units MS:1002814 ! volt-second per square centimeter
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003156
name: deconvoluted ion mobility drift time array
def: "Array of mean ion mobility values from a drift time device, reported in seconds (or milliseconds), as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003157
name: scanning quadrupole position lower bound m/z array
def: "Array of m/z values representing the lower bound m/z of the quadrupole position at each point in the spectrum." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000513 ! binary data array
relationship: has_units MS:1000040 ! m/z
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003158
name: scanning quadrupole position upper bound m/z array
def: "Array of m/z values representing the upper bound m/z of the quadrupole position at each point in the spectrum." [PSI:MS]
-xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000513 ! binary data array
relationship: has_units MS:1000040 ! m/z
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
id: MS:1003159
@@ -20566,376 +20843,3728 @@ is_a: MS:1001456 ! analysis software
synonym: "PTXQC" EXACT []
[Term]
-id: PEFF:0000001
-name: PEFF CV term
-def: "PSI Extended FASTA Format controlled vocabulary term." [PSI:PEFF]
-relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies
+id: MS:1003163
+name: analyte mixture members
+def: "The set of analyte identifiers that compose an interpretation of a spectrum." [PSI:PI]
+is_a: MS:1003078 ! interpreted spectrum attribute
+relationship: has_value_type MS:1002712 ! list of integers
[Term]
-id: PEFF:0000002
-name: PEFF file header section term
-def: "CV term that may appear in a PEFF file header section." [PSI:PEFF]
-is_a: PEFF:0000001 ! PEFF CV term
+id: MS:1003164
+name: QuaMeter IDFree
+def: "QuaMeter IDFree software for QC metric calculation." [DOI:10.1021/ac4034455, PMID:24494671]
+is_a: MS:1001456 ! analysis software
+synonym: "QuaMeter" EXACT []
[Term]
-id: PEFF:0000003
-name: PEFF file sequence entry term
-def: "CV term that may appear in a description line of a PEFF file individual sequence entry." [PSI:PEFF]
-is_a: PEFF:0000001 ! PEFF CV term
+id: MS:1003165
+name: iMonDB
+def: "iMonDB software to extract, store, and manage mass spectrometry instrument parameters from raw data files." [DOI:10.1021/acs.jproteome.5b00127, PMID:25798920, https://github.com/bittremieux/iMonDB]
+is_a: MS:1001456 ! analysis software
[Term]
-id: PEFF:0000008
-name: DbName
-def: "PEFF keyword for the sequence database name." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003166
+name: assigned intensity fraction
+def: "Fraction of intensity summed from all peaks that can be attributed to expected fragments of the analyte, divided by the intensity summed from all peaks in the spectrum" [PSI:PI]
+is_a: MS:1003078 ! interpreted spectrum attribute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
-id: PEFF:0000009
-name: Prefix
-def: "PEFF keyword for the sequence database prefix." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003167
+name: MSn-1 isolation window precursor purity
+def: "The fraction of total intensities in the isolation window in the previous round of MS (i.e. the MSn-1 scan) that can be assigned to this identified analyte" [PSI:PI]
+is_a: MS:1003078 ! interpreted spectrum attribute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
-id: PEFF:0000010
-name: DbDescription
-def: "PEFF keyword for the sequence database short description." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003168
+name: library spectrum comment
+def: "A free-text string providing additional information of the library spectrum not encoded otherwise, usually for human use and not parsed by software tools." [PSI:PI]
+is_a: MS:1003234 ! library spectrum attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
-id: PEFF:0000011
-name: Decoy
-def: "PEFF keyword for the specifying whether the sequence database is a decoy database." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
+id: MS:1003169
+name: proforma peptidoform sequence
+def: "Sequence string describing the amino acids and mass modifications of a peptidoform using the PSI ProForma notation" [PSI:PI]
+is_a: MS:1000889 ! peptidoform sequence
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
-id: PEFF:0000012
-name: DbSource
-def: "PEFF keyword for the source of the database file." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003170
+name: spectral library
+def: "A collection of spectra organized by their originating analyte, compiled deliberately for use in MS data analysis in future experiments" [PSI:PI]
+relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies
[Term]
-id: PEFF:0000013
-name: DbVersion
-def: "PEFF keyword for the database version (release date) according to database provider." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003171
+name: spectral library attribute
+def: "An attribute of a spectral library" [PSI:PI]
+relationship: part_of MS:1003170 ! spectral library
[Term]
-id: PEFF:0000014
-name: DbDate
-def: "OBSOLETE PEFF keyword for the database date (release or file date of the source) according to database provider." [PSI:PEFF]
-comment: This term was obsoleted.
-is_a: PEFF:0000002 ! PEFF file header section term
-is_obsolete: true
+id: MS:1003172
+name: library spectrum
+def: "An entry in a spectral library representing a spectrum" [PSI:PI]
+relationship: part_of MS:1003170 ! spectral library
[Term]
-id: PEFF:0000015
-name: NumberOfEntries
-def: "PEFF keyword for the sumber of sequence entries in the database." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:integer "The allowed value-type for this CV term."
+id: MS:1003173
+name: numeric attribute
+def: "An attribute that takes on a numeric value" [PSI:PI]
+is_a: MS:1000547 ! object attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
-id: PEFF:0000016
-name: Conversion
-def: "PEFF keyword for the description of the conversion from original format to this current one." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003174
+name: attribute maximum
+def: "The maximum value for this attribute" [PSI:PI]
+relationship: part_of MS:1003171 ! numeric attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
-id: PEFF:0000017
-name: SequenceType
-def: "PEFF keyword for the molecular type of the sequences." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
-relationship: has_regexp PEFF:1002002 ! regular expression for PEFF molecular sequence type
+id: MS:1003175
+name: attribute minimum
+def: "The minimum value for this attribute" [PSI:PI]
+relationship: part_of MS:1003171 ! numeric attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
-id: PEFF:0000018
-name: SpecificKey
-def: "PEFF keyword for database specific keywords not included in the current controlled vocabulary." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003176
+name: attribute mean
+def: "The arithmetic mean value for this attribute" [PSI:PI]
+relationship: part_of MS:1003171 ! numeric attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
-id: PEFF:0000019
-name: SpecificValue
-def: "PEFF keyword for the specific values for a custom key." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003177
+name: attribute standard deviation
+def: "The standard deviation (exact value of population, or estimate from sample) of this attribute" [PSI:PI]
+relationship: part_of MS:1003171 ! numeric attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
-id: PEFF:0000020
-name: DatabaseDescription
-def: "PEFF keyword for the short description of the PEFF file." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003178
+name: attribute coefficient of variation
+def: "The coefficient of variation of this attribute, i.e. standard deviation divided by the mean" [PSI:PI]
+relationship: part_of MS:1003171 ! numeric attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
-id: PEFF:0000021
-name: GeneralComment
-def: "PEFF keyword for a general comment." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003179
+name: attribute summary value
+def: "The most appropriate summary value of the attribute, usually but not necessarily the mean" [PSI:PI]
+relationship: part_of MS:1003171 ! numeric attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
-id: PEFF:0000022
-name: ProteoformDb
-def: "PEFF keyword that when set to 'true' indicates that the database contains complete proteoforms." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003180
+name: attribute median
+def: "The median of this attribute" [PSI:PI]
+relationship: part_of MS:1003171 ! numeric attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
[Term]
-id: PEFF:0000023
-name: OptionalTagDef
-def: "PEFF keyword for the short tag (abbreviation) and longer definition used to annotate a sequence annotation (such as variant or modification) in the OptionalTag location." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003181
+name: combined dissociation method
+def: "Combination of two or more dissociation methods that are known by a special term." [PSI:PI]
+is_a: MS:1000044 ! dissociation method
[Term]
-id: PEFF:0000024
-name: HasAnnotationIdentifiers
-def: "PEFF keyword that when set to 'true' indicates that entries in the database have identifiers for each annotation." [PSI:PEFF]
-is_a: PEFF:0000002 ! PEFF file header section term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003182
+name: electron-transfer/collision-induced dissociation
+def: "Dissociation process combining electron-transfer dissociation (ETD) and collision-induced dissociation (CID)." [PSI:PI]
+synonym: "ETciD" EXACT []
+is_a: MS:1003181 ! combined dissociation method
[Term]
-id: PEFF:0001001
-name: DbUniqueId
-def: "OBSOLETE Sequence database unique identifier." [PSI:PEFF]
-comment: This term was made obsolete because decided in Heidelberg 2018-04 that this is redundant.
-is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
-is_obsolete: true
+id: MS:1003183
+name: Synapt XS
+def: "Waters oa-ToF based Synapt XS." [PSI:PI]
+is_a: MS:1000126 ! Waters instrument model
[Term]
-id: PEFF:0001002
-name: PName
-def: "PEFF keyword for the protein full name." [PSI:PEFF]
-is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003184
+name: SELECT SERIES Cyclic IMS
+def: "Waters oa-ToF based SELECT SERIES Cyclic IMS." [PSI:PI]
+is_a: MS:1000126 ! Waters instrument model
[Term]
-id: PEFF:0001003
-name: NcbiTaxId
-def: "PEFF keyword for the NCBI taxonomy identifier." [PSI:PEFF]
-is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
+id: MS:1003185
+name: SELECT SERIES MRT
+def: "Waters oa-ToF based SELECT SERIES MRT." [PSI:PI]
+is_a: MS:1000126 ! Waters instrument model
[Term]
-id: PEFF:0001004
-name: TaxName
-def: "PEFF keyword for the taxonomy name (latin or common name)." [PSI:PEFF]
-is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003186
+name: library format version
+def: "Version number of the [PSI] library format specification" [PSI:PI]
+is_a: MS:1003171 ! spectral library attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
-id: PEFF:0001005
-name: GName
-def: "PEFF keyword for the gene name." [PSI:PEFF]
-is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003187
+name: library identifier
+def: "Short identifier for the library for easy reference, preferably but not necessarily globally unique" [PSI:PI]
+is_a: MS:1003171 ! spectral library attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
-id: PEFF:0001006
-name: Length
-def: "PEFF keyword for the sequence length." [PSI:PEFF]
-is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
+id: MS:1003188
+name: library name
+def: "A short name identifying the library to potential users. The same name may refer to multiple versions of the same continually updated library." [PSI:PI]
+is_a: MS:1003171 ! spectral library attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
-id: PEFF:0001007
-name: SV
-def: "PEFF keyword for the sequence version." [PSI:PEFF]
-is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003189
+name: library description
+def: "Extended free-text description of the library" [PSI:PI]
+is_a: MS:1003171 ! spectral library attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
-id: PEFF:0001008
-name: EV
-def: "PEFF keyword for the entry version." [PSI:PEFF]
-is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003190
+name: library version
+def: "Version number of the library, usually refering to a certain release of a continually updated library " [PSI:PI]
+is_a: MS:1003171 ! spectral library attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
-id: PEFF:0001009
-name: PE
-def: "PEFF keyword for the Protein Evidence; A UniProtKB code 1-5." [PSI:PEFF]
-is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:int "The allowed value-type for this CV term."
+id: MS:1003191
+name: library URI
+def: "URI or URL that uniquely identifies the library" [PSI:PI]
+is_a: MS:1003171 ! spectral library attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
-id: PEFF:0001010
-name: Processed
-def: "PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains." [PSI:PEFF]
-is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
-relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+id: MS:1003192
+name: decoy spectrum
+def: "A spectrum deliberately introduced into a spectral library that necessarily produces incorrect identifications when matched, for the purpose of error control in spectral library searching" [PSI:PI]
+is_a: MS:1003072 ! spectrum origin type
[Term]
-id: PEFF:0001011
-name: Variant
-def: "OBSOLETE Sequence variation (substitution, insertion, deletion)." [PSI:PEFF]
-comment: This term was made obsolete in favor of VariantSimple and VariantComplex.
-is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
-relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
-is_obsolete: true
+id: MS:1003193
+name: shuffle-and-reposition decoy spectrum
+def: "A decoy spectrum generated from a real spectrum, by shuffling the amino acid sequence of the identification of the real spectrum, followed by re-positioning annotated peaks to match the shuffled sequence." [PSI:PI]
+is_a: MS:1003192 ! decoy spectrum
[Term]
-id: PEFF:0001012
-name: ModResPsi
-def: "PEFF keyword for the modified residue with PSI-MOD identifier." [PSI:PEFF]
-is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
-relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+id: MS:1003194
+name: precursor shift decoy spectrum
+def: "A decoy spectrum generated from a real spectrum, by changing the precursor m/z value of the real spectrum." [PSI:PI]
+is_a: MS:1003192 ! decoy spectrum
[Term]
-id: PEFF:0001013
-name: ModRes
-def: "PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier." [PSI:PEFF]
-is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
-relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+id: MS:1003195
+name: unnatural peptidoform decoy spectrum
+def: "A decoy spectrum that is either a real spectrum of an unnatural peptidoform (e.g. a synthetic peptide that cannot be found in nature), or an artificial spectrum predicted for such unnatural peptidoform" [PSI:PI]
+is_a: MS:1003192 ! decoy spectrum
[Term]
-id: PEFF:0001014
-name: AltAC
-def: "PEFF keyword for the Alternative Accession Code." [PSI:PEFF]
-is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003196
+name: unrelated species decoy spectrum
+def: "A decoy spectrum that is a real spectrum of a naturally occuring peptidoform of an unrelated species that should not be found in the sample" [PSI:PI]
+is_a: MS:1003192 ! decoy spectrum
[Term]
-id: PEFF:0001015
-name: SeqStatus
-def: "PEFF keyword for the sequence status. Complete or Fragment." [PSI:PEFF]
-is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+id: MS:1003197
+name: license URI
+def: "URI of the license controlling use of the library (e.g. https://creativecommons.org/publicdomain/zero/1.0/)" [PSI:PI]
+is_a: MS:1003171 ! spectral library attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003198
+name: copyright notice
+def: "Notice of statutorily prescribed form that informs users of the underlying claim to copyright ownership in a published work" [PSI:PI]
+is_a: MS:1003171 ! spectral library attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003199
+name: change log
+def: "Extended free-text description of the difference from the previous version" [PSI:PI]
+is_a: MS:1003171 ! spectral library attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003200
+name: software version
+def: "Version number of the software package used for library creation" [PSI:PI]
+is_a: MS:1003171 ! spectral library attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003201
+name: library provenance attribute
+def: "Abstract term containing several different types of provenance information" [PSI:PI]
+is_a: MS:1003171 ! spectral library attribute
+
+[Term]
+id: MS:1003202
+name: BiblioSpec
+def: "A suite of software tools for creating and searching MS/MS peptide spectrum libraries, developed at the University of Washington" [PSI:PI]
+is_a: MS:1001456 ! analysis software
+is_a: MS:1003207 ! library creation software
+
+[Term]
+id: MS:1003203
+name: constituent spectrum file
+def: "Spectrum data file from which (at least) a subset of spectra were extracted from. Should use USI notation mzspec:PXDxxxx:msRunName if possible, or a URI if USI notation is not possible." [PSI:PI]
+is_a: MS:1003201 ! library provenance attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003204
+name: constituent identification file
+def: "Identification file where (at least) a subset of identifications were extracted from. Should use a URI if possible" [PSI:PI]
+is_a: MS:1003201 ! library provenance attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003205
+name: constituent library file
+def: "Source library URI which(at least) a subset of spectra were extracted from." [PSI:PI]
+is_a: MS:1003201 ! library provenance attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003206
+name: library creation log
+def: "String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped \n" [PSI:PI]
+is_a: MS:1003201 ! library provenance attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003207
+name: library creation software
+def: "Library creation software" [PSI:MS]
+is_a: MS:1000531 ! software
+is_a: MS:1003171 ! spectral library attribute
+
+[Term]
+id: MS:1003208
+name: experimental precursor monoisotopic m/z
+def: "The measured or inferred m/z (as reported by the mass spectrometer acquisition software or post-processing software) of the monoisotopic peak of the precursor ion based on the MSn-1 spectrum." [PSI:MS]
+is_a: MS:1000455 ! ion selection attribute
+is_a: MS:1003295 ! summary statistics of replicates
+relationship: has_units MS:1000040 ! m/z
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003209
+name: monoisotopic m/z deviation
+def: "The measured monoisotopic m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical monoisotopic m/z of the analyte assigned to the spectrum." [PSI:MS]
+is_a: MS:1003078 ! interpreted spectrum attribute
+is_a: MS:1003295 ! summary statistics of replicates
+relationship: has_units MS:1000040 ! m/z
+relationship: has_units UO:0000169 ! parts per million
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003210
+name: average m/z deviation
+def: "The measured average m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical average m/z of the analyte assigned to the spectrum." [PSI:MS]
+is_a: MS:1003078 ! interpreted spectrum attribute
+is_a: MS:1003295 ! summary statistics of replicates
+relationship: has_units MS:1000040 ! m/z
+relationship: has_units UO:0000169 ! parts per million
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003211
+name: library spectrum attribute set
+def: "A set of spectrum-related attributes that is shared by a subset of spectra within the same spectral library" [PSI:PI]
+is_a: MS:1003171 ! spectral library attribute
+
+[Term]
+id: MS:1003212
+name: library attribute set name
+def: "A name to refer to a library attribute set" [PSI:PI]
+relationship: part_of MS:1003211 ! library spectrum attribute set
+relationship: part_of MS:1003238 ! library analyte attribute set
+relationship: part_of MS:1003239 ! library interpretation attribute set
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003213
+name: mass spectrometry acquisition method
+def: "Mode of running a mass spectrometer method by which mass ranges are selected and possibly dissociated." [PSI:MS]
+is_a: MS:1000524 ! data file content
+is_a: MS:1001954 ! acquisition parameter
+relationship: part_of MS:1003350 ! mass spectrometry proteomics
+
+[Term]
+id: MS:1003214
+name: mass spectrometry acquisition method aspect
+def: "Specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated." [PSI:MS]
+is_a: MS:1001458 ! spectrum generation information
+relationship: part_of MS:1003213 ! mass spectrometry acquisition method
+
+[Term]
+id: MS:1003215
+name: data-independent acquisition
+def: "Mass spectrometer data acquisition method wherein mass selection for fragmentation is configured according to a pre-determined program, rather than based on any detected precursor ions." [PSI:MS]
+synonym: "DIA" EXACT []
+is_a: MS:1003214 ! mass spectrometry acquisition method aspect
+
+[Term]
+id: MS:1003216
+name: dissociation of full mass range
+def: "Mass spectrometer data acquisition method wherein all precursor ions of which the instrument is capable are fragmented at once.." [PSI:MS]
+is_a: MS:1003214 ! mass spectrometry acquisition method aspect
+
+[Term]
+id: MS:1003217
+name: dissociation of scanning quadrupole across a specified mass range
+def: "Mass spectrometer data acquisition method wherein ????." [PSI:MS]
+is_a: MS:1003214 ! mass spectrometry acquisition method aspect
+
+[Term]
+id: MS:1003218
+name: dissociation of sequential mass ranges
+def: "Mass spectrometer data acquisition method wherein a series of limited mass range fragmentation selection windows are preconfigured." [PSI:MS]
+is_a: MS:1003214 ! mass spectrometry acquisition method aspect
+
+[Term]
+id: MS:1003219
+name: ion mobility separation
+def: "Mass spectrometer data acquisition method wherein precursor ions are separated by their ion mobility properties prior to measurement." [PSI:MS]
+is_a: MS:1003214 ! mass spectrometry acquisition method aspect
+
+[Term]
+id: MS:1003220
+name: adduct deconvolution
+def: "Data processing action of merging of the measurements of potentially multiple adducts into a single representation that is independent of the small ion that adds charge to a larger molecule." [PSI:MS]
+is_a: MS:1000543 ! data processing action
+
+[Term]
+id: MS:1003221
+name: data-dependent acquisition
+def: "Mass spectrometer data acquisition method wherein MSn spectra are triggered based on the m/z of precursor ions detected in the same run." [PSI:MS]
+is_a: MS:1003214 ! mass spectrometry acquisition method aspect
+is_a: MS:1003213 ! mass spectrometry acquisition method
+synonym: "DDA" EXACT []
+
+[Term]
+id: MS:1003222
+name: ion mobility deconvolution
+def: "Data processing action of merging multiple ion peaks acquired at different ion mobility steps into a single mass spectrum representing a single analyte." [PSI:MS]
+is_a: MS:1000543 ! data processing action
+
+[Term]
+id: MS:1003224
+name: data independent acquisition from dissociation of sequential mass ranges
+def: "Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented. Examples of such an approach include SWATH-MS, FT-ARM, HRM, and PAcIFIC." [PSI:MS]
+is_a: MS:1003218 ! dissociation of sequential mass ranges
+is_a: MS:1003215 ! data-independent acquisition
+is_a: MS:1003213 ! mass spectrometry acquisition method
+
+[Term]
+id: MS:1003225
+name: data independent acquisition from dissociation of sequential mass ranges after ion mobility separation
+def: "Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented after being separated by ion mobility. An example of such an approach is Bruker diaPASEF." [PSI:MS]
+is_a: MS:1003218 ! dissociation of sequential mass ranges
+is_a: MS:1003219 ! ion mobility separation
+is_a: MS:1003215 ! data-independent acquisition
+is_a: MS:1003213 ! mass spectrometry acquisition method
+
+[Term]
+id: MS:1003226
+name: data independent acquisition from dissociation of full mass range after ion mobility separation
+def: "Data independent mass spectrometer acquisition method wherein the full mass range is fragmented after being separated by ion mobility. Examples of such an approach include HDMS^E and IMS-AIF." [PSI:MS]
+is_a: MS:1003216 ! dissociation of full mass range
+is_a: MS:1003219 ! ion mobility separation
+is_a: MS:1003215 ! data-independent acquisition
+is_a: MS:1003213 ! mass spectrometry acquisition method
+
+[Term]
+id: MS:1003227
+name: data independent acquisition from dissociation of full mass range
+def: "Data independent mass spectrometer acquisition method wherein the full mass range is fragmented. Examples of such an approach include MS^E, AIF, and bbCID." [PSI:MS]
+is_a: MS:1003216 ! dissociation of full mass range
+is_a: MS:1003219 ! ion mobility separation
+is_a: MS:1003215 ! data-independent acquisition
+is_a: MS:1003213 ! mass spectrometry acquisition method
+
+[Term]
+id: MS:1003228
+name: data independent acquisition from dissociation of scanning quadrupole across mass range
+def: "Data independent mass spectrometer acquisition method wherein ???. An example of such an approach is Waters SONAR." [PSI:MS]
+is_a: MS:1003215 ! data-independent acquisition
+is_a: MS:1003217 ! dissociation of scanning quadrupole across a specified mass range
+is_a: MS:1003213 ! mass spectrometry acquisition method
+
+[Term]
+id: MS:1003229
+name: timsTOF
+def: "Bruker Daltonics' timsTOF." [PSI:MS]
+is_a: MS:1003123 ! Bruker Daltonics timsTOF series
+
+[Term]
+id: MS:1003230
+name: timsTOF Pro 2
+def: "Bruker Daltonics' timsTOF Pro 2." [PSI:MS]
+is_a: MS:1003123 ! Bruker Daltonics timsTOF series
+
+[Term]
+id: MS:1003231
+name: timsTOF SCP
+def: "Bruker Daltonics' timsTOF SCP." [PSI:MS]
+is_a: MS:1003123 ! Bruker Daltonics timsTOF series
+
+[Term]
+id: MS:1003232
+name: PeakForest
+def: "comprehensive infrastructure to organize, curate and share a multi- instrument spectral library for metabolomics data annotation developed and distributed by the French National infrastructure in metabolomics and fluxomics (MetaboHUB)." [https://peakforest.org/]
+is_a: MS:1001456 ! analysis software
+is_a: MS:1003207 ! library creation software
+is_a: MS:1002878 ! small molecule analysis software
+
+[Term]
+id: MS:1003234
+name: library spectrum attribute
+def: "An attribute that describes information about an entry in a spectral library" [PSI:PI]
+relationship: part_of MS:1003172 ! library spectrum
+
+[Term]
+id: MS:1003235
+name: paper spray ionization
+def: "The ionization of analytes from a piece of paper by applying a solvent and voltage." [PSI:MS]
+is_a: MS:1000008 ! ionization type
+
+[Term]
+id: MS:1003237
+name: library spectrum key
+def: "An ordinal number uniquely identifying a spectrum in a library. Library spectrum keys should start at 1. Library spectrum keys SHOULD not change if entries are re-ordered or removed from a library." [PSI:PI]
+is_a: MS:1003234 ! library spectrum attribute
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003238
+name: library analyte attribute set
+def: "A set of analyte-related attributes that is shared by a subset of spectra within the same spectral library" [PSI:PI]
+is_a: MS:1003171 ! spectral library attribute
+
+[Term]
+id: MS:1003239
+name: library interpretation attribute set
+def: "A set of interpretation-related attributes that is shared by a subset of spectra within the same spectral library" [PSI:PI]
+is_a: MS:1003171 ! spectral library attribute
+
+[Term]
+id: MS:1003240
+name: peak intensity transform
+def: "A mathematical transformation applied to peak intensities, for example, as a way to modify the weight put on each peak when computing spectral match scores" [PSI:PI]
+is_a: MS:1000543 ! data processing action
+
+[Term]
+id: MS:1003241
+name: square root transform
+def: "A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their square roots" [PSI:PI]
+is_a: MS:1003240 ! peak intensity transform
+
+[Term]
+id: MS:1003242
+name: rank transform
+def: "A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their ranks" [PSI:PI]
+is_a: MS:1003240 ! peak intensity transform
+
+[Term]
+id: MS:1003243
+name: adduct ion mass
+def: "The theoretical mass of the adduct ion (e.g. for a singly-charged protonated peptide ion, this value would be the neutral peptide molecule's mass plus the mass of a proton)" [PSI:PI]
+is_a: MS:1003056 ! adduct ion property
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003244
+name: peptide accession number
+def: "Accession number (e.g. in PeptideAtlas) of the peptide sequence" [PSI:PI]
+is_a: MS:1003050 ! peptidoform attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003245
+name: Q Exactive UHMR
+def: "Thermo Scientific Q Exactive UHMR (Ultra High Mass Range) Hybrid Quadrupole Orbitrap MS." [PSI:PI]
+is_a: MS:1000494 ! Thermo Scientific instrument model
+
+[Term]
+id: MS:1003246
+name: ultraviolet photodissociation
+def: "Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple UV photons." [PSI:MS]
+synonym: "UVPD" EXACT []
+is_a: MS:1000435 ! photodissociation
+
+[Term]
+id: MS:1003247
+name: negative electron transfer dissociation
+def: "A process to fragment ions in a mass spectrometer by inducing fragmentation of anions (e.g. peptides or proteins) by transferring electrons to a radical-cation." [DOI:10.1016/j.jasms.2005.01.015, PSI:MS]
+synonym: "NETD" EXACT []
+is_a: MS:1000044 ! dissociation method
+
+[Term]
+id: MS:1003248
+name: proton transfer reaction
+def: "Process to transfer a proton from a hydronium ion (H3O+) to neutral analyte, leading to a protonated analyte, which typically does not lead to fragmentation." [DOI:10.1002/mas.20048, PSI:MS]
+synonym: "PTR" EXACT []
+is_a: MS:1000008 ! ionization type
+
+[Term]
+id: MS:1003249
+name: proton transfer charge reduction
+def: "Process to transfer one or more protons from a multiply charged cation (peptide or protein ion) to a proton acceptor anion or neutral basic compound, thereby reducing the charge of the original analyte." [PSI:MS]
+synonym: "PTCR" EXACT []
+is_a: MS:1000008 ! ionization type
+
+[Term]
+id: MS:1003250
+name: count of identified peptidoforms
+def: "The number of peptidoforms that pass the threshold to be considered identified with sufficient confidence." [PSI:PI]
+is_a: MS:1002702 ! peptide sequence-level result list attribute
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003251
+name: count of identified spectra
+def: "The number of spectra that pass the threshold to be considered identified with sufficient confidence." [PSI:PI]
+is_a: MS:1002700 ! PSM-level result list attribute
+is_a: MS:4000003 ! single value
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_metric_category MS:4000008 ! ID based metric
+
+[Term]
+id: MS:1003252
+name: Xevo G2-XS QTof
+def: "Waters Corporation Xevo G2-XS QTof quadrupole time-of-flight mass spectrometer." [PSI:PI]
+is_a: MS:1000126 ! Waters instrument model
+
+[Term]
+id: MS:1003253
+name: DIA-NN
+def: "A universal software for data-independent acquisition (DIA) proteomics data processing" [PMID:31768060, https://github.com/vdemichev/DiaNN]
+is_a: MS:1001139 ! quantitation software name
+is_a: MS:1001456 ! analysis software
+
+[Term]
+id: MS:1003254
+name: peak attribute
+def: "An attribute of a peak in a mass spectrum other than its m/z, intensity, and annotation. " [PSI:PI]
+relationship: part_of MS:1000231 ! peak
+
+[Term]
+id: MS:1003255
+name: pre-decharged charge state
+def: "For a de-charged spectrum, the original charge state of the ion observed in a mass spectrum determined by charge deconvolution. " [PSI:PI]
+is_a: MS:1003254 ! peak attribute
+
+[Term]
+id: MS:1003256
+name: peptidoform ion attribute
+def: "Non-inherent characteristic attributed to a peptidoform" [PSI:PI]
+relationship: part_of MS:1003051 ! peptidoform ion
+
+[Term]
+id: MS:1003257
+name: library spectrum cross reference
+def: "A link from one spectrum to another spectrum of interest " [PSI:PI]
+is_a: MS:1003234 ! library spectrum attribute
+
+[Term]
+id: MS:1003258
+name: related spectrum
+def: "A cross reference to another spectrum that has some relationship with this one, but is not necessarily spectrally similar. " [PSI:PI]
+is_a: MS:1003257 ! library spectrum cross reference
+
+[Term]
+id: MS:1003259
+name: related spectrum keys
+def: "A list of cross references to a related spectrum in the same library, in the form of the library spectrum key. " [PSI:PI]
+is_a: MS:1003258 ! related spectrum
+relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003260
+name: related spectrum USI
+def: "A cross reference to a related spectrum in the form of a PSI Universal Spectrum Identifier" [PSI:PI]
+is_a: MS:1003258 ! related spectrum
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003261
+name: related spectrum description
+def: "A free-text string describing the related spectrum and/or its relationship to this spectrum" [PSI:PI]
+relationship: part_of MS:1003258 ! related spectrum
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003262
+name: similar spectrum
+def: "A cross reference to another spectrum that has high spectral similarity with this one, usually assumed to originate from the same analyte ion." [PSI:PI]
+is_a: MS:1003257 ! library spectrum cross reference
+
+[Term]
+id: MS:1003263
+name: similar spectrum keys
+def: "A list of cross references to a similar spectrum in the same library, in the form of the library spectrum key. " [PSI:PI]
+is_a: MS:1003262 ! similar spectrum
+relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003264
+name: similar spectrum USI
+def: "A cross reference to a similar spectrum in the form of a PSI Universal Spectrum Identifier" [PSI:PI]
+is_a: MS:1003262 ! similar spectrum
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003265
+name: spectrum cluster
+def: "A group of spectra that are spectrally similar to each other" [PSI:PI]
+relationship: part_of MS:1003170 ! spectral library
+
+[Term]
+id: MS:1003266
+name: spectrum cluster attribute
+def: "A non-inherent characteristic of a spectrum cluster" [PSI:PI]
+relationship: part_of MS:1003265 ! spectrum cluster
+
+[Term]
+id: MS:1003267
+name: spectrum cluster key
+def: "An ordinal number uniquely identifying a spectrum cluster. It should start with 1." [PSI:PI]
+is_a: MS:1003266 ! spectrum cluster attribute
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003268
+name: spectrum cluster member spectrum keys
+def: "A list of integers corresponding to the library spectrum keys of the members of this cluster. These members must be in the same library." [PSI:PI]
+is_a: MS:1003266 ! spectrum cluster attribute
+relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003269
+name: spectrum cluster member USI
+def: "A member of this cluster external to the library, specified using a PSI Universal Spectrum Identifier." [PSI:PI]
+is_a: MS:1003266 ! spectrum cluster attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003270
+name: proforma peptidoform ion notation
+def: "A string describing the peptidoform ion using the PSI ProForma notation, which should include the charge state, and optionally the adduct type." [PSI:PI]
+is_a: MS:1003256 ! peptidoform ion attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003271
+name: peak annotation
+def: "The molecular identity(-ies) of the ion(s) producing this peak, inferred manually or computationally based on its m/z and the molecular interpretation of the spectrum." [PSI:PI]
+relationship: part_of MS:1000231 ! peak
+
+[Term]
+id: MS:1003272
+name: peak annotation string
+def: "A string representing the peak annotation, in a defined format specified by the attribute 'ion annotation format'." [PSI:PI]
+relationship: part_of MS:1003271 ! peak annotation
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003273
+name: peak annotation confidence
+def: "A confidence value of assigning a peak annotation to a peak, as defined by the attribute 'peak annotation confidence metric'." [PSI:PI]
+relationship: part_of MS:1003271 ! peak annotation
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003274
+name: peak annotation confidence metric
+def: "A confidence metric of assigning a peak annotation to a peak. By default, this should range from 0 (no confidence) to 1 (certain), and if there are multiple annotations of the same peak, the sum of their confidence levels should be no more than 1." [PSI:PI]
+is_a: MS:1003078 ! interpreted spectrum attribute
+
+[Term]
+id: MS:1003275
+name: other attribute name
+def: "A user-provided name for a user-defined value describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003276 to provide the attribute's value" [PSI:MS]
+is_a: MS:1003078 ! interpreted spectrum attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003276
+name: other attribute value
+def: "A user-provided value for a user-defined name describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003275 to provide the attribute's name" [PSI:MS]
+is_a: MS:1003078 ! interpreted spectrum attribute
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_value_type MS:1002711 ! The allowed value-type for this CV term
+relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term
+relationship: has_value_type MS:1002713 ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003277
+name: value between -1 and 1 inclusive
+def: "Value range for signed normalized score values." [PSI:PI]
+is_a: MS:1002304 ! domain range
+
+[Term]
+id: MS:1003278
+name: m/z variability of peak
+def: "A measure of the statistical variability of the m/z value of this peak, usually estimated from replicate spectra of the same analyte." [PSI:PI]
+is_a: MS:1003254 ! peak attribute
+
+[Term]
+id: MS:1003279
+name: observation frequency of peak
+def: "The frequency at which this peak is observed among replicate spectra of the same analyte." [PSI:PI]
+is_a: MS:1003254 ! peak attribute
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003280
+name: intensity variability of peak
+def: "A measure of the statistical variability of the intensity of this peak, usually estimated from replicate spectra of the same analyte." [PSI:PI]
+is_a: MS:1003254 ! peak attribute
+
+[Term]
+id: MS:1003281
+name: Casanovo
+def: "Casanovo is a deep learning-based de novo spectrum identification tool. Official website https://github.com/Noble-Lab/casanovo/." [https://github.com/Noble-Lab/casanovo/]
+is_a: MS:1001456 ! analysis software
+
+[Term]
+id: MS:1003282
+name: Bruker TSF format
+def: "Bruker TSF raw file format." [PSI:MS]
+is_a: MS:1000560 ! mass spectrometer file format
+
+[Term]
+id: MS:1003283
+name: Bruker TSF nativeID format
+def: "Native format defined by frame=xsd:nonNegativeInteger." [PSI:MS]
+is_a: MS:1000767 ! native spectrum identifier format
+
+[Term]
+id: MS:1003284
+name: Bruker TSF nativeID format, combined spectra
+def: "Bruker TSF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI]
+is_a: MS:1002646 ! native spectrum identifier format, combined spectra
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+
+[Term]
+id: MS:1003285
+name: standard deviation of m/z values of peak among replicates
+def: "The standard deviation of the m/z values of this peak among the replicate spectra of the same analyte." [PSI:PI]
+is_a: MS:1003278 ! m/z variability of peak
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003286
+name: coefficient of variation of intensity of peak among replicates
+def: "The coefficient of variation (standard deviation divided by mean) of the intensities of this peak among the replicate spectra of the same analyte." [PSI:PI]
+is_a: MS:1003280 ! intensity variability of peak
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003287
+name: standard deviation of intensity of peak among replicates
+def: "The standard deviation of the intensities of this peak among the replicate spectra of the same analyte." [PSI:PI]
+is_a: MS:1003280 ! intensity variability of peak
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003288
+name: number of unassigned peaks
+def: "The number of unassigned peaks in the spectrum." [NIST]
+is_a: MS:1003078 ! interpreted spectrum attribute
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003289
+name: intensity of highest unassigned peak
+def: "The intensity of the highest unassigned peak in the spectrum." [NIST]
+is_a: MS:1003078 ! interpreted spectrum attribute
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003290
+name: number of unassigned peaks among top 20 peaks
+def: "The number of unassigned peaks among the most intense 20 peaks in the spectrum." [NIST]
+is_a: MS:1003078 ! interpreted spectrum attribute
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003291
+name: Luciphor deltaScore
+def: "Luciphor phosphosite localization score" [PSI:MS]
+is_a: MS:1001968 ! PTM localization PSM-level statistic
+relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
+
+[Term]
+id: MS:1003292
+name: TSQ Altis Plus
+def: "Thermo Scientific TSQ Altis Plus Triple Quadrupole MS." [PSI:PI]
+is_a: MS:1000494 ! Thermo Scientific instrument model
+
+[Term]
+id: MS:1003293
+name: ZenoTOF 7600
+def: "SCIEX ZenoTOF 7600." [PSI:MS]
+is_a: MS:1000121 ! SCIEX instrument model
+
+[Term]
+id: MS:1003294
+name: electron activated dissociation
+def: "A process to fragment ions in a high intensity electron beam which results in a dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins." [PSI:MS]
+synonym: "EAD" EXACT []
+is_a: MS:1000250 ! electron capture dissociation
+
+[Term]
+id: MS:1003295
+name: summary statistics of replicates
+def: "Summary statistics of an attribute among all replicates that are aggregated to generate this spectrum." [PSI:PI]
+is_a: MS:1003064 ! spectrum aggregation attribute
+
+[Term]
+id: MS:1003296
+name: number of replicates spectra used from source
+def: "The number of replicate spectra used during the aggregation process that originate from a specified source (e.g. a file, a dataset, a sample type, etc.). This term must appear in a group alongside a source term, which is one of: 'ProteomeXchange accession number', 'constituent spectrum file', or 'sample name'" [PSI:PI]
+is_a: MS:1003064 ! spectrum aggregation attribute
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003297
+name: contributing replicate spectrum
+def: "A cross reference to another spectrum that is a replicate spectrum of the same analyte and contributes to the generation of this aggregated spectrum." [PSI:PI]
+is_a: MS:1003257 ! library spectrum cross reference
+
+[Term]
+id: MS:1003298
+name: contributing replicate spectrum keys
+def: "A list of cross references to contributing replicate spectra in the same library, in the form of library spectrum keys." [PSI:PI]
+relationship: part_of MS:1003297 ! contributing replicate spectrum
+relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003299
+name: contributing replicate spectrum USI
+def: "A list of cross references to contributing replicate spectra, in the form of PSI Universal Spectrum Identifiers." [PSI:PI]
+relationship: part_of MS:1003297 ! contributing replicate spectrum
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003300
+name: spectrum match
+def: "Result of a comparison of a spectrum to another spectrum, usually to assess the plausibility that the two spectra originate from the same analyte." [PSI:PI]
+relationship: part_of MS:1001000 ! spectrum interpretation
+
+[Term]
+id: MS:1003301
+name: peptide-spectrum match
+def: "Result of a comparison of an observed fragment ion spectrum to the theoretically predicted fragmentation pattern of a peptide sequence, to assess the plausibility that the observed spectrum originates from the putative peptide sequence." [PSI:PI]
+is_a: MS:1003300 ! spectrum match
+synonym: "PSM" EXACT []
+
+[Term]
+id: MS:1003302
+name: spectrum-spectrum match
+def: "Result of a comparison of an observed fragment ion spectrum to another observed fragment ion spectrum, to assess the plausibility that two spectra originate from the same analyte, e.g., in spectral library searching and spectrum clustering." [PSI:PI]
+is_a: MS:1003300 ! spectrum match
+synonym: "SSM" EXACT []
+
+[Term]
+id: MS:1003303
+name: spectral similarity
+def: "A measure of how similar two spectra are, based on the features of the spectra (the locations and intensities of peaks) alone." [PSI:PI]
+is_a: MS:1002694 ! single identification result attribute
+relationship: part_of MS:1003302 ! spectrum-spectrum match
+
+[Term]
+id: MS:1003304
+name: spectral dot product
+def: "The dot (inner) product of two vectorized spectra divided by the product of their vector norms. It ranges from 0 (orthogonal vectors) to 1 (collinear vectors). Also known as cosine similarity." [PSI:PI]
+is_a: MS:1003303 ! spectral similarity
+synonym: "cosine similarity" EXACT []
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003305
+name: spectral Euclidean distance
+def: "The Euclidean distance between a pair of points representing two vectorized spectra in high-dimensional space." [PSI:PI]
+is_a: MS:1003303 ! spectral similarity
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003306
+name: shared peak count
+def: "The number of peaks with closely matching m/z values that are common to two spectra." [PSI:PI]
+is_a: MS:1003303 ! spectral similarity
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003307
+name: normalized spectral angle
+def: "The angle subtended by two vectorized spectra in high-dimensional space. It is equal to the 1 - (2 * inverse cosine of the spectral dot product) / pi." [https://doi.org/10.1074/mcp.O113.036475]
+is_a: MS:1003303 ! spectral similarity
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003308
+name: spectral Pearson correlation
+def: "The Pearson's rho statistic between a pair of points representing two vectorized spectra." [PSI:PI]
+is_a: MS:1003303 ! spectral similarity
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+
+[Term]
+id: MS:1003309
+name: Goslin
+def: "The Goslin implementations parse common lipid name dialects and normalize them to the recent lipid shorthand nomenclature based on grammars on succinct lipid nomenclature." [PMID:32589019, https://github.com/lifs-tools/goslin]
+is_a: MS:1001457 ! data processing software
+is_a: MS:1002414 ! postprocessing software
+is_a: MS:1002964 ! lipidomics analysis software
+
+[Term]
+id: MS:1003310
+name: Lipid shorthand identification confidence level
+def: "Identification confidence levels based on the updated lipid shorthand nomenclature. The value slot can have the values 'Category', 'Class', 'Species', 'Phosphate-position', 'Molecular species', 'sn-position', 'DBE position', 'Structure defined', 'Full structure', 'Complete structure'." [PMID:33037133]
+is_a: MS:1002895 ! small molecule identification attribute
+
+[Term]
+id: MS:1003311
+name: Lipid empirical score
+def: "The lipid empirical score is a point-based lipid class-specific scoring system based on MS and other evidence sources as defined by the Lipidomics Standards Initiative (LSI). The score has a numeric value between 0 and 100. Score values are lipid class-specific and are therefore not immediately comparable between lipid classes." []
+is_a: MS:1002888 ! small molecule confidence measure
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003312
+name: Lipid shorthand identification confidence - Category
+def: "Lipid shorthand identification confidence level 'Category'." [PMID:33037133]
+is_a: MS:1003310 ! Lipid shorthand identification confidence level
+
+[Term]
+id: MS:1003313
+name: Lipid shorthand identification confidence - Class
+def: "Lipid shorthand identification confidence level 'Class'." [PMID:33037133]
+is_a: MS:1003310 ! Lipid shorthand identification confidence level
+
+[Term]
+id: MS:1003314
+name: Lipid shorthand identification confidence - Species
+def: "Lipid shorthand identification confidence level 'Species'." [PMID:33037133]
+is_a: MS:1003310 ! Lipid shorthand identification confidence level
+
+[Term]
+id: MS:1003315
+name: Lipid shorthand identification confidence - Phosphate-position
+def: "Lipid shorthand identification confidence level 'Phosphate-position'." [PMID:33037133]
+is_a: MS:1003310 ! Lipid shorthand identification confidence level
+
+[Term]
+id: MS:1003316
+name: Lipid shorthand identification confidence - Molecular species
+def: "Lipid shorthand identification confidence level 'Molecular species'." [PMID:33037133]
+is_a: MS:1003310 ! Lipid shorthand identification confidence level
+
+[Term]
+id: MS:1003317
+name: Lipid shorthand identification confidence - sn-position
+def: "Lipid shorthand identification confidence level 'sn-position'." [PMID:33037133]
+is_a: MS:1003310 ! Lipid shorthand identification confidence level
+
+[Term]
+id: MS:1003318
+name: Lipid shorthand identification confidence - DBE pos
+def: "Lipid shorthand identification confidence level 'DBE pos'." [PMID:33037133]
+is_a: MS:1003310 ! Lipid shorthand identification confidence level
+
+[Term]
+id: MS:1003319
+name: Lipid shorthand identification confidence - Structure defined
+def: "Lipid shorthand identification confidence level 'Structure defined'." [PMID:33037133]
+is_a: MS:1003310 ! Lipid shorthand identification confidence level
+
+[Term]
+id: MS:1003320
+name: spectrum cluster size
+def: "The number of spectra in a spectrum cluster." [PSI:PI]
+is_a: MS:1003266 ! spectrum cluster attribute
+relationship: has_value_type xsd:integer
+
+[Term]
+id: MS:1003321
+name: summary statistics of clustered spectra
+def: "Summary statistics of an attribute among all spectra of a spectrum cluster." [PSI:PI]
+is_a: MS:1003266 ! spectrum cluster attribute
+
+[Term]
+id: MS:1003322
+name: spectrum cluster best representative
+def: "Cross reference to the spectrum that is considered the most representative among spectra in a cluster, either as a library spectrum key if the best representative is in the same library, or a universal spectrum identifier if it is not." [PSI:PI]
+is_a: MS:1003266 ! spectrum cluster attribute
+relationship: has_value_type xsd:string
+
+[Term]
+id: MS:1003323
+name: spectrum cluster consensus spectrum
+def: "Cross reference to a consensus spectrum that is constructed from aggregating spectra in a cluster, either as a library spectrum key if the consensus spectrum is in the same library, or a universal spectrum identifier if it is not." [PSI:PI]
+is_a: MS:1003266 ! spectrum cluster attribute
+relationship: has_value_type xsd:string
+
+[Term]
+id: MS:1003324
+name: spectral dot product to aggregated spectrum
+def: "Spectral similarity measured by the spectral dot product between a replicate to its corresponding aggregated (e.g. consensus) spectrum." [PSI:PI]
+is_a: MS:1003295 ! summary statistics of replicates
+is_a: MS:1003304 ! spectral dot product
+relationship: has_value_type xsd:float
+
+[Term]
+id: MS:1003325
+name: Lipid shorthand identification confidence - Full structure
+def: "Lipid shorthand identification confidence level 'Full structure'." [PMID:33037133]
+is_a: MS:1003310 ! Lipid shorthand identification confidence level
+
+[Term]
+id: MS:1003326
+name: Lipid shorthand identification confidence - Complete structure
+def: "Lipid shorthand identification confidence level 'Complete structure'." [PMID:33037133]
+is_a: MS:1003310 ! Lipid shorthand identification confidence level
+
+[Term]
+id: MS:1003327
+name: number of identified protein groups
+def: "The number of protein groups that pass the threshold to be considered identified with sufficient confidence." [PSI:PI]
+is_a: MS:1002405 ! protein group-level result list attribute
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_units UO:0000189 ! count unit
+
+[Term]
+id: MS:1003328
+name: number of identified proteoforms
+def: "The number of proteoforms that pass the threshold to be considered identified with sufficient confidence." [PSI:PI]
+is_a: MS:1001085 ! protein-level identification attribute
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_units UO:0000189 ! count unit
+
+[Term]
+id: MS:1003329
+name: looplink spectrum identification item
+def: "Identification of an internally linked peptide (a peptide that contains both ends of a crosslink), also known as a looplink." [PSI:MS]
+synonym: "loop-link spectrum identification item" EXACT []
+is_a: MS:1002508 ! crosslinking attribute
+
+[Term]
+id: MS:1003330
+name: noncovalently associated peptides search
+def: "Noncovalently associated peptides search performed. Noncovalently associated peptides are two different peptides which were not crosslinked but stayed associated with each other throughout the workflow, due to noncovalent interactions." [PSI:MS]
+is_a: MS:1002489 ! special processing
+
+
+[Term]
+id: MS:1003331
+name: noncovalently associated peptides spectrum identification item
+def: "Noncovalently associated peptides spectrum identification item." [PSI:MS]
+is_a: MS:1002508 ! crosslinking attribute
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003332
+name: identification based on multiple spectra
+def: "Provides an identifier to encode identifications based on multiple spectra." [PSI:MS]
+is_a: MS:1002345 ! PSM-level attribute
+relationship: has_regexp MS:1003333 ! regular expression for encoding identifications based on multiple spectra.
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003333
+name: regular expression for encoding identifications based on multiple spectra.
+def: "^(?[0-9]+)(?::(?P|C))$" [PSI:MS]
+is_a: MS:1002479 ! regular expression
+
+[Term]
+id: MS:1003334
+name: parent term for PSM-level scores for identifications based on multiple spectra
+def: "Parent term for PSM-level scores for identifications based on multiple spectra." [PSI:MS]
+is_a: MS:1002347 ! PSM-level identification statistic
+is_a: MS:1002483 ! PSM-level statistical threshold
+relationship: has_regexp MS:1003335 ! regular expression for PSM-level scores for identifications based on multiple spectra
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003335
+name: regular expression for PSM-level scores for identifications based on multiple spectra
+def: "^(?[0-9]+):(?[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+))$" [PSI:MS]
+is_a: MS:1002479 ! regular expression
+
+[Term]
+id: MS:1003336
+name: posterior error probability from identification based on multiple spectra
+def: "PEP score for identifications based on multiple spectra." [PSI:MS]
+is_a: MS:1003334 ! Parent term for PSM-level scores for identifications based on multiple spectra
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003337
+name: crosslinked PSM-level global FDR
+def: "Estimation of the global false discovery rate of crosslinked peptide spectrum matches." [PSI:MS]
+is_a: MS:1002701 ! PSM-level result list statistic
+is_a: MS:1002483 ! PSM-level statistical threshold
+is_a: MS:1002664 ! interaction score derived from crosslinking
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003338
+name: peptide-pair sequence-level global FDR
+def: "Estimation of the global false discovery rate for distinct peptide-pairs (id est multiple PSMs have been collapsed to one entry). Applicable in the case of crosslinked peptides or noncovalently associated peptides." [PSI:MS]
+is_a: MS:1002703 ! peptide sequence-level result list statistic
+is_a: MS:1002484 ! peptide-level statistical threshold
+is_a: MS:1002664 ! interaction score derived from crosslinking
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003339
+name: peptide-pair passes threshold
+def: "Peptide-pair passes threshold. Applicable in the case of crosslinked peptides or noncovalently associated peptides." [PSI:MS]
+is_a: MS:1001105 ! peptide sequence-level identification attribute
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003340
+name: residue-pair passes threshold
+def: "Residue-pair passes threshold. In the context of crosslinking experiments, a residue-pair is a unique pair of crosslinked residues, irrespective of the peptides identified (A level of consolidation higher than unique peptide but lower than PPI)." [PSI:MS]
+is_a: MS:1001060 ! quality estimation method details
+relationship: has_regexp MS:1003342 ! regular expression for whether interaction score derived from crosslinking passes threshold
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003341
+name: protein-protein interaction passes threshold
+def: "Protein-protein interaction passes threshold." [PSI:MS]
+is_a: MS:1001060 ! quality estimation method details
+relationship: has_regexp MS:1003342 ! regular expression for whether interaction score derived from crosslinking passes threshold
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003342
+name: regular expression for whether interaction score derived from crosslinking passes threshold
+def: "^((?[0-9]+):(?true|false))$" [PSI:MS]
+is_a: MS:1002479 ! regular expression
+
+[Term]
+id: MS:1003343
+name: FDR applied separately to self crosslinks and protein heteromeric crosslinks
+def: "States whether FDR was applied separately to self crosslinks (crosslinks between peptides within one protein sequence) and protein heteromeric crosslinks (crosslinks between distinct protein sequences)." [PSI:MS]
+is_a: MS:1002489 ! special processing
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003344
+name: residue-pair ref
+def: "Reference to a residue-pair supported by this identification item, the value is the identifier for the residue-pair. In the context of crosslinking experiments, a residue-pair is a unique pair of crosslinked residues, irrespective of the peptides identified (A level of consolidation higher than unique peptide but lower than PPI)." [PSI:MS]
+is_a: MS:1002508 ! crosslinking attribute
+relationship: has_regexp MS:1003345 ! regular expression for residue-pair ref
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003345
+name: regular expression for residue-pair ref
+def: "^(([0-9]+).(a|b))$" [PSI:MS]
+is_a: MS:1002479 ! regular expression
+
+[Term]
+id: MS:1003346
+name: cleavable crosslinker stub
+def: "This term indicates that a given protein modification is a derivative of a cleavable crosslinker." [PSI:MS]
+is_a: MS:1001471 ! peptide modification details
+
+[Term]
+id: MS:1003347
+name: Unimod derivative code
+def: "The single letter code in Unimod that identifies a specific derivative of a modification. For example, in UNIMOD:1842 (http://www.unimod.org/modifications_view.php?editid1=1842) the letter ‘W’ represents the derivative ‘water quenched monolink’." [PSI:MS]
+is_a: MS:1001471 ! peptide modification details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003348
+name: proteomics
+def: "large-scale study of proteins and proteomes." [PSI:MS]
+relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies
+
+[Term]
+id: MS:1003349
+name: affinity proteomics
+def: "large-scale study of proteins and proteomes via the use of affinity reagents." [PSI:MS]
+is_a: MS:1003348 ! proteomics
+
+[Term]
+id: MS:1003350
+name: mass spectrometry proteomics
+def: "large-scale study of proteins and proteomes via the use of mass spectrometers to measure the masses and abundances of charged proteins or protein fragments." [PSI:MS]
+is_a: MS:1003348 ! proteomics
+
+[Term]
+id: MS:1003351
+name: top-down proteomics
+def: "study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact proteins." [PSI:MS]
+is_a: MS:1003350 ! mass spectrometry proteomics
+
+[Term]
+id: MS:1003352
+name: native top-down proteomics
+def: "study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact folded proteins." [PSI:MS]
+is_a: MS:1003351 ! top-down proteomics
+
+[Term]
+id: MS:1003353
+name: non-native top-down proteomics
+def: "study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact denatured proteins." [PSI:MS]
+is_a: MS:1003351 ! top-down proteomics
+
+[Term]
+id: MS:1003354
+name: middle-down proteomics
+def: "study of proteins via the use of mass spectrometers to measure the masses and abundances of large protein fragments after partial digestion of denatured proteins." [PSI:MS]
+is_a: MS:1003350 ! mass spectrometry proteomics
+
+[Term]
+id: MS:1003355
+name: bottom-up proteomics
+def: "study of proteins via the use of mass spectrometers to measure the masses and abundances of peptides after complete digestion of denatured proteins." [PSI:MS]
+is_a: MS:1003350 ! mass spectrometry proteomics
+
+[Term]
+id: MS:1003356
+name: Orbitrap Ascend
+def: "Thermo Scientific Orbitrap Ascend mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI]
+is_a: MS:1000494 ! Thermo Scientific instrument model
+
+[Term]
+id: MS:1003357
+name: ANN-SoLo
+def: "ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up open modification searching by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate and the shifted dot product score to sensitively match modified spectra to their unmodified counterpart." [doi:10.1021/acs.jproteome.8b00359, doi:10.1021/acs.jproteome.9b00291]
+is_a: MS:1001456 ! analysis software
+
+[Term]
+id: MS:1003358
+name: XCorr rank
+def: "The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the XCorr score." [PSI:MS]
+is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003359
+name: exact p-value
+def: "A p-value for the XCorr score, calculated using dynamic programming." [PMID:24895379]
+is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003360
+name: refactored XCorr
+def: "A modified version of the XCorr score that is made amenable to dynamic programming calculation of p-values by changing a max operation to a sum." [PMID:30221945]
+is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003361
+name: res-ev score
+def: "The residue-evidence (res-ev) score measures the quality of a match between a peptide and observed spectrum using a method similar to XCorr, but considering all pairs of observed peaks." [PMID:30221945]
+is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003362
+name: res-ev rank
+def: "The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the res-ev score." [PMID:30221945]
+is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003363
+name: res-ev p-value
+def: "The residue-evidence p-value is computed from the residue-evidence score using a dynamic programming procedure." [PMID:30221945]
+is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003364
+name: combined p-value
+def: "A p-value that is computed by taking the product of the exact p-value and the res-ev p-value and then adjusting for dependencies between them." [PMID:30221945]
+is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003365
+name: combined p-value rank
+def: "The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the combined p-value." [PMID:30221945]
+is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003366
+name: tailor score
+def: "A calibrated version of the XCorr score, computed by dividing the XCorr by the 99th percentile of the distribution of all scores for a particular spectrum." [PMID:32175744]
+is_a: MS:1001143 ! PSM-level search engine specific statistic
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003367
+name: monoisotopic mass deisotoping
+def: "The removal of isotope peaks to represent each ion as one data point corresponding to the ion's monoisotopic mass. It is done in conjunction with the charge state deconvolution." [PSI:MS]
+is_a: MS:1000033 ! deisotoping
+
+[Term]
+id: MS:1003368
+name: most abundant mass deisotoping
+def: "The removal of isotope peaks to represent each ion as one data point corresponding to the ion's most abundant isotopic mass. It is done in conjunction with the charge state deconvolution." [PSI:MS]
+is_a: MS:1000033 ! deisotoping
+
+[Term]
+id: MS:1003369
+name: average mass deisotoping
+def: "The removal of isotope peaks to represent each ion as one data point corresponding to the ion's average mass. It is done in conjunction with the charge state deconvolution." [PSI:MS]
+is_a: MS:1000033 ! deisotoping
+
+[Term]
+id: MS:1003370
+name: reduction to summed singly charged peak list
+def: "The summing of peaks corresponding to the same mass at multiple charge states and presented as singly charged m/z." [PSI:MS]
+is_a: MS:1000543 ! data processing action
+
+[Term]
+id: MS:1003371
+name: SelexION compensation voltage
+def: "The voltage applied in the SelexION device to allow certain ions to transmit through to the mass spectrometer." [PSI:MS]
+is_a: MS:1002892 ! ion mobility attribute
+is_a: MS:1000455 ! ion selection attribute
+is_a: MS:1003254 ! peak attribute
+relationship: has_units UO:0000218 ! volt
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003372
+name: specification document extension version
+def: "The versioning of a an extension to a specification document that the current file requires to be read correctly. The version should encode the name of the extension, and some ordinal expression of its revision, preferably in semantic versioning notation. Signals that readers that do not know this extension should return an appropriately informative error if they do not think they can or should try to interpret the file." [PSI:MS]
+relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies
+relationship: has_regexp MS:1003384 ! semantic version regexp
+
+[Term]
+id: MS:1003373
+name: mzIdentML extension version
+def: "The versioning of an mzIdentML extension document." [PSI:PI]
+is_a: MS:1003372 ! specification document extension version
+relationship: part_of MS:1002073 ! mzIdentML format
+
+[Term]
+id: MS:1003374
+name: Open Chromatography Binary OCB format
+def: "ChemClipse/OpenChrom file format." [PSI:MS]
+is_a: MS:1000560 ! mass spectrometer file format
+
+[Term]
+id: MS:1003375
+name: Conversion to OCB
+def: "Conversion of a file format to Open Chromatography Binary OCB file format." [PSI:MS]
+is_a: MS:1000530 ! file format conversion
+
+[Term]
+id: MS:1003376
+name: ChemClipse
+def: "ChemClipse is part of the Eclipse Science project. Primarily developed by Lablicate GmbH." [https://projects.eclipse.org/projects/science.chemclipse]
+synonym: "chemclipse" EXACT []
+is_a: MS:1001456 ! analysis software
+is_a: MS:1001457 ! data processing software
+
+[Term]
+id: MS:1003377
+name: OpenChrom
+def: "OpenChrom is an Open Source software for data processing and analysis. Based upon Eclipse ChemClipse." [PMID:20673335, DOI:10.1186/1471-2105-11-405, https://www.openchrom.net/]
+synonym: "openchrom" EXACT []
+is_a: MS:1001456 ! analysis software
+is_a: MS:1001457 ! data processing software
+
+[Term]
+id: MS:1003378
+name: Orbitrap Astral
+def: "Thermo Scientific Orbitrap Astral mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and the Astral analyzer." [PSI:MS]
+is_a: MS:1000494 ! Thermo Scientific instrument model
+
+[Term]
+id: MS:1003379
+name: asymmetric track lossless time-of-flight analyzer
+def: "A TOF-like mass analyzer with asymmetric ion mirrors to direct ions into transversal asymmetric oscillations and ion foil shapes and maintains ion packet for transmission and resolution." [PSI:MS]
+synonym: "Astral" EXACT []
+is_a: MS:1000084 ! time-of-flight
+
+[Term]
+id: MS:1003380
+name: Xevo G3 QTof
+def: "Waters Corporation Xevo G3 QTof quadrupole time-of-flight mass spectrometer." [PSI:MS]
+is_a: MS:1000126 ! Waters instrument model
+
+[Term]
+id: MS:1003381
+name: ACQUITY RDa Detector
+def: "Waters Corporation RDa time-of-flight mass detector." [PSI:MS]
+is_a: MS:1000126 ! Waters instrument model
+
+[Term]
+id: MS:1003382
+name: waters_connect
+def: "Waters Corporation waters_connect software for liquid chromatography and mass spectrometry acquisition and processing." [PSI:MS]
+is_a: MS:1000694 ! Waters software
+is_a: MS:1001455 ! acquisition software
+is_a: MS:1001456 ! analysis software
+is_a: MS:1001457 ! data processing software
+
+[Term]
+id: MS:1003383
+name: timsTOF Ultra
+def: "Bruker Daltonics' timsTOF Ultra." [PSI:MS]
+is_a: MS:1003123 ! Bruker Daltonics timsTOF series
+
+[Term]
+id: MS:1003384
+name: semantic version regexp
+def: "v?(\d+)\.(\d+)\.(\d+)(?:-(\S+))?" [PSI:PI]
+is_a: MS:1002479 ! regular expression
+
+[Term]
+id: MS:1003385
+name: mzIdentML crosslinking extension document version
+def: "The versioning of the crosslinking mzIdentML extension document." [PSI:PI]
+is_a: MS:1003373 ! mzIdentML extension version
+relationship: has_value_type xsd:string
+
+[Term]
+id: MS:1003386
+name: Spectra
+def: "Bioconductor package Spectra for mass spectrometry data representation and processing." [PSI:MS, https://doi.org/doi:10.18129/B9.bioc.Spectra]
+is_a: MS:1001456 ! analysis software
+is_a: MS:1001457 ! data processing software
+
+[Term]
+id: MS:1003387
+name: MetaboAnnotation
+def: "Bioconductor package MetaboAnnotation for annotation of untargeted metabolomics data." [PSI:MS, https://doi.org/doi:10.18129/B9.bioc.MetaboAnnotation, https://doi.org/10.3390/metabo12020173, PMID:35208247]
+is_a: MS:1001456 ! analysis software
+is_a: MS:1001457 ! data processing software
+
+[Term]
+id: MS:1003388
+name: CompoundDb
+def: "Bioconductor package CompoundDb for creation, usage and maintenance of public or library-specific annotation databases and spectra libraries." [PSI:MS, https://doi.org/doi:10.18129/B9.bioc.CompoundDb, https://doi.org/10.3390/metabo12020173, PMID:35208247]
+is_a: MS:1001456 ! analysis software
+is_a: MS:1001457 ! data processing software
+is_a: MS:1003207 ! library creation software
+
+[Term]
+id: MS:1003389
+name: mzTab-M
+def: "Expanded tabular result format for metabolomics experiments reporting quantitative summary data, MS features and identification evidence." [PMID:30688441, PMID:31525911, https://www.psidev.info/mztab]
+is_a: MS:1000914 ! tab delimited text format
+
+[Term]
+id: MS:1003390
+name: crosslinker cleavage characteristics
+def: "Signifies that the crosslinker is cleavable and on cleavage can leave a given stub. The pattern specifies three slots ::." [PSI:PI]
+is_a: MS:1001471 ! peptide modification details
+relationship: has_regexp MS:1003391 ! crosslinker cleavage regular expression
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003391
+name: crosslinker cleavage regular expression
+def: "^(?[A-Za-z]):(?[+-]?[0-9]+(\.[0-9]+)?([eE][+-]?[0-9]+(\.[0-9]+)?)?):(?[A-Za-z]+)$" [PSI:PI]
+is_a: MS:1002479 ! regular expression
+
+[Term]
+id: MS:1003392
+name: search modification id
+def: "A unique identifier within an in mzIdentML document denoting a search modification rule. The same modification may be present multiple times with different id values to reflect different specificities or neutral losses." [PSI:PI]
+is_a: MS:1001471 ! peptide modification details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003393
+name: search modification id ref
+def: "A reference to a `search modification id` in the current mzIdentML document that defines the properties of this modification instance." [PSI:PI]
+is_a: MS:1001471 ! peptide modification details
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003394
+name: SelexION separation voltage
+def: "RF voltage applied in the SelexION device to separate ions in trajectory based on the difference in their mobility between the high field and low field portions of the applied RF." [PSI:MS]
+is_a: MS:1002892 ! ion mobility attribute
+is_a: MS:1000455 ! ion selection attribute
+is_a: MS:1003254 ! peak attribute
+relationship: has_units UO:0000218 ! volt
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003395
+name: Q Exactive GC Orbitrap
+def: "Q Exactive GC Orbitrap GC-MS/MS hybrid quadrupole Orbitrap mass spectrometer." [PSI:MS]
+is_a: MS:1000483 ! Thermo Fisher Scientific instrument model
+
+[Term]
+id: MS:1003396
+name: 8890 GC/MS
+def: "Agilent 8890 Gas Chromatograph System." [PSI:MS]
+is_a: MS:1000490 ! Agilent instrument model
+
+[Term]
+id: MS:1003397
+name: timsTOF fleX MALDI-2
+def: "Bruker Daltonics' timsTOF fleX MALDI-2." [PSI:MS]
+is_a: MS:1003123 ! Bruker Daltonics timsTOF series
+
+[Term]
+id: MS:1003398
+name: deconvoluted data
+def: "The data contained in this file have been processed to remove, collapse, or label one or more dimensions of the original dataset, such as charge deconvolution or ion mobility deconvolution. To determine the type of deconvolution done, the reader should consult the appropriate section of the file, such as the data processing methods in an mzML file." [PSI:MS]
+is_a: MS:1000524 ! data file content
+
+[Term]
+id: MS:1003399
+name: quality control software
+def: "Software that creates or manipulates QC-related data." [PSI:MS]
+is_a: MS:1001457 ! data processing software
+
+[Term]
+id: MS:1003400
+name: rmzqc
+def: "An R package for reading, validating, and writing mzQC files." [https://github.com/MS-Quality-hub/rmzqc]
+is_a: MS:1003399 ! quality control software
+
+[Term]
+id: MS:1003401
+name: jmzqc
+def: "A Java package for reading, validating, and writing mzQC files." [https://github.com/MS-Quality-hub/jmzqc]
+is_a: MS:1003399 ! quality control software
+
+[Term]
+id: MS:1003402
+name: pymzqc
+def: "A Python package for reading, validating, and writing mzQC files." [https://github.com/MS-Quality-hub/pymzqc]
+is_a: MS:1003399 ! quality control software
+
+[Term]
+id: MS:1003403
+name: InChI
+def: "IUPAC International Chemical Identifier." [PMID:26136848]
+is_a: MS:1001405 ! spectrum identification result details
+is_a: MS:1000867 ! structural formula
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:1003404
+name: timsTOF HT
+def: "Bruker Daltonics' timsTOF HT." [PSI:MS]
+is_a: MS:1003123 ! Bruker Daltonics timsTOF series
+
+[Term]
+id: MS:1003405
+name: mzRecal
+def: "MS1 recalibration using identified peptides as internal calibrants." [DOI:10.1093/bioinformatics/btab056, PMID:33538780, https://github.com/524D/mzrecal]
+is_a: MS:1001457 ! data processing software
+
+[Term]
+id: MS:1003406
+name: spectrum clustering software
+def: "Software designed to group multiple mass spectra by high similarity, generally with the goal of grouping replicate spectra derived from the same analyte." [PSI:MS]
+is_a: MS:1000531 ! software
+
+[Term]
+id: MS:1003409
+name: Stellar
+def: "Thermo Scientific Stellar mass spectrometer contains a quadrupole mass filter, a collision cell, and a quadrupole linear ion trap mass analyzer." [PSI:MS]
+is_a: MS:1000494 ! Thermo Scientific instrument model
+
+[Term]
+id: MS:4000000
+name: PSI-MS CV Quality Control Vocabulary
+def: "PSI Quality Control controlled vocabulary term." [PSI:MS]
+relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies
+
+[Term]
+id: MS:4000001
+name: QC metric
+def: "Parent term for QC metrics, each metric MUST have this as an ancestor in its is_a relations." [PSI:MS]
+relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary
+
+[Term]
+id: MS:4000002
+name: QC metric value type
+def: "The QC metric type describes what type the corresponding metric is. Possible types are single value, n-tuple, table, or matrix." [PSI:MS]
+relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary
+
+[Term]
+id: MS:4000003
+name: single value
+def: "Metrics consisting of a single value. The value must have a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value)." [PSI:MS]
+is_a: MS:4000002 ! QC metric value type
+
+[Term]
+id: MS:4000004
+name: n-tuple
+def: "Metrics consisting of multiple values, with the number of values implicitly specified by length of the JSON array (e.g. length 4 for quartiles). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the tuple must have the same unit and type (if applicable)." [PSI:MS]
+is_a: MS:4000002 ! QC metric value type
+
+[Term]
+id: MS:4000005
+name: table
+def: "Metrics consisting of a table or data frame. The values of the table may have different types in each column (in contrast to a matrix). Each column must have a unit (identical for all entries of this column) and may have a value type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value)." [PSI:MS]
+comment: The actual structure of the table is defined in the mzQC specification document. In short: it must have at least one column, and MAY have optional columns.
+is_a: MS:4000002 ! QC metric value type
+
+[Term]
+id: MS:4000006
+name: matrix
+def: "A matrix is a rectangular array of values of the same type (in contrast to a table). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the matrix must have the same unit and type (if applicable)." [PSI:MS]
+comment: The actual structure of the matrix is defined in the mzQC specification document.
+is_a: MS:4000002 ! QC metric value type
+
+[Term]
+id: MS:4000007
+name: QC metric category
+def: "Categorization of the QC metric." [PSI:MS]
+relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary
+
+[Term]
+id: MS:4000008
+name: ID based metric
+def: "QC metric based on identification results." [PSI:MS]
+is_a: MS:4000007 ! QC metric category
+
+[Term]
+id: MS:4000009
+name: ID free metric
+def: "QC metric not based on identification results." [PSI:MS]
+is_a: MS:4000007 ! QC metric category
+
+[Term]
+id: MS:4000010
+name: quantification based metric
+def: "QC metric based on quantification results." [PSI:MS]
+is_a: MS:4000007 ! QC metric category
+
+[Term]
+id: MS:4000012
+name: single run based metric
+def: "QC metric calculated from a single run (e.g. one .raw file)." [PSI:MS]
+is_a: MS:4000007 ! QC metric category
+
+[Term]
+id: MS:4000013
+name: multiple runs based metric
+def: "QC metric calculated from multiple runs (e.g. multiple .raw files)." [PSI:MS]
+is_a: MS:4000007 ! QC metric category
+
+[Term]
+id: MS:4000014
+name: single spectrum based metric
+def: "QC metric calculated from a single spectrum." [PSI:MS]
+is_a: MS:4000007 ! QC metric category
+
+[Term]
+id: MS:4000015
+name: multiple spectra based metric
+def: "QC metric calculated from multiple spectra." [PSI:MS]
+is_a: MS:4000007 ! QC metric category
+
+[Term]
+id: MS:4000016
+name: retention time metric
+def: "QC metric related to retention time." [PSI:MS]
+is_a: MS:4000001 ! QC metric
+
+[Term]
+id: MS:4000017
+name: chromatogram metric
+def: "QC metric related to a chromatogram." [PSI:MS]
+is_a: MS:4000001 ! QC metric
+
+[Term]
+id: MS:4000018
+name: XIC metric
+def: "QC metric related to an extracted ion chromatogram." [PSI:MS]
+is_a: MS:4000017 ! chromatogram metric
+
+[Term]
+id: MS:4000019
+name: MS metric
+def: "QC metric related to the mass spectrometry acquisition." [PSI:MS]
+is_a: MS:4000001 ! QC metric
+
+[Term]
+id: MS:4000020
+name: ion source metric
+def: "QC metric related to events in the ion source." [PSI:MS]
+is_a: MS:4000019 ! MS metric
+
+[Term]
+id: MS:4000021
+name: MS1 metric
+def: "QC metric based on MS1 events." [PSI:MS]
+is_a: MS:4000019 ! MS metric
+
+[Term]
+id: MS:4000022
+name: MS2 metric
+def: "QC metric based on MS2 events." [PSI:MS]
+is_a: MS:4000019 ! MS metric
+
+[Term]
+id: MS:4000023
+name: sample preparation metric
+def: "QC metric related to the sample preparation." [PSI:MS]
+is_a: MS:4000001 ! QC metric
+
+[Term]
+id: MS:4000024
+name: environment metric
+def: "QC metric related to measurements of the ambient environment, such as the laboratory." [PSI:MS]
+is_a: MS:4000001 ! QC metric
+
+[Term]
+id: MS:4000050
+name: XIC50 fraction
+def: "The number of XIC that account for the top half of all XIC-FWHM divided by the number of all XIC." [PSI:MS]
+comment: This metric characterises the distribution of precursor peak widths, much as the N50 characterises contig sizes in genome assembly.
+synonym: "XIC-WideFrac" EXACT [PMID:24494671]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_value_concept UO:0000191 ! fraction
+
+[Term]
+id: MS:4000051
+name: XIC-FWHM quantiles
+def: "The first to n-th quantile of peak widths for XICs. A metric's value triplet represents the related QuaMeter metrics of XIC-FWHM-Q1,Q2,Q3." [PSI:MS]
+synonym: "XIC-FWHM-Q1" RELATED [PMID:24494671]
+synonym: "XIC-FWHM-Q2" RELATED [PMID:24494671]
+synonym: "XIC-FWHM-Q3" RELATED [PMID:24494671]
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000018 ! XIC metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_value_concept MS:1000086 ! full width at half-maximum
+relationship: has_value_concept STATO:0000291 ! quantile
+relationship: has_units UO:0000010 ! second
+
+[Term]
+id: MS:4000052
+name: XIC-Height quartile ratios
+def: "The log ratio of successive XIC height quartiles. The metric's value triplet represents the log ratios of XIC-height-Q2 to XIC-height-Q1, XIC-height-Q3 to XIC-height-Q2, XIC-height max to XIC-height-Q3." [PSI:MS]
+synonym: "XIC-Height-Q2" RELATED [PMID:24494671]
+synonym: "XIC-Height-Q3" RELATED [PMID:24494671]
+synonym: "XIC-Height-Q4" RELATED [PMID:24494671]
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000018 ! XIC metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_value_concept STATO:0000105 ! log signal intensity ratio
+relationship: has_value_concept UO:0000191 ! fraction
+
+[Term]
+id: MS:4000053
+name: chromatography duration
+def: "The retention time duration of the chromatography in seconds." [PSI:MS]
+comment: Longer duration may indicate a better chromatographic separation of compounds which depends, however, also on the sampling/scan rate of the MS instrument.
+synonym: "RT-Duration" RELATED [PMID:24494671]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000016 ! retention time metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_value_concept NCIT:C25330 ! Duration
+relationship: has_units UO:0000010 ! second
+
+[Term]
+id: MS:4000054
+name: TIC quarters RT fraction
+def: "The interval when the respective quarter of the TIC accumulates divided by retention time duration." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. The metric provides information on the sample (compound) flow along the chromatographic run, potentially revealing poor chromatographic performance, such as the absence of a signal for a significant portion of the run.
+synonym: "RT-TIC-Q1" RELATED [PMID:24494671]
+synonym: "RT-TIC-Q2" RELATED [PMID:24494671]
+synonym: "RT-TIC-Q3" RELATED [PMID:24494671]
+synonym: "RT-TIC-Q4" RELATED [PMID:24494671]
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000016 ! retention time metric
+relationship: has_metric_category MS:4000017 ! chromatogram metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units UO:0000191 ! fraction
+
+[Term]
+id: MS:4000055
+name: MS1 quarter RT fraction
+def: "The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS1 scans, the values are expected to be in a similar range across samples of the same type.
+synonym: "RT-MS-Q1" RELATED [PMID:24494671]
+synonym: "RT-MS-Q2" RELATED [PMID:24494671]
+synonym: "RT-MS-Q3" RELATED [PMID:24494671]
+synonym: "RT-MS-Q4" RELATED [PMID:24494671]
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000016 ! retention time metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units UO:0000191 ! fraction
+
+[Term]
+id: MS:4000056
+name: MS2 quarter RT fraction
+def: "The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation.
+synonym: "RT-MSMS-Q1" RELATED [PMID:24494671]
+synonym: "RT-MSMS-Q2" RELATED [PMID:24494671]
+synonym: "RT-MSMS-Q3" RELATED [PMID:24494671]
+synonym: "RT-MSMS-Q4" RELATED [PMID:24494671]
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000016 ! retention time metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units UO:0000191 ! fraction
+
+[Term]
+id: MS:4000057
+name: MS1 TIC-change quartile ratios
+def: "The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3" [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation.This metric evaluates the stability (similarity) of MS1 TIC values from scan to scan along the LC run. High log ratios representing very large intensity differences between pairs of scans might be due to electrospray instability or presence of a chemical contaminant.
+synonym: "MS1-TIC-Change-Q2" RELATED [PMID:24494671]
+synonym: "MS1-TIC-Change-Q3" RELATED [PMID:24494671]
+synonym: "MS1-TIC-Change-Q4" RELATED [PMID:24494671]
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000017 ! chromatogram metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_value_concept STATO:0000105 ! log signal intensity ratio
+
+[Term]
+id: MS:4000058
+name: MS1 TIC quartile ratios
+def: "The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. The ratios provide information on the distribution of the TIC values for one LC-MS run. Within an experiment, with the same LC setup, values should be comparable between samples.
+synonym: "MS1-TIC-Q2" RELATED [PMID:24494671]
+synonym: "MS1-TIC-Q3" RELATED [PMID:24494671]
+synonym: "MS1-TIC-Q4" RELATED [PMID:24494671]
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000017 ! chromatogram metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_value_concept STATO:0000105 ! log signal intensity ratio
+
+[Term]
+id: MS:4000059
+name: number of MS1 spectra
+def: "The number of MS1 events in the run." [PSI:MS]
+comment: An unusual low number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample.
+synonym: "MS1-Count" EXACT [PMID:24494671]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_units UO:0000189 ! count unit
+
+[Term]
+id: MS:4000060
+name: number of MS2 spectra
+def: "The number of MS2 events in the run." [PSI:MS]
+comment: An unusual low number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample.
+synonym: "MS2-Count" EXACT [PMID:24494671]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_units UO:0000189 ! count unit
+
+[Term]
+id: MS:4000061
+name: MS1 density quantiles
+def: "The first to n-th quantile of MS1 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS1 density. The number of values in the tuple implies the quantile mode." [PSI:MS]
+synonym: "MS1-Density-Q1" RELATED [PMID:24494671]
+synonym: "MS1-Density-Q2" RELATED [PMID:24494671]
+synonym: "MS1-Density-Q3" RELATED [PMID:24494671]
+synonym: "MS1 peak density distribution - quantiles" EXACT []
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_value_concept NCIT:C45781 ! Density
+relationship: has_value_concept STATO:0000291 ! quantile
+relationship: has_units UO:0000189 ! count unit
+
+[Term]
+id: MS:4000062
+name: MS2 density quantiles
+def: "The first to n-th quantile of MS2 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS2 density. The number of values in the tuple implies the quantile mode." [PSI:MS]
+synonym: "MS2-Density-Q1" RELATED [PMID:24494671]
+synonym: "MS2-Density-Q2" RELATED [PMID:24494671]
+synonym: "MS2-Density-Q3" RELATED [PMID:24494671]
+synonym: "MS2 peak density distribution - quantiles" EXACT []
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_value_concept NCIT:C45781 ! Density
+relationship: has_value_concept STATO:0000291 ! quantile
+relationship: has_units UO:0000189 ! count unit
+
+[Term]
+id: MS:4000063
+name: MS2 known precursor charges fractions
+def: "The fraction of MS/MS precursors of the corresponding charge. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. The highest charge state is to be interpreted as that charge state or higher." [PSI:MS]
+comment: the MS2-PrecZ metrics can be directly read from the table respective table rows, the ratios of IS-3 metrics must be derived from the respective table rows, IS-3A as ratio of +1 over +2, IS-3B as ratio of +3 over +2, IS-3C as +4 over +2.
+synonym: "MS2-PrecZ-1" NARROW [PMID:24494671]
+synonym: "MS2-PrecZ-2" NARROW [PMID:24494671]
+synonym: "MS2-PrecZ-3" NARROW [PMID:24494671]
+synonym: "MS2-PrecZ-4" NARROW [PMID:24494671]
+synonym: "MS2-PrecZ-5" NARROW [PMID:24494671]
+synonym: "MS2-PrecZ-more" NARROW [PMID:24494671]
+synonym: "IS-3A" RELATED [PMID:19837981]
+synonym: "IS-3B" RELATED [PMID:19837981]
+synonym: "IS-3C" RELATED [PMID:19837981]
+is_a: MS:4000005 ! table
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000020 ! ion source metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_column MS:1000041 ! charge state
+relationship: has_column UO:0000191 ! fraction
+
+[Term]
+id: MS:4000064
+name: MS2 unknown and likely precursor charges fractions
+def: "The fractions of inferred charge state of MS/MS precursors. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. Charge 0 represents unknown charge states." [PSI:MS]
+synonym: "MS2-PrecZ-likely-1" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-likely-multi" RELATED [PMID:24494671]
+is_a: MS:4000005 ! table
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000020 ! ion source metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_column MS:1000041 ! charge state
+relationship: has_column UO:0000191 ! fraction
+
+[Term]
+id: MS:4000065
+name: fastest frequency for MS level 1 collection
+def: "Fastest frequency for MS level 1 collection" [PSI:MS]
+comment: Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used.
+synonym: "MS1-Freq-Max" EXACT [PMID:24494671]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units UO:0000106 ! hertz
+
+[Term]
+id: MS:4000066
+name: fastest frequency for MS level 2 collection
+def: "Fastest frequency for MS level 2 collection" [PSI:MS]
+comment: Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used.
+synonym: "MS2-Freq-Max" EXACT [PMID:24494671]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units UO:0000106 ! hertz
+
+[Term]
+id: MS:4000067
+name: MS run duration
+def: "The duration of the mass spectrometry acquisition (as measured by the time between the last scan and first scan) in seconds." [PSI:MS]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000019 ! MS metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_value_concept NCIT:C25330 ! Duration
+relationship: has_units UO:0000010 ! second
+
+[Term]
+id: MS:4000068
+name: spectra half-TIC
+def: "The minimal proportion of peaks needed to account for at least 50% of the total ion current in each individual spectrum considered, recorded in a mandatory fraction column. Either USI or native spectrum identifier columns must be present as well." [PSI:MS]
+is_a: MS:4000005 ! table
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_optional_column MS:1003063 ! universal spectrum identifier
+relationship: has_optional_column MS:1000767 ! native spectrum identifier format
+relationship: has_column UO:0000191 ! fraction
+relationship: has_relation MS:1000285 ! total ion current
+
+[Term]
+id: MS:4000069
+name: m/z acquisition range
+def: "Upper and lower limit of m/z precursor values at which MSn spectra are recorded." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition. Based on the used MS instrument configuration, the values should be similar. Variations between measurements may arise when employing acquisition in DDA mode.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000019 ! MS metric
+relationship: has_units MS:1000040 ! m/z
+relationship: has_value_concept STATO:0000035 ! range
+
+[Term]
+id: MS:4000070
+name: retention time acquisition range
+def: "Upper and lower limit of retention time at which spectra are recorded." [PSI:MS]
+comment: An unusual low range may indicate incomplete sampling and/or a premature or failed LC run.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000016 ! retention time metric
+relationship: has_units UO:0000010 ! second
+relationship: has_value_concept STATO:0000035 ! range
+
+[Term]
+id: MS:4000071
+name: number of chromatograms
+def: "The number of chromatograms recorded for the run." [PSI:MS]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000017 ! chromatogram metric
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_units UO:0000189 ! count unit
+
+[Term]
+id: MS:4000072
+name: observed mass accuracy
+def: "Observed mass accuracy in ppm, calculated by 1E6 x (observed m/z - theoretical m/z)/theoretical m/z of a selected and identified ion in a mass spectrum." [PSI:MS]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000014 ! single spectrum based metric
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_units UO:0000169 ! parts per million
+relationship: has_value_concept MS:1000014 ! accuracy
+
+[Term]
+id: MS:4000073
+name: QC sample metric
+def: "A QC metric based on a QC sample of known content." [PSI:MS]
+is_a: MS:4000007 ! QC metric category
+
+[Term]
+id: MS:4000074
+name: high complexity QC sample metric
+def: "A QC metric based on a QC sample of known and high complexity content." [PSI:MS]
+is_a: MS:4000073 ! QC sample metric
+
+[Term]
+id: MS:4000075
+name: low complexity QC sample metric
+def: "A QC metric based on a QC sample of known and low complexity content." [PSI:MS]
+is_a: MS:4000073 ! QC sample metric
+
+[Term]
+id: MS:4000076
+name: QC2 sample metric
+def: "A QC metric based on the results of a QC2 sample measurement. A QC2 sample is made from Pierce HeLa protein digest standard, see Pichler et al. Chiva et al. for details on QC sample design." [PSI:MS, PMID:23088386, PMID:29324744]
+comment: Expected peptides from QC2 sample measurement are: 'YAEAVTR','STLTDSLVC(Carbamidomethyl)K','SLADELALVDVLEDK','NPDDITNEEYGEFYK','LAVDEEENADNNTK','FEELNMDLFR','EAALSTALSEK','DDVAQTDLLQIDPNFGSK','RFPGYDSESK','EATTEFSVDAR','EQFLDGDGWTSR','TPAQFDADELR','LGDLYEEEMR','EVSTYIK','FAFQAEVNR'
+is_a: MS:4000074 ! high complexity QC sample metric
+
+[Term]
+id: MS:4000077
+name: QC1 sample metric
+def: "A QC metric based on the results of a QC1 sample measurement. A QC1 sample is made from trypsin-digested BSA MS Standard (CAM modified), see Pichler et al. Chiva et al. for details on QC sample design)." [PSI:MS, PMID:23088386, PMID:29324744]
+comment: Expected peptides from QC1 sample measurement are: 'LVNELTEFAK','HLVDEPQNLIK','VPQVSTPTLVEVSR','EAC(Carbamidomethyl)FAVEGPK','EYEATLEEC(Carbamidomethyl)C(Carbamidomethyl)AK','EC(Carbamidomethyl)C(Carbamidomethyl)HGDLLEC(Carbamidomethyl)ADDR','SLHTLFGDELC(Carbamidomethyl)K','TC(Carbamidomethyl)VADESHAGC(Carbamidomethyl)EK','YIC(Carbamidomethyl)DNQDTISSK','NEC(Carbamidomethyl)FLSHK'
+is_a: MS:4000075 ! low complexity QC sample metric
+
+[Term]
+id: MS:4000078
+name: QC2 sample mass accuracies
+def: "Observed mass accuracy for the peptides of a QC2 sample measurement. The table should contain the peptides as described in the QC2 sample metric term, missing are interpreted as not detected." [PSI:MS]
+is_a: MS:4000005 ! table
+relationship: has_metric_category MS:4000076 ! QC2 sample metric
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_column MS:1003169 ! proforma peptidoform sequence
+relationship: has_column MS:4000072 ! observed mass accuracy
+
+[Term]
+id: MS:4000079
+name: QC2 sample intensities
+def: "Observed intensities for the peptides of a QC2 sample measurement within 5 ppm and +/- 240 s RT tolerance. Different metrics of observed intensities are possible, at least one must be present. The table should contain the peptides as defined in the parent QC2 sample metric term, missing are interpreted as not detected." [PSI:MS]
+is_a: MS:4000005 ! table
+relationship: has_metric_category MS:4000076 ! QC2 sample metric
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_column MS:1003169 ! proforma peptidoform sequence
+relationship: has_optional_column MS:1001858 ! XIC area
+relationship: has_optional_column MS:1001859 ! normalized XIC area
+relationship: has_optional_column MS:1001844 ! MS1 feature area
+relationship: has_optional_column MS:1001843 ! MS1 feature maximum intensity
+relationship: has_optional_column MS:1003085 ! previous MSn-1 scan precursor intensity
+
+[Term]
+id: MS:4000080
+name: QC non-metric term
+def: "QC terms associated but not directly metrics themselves." [PSI:MS]
+relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary
+
+[Term]
+id: MS:4000081
+name: first principal component
+def: "Data from the first principal component of a PCA." [PSI:MS]
+relationship: has_value_concept NCIT:C60694 ! Principal Component
+is_a: MS:4000080 ! QC non-metric term
+synonym: "1st PC" EXACT []
+
+[Term]
+id: MS:4000082
+name: second principal component
+def: "Data from the second principal component of a PCA." [PSI:MS]
+relationship: has_value_concept NCIT:C60694 ! Principal Component
+is_a: MS:4000080 ! QC non-metric term
+synonym: "2nd PC" EXACT []
+
+[Term]
+id: MS:4000083
+name: third principal component
+def: "Data from the third principal component of a PCA." [PSI:MS]
+relationship: has_value_concept NCIT:C60694 ! Principal Component
+is_a: MS:4000080 ! QC non-metric term
+synonym: "3rd PC" EXACT []
+
+[Term]
+id: MS:4000084
+name: fourth principal component
+def: "Data from the fourth principal component of a PCA." [PSI:MS]
+relationship: has_value_concept NCIT:C60694 ! Principal Component
+is_a: MS:4000080 ! QC non-metric term
+synonym: "4th PC" EXACT []
+
+[Term]
+id: MS:4000085
+name: fifth principal component
+def: "Data from the fifth principal component of a PCA." [PSI:MS]
+relationship: has_value_concept NCIT:C60694 ! Principal Component
+is_a: MS:4000080 ! QC non-metric term
+synonym: "5th PC" EXACT []
+
+[Term]
+id: MS:4000086
+name: mzQC input reference
+def: "Used to refer to data elements of input sections in mzQC, either inputFile names or metadata labels." [PSI:MS]
+is_a: MS:4000080 ! QC non-metric term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000087
+name: mzQC plot label
+def: "Used to supply alternative labels for plotting figures." [PSI:MS]
+is_a: MS:4000080 ! QC non-metric term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000088
+name: batch label
+def: "Used to supply batch label information with any string value." [PSI:MS]
+is_a: MS:4000080 ! QC non-metric term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000089
+name: injection sequence label
+def: "Used to supply injection sequence information with consecutive whole numbers." [PSI:MS]
+is_a: MS:4000080 ! QC non-metric term
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000090
+name: principal component analysis of MaxQuant's protein group raw intensities
+def: "A table with the PCA results of MaxQuant's protein group raw intensities." [PSI:MS] {http://coxdocs.org/doku.php?id="maxquant:table:directory&s[]=output"}
+is_a: MS:4000005 ! table
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_metric_category MS:4000013 ! multiple runs based metric
+relationship: has_column MS:4000081 ! first principal component
+relationship: has_column MS:4000086 ! mzQC input reference
+relationship: has_optional_column MS:4000082 ! second principal component
+relationship: has_optional_column MS:4000083 ! third principal component
+relationship: has_optional_column MS:4000084 ! fourth principal component
+relationship: has_optional_column MS:4000085 ! fifth principal component
+
+[Term]
+id: MS:4000091
+name: principal component analysis of MaxQuant's protein group lfq intensities
+def: "A table with the PCA results of MaxQuant's protein group lfq intensities." [PSI:MS] {http://coxdocs.org/doku.php?id="maxquant:table:directory&s[]=output"}
+is_a: MS:4000005 ! table
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_metric_category MS:4000013 ! multiple runs based metric
+relationship: has_column MS:4000081 ! first principal component
+relationship: has_column MS:4000086 ! mzQC input reference
+relationship: has_optional_column MS:4000082 ! second principal component
+relationship: has_optional_column MS:4000083 ! third principal component
+relationship: has_optional_column MS:4000084 ! fourth principal component
+relationship: has_optional_column MS:4000085 ! fifth principal component
+
+[Term]
+id: MS:4000092
+name: identified MS1 feature area principal component analysis result
+def: "A table with the PCA results of identified MS1 feature areas." [PSI:MS]
+is_a: MS:4000005 ! table
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_metric_category MS:4000013 ! multiple runs based metric
+relationship: has_column MS:4000081 ! first principal component
+relationship: has_column MS:4000086 ! mzQC input reference
+relationship: has_optional_column MS:4000082 ! second principal component
+relationship: has_optional_column MS:4000083 ! third principal component
+relationship: has_optional_column MS:4000084 ! fourth principal component
+relationship: has_optional_column MS:4000085 ! fifth principal component
+relationship: has_optional_column MS:4000087 ! mzQC plot label
+relationship: has_optional_column MS:4000088 ! batch label
+relationship: has_optional_column MS:4000089 ! injection sequence label
+
+[Term]
+id: MS:4000093
+name: unidentified MS1 feature area principal component analysis result
+def: "A table with the PCA results of unidentified but multiple-run-matched MS1 feature areas." [PSI:MS]
+is_a: MS:4000005 ! table
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_metric_category MS:4000013 ! multiple runs based metric
+relationship: has_column MS:4000081 ! first principal component
+relationship: has_column MS:4000086 ! mzQC input reference
+relationship: has_optional_column MS:4000082 ! second principal component
+relationship: has_optional_column MS:4000083 ! third principal component
+relationship: has_optional_column MS:4000084 ! fourth principal component
+relationship: has_optional_column MS:4000085 ! fifth principal component
+relationship: has_optional_column MS:4000087 ! mzQC plot label
+relationship: has_optional_column MS:4000088 ! batch label
+relationship: has_optional_column MS:4000089 ! injection sequence label
+
+[Term]
+id: MS:4000094
+name: batch-corrected identified MS1 feature area principal component analysis result
+def: "A table with the PCA results of identified MS1 feature areas after batch-correction." [PSI:MS]
+is_a: MS:4000005 ! table
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_metric_category MS:4000013 ! multiple runs based metric
+relationship: has_column MS:4000081 ! first principal component
+relationship: has_column MS:4000086 ! mzQC input reference
+relationship: has_optional_column MS:4000082 ! second principal component
+relationship: has_optional_column MS:4000083 ! third principal component
+relationship: has_optional_column MS:4000084 ! fourth principal component
+relationship: has_optional_column MS:4000085 ! fifth principal component
+relationship: has_optional_column MS:4000087 ! mzQC plot label
+relationship: has_optional_column MS:4000088 ! batch label
+relationship: has_optional_column MS:4000089 ! injection sequence label
+
+[Term]
+id: MS:4000095
+name: slowest frequency for MS level 1 collection
+def: "The slowest acquisition speed with which precursor MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used." [PSI:MS]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_units UO:0000106 ! hertz
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_metric_category MS:4000021 ! MS1 metric
+
+[Term]
+id: MS:4000096
+name: slowest frequency for MS level 2 collection
+def: "The slowest acquisition speed with which product MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used." [PSI:MS]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_units UO:0000106 ! hertz
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_metric_category MS:4000022 ! MS2 metric
+
+[Term]
+id: MS:4000097
+name: MS1 signal jump (10x) count
+def: "The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans." [PSI:MS]
+comment: An unusual high count of signal jumps or falls may indicate ESI stability issues.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_units UO:0000189 ! count unit
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
+synonym: "IS-1A" RELATED []
+
+[Term]
+id: MS:4000098
+name: MS1 signal fall (10x) count
+def: "The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans." [PSI:MS]
+comment: An unusual high count of signal jumps or falls may indicate ESI stability issues.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_units UO:0000189 ! count unit
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
+synonym: "IS-1B" RELATED []
+
+[Term]
+id: MS:4000099
+name: number of empty MS1 scans
+def: "Number of MS1 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks)." [PSI:MS]
+comment: An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_units UO:0000189 ! count unit
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000100
+name: number of empty MS2 scans
+def: "Number of MS2 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks)." [PSI:MS]
+comment: An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_units UO:0000189 ! count unit
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000101
+name: number of empty MS3 scans
+def: "Number of MS3 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks)." [PSI:MS]
+comment: An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_units UO:0000189 ! count unit
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000102
+name: number of detected quantification data points
+def: "The number of data points detected for quantification purposes within the run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run." [PSI:MS]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_units UO:0000189 ! count unit
+
+[Term]
+id: MS:4000103
+name: number of identified quantification data points
+def: "The number of identified data points for quantification purposes within the run after user defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+relationship: has_units UO:0000189 ! count unit
+
+[Term]
+id: MS:4000104
+name: total ion currents
+def: "Tabular representation of the total ion current detected in each of a series of mass spectra." [PSI:MS]
+is_a: MS:4000005 ! table
+is_a: MS:1000235 ! total ion current chromatogram
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000016 ! retention time metric
+relationship: has_column MS:1000767 ! native spectrum identifier format
+relationship: has_optional_column MS:1000894 ! retention time
+relationship: has_optional_column MS:1003059 ! number of peaks
+relationship: has_column MS:1000285 ! total ion current
+
+[Term]
+id: MS:4000105
+name: ion injection parameters
+def: "Tabular representation of the parameters around ion selection like the amount of time spent filling an ion trapping device for each scan acquisition." [PSI:MS]
+is_a: MS:4000005 ! table
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_column MS:1000767 ! native spectrum identifier format
+relationship: has_column MS:1000927 ! ion injection time
+relationship: has_optional_column MS:1000511! ms level
+relationship: has_optional_column MS:1000465 ! scan polarity
+relationship: has_optional_column MS:1000500 ! scan window upper limit
+relationship: has_optional_column MS:1000501 ! scan window lower limit
+
+[Term]
+id: MS:4000106
+name: MS1 frequency in equal parts of subsequent RT
+def: "Average MS1 frequency during retention time periods between adjacent retention time quantiles. (Four values implies values for 1st, 2nd, 3rd, 4th quarter.)" [PSI:MS]
+comment: Acquisition frequency can be used to gauge the suitability of instrument settings depending on the sample content.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_units UO:0000106 ! hertz
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000107
+name: MS2 frequency in equal parts of subsequent RT
+def: "Average MS2 frequency during retention time periods between adjacent retention time quantiles. (Four values implies values for 1st, 2nd, 3rd, 4th quarter.)" [PSI:MS]
+comment: Acquisition frequency can be used to gauge the suitability of instrument settings depending on the sample content.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_units UO:0000106 ! hertz
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000108
+name: MS1 peak density distribution mean
+def: "From the distribution of peak densities in MS1, the mean" [PSI:MS]
+comment: The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000401 ! sample mean
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000109
+name: MS1 peak density distribution sigma
+def: "From the distribution of peak densities in MS1, the sigma value" [PSI:MS]
+comment: The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000237 ! standard deviation
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000110
+name: MS1 peak density distribution low outliers
+def: "From the distribution of peak densities in MS1, the list of outliers below a in-file defined threshold" [PSI:MS]
+comment: The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000036 ! outlier
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000111
+name: MS1 peak density distribution high outliers
+def: "From the distribution of peak densities in MS1, the list of outliers above a in-file defined threshold" [PSI:MS]
+comment: The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000036 ! outlier
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000112
+name: MS2 peak density distribution mean
+def: "From the distribution of peak densities in MS2, the mean" [PSI:MS]
+comment: The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000401 ! sample mean
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000113
+name: MS2 peak density distribution sigma
+def: "From the distribution of peak densities in MS2, the sigma value" [PSI:MS]
+comment: The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000237 ! standard deviation
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000114
+name: MS2 peak density distribution low outliers
+def: "From the distribution of peak densities in MS2, the list of outliers below a in-file defined threshold" [PSI:MS]
+comment: The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000036 ! outlier
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000115
+name: MS2 peak density distribution high outliers
+def: "From the distribution of peak densities in MS2, the list of outliers above a in-file defined threshold" [PSI:MS]
+comment: The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000036 ! outlier
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000116
+name: MS2 precursor intensity distribution
+def: "From the distribution of MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3." [PSI:MS]
+comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000291 ! quantile
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units MS:1000043 ! intensity unit
+
+[Term]
+id: MS:4000117
+name: MS2 precursor intensity distribution mean
+def: "From the distribution of MS2 precursor intensities, the mean" [PSI:MS]
+comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000401 ! sample mean
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units MS:1000043 ! intensity unit
+
+[Term]
+id: MS:4000118
+name: MS2 precursor intensity distribution sigma
+def: "From the distribution of MS2 precursor intensities, the sigma value" [PSI:MS]
+comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000237 ! standard deviation
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units MS:1000043 ! intensity unit
+
+[Term]
+id: MS:4000119
+name: MS2 precursor intensity distribution low outliers
+def: "From the distribution of precursor intensities, the list of outliers below a in-file defined threshold" [PSI:MS]
+comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000036 ! outlier
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units MS:1000043 ! intensity unit
+
+[Term]
+id: MS:4000120
+name: MS2 precursor intensity distribution high outliers
+def: "From the distribution of precursor intensities, the list of outliers above a in-file defined threshold" [PSI:MS]
+comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000036 ! outlier
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units MS:1000043 ! intensity unit
+
+[Term]
+id: MS:4000121
+name: MS1 signal-to-noise ratio quantiles
+def: "From the distribution of signal-to-noise ratio in MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3" [PSI:MS]
+comment: The Signal-to-noise ratio in MS1 distribution can provide insight to the presence of nuisance factors.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000291 ! quantile
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000122
+name: MS1 signal-to-noise ratio mean
+def: "From the distribution of signal-to-noise ratio in MS1, the mean" [PSI:MS]
+comment: The signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000401 ! sample mean
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000123
+name: MS1 signal-to-noise ratio sigma
+def: "From the distribution of signal-to-noise ratio in MS1, the sigma value" [PSI:MS]
+comment: The Signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000237 ! standard deviation
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000124
+name: MS1 signal-to-noise ratio low outliers
+def: "From the distribution of signal-to-noise ratio in MS1, the list of outliers below a in-file defined threshold" [PSI:MS]
+comment: The Signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000036 ! outlier
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000125
+name: MS1 signal-to-noise ratio high outliers
+def: "From the distribution of signal-to-noise ratio in MS1, the list of outliers above a in-file defined threshold" [PSI:MS]
+comment: The Signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000036 ! outlier
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000126
+name: MS2 signal-to-noise ratio quantiles
+def: "From the distribution of signal-to-noise ratio in MS2, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3" [PSI:MS]
+comment: A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000291 ! quantile
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000127
+name: MS2 signal-to-noise ratio mean
+def: "From the distribution of signal-to-noise ratio in MS2, the mean" [PSI:MS]
+comment: A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000401 ! sample mean
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000128
+name: MS2 signal-to-noise ratio sigma
+def: "From the distribution of signal-to-noise ratio in MS2, the sigma value" [PSI:MS]
+comment: A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000237 ! standard deviation
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000129
+name: MS2 signal-to-noise ratio low outliers
+def: "From the distribution of signal-to-noise ratio in MS2, the list of outliers below a in-file defined threshold" [PSI:MS]
+comment: A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000036 ! outlier
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000130
+name: MS2 signal-to-noise ratio high outliers
+def: "From the distribution of signal-to-noise ratio in MS2, the list of outliers above a in-file defined threshold" [PSI:MS]
+comment: A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware').
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000036 ! outlier
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000131
+name: MS1 ion collection time quantiles
+def: "From the distribution of ion injection times (MS:1000927) for MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3" [PSI:MS]
+comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000291 ! quantile
+relationship: has_units UO:0000028 ! millisecond
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000132
+name: MS1 ion collection time mean
+def: "From the distribution of ion injection times (MS:1000927) for MS1, the mean" [PSI:MS]
+comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000401 ! sample mean
+relationship: has_units UO:0000028 ! millisecond
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000133
+name: MS1 ion collection time sigma
+def: "From the distribution of ion injection times (MS:1000927) for MS1, the sigma value" [PSI:MS]
+comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000237 ! standard deviation
+relationship: has_units UO:0000028 ! millisecond
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000134
+name: MS1 ion collection time low outliers
+def: "From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers below a in-file defined threshold" [PSI:MS]
+comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000036 ! outlier
+relationship: has_units UO:0000028 ! millisecond
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000135
+name: MS1 ion collection time high outliers
+def: "From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers above a in-file defined threshold" [PSI:MS]
+comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000036 ! outlier
+relationship: has_units UO:0000028 ! millisecond
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000136
+name: MS2 ion collection time quantiles
+def: "From the distribution of ion injection times (MS:1000927) for MS2, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3" [PSI:MS]
+comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_value_concept STATO:0000291 ! quantile
+relationship: has_units UO:0000028 ! millisecond
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000137
+name: MS2 ion collection time mean
+def: "From the distribution of ion injection times (MS:1000927) for MS2, the mean" [PSI:MS]
+comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000401 ! sample mean
+relationship: has_units UO:0000028 ! millisecond
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000138
+name: MS2 ion collection time sigma
+def: "From the distribution of ion injection times (MS:1000927) for MS2, the sigma value" [PSI:MS]
+comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000237 ! standard deviation
+relationship: has_units UO:0000028 ! millisecond
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000139
+name: MS2 ion collection time low outliers
+def: "From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers below a in-file defined threshold" [PSI:MS]
+comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000036 ! outlier
+relationship: has_units UO:0000028 ! millisecond
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000140
+name: MS2 ion collection time high outliers
+def: "From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers above a in-file defined threshold" [PSI:MS]
+comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000036 ! outlier
+relationship: has_units UO:0000028 ! millisecond
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000141
+name: outlier threshold criterion
+def: "The definition of the outlier criteria applied." [PSI:MS]
+is_a: MS:4000080 ! QC non-metric term
+
+[Term]
+id: MS:4000142
+name: Tukey's fence
+def: "Defines outliers with Tukey's fence as <(Q1-x*IQR) for low outliers and >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5." [PSI:MS]
+is_a: MS:4000141 ! outlier threshold criterion
+
+[Term]
+id: MS:4000143
+name: Tukey's fence high outliers
+def: "Defines high outliers with Tukey's fence as >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5." [PSI:MS]
+is_a: MS:4000141 ! outlier threshold criterion
+
+[Term]
+id: MS:4000144
+name: Tukey's fence low outliers
+def: "Defines low outliers with Tukey's fence as <(Q1-x*IQR) for low outliers, where x is defined by the term's value. The default is x=1.5." [PSI:MS]
+is_a: MS:4000141 ! outlier threshold criterion
+
+[Term]
+id: MS:4000145
+name: Z-score threshold
+def: "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3." [PSI:MS]
+is_a: MS:4000141 ! outlier threshold criterion
+
+[Term]
+id: MS:4000146
+name: Z-score threshold high outliers
+def: "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3." [PSI:MS]
+is_a: MS:4000141 ! outlier threshold criterion
+
+[Term]
+id: MS:4000147
+name: Z-score threshold low outliers
+def: "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3." [PSI:MS]
+is_a: MS:4000141 ! outlier threshold criterion
+
+[Term]
+id: MS:4000148
+name: algorithmical threshold
+def: "Defines outliers algorithmically, where a single value threshold might not be applicable or p.r.n. multivariate decision making is applied. The value of the term should name the algorithmical method used." [PSI:MS]
+is_a: MS:4000141 ! outlier threshold criterion
+
+[Term]
+id: MS:4000149
+name: iRT calibration formula
+def: "A polynomial formula to calibrate retention time based on iRT reference peptides. The order of the values corresponds to polynomial terms. I.e. a linear equation is represented by a two-tuple consisting of (slope, intercept). More general, the position in the n_tuple indicates the power of `x`: position `n → x^0`, position `n - 1 → x^1`, position `n - 2 → x^2`, etc." [PSI:MS]
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000016 ! retention time metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000150
+name: iRT calibration adjusted r-squared
+def: "The goodness of fit statistic between observed retention times and iRT calibrated retention times." [PSI:MS]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000016 ! retention time metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000151
+name: MsQuality
+def: "MsQuality – an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data." [DOI:10.1101/2023.05.12.540477, https://github.com/tnaake/MsQuality/]
+is_a: MS:1001456 ! analysis software
+
+[Term]
+id: MS:4000152
+name: MS2 precursor median m/z of identified quantification data points
+def: "Median m/z value for MS2 precursors of all quantification data points after user-defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: The m/z distribution informs about the dynamic range of the acquisition.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000020 ! ion source metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_units MS:1000040 ! m/z
+
+[Term]
+id: MS:4000153
+name: interquartile RT period for identified quantification data points
+def: "The interquartile retention time period, in seconds, for all quantification data points after user-defined acceptance criteria are applied over the complete run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: Longer duration may indicate a better chromatographic separation of compounds which depends, however, also on the sampling/scan rate of the MS instrument.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000017 ! chromatogram metric
+relationship: has_units UO:0000010 ! second
+synonym: "C-2A" RELATED [PMID:19837981]
+
+[Term]
+id: MS:4000154
+name: rate of the interquartile RT period for identified quantification data points
+def: "The rate of identified quantification data points for the interquartile retention time period, in identified quantification data points per second. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: Higher rates may indicate a more efficient sampling and identification.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000017 ! chromatogram metric
+relationship: has_units UO:0000106 ! hertz
+synonym: "C-2B" RELATED [PMID:19837981]
+
+[Term]
+id: MS:4000155
+name: area under TIC
+def: "The area under the total ion chromatogram." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition. Differences between samples of an experiment may indicate differences in the dynamic range and/or in the sample content.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free
+relationship: has_metric_category MS:4000017 ! chromatogram metric
+
+[Term]
+id: MS:4000156
+name: area under TIC RT quantiles
+def: "The area under the total ion chromatogram of the retention time quantiles. Number of quantiles are given by the n-tuple." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. Differences between samples of an experiment may indicate differences in chromatographic performance, differences in the dynamic range and/or in the sample content.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free
+relationship: has_metric_category MS:4000017 ! chromatogram metric
+
+[Term]
+id: MS:4000157
+name: extent of identified MS2 precursor intensity
+def: "Ratio of 95th over 5th percentile of MS2 precursor intensity for all quantification data points after user-defined acceptance criteria are applied. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+synonym: "MS1-3A" RELATED [PMID:19837981]
+
+[Term]
+id: MS:4000158
+name: median of TIC values in the RT range in which the middle half of quantification data points are identified
+def: "Median of TIC values in the RT range in which half of quantification data points are identified (RT values of Q1 to Q3 of identifications). These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+
+[Term]
+id: MS:4000159
+name: median of TIC values in the shortest RT range in which half of the quantification data points are identified
+def: "Median of TIC values in the shortest RT range in which half of the quantification data points are identified. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+synonym: "MS1-2B" RELATED [PMID:19837981]
+
+[Term]
+id: MS:4000160
+name: MS2 precursor intensity range
+def: "Minimum and maximum MS2 precursor intensity recorded." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000009 ! ID free
+relationship: has_metric_category MS:4000022 ! MS2 metric
+
+[Term]
+id: MS:4000161
+name: identified MS2 precursor intensity distribution
+def: "From the distribution of identified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition in relation to identifiability.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000291 ! quantile
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units MS:1000043 ! intensity unit
+
+[Term]
+id: MS:4000162
+name: unidentified MS2 precursor intensity distribution
+def: "From the distribution of unidentified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition in relation to identifiability.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000291 ! quantile
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units MS:1000043 ! intensity unit
+
+[Term]
+id: MS:4000163
+name: identified MS2 precursor intensity distribution mean
+def: "From the distribution of identified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition in relation to identifiability.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000401 ! sample mean
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units MS:1000043 ! intensity unit
+
+[Term]
+id: MS:4000164
+name: unidentified MS2 precursor intensity distribution mean
+def: "From the distribution of unidentified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition in relation to identifiability.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000401 ! sample mean
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units MS:1000043 ! intensity unit
+
+[Term]
+id: MS:4000165
+name: identified MS2 precursor intensity distribution sigma
+def: "From the distribution of identified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition in relation to identifiability.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000237 ! standard deviation
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units MS:1000043 ! intensity unit
+
+[Term]
+id: MS:4000166
+name: unidentified MS2 precursor intensity distribution sigma
+def: "From the distribution of unidentified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: The metric informs about the dynamic range of the acquisition in relation to identifiability.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_value_concept STATO:0000237 ! standard deviation
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units MS:1000043 ! intensity unit
+
+[Term]
+id: MS:4000167
+name: ratio of 1+ over 2+ of all MS2 known precursor charges
+def: "The ratio of 1+ over 2+ MS2 precursor charge count of all spectra." [PSI:MS]
+comment: High ratios of 1+/2+ MS2 precursor charge count may indicate inefficient ionization.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000020 ! ion source metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+synonym: "IS-3A" RELATED [PMID:19837981]
+synonym: "MS2 known precursor charges fractions" RELATED []
+synonym: "MS2-PrecZ-1" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-2" RELATED [PMID:24494671]
+
+[Term]
+id: MS:4000168
+name: ratio of 1+ over 2+ of identified MS2 known precursor charges
+def: "The ratio of 1+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: High ratios of 1+/2+ MS2 precursor charge count may indicate inefficient ionization in relation to identifiability.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000020 ! ion source metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+synonym: "IS-3A" RELATED [PMID:19837981]
+synonym: "MS2 known precursor charges fractions" RELATED []
+synonym: "MS2-PrecZ-1" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-2" RELATED [PMID:24494671]
+
+[Term]
+id: MS:4000169
+name: ratio of 3+ over 2+ of all MS2 known precursor charges
+def: "The ratio of 3+ over 2+ MS2 precursor charge count of all spectra." [PSI:MS]
+comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000020 ! ion source metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+synonym: "IS-3B" RELATED [PMID:19837981]
+synonym: "MS2 known precursor charges fractions" RELATED []
+synonym: "MS2-PrecZ-2" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-3" RELATED [PMID:24494671]
+
+[Term]
+id: MS:4000170
+name: ratio of 3+ over 2+ of identified MS2 known precursor charges
+def: "The ratio of 3+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides in relation to identifiability.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000020 ! ion source metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+synonym: "IS-3B" RELATED [PMID:19837981]
+synonym: "MS2 known precursor charges fractions" RELATED []
+synonym: "MS2-PrecZ-2" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-3" RELATED [PMID:24494671]
+
+[Term]
+id: MS:4000171
+name: ratio of 4+ over 2+ of all MS2 known precursor charges
+def: "The ratio of 4+ over 2+ MS2 precursor charge count of all spectra." [PSI:MS]
+comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000020 ! ion source metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+synonym: "IS-3C" RELATED [PMID:19837981]
+synonym: "MS2 known precursor charges fractions" RELATED []
+synonym: "MS2-PrecZ-2" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-4" RELATED [PMID:24494671]
+
+[Term]
+id: MS:4000172
+name: ratio of 4+ over 2+ of identified MS2 known precursor charges
+def: "The ratio of 4+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides in relation to identifiability.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000020 ! ion source metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+synonym: "IS-3C" RELATED [PMID:19837981]
+synonym: "MS2 known precursor charges fractions" RELATED []
+synonym: "MS2-PrecZ-2" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-4" RELATED [PMID:24494671]
+
+[Term]
+id: MS:4000173
+name: mean MS2 precursor charge in all spectra
+def: "Mean MS2 precursor charge in all spectra" [PSI:MS]
+comment: Higher charges may indicate inefficient ionization or e.g. preference for longer peptides.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000020 ! ion source metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+synonym: "MS2 known precursor charges fractions" RELATED []
+synonym: "MS2-PrecZ-1" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-2" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-3" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-4" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-5" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-more" RELATED [PMID:24494671]
+
+[Term]
+id: MS:4000174
+name: mean MS2 precursor charge in identified spectra
+def: "Mean MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: Higher charges may indicate inefficient ionization or e.g. preference for longer peptides in relation to identifiability.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000020 ! ion source metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+synonym: "MS2 known precursor charges fractions" RELATED []
+synonym: "MS2-PrecZ-1" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-2" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-3" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-4" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-5" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-more" RELATED [PMID:24494671]
+
+[Term]
+id: MS:4000175
+name: median MS2 precursor charge in all spectra
+def: "Median MS2 precursor charge in all spectra" [PSI:MS]
+comment: Higher charges may indicate inefficient ionization and/or e.g. preference for longer peptides.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000009 ! ID free metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000020 ! ion source metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+synonym: "MS2 known precursor charges fractions" RELATED []
+synonym: "MS2-PrecZ-1" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-2" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-3" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-4" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-5" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-more" RELATED [PMID:24494671]
+
+[Term]
+id: MS:4000176
+name: median MS2 precursor charge in identified spectra
+def: "Median MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]
+comment: Higher charges may indicate inefficient ionization and/or e.g. preference for longer peptides in relation to identifiability.
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000020 ! ion source metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+synonym: "MS2 known precursor charges fractions" RELATED []
+synonym: "MS2-PrecZ-1" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-2" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-3" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-4" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-5" RELATED [PMID:24494671]
+synonym: "MS2-PrecZ-more" RELATED [PMID:24494671]
+
+[Term]
+id: MS:4000177
+name: contaminant protein abundance fraction
+def: "The fraction of total protein abundance in a mass spectrometry run or a group of runs which can be attributed to a user-defined list of contaminant proteins (e.g. using the cRAP contaminant database)." [PSI:MS]
+comment: "High values may indicate a sample handling issue, and/or insufficient sample concentration."
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV
+relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
+relationship: has_order MS:1002109 ! lower score better
+synonym: "PG: Contaminants" NARROW []
+
+[Term]
+id: MS:4000178
+name: precursor ppm deviation mean
+def: "The mean of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied" [PSI:MS]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000401 ! sample mean
+relationship: has_value_concept MS:1000014 ! accuracy
+relationship: has_units UO:0000169 ! parts per million
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000179
+name: precursor ppm deviation sigma
+def: "The standard deviation of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied" [PSI:MS]
+is_a: MS:4000003 ! single value
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000021 ! MS1 metric
+relationship: has_value_concept STATO:0000237 ! standard deviation
+relationship: has_value_concept MS:1000830 ! precision
+relationship: has_units UO:0000169 ! parts per million
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+
+[Term]
+id: MS:4000180
+name: table of missed cleavage counts
+def: "The number of identified peptides with corresponding number of missed cleavages after user-defined acceptance criteria are applied. The number of missed cleavages per peptide is given in the 'number of missed cleavages' column, the respective count of such peptides identified in the 'Number of Occurrences' column. The highest 'missed cleavages' row is to be interpreted as that number of missed cleavages or higher." [PSI:MS]
+is_a: MS:4000005 ! table
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_column MS:1003044 ! number of missed cleavages
+relationship: has_column NCIT:C150827 ! Number of Occurrences
+
+[Term]
+id: MS:4000181
+name: identified MS2 quarter RT fraction
+def: "The interval used for acquisition of the first, second, third, and fourth quarter of all identified MS2 events divided by retention time duration." [PSI:MS]
+comment: The metric informs about the dynamic range of the MS2 identification process along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation.
+is_a: MS:4000004 ! n-tuple
+relationship: has_metric_category MS:4000012 ! single run based metric
+relationship: has_metric_category MS:4000008 ! ID based metric
+relationship: has_metric_category MS:4000022 ! MS2 metric
+relationship: has_metric_category MS:4000016 ! retention time metric
+relationship: has_value_type xsd:float ! The allowed value-type for this CV term
+relationship: has_units UO:0000191 ! fraction
+synonym: "RT-MSMS-Q1" RELATED [PMID:24494671]
+synonym: "RT-MSMS-Q2" RELATED [PMID:24494671]
+synonym: "RT-MSMS-Q3" RELATED [PMID:24494671]
+synonym: "RT-MSMS-Q4" RELATED [PMID:24494671]
+
+[Term]
+id: MS:1003407
+name: Scout
+def: "Identifying crosslinked peptides in complex protein mixtures" [PSI:MS]
+is_a: MS:1001456 ! analysis software
+
+[Term]
+id: MS:1003408
+name: Scout score
+def: "Scout identification search engine score" [PSI:MS]
+is_a: MS:1003407 ! Scout
+relationship: has_order MS:1003407 ! higher score better
+relationship: has_value_type xsd:double ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000001
+name: PEFF CV term
+def: "PSI Extended FASTA Format controlled vocabulary term." [PSI:PEFF]
+relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies
+
+[Term]
+id: PEFF:0000002
+name: PEFF file header section term
+def: "CV term that may appear in a PEFF file header section." [PSI:PEFF]
+is_a: PEFF:0000001 ! PEFF CV term
+
+[Term]
+id: PEFF:0000003
+name: PEFF file sequence entry term
+def: "CV term that may appear in a description line of a PEFF file individual sequence entry." [PSI:PEFF]
+is_a: PEFF:0000001 ! PEFF CV term
+
+[Term]
+id: PEFF:0000008
+name: DbName
+def: "PEFF keyword for the sequence database name." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000009
+name: Prefix
+def: "PEFF keyword for the sequence database prefix." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000010
+name: DbDescription
+def: "PEFF keyword for the sequence database short description." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000011
+name: Decoy
+def: "PEFF keyword for the specifying whether the sequence database is a decoy database." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000012
+name: DbSource
+def: "PEFF keyword for the source of the database file." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000013
+name: DbVersion
+def: "PEFF keyword for the database version (release date) according to database provider." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000014
+name: DbDate
+def: "OBSOLETE PEFF keyword for the database date (release or file date of the source) according to database provider." [PSI:PEFF]
+comment: This term was obsoleted.
+is_a: PEFF:0000002 ! PEFF file header section term
+is_obsolete: true
+
+[Term]
+id: PEFF:0000015
+name: NumberOfEntries
+def: "PEFF keyword for the sumber of sequence entries in the database." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000016
+name: Conversion
+def: "PEFF keyword for the description of the conversion from original format to this current one." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000017
+name: SequenceType
+def: "PEFF keyword for the molecular type of the sequences." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_regexp PEFF:1002002 ! regular expression for PEFF molecular sequence type
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000018
+name: SpecificKey
+def: "PEFF keyword for database specific keywords not included in the current controlled vocabulary." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000019
+name: SpecificValue
+def: "PEFF keyword for the specific values for a custom key." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000020
+name: DatabaseDescription
+def: "PEFF keyword for the short description of the PEFF file." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000021
+name: GeneralComment
+def: "PEFF keyword for a general comment." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000022
+name: ProteoformDb
+def: "PEFF keyword that when set to 'true' indicates that the database contains complete proteoforms." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000023
+name: OptionalTagDef
+def: "PEFF keyword for the short tag (abbreviation) and longer definition used to annotate a sequence annotation (such as variant or modification) in the OptionalTag location." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0000024
+name: HasAnnotationIdentifiers
+def: "PEFF keyword that when set to 'true' indicates that entries in the database have identifiers for each annotation." [PSI:PEFF]
+is_a: PEFF:0000002 ! PEFF file header section term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0001001
+name: DbUniqueId
+def: "OBSOLETE Sequence database unique identifier." [PSI:PEFF]
+comment: This term was made obsolete because decided in Heidelberg 2018-04 that this is redundant.
+is_a: PEFF:0000003 ! PEFF file sequence entry term
+is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0001002
+name: PName
+def: "PEFF keyword for the protein full name." [PSI:PEFF]
+is_a: PEFF:0000003 ! PEFF file sequence entry term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0001003
+name: NcbiTaxId
+def: "PEFF keyword for the NCBI taxonomy identifier." [PSI:PEFF]
+is_a: PEFF:0000003 ! PEFF file sequence entry term
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0001004
+name: TaxName
+def: "PEFF keyword for the taxonomy name (latin or common name)." [PSI:PEFF]
+is_a: PEFF:0000003 ! PEFF file sequence entry term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0001005
+name: GName
+def: "PEFF keyword for the gene name." [PSI:PEFF]
+is_a: PEFF:0000003 ! PEFF file sequence entry term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0001006
+name: Length
+def: "PEFF keyword for the sequence length." [PSI:PEFF]
+is_a: PEFF:0000003 ! PEFF file sequence entry term
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0001007
+name: SV
+def: "PEFF keyword for the sequence version." [PSI:PEFF]
+is_a: PEFF:0000003 ! PEFF file sequence entry term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0001008
+name: EV
+def: "PEFF keyword for the entry version." [PSI:PEFF]
+is_a: PEFF:0000003 ! PEFF file sequence entry term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0001009
+name: PE
+def: "PEFF keyword for the Protein Evidence; A UniProtKB code 1-5." [PSI:PEFF]
+is_a: PEFF:0000003 ! PEFF file sequence entry term
+relationship: has_value_type xsd:int ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0001010
+name: Processed
+def: "PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains." [PSI:PEFF]
+is_a: PEFF:0000003 ! PEFF file sequence entry term
+relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0001011
+name: Variant
+def: "OBSOLETE Sequence variation (substitution, insertion, deletion)." [PSI:PEFF]
+comment: This term was made obsolete in favor of VariantSimple and VariantComplex.
+is_a: PEFF:0000003 ! PEFF file sequence entry term
+relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+is_obsolete: true
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0001012
+name: ModResPsi
+def: "PEFF keyword for the modified residue with PSI-MOD identifier." [PSI:PEFF]
+is_a: PEFF:0000003 ! PEFF file sequence entry term
+relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0001013
+name: ModRes
+def: "PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier." [PSI:PEFF]
+is_a: PEFF:0000003 ! PEFF file sequence entry term
+relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0001014
+name: AltAC
+def: "PEFF keyword for the Alternative Accession Code." [PSI:PEFF]
+is_a: PEFF:0000003 ! PEFF file sequence entry term
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
+
+[Term]
+id: PEFF:0001015
+name: SeqStatus
+def: "PEFF keyword for the sequence status. Complete or Fragment." [PSI:PEFF]
+is_a: PEFF:0000003 ! PEFF file sequence entry term
relationship: has_regexp PEFF:1002003 ! regular expression for PEFF sequence status
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001016
name: CC
def: "PEFF keyword for the entry associated comment." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001017
name: KW
def: "PEFF keyword for the entry associated keyword(s)." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001018
name: GO
def: "PEFF keyword for the Gene Ontology code." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001019
name: XRef
def: "PEFF keyword for the cross-reference to an external resource." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001020
name: mature protein
def: "Portion of a newly synthesized protein that contributes to a final structure after other components such as signal peptides are removed." [PSI:PEFF]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001021
name: signal peptide
def: "Short peptide present at the N-terminus of a newly synthesized protein that is cleaved off and is not part of the final mature protein." [PSI:PEFF]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001022
name: transit peptide
def: "Short peptide present at the N-terminus of a newly synthesized protein that helps the protein through the membrane of its destination organelle." [PSI:PEFF]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001023
name: Conflict
def: "PEFF keyword for the sequence conflict; a UniProtKB term." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001024
name: Crc64
def: "PEFF keyword for the Sequence checksum in crc64." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001025
name: Domain
def: "PEFF keyword for the sequence range of a domain." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001026
name: ID
def: "PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001027
name: ModResUnimod
def: "PEFF keyword for the modified residue with UniMod identifier." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001028
name: VariantSimple
def: "PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001029
name: VariantComplex
def: "PEFF keyword for a sequence variation that is more complex than a single amino acid change or change to a stop codon." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001030
name: Proteoform
def: "PEFF keyword for the proteoforms of this protein, constructed as a set of annotation identifiers." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001031
name: DisulfideBond
def: "PEFF keyword for the disulfide bonds in this protein, constructed as a sets of annotation identifiers of two half-cystine modifications." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001032
@@ -20948,23 +24577,23 @@ id: PEFF:0001033
name: Comment
def: "PEFF keyword for the individual protein entry comment. It is discouraged to put parsable information here. This is only for free-text commentary." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001034
name: propeptide
def: "Short peptide that is cleaved off a newly synthesized protein and generally immediately degraded in the process of protein maturation, and is not a signal peptide or transit peptide." [PSI:PEFF]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:0001035
name: initiator methionine
def: "N-terminal methionine residue of a protein that can be co-translationally cleaved." [PSI:PEFF]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
-xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment
+relationship: has_value_type xsd:string ! The allowed value-type for this CV term
[Term]
id: PEFF:1002001
@@ -20983,3 +24612,534 @@ id: PEFF:1002003
name: regular expression for PEFF sequence status
def: "(Complete|Fragment|[a-z0-9A-Z]+)." [PSI:PEFF]
is_a: MS:1002479 ! regular expression
+
+
+[Term]
+id: UO:0000000
+name: unit
+namespace: unit.ontology
+def: "A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia]
+created_by: george gkoutos
+
+[Term]
+id: UO:0000001
+name: length unit
+namespace: unit.ontology
+def: "A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia]
+subset: unit_group_slim
+is_a: UO:0000000
+relationship: is_unit_of PATO:0001708
+created_by: george gkoutos
+
+[Term]
+id: UO:0000002
+name: mass unit
+namespace: unit.ontology
+def: "A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia]
+subset: unit_group_slim
+is_a: UO:0000000
+relationship: is_unit_of PATO:0000125
+relationship: is_unit_of PATO:0000128
+created_by: george gkoutos
+
+[Term]
+id: UO:0000003
+name: time unit
+namespace: unit.ontology
+alt_id: UO:0000149
+def: "A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia]
+subset: unit_group_slim
+synonym: "time derived unit" EXACT []
+is_a: UO:0000000
+relationship: is_unit_of PATO:0000165
+relationship: is_unit_of PATO:0001309
+created_by: george gkoutos
+
+[Term]
+id: UO:0000005
+name: temperature unit
+namespace: unit.ontology
+alt_id: UO:0000126
+def: "A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter." [Wikipedia:Wikipedia]
+subset: unit_group_slim
+synonym: "temperature derived unit" EXACT []
+is_a: UO:0000000
+relationship: is_unit_of PATO:0000146
+created_by: george gkoutos
+
+[Term]
+id: UO:0000008
+name: meter
+namespace: unit.ontology
+def: "A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second." [BIPM:BIPM, NIST:NIST]
+subset: unit_slim
+synonym: "m" EXACT []
+synonym: "metre" EXACT []
+is_a: UO:0000001
+is_a: UO:0000045
+created_by: george gkoutos
+
+[Term]
+id: UO:0000010
+name: second
+namespace: unit.ontology
+def: "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom." [BIPM:BIPM, NIST:NIST]
+subset: unit_slim
+synonym: "s" EXACT []
+is_a: UO:0000003
+is_a: UO:0000045
+created_by: george gkoutos
+
+[Term]
+id: UO:0000012
+name: kelvin
+namespace: unit.ontology
+def: "A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water." [BIPM:BIPM, NIST:NIST]
+subset: unit_slim
+synonym: "K" EXACT []
+is_a: UO:0000005
+is_a: UO:0000045
+created_by: george gkoutos
+
+[Term]
+id: UO:0000017
+name: micrometer
+namespace: unit.ontology
+def: "A length unit which is equal to one millionth of a meter or 10^[-6] m." [NIST:NIST]
+subset: unit_slim
+synonym: "micrometre" EXACT []
+synonym: "micron" EXACT []
+synonym: "um" EXACT []
+is_a: UO:0000001
+created_by: george gkoutos
+
+[Term]
+id: UO:0000018
+name: nanometer
+namespace: unit.ontology
+def: "A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." [NIST:NIST]
+subset: unit_slim
+synonym: "nanometre" EXACT []
+synonym: "nm" EXACT []
+is_a: UO:0000001
+created_by: george gkoutos
+
+[Term]
+id: UO:0000021
+name: gram
+namespace: unit.ontology
+def: "A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg." [NIST:NIST]
+subset: unit_slim
+synonym: "g" EXACT []
+is_a: UO:0000002
+created_by: george gkoutos
+
+[Term]
+id: UO:0000027
+name: degree Celsius
+namespace: unit.ontology
+def: "A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K." [NIST:NIST]
+subset: unit_slim
+synonym: "C" EXACT []
+is_a: UO:0000005
+created_by: george gkoutos
+
+[Term]
+id: UO:0000028
+name: millisecond
+namespace: unit.ontology
+def: "A time unit which is equal to one thousandth of a second or 10^[-3] s." [NIST:NIST]
+subset: unit_slim
+synonym: "ms" EXACT []
+is_a: UO:0000003
+created_by: george gkoutos
+
+[Term]
+id: UO:0000031
+name: minute
+namespace: unit.ontology
+def: "A time unit which is equal to 60 seconds." [Wikipedia:Wikipedia]
+subset: unit_slim
+synonym: "min" EXACT []
+is_a: UO:0000003
+created_by: george gkoutos
+
+[Term]
+id: UO:0000045
+name: base unit
+namespace: unit.ontology
+def: "A unit which is one of a particular measure to which all measures of that type can be related." [NIST:NIST]
+subset: unit_group_slim
+is_a: UO:0000000
+created_by: george gkoutos
+
+[Term]
+id: UO:0000047
+name: area unit
+namespace: unit.ontology
+def: "A unit which is a standard measure of the amount of a 2-dimensional flat surface." [UOC:GVG]
+subset: unit_group_slim
+is_a: UO:0000000
+relationship: is_unit_of PATO:0001709
+created_by: george gkoutos
+
+[Term]
+id: UO:0000052
+name: mass density unit
+namespace: unit.ontology
+def: "A density unit which is a standard measure of the mass of a substance in a given volume." [UOC:GVG]
+subset: unit_group_slim
+synonym: "mass per unit volume" EXACT []
+is_a: UO:0000182
+relationship: is_unit_of PATO:0001353
+created_by: george gkoutos
+
+[Term]
+id: UO:0000095
+name: volume unit
+namespace: unit.ontology
+def: "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST]
+subset: unit_group_slim
+is_a: UO:0000000
+relationship: is_unit_of PATO:0001710
+created_by: george gkoutos
+
+[Term]
+id: UO:0000098
+name: milliliter
+namespace: unit.ontology
+def: "A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter." [NIST:NIST]
+subset: unit_slim
+synonym: "millilitre" EXACT []
+synonym: "ml" EXACT []
+is_a: UO:0000095
+created_by: george gkoutos
+
+[Term]
+id: UO:0000105
+name: frequency unit
+namespace: unit.ontology
+def: "A unit which is a standard measure of the number of repetitive actions in a particular time." [NIST:NIST]
+subset: unit_group_slim
+is_a: UO:0000000
+relationship: is_unit_of PATO:0000044
+created_by: george gkoutos
+
+[Term]
+id: UO:0000106
+name: hertz
+namespace: unit.ontology
+def: "A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second." [NIST:NIST]
+subset: unit_slim
+synonym: "Hz" EXACT []
+synonym: "s^1" EXACT []
+is_a: UO:0000105
+created_by: george gkoutos
+
+[Term]
+id: UO:0000109
+name: pressure unit
+namespace: unit.ontology
+def: "A unit which is a standard measure of the force applied to a given area." [NIST:NIST]
+subset: unit_group_slim
+is_a: UO:0000000
+relationship: is_unit_of PATO:0001025
+created_by: george gkoutos
+
+[Term]
+id: UO:0000110
+name: pascal
+namespace: unit.ontology
+def: "A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2]." [NIST:NIST]
+subset: unit_slim
+synonym: "Pa" EXACT []
+is_a: UO:0000109
+created_by: george gkoutos
+
+[Term]
+id: UO:0000111
+name: energy unit
+namespace: unit.ontology
+def: "A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc)." [NIST:NIST]
+subset: unit_group_slim
+is_a: UO:0000000
+relationship: is_unit_of PATO:0001021
+relationship: is_unit_of PATO:0001026
+created_by: george gkoutos
+
+[Term]
+id: UO:0000112
+name: joule
+namespace: unit.ontology
+def: "An energy unit which is equal to the energy required when a force of 1 newton moves an object 1 meter in the direction of the force." [NIST:NIST]
+subset: unit_slim
+synonym: "J" EXACT []
+is_a: UO:0000111
+created_by: george gkoutos
+
+[Term]
+id: UO:0000121
+name: angle unit
+namespace: unit.ontology
+def: "A unit which is a standard measure of the figure or space formed by the junction of two lines or planes." [Wikipedia:Wikipedia]
+subset: unit_group_slim
+is_a: UO:0000000
+relationship: is_unit_of PATO:0000133
+created_by: george gkoutos
+
+[Term]
+id: UO:0000122
+name: plane angle unit
+namespace: unit.ontology
+def: "A unit which is a standard measure of the angle formed by two straight lines in the same plane." [Wikipedia:Wikipedia]
+subset: unit_group_slim
+is_a: UO:0000121
+created_by: george gkoutos
+
+[Term]
+id: UO:0000150
+name: nanosecond
+namespace: unit.ontology
+def: "A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s." [NIST:NIST]
+subset: unit_slim
+synonym: "ns" EXACT []
+is_a: UO:0000003
+created_by: george gkoutos
+
+[Term]
+id: UO:0000166
+name: parts per notation unit
+namespace: unit.ontology
+def: "A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance." [Wikipedia:Wikipedia]
+subset: unit_group_slim
+is_a: UO:0000186
+created_by: george gkoutos
+
+[Term]
+id: UO:0000169
+name: parts per million
+namespace: unit.ontology
+def: "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]." [UOC:GVG]
+subset: unit_slim
+synonym: "10^[-6]" EXACT []
+synonym: "ppm" EXACT []
+is_a: UO:0000166
+created_by: george gkoutos
+
+[Term]
+id: UO:0000175
+name: gram per liter
+namespace: unit.ontology
+def: "A mass unit density which is equal to mass of an object in grams divided by the volume in liters." [UOC:GVG]
+subset: unit_slim
+synonym: "g/L" EXACT []
+synonym: "gram per litre" EXACT []
+is_a: UO:0000052
+created_by: george gkoutos
+
+[Term]
+id: UO:0000182
+name: density unit
+namespace: unit.ontology
+def: "A unit which is a standard measure of the influence exerted by some mass." [Wikipedia:Wikipedia]
+subset: unit_group_slim
+is_a: UO:0000000
+relationship: is_unit_of PATO:0001019
+created_by: george gkoutos
+
+[Term]
+id: UO:0000185
+name: degree
+namespace: unit.ontology
+def: "A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad." [Wikipedia:Wikipedia]
+subset: unit_slim
+is_a: UO:0000122
+created_by: george gkoutos
+
+[Term]
+id: UO:0000186
+name: dimensionless unit
+namespace: unit.ontology
+def: "A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia]
+subset: unit_group_slim
+is_a: UO:0000000
+created_by: george gkoutos
+
+[Term]
+id: UO:0000187
+name: percent
+namespace: unit.ontology
+def: "A dimensionless ratio unit which denotes numbers as fractions of 100." [Wikipedia:Wikipedia]
+subset: unit_group_slim
+synonym: "%" EXACT []
+is_a: UO:0000190
+created_by: george gkoutos
+
+[Term]
+id: UO:0000189
+name: count unit
+namespace: unit.ontology
+def: "A dimensionless unit which denotes a simple count of things." [MGED:MGED]
+subset: unit_group_slim
+synonym: "count" EXACT []
+is_a: UO:0000186
+created_by: george gkoutos
+
+[Term]
+id: UO:0000190
+name: ratio
+namespace: unit.ontology
+def: "A dimensionless unit which denotes an amount or magnitude of one quantity relative to another." [Wikipedia:Wikipedia]
+subset: unit_group_slim
+is_a: UO:0000186
+created_by: george gkoutos
+
+[Term]
+id: UO:0000191
+name: fraction
+namespace: unit.ontology
+def: "A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator)." [Wikipedia:Wikipedia]
+subset: unit_group_slim
+is_a: UO:0000190
+created_by: george gkoutos
+
+[Term]
+id: UO:0000217
+name: electric potential difference unit
+namespace: unit.ontology
+def: "A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field." [Wikipedia:Wikipedia]
+subset: unit_group_slim
+is_a: UO:0000000
+relationship: is_unit_of PATO:0001464
+created_by: george gkoutos
+
+[Term]
+id: UO:0000218
+name: volt
+namespace: unit.ontology
+def: "An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy." [Wikipedia:Wikipedia]
+subset: unit_slim
+synonym: "V" EXACT []
+is_a: UO:0000217
+created_by: george gkoutos
+
+[Term]
+id: UO:0000221
+name: dalton
+namespace: unit.ontology
+def: "An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state." [Wikipedia:Wikipedia]
+subset: unit_slim
+synonym: "amu" EXACT []
+synonym: "Da" EXACT []
+synonym: "u" EXACT []
+synonym: "unified atomic mass unit" EXACT []
+is_a: UO:0000002
+created_by: george gkoutos
+
+[Term]
+id: UO:0000222
+name: kilodalton
+namespace: unit.ontology
+def: "A mass unit which is equal to one thousand daltons." [Wikipedia:Wikipedia]
+subset: unit_slim
+synonym: "kDa" EXACT []
+is_a: UO:0000002
+created_by: george gkoutos
+
+[Term]
+id: UO:0000227
+name: magnetic flux density unit
+namespace: unit.ontology
+def: "A unit which is a standard measure of the strength of a magnetic field." [allnet:allnet]
+subset: unit_group_slim
+synonym: "B" EXACT []
+is_a: UO:0000000
+created_by: george gkoutos
+
+[Term]
+id: UO:0000228
+name: tesla
+namespace: unit.ontology
+def: "A magnetic flux density unit which is equal to one weber per square meter." [WordNet:WordNet]
+subset: unit_slim
+synonym: "T" EXACT []
+synonym: "Wb/m2" EXACT []
+is_a: UO:0000227
+created_by: george gkoutos
+
+[Term]
+id: UO:0000266
+name: electronvolt
+namespace: unit.ontology
+def: "A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J." [Wikipedia:Wikipedia]
+subset: unit_slim
+synonym: "electron volt" EXACT []
+synonym: "eV" EXACT []
+is_a: UO:0000111
+created_by: george gkoutos
+
+[Term]
+id: UO:0000267
+name: electric field strength unit
+namespace: unit.ontology
+def: "The electric field strength is a unit which is a measure of the potential difference between two points some distance apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field]
+subset: unit_group_slim
+synonym: "E-field strength " EXACT []
+is_a: UO:0000000
+created_by: george gkoutos
+creation_date: 2009-03-03T12:23:16Z
+
+[Term]
+id: UO:0000268
+name: volt per meter
+namespace: unit.ontology
+def: "The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field]
+subset: unit_slim
+synonym: "V/m" EXACT []
+synonym: "volt per metre" EXACT []
+is_a: UO:0000267
+created_by: george gkoutos
+creation_date: 2009-03-03T12:28:17Z
+
+[Term]
+id: UO:0000269
+name: absorbance unit
+namespace: unit.ontology
+def: "A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light." [Wikipedia:http\://en.wikipedia.org/wiki/Absorbance]
+subset: unit_slim
+synonym: "AU" EXACT []
+is_a: UO:0000186
+created_by: george gkoutos
+creation_date: 2009-07-14T12:33:48Z
+
+[Term]
+id: UO:0000270
+name: volumetric flow rate unit
+namespace: unit.ontology
+def: "A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time ." [Wikipedia:Wikipedia]
+subset: unit_group_slim
+is_a: UO:0000000
+created_by: george gkoutos
+
+[Term]
+id: UO:0000271
+name: microliters per minute
+namespace: unit.ontology
+def: "A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute." [UOC:GVG]
+subset: unit_slim
+synonym: "microlitres per minute" EXACT []
+synonym: "uL/min" EXACT []
+is_a: UO:0000270
+relationship: is_unit_of PATO:0001574
+created_by: george gkoutos
+
+[Term]
+id: UO:0000324
+name: square angstrom
+namespace: unit.ontology
+def: "An area unit which is equal to an area enclosed by a square with sides each 1 angstrom long." [UOC:GVG]
+synonym: "A^[2]" RELATED []
+is_a: UO:0000047
+created_by: gkoutos
+creation_date: 2013-06-27T05:06:40Z
+
diff --git a/share/OpenMS/CV/qc-cv.obo b/share/OpenMS/CV/qc-cv.obo
index 0e3374afa92..5675698c2d5 100755
--- a/share/OpenMS/CV/qc-cv.obo
+++ b/share/OpenMS/CV/qc-cv.obo
@@ -13,7 +13,7 @@ remark: creator: Mathias Walzer ebi.ac.uk>
remark: namespace: MS
remark: namespace: QC
import: http://ontologies.berkeleybop.org/uo.obo
-import: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
+import: http://purl.obolibrary.org/obo/ms/psi-ms.obo
import: https://raw.githubusercontent.com/obi-ontology/obi/master/obi.owl
import: https://raw.githubusercontent.com/ISA-tools/stato/dev/releases/1.4/stato.obo
ontology: qc
diff --git a/share/OpenMS/examples/FRACTIONS/BSA1_F1_ION.mzML b/share/OpenMS/examples/FRACTIONS/BSA1_F1_ION.mzML
index 8a69b8fc497..5bdadfdfe2f 100644
--- a/share/OpenMS/examples/FRACTIONS/BSA1_F1_ION.mzML
+++ b/share/OpenMS/examples/FRACTIONS/BSA1_F1_ION.mzML
@@ -2,7 +2,7 @@
-
+
diff --git a/src/openms/include/OpenMS/FORMAT/HANDLERS/MzIdentMLDOMHandler.h b/src/openms/include/OpenMS/FORMAT/HANDLERS/MzIdentMLDOMHandler.h
index 214f60d01fc..bf8528d9b2f 100644
--- a/src/openms/include/OpenMS/FORMAT/HANDLERS/MzIdentMLDOMHandler.h
+++ b/src/openms/include/OpenMS/FORMAT/HANDLERS/MzIdentMLDOMHandler.h
@@ -252,9 +252,9 @@ namespace OpenMS
std::list > hit_pev_; ///< writing help only
bool xl_ms_search_; ///< is true when reading a file containing Cross-Linking MS search results
- std::map xl_id_donor_map_; ///< mapping Peptide id -> cross-link donor value
- //std::map xl_id_acceptor_map_; ///< mapping Peptide id -> cross-link acceptor value
- std::map xl_id_acceptor_map_; ///< mapping peptide id of acceptor peptide -> cross-link acceptor value
+ std::map xl_id_donor_map_; ///< mapping Peptide id -> crosslink donor value
+ //std::map xl_id_acceptor_map_; ///< mapping Peptide id -> crosslink acceptor value
+ std::map xl_id_acceptor_map_; ///< mapping peptide id of acceptor peptide -> crosslink acceptor value
std::map xl_donor_pos_map_; ///< mapping donor value -> cross-link modification location
std::map xl_acceptor_pos_map_; ///< mapping acceptor value -> cross-link modification location
std::map xl_mass_map_; ///< mapping Peptide id -> cross-link mass
diff --git a/src/openms/source/FORMAT/ControlledVocabulary.cpp b/src/openms/source/FORMAT/ControlledVocabulary.cpp
index 9c3f203d6b3..6b48aac62ae 100644
--- a/src/openms/source/FORMAT/ControlledVocabulary.cpp
+++ b/src/openms/source/FORMAT/ControlledVocabulary.cpp
@@ -183,8 +183,22 @@ namespace OpenMS
}
if (line_wo_spaces.hasPrefix("remark:URL:"))
{
- // https://
- url_ = line.substr(line.find_first_of('/') - 7).trim();
+ // Find the position of "http://" or "https://"
+ size_t httpPos = line.find("http://");
+ size_t httpsPos = line.find("https://");
+
+ // Determine the starting position of the URL
+ if (httpPos != std::string::npos)
+ {
+ url_ = line.substr(httpPos).trim();
+ } else if (httpsPos != std::string::npos)
+ {
+ url_ = line.substr(httpsPos).trim();
+ } else
+ {
+ // No URL found
+ std::cerr << "No URL found in the line." << std::endl;
+ }
}
//********************************************************************************
@@ -316,7 +330,9 @@ namespace OpenMS
{
term.obsolete = true;
}
- else if (line_wo_spaces.hasPrefix("xref:value-type") || line_wo_spaces.hasPrefix("xref_analog:value-type"))
+ else if (line_wo_spaces.hasPrefix("xref:value-type")
+ || line_wo_spaces.hasPrefix("xref_analog:value-type")
+ )
{
line_wo_spaces.remove('\\');
if (line_wo_spaces.hasSubstring("value-type:xsd:string"))
@@ -373,6 +389,73 @@ namespace OpenMS
}
cerr << "ControlledVocabulary: OBOFile: unknown xsd type: " << line_wo_spaces << ", ignoring" << "\n";
}
+ else if (line_wo_spaces.hasPrefix("relationship:has_value_type")) // since newer obo type in relationship instead of xref
+ {
+ if (line_wo_spaces.hasSubstring("xsd:string"))
+ {
+ term.xref_type = CVTerm::XSD_STRING;
+ continue;
+ }
+ if (line_wo_spaces.hasSubstring("xsd:integer")
+ || line_wo_spaces.hasSubstring("xsd:int"))
+ {
+ term.xref_type = CVTerm::XSD_INTEGER;
+ continue;
+ }
+ if (line_wo_spaces.hasSubstring("xsd:decimal") ||
+ line_wo_spaces.hasSubstring("xsd:float") ||
+ line_wo_spaces.hasSubstring("xsd:double"))
+ {
+ term.xref_type = CVTerm::XSD_DECIMAL;
+ continue;
+ }
+ if (line_wo_spaces.hasSubstring("xsd:negativeInteger"))
+ {
+ term.xref_type = CVTerm::XSD_NEGATIVE_INTEGER;
+ continue;
+ }
+ if (line_wo_spaces.hasSubstring("xsd:positiveInteger"))
+ {
+ term.xref_type = CVTerm::XSD_POSITIVE_INTEGER;
+ continue;
+ }
+ if (line_wo_spaces.hasSubstring("xsd:nonNegativeInteger"))
+ {
+ term.xref_type = CVTerm::XSD_NON_NEGATIVE_INTEGER;
+ continue;
+ }
+ if (line_wo_spaces.hasSubstring("xsd:nonPositiveInteger"))
+ {
+ term.xref_type = CVTerm::XSD_NON_POSITIVE_INTEGER;
+ continue;
+ }
+ if (line_wo_spaces.hasSubstring("xsd:boolean")
+ || line_wo_spaces.hasSubstring("xsd:bool"))
+ {
+ term.xref_type = CVTerm::XSD_BOOLEAN;
+ continue;
+ }
+ if (line_wo_spaces.hasSubstring("xsd:date"))
+ {
+ term.xref_type = CVTerm::XSD_DATE;
+ continue;
+ }
+ if (line_wo_spaces.hasSubstring("xsd:anyURI"))
+ {
+ term.xref_type = CVTerm::XSD_ANYURI;
+ continue;
+ }
+ if (
+ line_wo_spaces.hasSubstring("MS:1002711") ||
+ line_wo_spaces.hasSubstring("MS:1002712") ||
+ line_wo_spaces.hasSubstring("MS:1002713")
+ )
+ {
+ term.xref_type = CVTerm::XSD_STRING; // store list as string
+ continue;
+ }
+ cerr << "ControlledVocabulary: OBOFile: unknown xsd type: " << line_wo_spaces << ", ignoring" << "\n";
+ }
else if (line_wo_spaces.hasPrefix("xref:binary-data-type") || line_wo_spaces.hasPrefix("xref_analog:binary-data-type"))
{
line_wo_spaces.remove('\\');
diff --git a/src/openms/source/FORMAT/HANDLERS/MzIdentMLDOMHandler.cpp b/src/openms/source/FORMAT/HANDLERS/MzIdentMLDOMHandler.cpp
index 93bb6239164..2e6325a72cb 100644
--- a/src/openms/source/FORMAT/HANDLERS/MzIdentMLDOMHandler.cpp
+++ b/src/openms/source/FORMAT/HANDLERS/MzIdentMLDOMHandler.cpp
@@ -196,7 +196,7 @@ namespace OpenMS::Internal
while (child && !xl_ms_search_)
{
String accession = StringManager::convert(child->getAttribute(CONST_XMLCH("accession")));
- if (accession == "MS:1002494") // accession for "cross-linking search"
+ if (accession == "MS:1002494") // accession for "crosslinking search"
{
xl_ms_search_ = true;
}
@@ -2343,7 +2343,7 @@ namespace OpenMS::Internal
while (cvp)
{
- if (XMLString::equals(cvp->getAttribute(CONST_XMLCH("accession")), CONST_XMLCH("MS:1002509"))) // cross-link donor
+ if (XMLString::equals(cvp->getAttribute(CONST_XMLCH("accession")), CONST_XMLCH("MS:1002509"))) // crosslink donor
{
String donor_val = StringManager::convert(cvp->getAttribute(CONST_XMLCH("value")));
xl_id_donor_map_.insert(make_pair(pep_id, donor_val));
@@ -2357,7 +2357,7 @@ namespace OpenMS::Internal
xl_mod_map_.insert(make_pair(pep_id, xl_mod_name));
donor_acceptor_found = true;
}
- else if (XMLString::equals(cvp->getAttribute(CONST_XMLCH("accession")), CONST_XMLCH("MS:1002510"))) // cross-link acceptor
+ else if (XMLString::equals(cvp->getAttribute(CONST_XMLCH("accession")), CONST_XMLCH("MS:1002510"))) // crosslink acceptor
{
String acceptor_val = StringManager::convert(cvp->getAttribute(CONST_XMLCH("value")));
xl_id_acceptor_map_.insert(make_pair(pep_id, acceptor_val));
diff --git a/src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp b/src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp
index 915fe9f8bbc..e9d7539e2f0 100644
--- a/src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp
+++ b/src/openms/source/FORMAT/HANDLERS/MzIdentMLHandler.cpp
@@ -628,7 +628,7 @@ namespace OpenMS::Internal
sip += "\t\t\n";
if (is_ppxl)
{
- sip += "\n\t\t\t" + cv_.getTermByName("cross-linking search").toXMLString(cv_ns) + "\n";
+ sip += "\n\t\t\t" + cv_.getTermByName("crosslinking search").toXMLString(cv_ns) + "\n";
}
//remove MS:1001029 written if present in as of SearchDatabase_may rule
ProteinIdentification::SearchParameters search_params = it->getSearchParameters();
@@ -971,7 +971,7 @@ namespace OpenMS::Internal
//--------------------------------------------------------------------------------------------
os << "\n"
<< "\t\n "
<< "\t\n"
<< "\tprot_ids_->push_back(prot_id);
// Fetch the enzymes database
diff --git a/src/openms/source/FORMAT/MzQCFile.cpp b/src/openms/source/FORMAT/MzQCFile.cpp
index 27cfea8f1e6..1bd152e6b9f 100644
--- a/src/openms/source/FORMAT/MzQCFile.cpp
+++ b/src/openms/source/FORMAT/MzQCFile.cpp
@@ -268,8 +268,8 @@ namespace OpenMS
},
{
{"name", "Proteomics Standards Initiative Mass Spectrometry Ontology"},
- {"uri", "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"},
- {"version", "4.1.56"}
+ {"uri", "http://purl.obolibrary.org/obo/ms/psi-ms.obo"},
+ {"version", "4.1.155"}
}
};
os << out.dump(2);
diff --git a/src/pyOpenMS/pxds/OpenSwathOSWWriter.pxd b/src/pyOpenMS/pxds/OpenSwathOSWWriter.pxd
index fa871eced01..a6a38c4cdab 100644
--- a/src/pyOpenMS/pxds/OpenSwathOSWWriter.pxd
+++ b/src/pyOpenMS/pxds/OpenSwathOSWWriter.pxd
@@ -7,7 +7,7 @@ cdef extern from "" namespace "O
cdef cppclass OpenSwathOSWWriter "OpenMS::OpenSwathOSWWriter":
- OpenSwathOSWWriter(String output_filename, UInt64 run_id, String input_filename, bool ms1_scores, bool sonar, bool uis_scores) except + nogil
+ OpenSwathOSWWriter(String output_filename, UInt64 run_id, String input_filename, bool uis_scores) except + nogil
OpenSwathOSWWriter(OpenSwathOSWWriter &) except + nogil # compiler
bool isActive() except + nogil
diff --git a/src/pyOpenMS/pyopenms-docs b/src/pyOpenMS/pyopenms-docs
index df06fc86eba..9875a9ef8d2 160000
--- a/src/pyOpenMS/pyopenms-docs
+++ b/src/pyOpenMS/pyopenms-docs
@@ -1 +1 @@
-Subproject commit df06fc86eba99a5e8913de69e2500595fc71ee73
+Subproject commit 9875a9ef8d2fab46773f2d7f7a52cc150e6ba2b0
diff --git a/src/pyOpenMS/pyopenms/_dataframes.py b/src/pyOpenMS/pyopenms/_dataframes.py
index 7f3801dbe0d..33a5b17ff81 100644
--- a/src/pyOpenMS/pyopenms/_dataframes.py
+++ b/src/pyOpenMS/pyopenms/_dataframes.py
@@ -664,24 +664,12 @@ class _MSSpectrumDF(_MSSpectrum):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
- def get_df(self, export_ion_mobility: bool = True, export_meta_values: bool = True, export_peptide_identifications: bool = True) -> _pd.DataFrame:
+ def get_df(self, export_meta_values: bool = True) -> _pd.DataFrame:
"""
Returns a DataFrame representation of the MSSpectrum.
- mz: The mass-to-charge ratio (m/z) values of the peaks in the mass spectrum.
- intensity: The intensity (abundance) of the peaks in the mass spectrum.
- ion_mobility: The ion mobility values.
- ion_mobility_unit: The ion mobility unit.
- ms_level: The MS level of the mass spectrum (1 for MS1, 2 for MS2, etc.).
- precursor_mz: The mass-to-charge of the precursor ion.
- precursor_charge: The charge of the precursor ion.
- native_id: The native identifier of the spectrum.
- spectrum: The spectrum of annotated peptide identification hit.
-
Args:
- export_ion_mobility (bool): Whether to export ion mobility data.
export_meta_values (bool): Whether to export meta values.
- export_peptide_identifications (bool): Whether to export peptide identifications.
Returns:
pd.DataFrame: DataFrame representation of the MSSpectrum.
@@ -691,10 +679,10 @@ def get_df(self, export_ion_mobility: bool = True, export_meta_values: bool = Tr
df = _pd.DataFrame({'mz': mzs, 'intensity': intensities})
cnt = df.shape[0]
-
- if export_ion_mobility:
- df['ion_mobility'] = _np.array([i for i in self.getFloatDataArrays()[0]]) if self.containsIMData() else _np.nan
- df['ion_mobility_unit'] = _np.full(cnt, self.getDriftTimeUnitAsString(), dtype=_np.dtype('U20'))
+
+ # ion mobility
+ df['ion_mobility'] = _np.array([i for i in self.getFloatDataArrays()[0]]) if self.containsIMData() else _np.nan
+ df['ion_mobility_unit'] = _np.full(cnt, self.getDriftTimeUnitAsString(), dtype=_np.dtype(f'U{len(self.getDriftTimeUnitAsString())}'))
df['ms_level'] = _np.full(cnt, self.getMSLevel(), dtype=_np.dtype('uint16'))
@@ -704,14 +692,24 @@ def get_df(self, export_ion_mobility: bool = True, export_meta_values: bool = Tr
df['native_id'] = _np.full(cnt, self.getNativeID(), dtype=_np.dtype('U100'))
- if export_peptide_identifications:
- peps = self.getPeptideIdentifications()
- seq = ''
- if peps:
- hits = peps[0].getHits()
- if hits:
- seq = hits[0].getSequence().toString()
- df['sequence'] = _np.full(cnt, seq, dtype=_np.dtype(f'U{len(seq)}'))
+ # peptide sequence
+ peps = self.getPeptideIdentifications() # type: list[PeptideIdentification]
+ seq = ''
+ if peps:
+ hits = peps[0].getHits()
+ if hits:
+ seq = hits[0].getSequence().toString()
+ df['sequence'] = _np.full(cnt, seq, dtype=_np.dtype(f'U{len(seq)}'))
+
+ # ion annotations in string data array with names IonName or IonNames
+ ion_annotations = _np.full(cnt, '', dtype=_np.dtype('U1'))
+ for sda in self.getStringDataArrays():
+ if sda.getName() == 'IonNames':
+ decoded = [ion.decode() for ion in sda]
+ if len(decoded) == df.shape[0]:
+ ion_annotations = _np.array(decoded, dtype=_np.dtype(f'U{len(max(decoded))}'))
+ break
+ df['ion_annotation'] = ion_annotations
if export_meta_values:
df = _add_meta_values(df, self)
diff --git a/src/pyOpenMS/setup.py b/src/pyOpenMS/setup.py
index 786c72dbf65..191f9efeef6 100644
--- a/src/pyOpenMS/setup.py
+++ b/src/pyOpenMS/setup.py
@@ -254,7 +254,7 @@
'pyopenms': ['py.typed', '*.pyi']
},
install_requires=[
- 'numpy',
+ 'numpy<=1.26.4',
'pandas',
'matplotlib>=3.5'
],
diff --git a/src/pyOpenMS/tests/unittests/test000.py b/src/pyOpenMS/tests/unittests/test000.py
index b44625d87f9..fc82d0bed57 100644
--- a/src/pyOpenMS/tests/unittests/test000.py
+++ b/src/pyOpenMS/tests/unittests/test000.py
@@ -2859,6 +2859,7 @@ def testMSSpectrum():
assert ii[0] == 200.0
assert ii[1] == 400.0
+ spec.setMSLevel(2)
spec.setNativeID('scan=1')
prec = pyopenms.Precursor()
prec.setMZ(100.0)
@@ -2877,15 +2878,23 @@ def testMSSpectrum():
spec.setFloatDataArrays( f_da )
spec.setDriftTimeUnit( pyopenms.DriftTimeUnit.MILLISECOND )
+ s_da = pyopenms.StringDataArray()
+ for s in ['b3+', 'y4+']:
+ s_da.push_back(s)
+ s_da.setName("IonNames")
+ spec.setStringDataArrays([s_da])
+
df = spec.get_df()
- assert df.shape == (2, 10)
+ assert df.shape == (2, 11)
assert df.loc[0, 'mz'] == 1000.0
assert df.loc[0, 'intensity'] == 200.0
assert df.loc[0, 'ion_mobility'] == 5.0
assert df.loc[0, 'ion_mobility_unit'] == 'ms'
+ assert df.loc[0, 'ms_level'] == 2
assert df.loc[0, 'precursor_mz'] == 100.0
assert df.loc[0, 'precursor_charge'] == 1
assert df.loc[0, 'native_id'] == 'scan=1'
+ assert df.loc[0, 'ion_annotation'] == 'b3+'
assert df.loc[0, 'sequence'] == 'A'
assert df.loc[0, 'total ion current'] == 600
diff --git a/src/tests/class_tests/openms/data/AccurateMassSearchEngine_output1_mztabm_featureXML.mzTab b/src/tests/class_tests/openms/data/AccurateMassSearchEngine_output1_mztabm_featureXML.mzTab
index 09527a89409..8c45275c645 100644
--- a/src/tests/class_tests/openms/data/AccurateMassSearchEngine_output1_mztabm_featureXML.mzTab
+++ b/src/tests/class_tests/openms/data/AccurateMassSearchEngine_output1_mztabm_featureXML.mzTab
@@ -11,8 +11,8 @@ MTD study_variable[1]-assay_refs assay[1]
MTD study_variable[1]-description study_variable_NotARealFileJustATest
MTD cv[1]-label PSI-MS
MTD cv[1]-full_name MS
-MTD cv[1]-version 4.1.56
-MTD cv[1]-uri https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
+MTD cv[1]-version 4.1.155
+MTD cv[1]-uri http://purl.obolibrary.org/obo/ms/psi-ms.obo
MTD database[1] [, , HMDB, ]
MTD database[1]-prefix HMDB
MTD database[1]-version 3.5
diff --git a/src/tests/class_tests/openms/data/AccurateMassSearchEngine_output2_mztabm_featureXML.mzTab b/src/tests/class_tests/openms/data/AccurateMassSearchEngine_output2_mztabm_featureXML.mzTab
index e8b7cac968a..f66bb0d6951 100644
--- a/src/tests/class_tests/openms/data/AccurateMassSearchEngine_output2_mztabm_featureXML.mzTab
+++ b/src/tests/class_tests/openms/data/AccurateMassSearchEngine_output2_mztabm_featureXML.mzTab
@@ -11,8 +11,8 @@ MTD study_variable[1]-assay_refs assay[1]
MTD study_variable[1]-description study_variable_NotARealFileJustATest
MTD cv[1]-label PSI-MS
MTD cv[1]-full_name MS
-MTD cv[1]-version 4.1.56
-MTD cv[1]-uri https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
+MTD cv[1]-version 4.1.155
+MTD cv[1]-uri http://purl.obolibrary.org/obo/ms/psi-ms.obo
MTD database[1] [, , HMDB, ]
MTD database[1]-prefix HMDB
MTD database[1]-version 3.5
diff --git a/src/tests/class_tests/openms/data/IM_FAIMS_test.mzML b/src/tests/class_tests/openms/data/IM_FAIMS_test.mzML
index 6c133477511..8af966a4527 100755
--- a/src/tests/class_tests/openms/data/IM_FAIMS_test.mzML
+++ b/src/tests/class_tests/openms/data/IM_FAIMS_test.mzML
@@ -2,7 +2,7 @@
-
+
diff --git a/src/tests/class_tests/openms/data/MzIdentML_XLMS_labelled.mzid b/src/tests/class_tests/openms/data/MzIdentML_XLMS_labelled.mzid
index 5fd11244bb8..302994f7abb 100644
--- a/src/tests/class_tests/openms/data/MzIdentML_XLMS_labelled.mzid
+++ b/src/tests/class_tests/openms/data/MzIdentML_XLMS_labelled.mzid
@@ -6,7 +6,7 @@
id="OpenMS_11422463686885200558"
creationDate="2019-07-26T13:21:11">
-
+
@@ -37,14 +37,14 @@
FIVKASSGPR
-
+
FIVKASSGPR
-
+
@@ -63,90 +63,90 @@
FIVKASSGPR
-
+
SAVIKTSTR
-
+
FIVKASSGPR
-
+
FIVKASSGPR
-
+
SAVIKTSTR
-
+
FIVKASSGPR
-
+
FIVKASSGPR
-
+
SAVIKTSTR
-
+
FIVKASSGPR
-
+
SAVIKTSTR
-
+
SAVIKTSTR
-
+
SAVIKTSTR
-
+
SAVIKTSTR
-
+
SAVIKTSTR
-
+
@@ -181,7 +181,7 @@
-
+
@@ -293,7 +293,7 @@
-
+
@@ -376,7 +376,7 @@
-
+
@@ -468,7 +468,7 @@
-
+
@@ -558,7 +558,7 @@
-
+
@@ -611,7 +611,7 @@
-
+
@@ -664,7 +664,7 @@
-
+
@@ -756,7 +756,7 @@
-
+
@@ -846,7 +846,7 @@
-
+
@@ -899,7 +899,7 @@
-
+
@@ -952,7 +952,7 @@
-
+
@@ -1037,7 +1037,7 @@
-
+
@@ -1120,7 +1120,7 @@
-
+
@@ -1173,7 +1173,7 @@
-
+
@@ -1226,7 +1226,7 @@
-
+
@@ -1311,7 +1311,7 @@
-
+
@@ -1394,7 +1394,7 @@
-
+
@@ -1447,7 +1447,7 @@
-
+
@@ -1500,7 +1500,7 @@
-
+
@@ -1585,7 +1585,7 @@
-
+
@@ -1668,7 +1668,7 @@
-
+
@@ -1767,7 +1767,7 @@
-
+
@@ -1864,7 +1864,7 @@
-
+
@@ -1917,7 +1917,7 @@
-
+
@@ -1970,7 +1970,7 @@
-
+
@@ -2062,7 +2062,7 @@
-
+
@@ -2152,7 +2152,7 @@
-
+
@@ -2205,7 +2205,7 @@
-
+
@@ -2258,7 +2258,7 @@
-
+
@@ -2343,7 +2343,7 @@
-
+
@@ -2426,7 +2426,7 @@
-
+
@@ -2479,7 +2479,7 @@
-
+
@@ -2532,7 +2532,7 @@
-
+
@@ -2617,7 +2617,7 @@
-
+
@@ -2700,7 +2700,7 @@
-
+
@@ -2753,7 +2753,7 @@
-
+
@@ -2806,7 +2806,7 @@
-
+
diff --git a/src/tests/class_tests/openms/data/MzIdentML_XLMS_unlabelled.mzid b/src/tests/class_tests/openms/data/MzIdentML_XLMS_unlabelled.mzid
index d4263b55dcb..2d86703a480 100644
--- a/src/tests/class_tests/openms/data/MzIdentML_XLMS_unlabelled.mzid
+++ b/src/tests/class_tests/openms/data/MzIdentML_XLMS_unlabelled.mzid
@@ -6,7 +6,7 @@
id="OpenMS_17716858074023296841"
creationDate="2019-07-26T14:30:07">
-
+
@@ -31,13 +31,13 @@
KNVPIEFPVIDR
-
+
LGCKALHVLFER
-
+
@@ -70,7 +70,7 @@
-
+
@@ -242,7 +242,7 @@
-
+
@@ -294,7 +294,7 @@
-
+
diff --git a/src/tests/class_tests/openms/data/MzTabMFile_output_1.mztab b/src/tests/class_tests/openms/data/MzTabMFile_output_1.mztab
index 9efbafec20b..ff812452e60 100644
--- a/src/tests/class_tests/openms/data/MzTabMFile_output_1.mztab
+++ b/src/tests/class_tests/openms/data/MzTabMFile_output_1.mztab
@@ -14,8 +14,8 @@ MTD study_variable[1]-assay_refs assay[1]
MTD study_variable[1]-description study_variable_2012_02_03_PStd_10_1-50
MTD cv[1]-label PSI-MS
MTD cv[1]-full_name MS
-MTD cv[1]-version 4.1.56
-MTD cv[1]-uri https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
+MTD cv[1]-version 4.1.155
+MTD cv[1]-uri http://purl.obolibrary.org/obo/ms/psi-ms.obo
MTD database[1] [, , HMDB, ]
MTD database[1]-prefix HMDB
MTD database[1]-version 3.5
diff --git a/src/tests/class_tests/openms/data/degenerate_cases/empty_spec.mzML b/src/tests/class_tests/openms/data/degenerate_cases/empty_spec.mzML
index 7171c477b84..27f75cbcda6 100644
--- a/src/tests/class_tests/openms/data/degenerate_cases/empty_spec.mzML
+++ b/src/tests/class_tests/openms/data/degenerate_cases/empty_spec.mzML
@@ -1,7 +1,7 @@
-
+
diff --git a/src/tests/class_tests/openms/source/MzIdentMLFile_test.cpp b/src/tests/class_tests/openms/source/MzIdentMLFile_test.cpp
index 400fd707670..76c49f5c197 100644
--- a/src/tests/class_tests/openms/source/MzIdentMLFile_test.cpp
+++ b/src/tests/class_tests/openms/source/MzIdentMLFile_test.cpp
@@ -416,7 +416,7 @@ matched_linear_beta,ppm_error_abs_sum_linear_alpha,ppm_error_abs_sum_linear_beta
ppm_error_abs_sum_xlinks_beta,ppm_error_abs_sum_linear,ppm_error_abs_sum_xlinks,ppm_error_abs_sum_alpha,ppm_error_abs_sum_beta,\
ppm_error_abs_sum,precursor_total_intensity,precursor_target_intensity,precursor_signal_proportion,precursor_target_peak_count,\
precursor_residual_peak_count")
- TEST_EQUAL(protein_ids[0].getMetaValue("SpectrumIdentificationProtocol"), "MS:1002494") // cross-linking search
+ TEST_EQUAL(protein_ids[0].getMetaValue("SpectrumIdentificationProtocol"), "MS:1002494") // crosslinking search
// PeptideIdentification (Indices may change, without making the reading/writing invalid, if e.g. more is added to the test file)
@@ -474,7 +474,7 @@ START_SECTION(([EXTRA] XLMS data unlabeled cross-linker))
TEST_EQUAL(protein_ids2[0].getSearchParameters().getMetaValue("cross_link:residue1"), "[K, N-term]")
TEST_EQUAL(protein_ids2[0].getSearchParameters().getMetaValue("cross_link:residue2"), "[K, N-term]")
TEST_EQUAL(String(protein_ids2[0].getSearchParameters().getMetaValue("cross_link:mass")).toDouble(), 138.0680796)
- TEST_EQUAL(protein_ids[0].getMetaValue("SpectrumIdentificationProtocol"), "MS:1002494") // cross-linking search
+ TEST_EQUAL(protein_ids[0].getMetaValue("SpectrumIdentificationProtocol"), "MS:1002494") // crosslinking search
// PeptideIdentification (Indices may change, without making the reading/writing invalid, if e.g. more is added to the test file)
TEST_EQUAL(peptide_ids2.size(), 3)
diff --git a/src/tests/class_tests/openms/source/MzTabM_test.cpp b/src/tests/class_tests/openms/source/MzTabM_test.cpp
index 65687ecc225..b63222fbaeb 100644
--- a/src/tests/class_tests/openms/source/MzTabM_test.cpp
+++ b/src/tests/class_tests/openms/source/MzTabM_test.cpp
@@ -237,7 +237,7 @@ START_SECTION(Fill data structure)
MzTabCVMetaData meta_cv;
meta_cv.label = MzTabString("MS");
meta_cv.full_name = MzTabString("PSI-MS controlled vocabulary");
- meta_cv.version = MzTabString("4.1.56");
+ meta_cv.version = MzTabString("4.1.155");
meta_cv.url = MzTabString("share/OpenMS/CV/psi-ms.obo");
mztabm_meta.cv[0] = meta_cv;
diff --git a/src/tests/topp/AccurateMassSearch_5_output.mzTab b/src/tests/topp/AccurateMassSearch_5_output.mzTab
index 10771ebd08e..cb8332b0e5c 100644
--- a/src/tests/topp/AccurateMassSearch_5_output.mzTab
+++ b/src/tests/topp/AccurateMassSearch_5_output.mzTab
@@ -14,7 +14,7 @@ MTD study_variable[1]-description study_variable_PestMix1_1ngSolventDDA20-50
MTD cv[1]-label PSI-MS
MTD cv[1]-full_name MS
MTD cv[1]-version 4.1.49
-MTD cv[1]-uri https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
+MTD cv[1]-uri http://purl.obolibrary.org/obo/ms/psi-ms.obo
MTD database[1] [, , CustomDB, ]
MTD database[1]-prefix CustomDB
MTD database[1]-version 0.0
diff --git a/src/tests/topp/AccurateMassSearch_6_output.mzTab b/src/tests/topp/AccurateMassSearch_6_output.mzTab
index 10771ebd08e..cb8332b0e5c 100644
--- a/src/tests/topp/AccurateMassSearch_6_output.mzTab
+++ b/src/tests/topp/AccurateMassSearch_6_output.mzTab
@@ -14,7 +14,7 @@ MTD study_variable[1]-description study_variable_PestMix1_1ngSolventDDA20-50
MTD cv[1]-label PSI-MS
MTD cv[1]-full_name MS
MTD cv[1]-version 4.1.49
-MTD cv[1]-uri https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
+MTD cv[1]-uri http://purl.obolibrary.org/obo/ms/psi-ms.obo
MTD database[1] [, , CustomDB, ]
MTD database[1]-prefix CustomDB
MTD database[1]-version 0.0
diff --git a/src/tests/topp/AssayGeneratorMetabo-in-SIRIUS-project/report.mztab b/src/tests/topp/AssayGeneratorMetabo-in-SIRIUS-project/report.mztab
index 1b0f8e25f62..380a542ca5a 100644
--- a/src/tests/topp/AssayGeneratorMetabo-in-SIRIUS-project/report.mztab
+++ b/src/tests/topp/AssayGeneratorMetabo-in-SIRIUS-project/report.mztab
@@ -5,7 +5,7 @@ MTD software[1] [, , SIRIUS, 4.13.1]
MTD ms_run[1]-location /home/axel/dev/OpenMS/src/tests/topp/SiriusExport_2_output.ms
MTD ms_run[1]-scan_polarity[1] [MS, MS:1000130, positive scan, ]
MTD cv[1]-label MS
-MTD cv[1]-uri URL:https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
+MTD cv[1]-uri http://purl.obolibrary.org/obo/ms/psi-ms.obo
MTD cv[1]-version 4.1.16
MTD cv[1]-full_name PSI-MS controlled vocabulary
MTD small_molecule-identification_reliability [MS, MS:1002955, hr-ms compound identification confidence level, ]
diff --git a/src/tests/topp/IDFileConverter_26_input.mzid b/src/tests/topp/IDFileConverter_26_input.mzid
index ad820209814..badb45e62e8 100644
--- a/src/tests/topp/IDFileConverter_26_input.mzid
+++ b/src/tests/topp/IDFileConverter_26_input.mzid
@@ -1,7 +1,7 @@
-
+
diff --git a/src/tests/topp/IDFileConverter_31_input.mzid b/src/tests/topp/IDFileConverter_31_input.mzid
index 135c0a4e56a..85fa3ca6452 100644
--- a/src/tests/topp/IDFileConverter_31_input.mzid
+++ b/src/tests/topp/IDFileConverter_31_input.mzid
@@ -6,7 +6,7 @@
id="OpenMS_11115414975438642789"
creationDate="2019-07-30T12:13:41">
-
+
diff --git a/src/tests/topp/IDFileConverter_9_output.mzid b/src/tests/topp/IDFileConverter_9_output.mzid
index 135c0a4e56a..85fa3ca6452 100644
--- a/src/tests/topp/IDFileConverter_9_output.mzid
+++ b/src/tests/topp/IDFileConverter_9_output.mzid
@@ -6,7 +6,7 @@
id="OpenMS_11115414975438642789"
creationDate="2019-07-30T12:13:41">
-
+
diff --git a/src/tests/topp/OpenPepXLLF_output.mzid b/src/tests/topp/OpenPepXLLF_output.mzid
index d85ed1c7fce..931ae2bdbf1 100644
--- a/src/tests/topp/OpenPepXLLF_output.mzid
+++ b/src/tests/topp/OpenPepXLLF_output.mzid
@@ -6,7 +6,7 @@
id="OpenMS_17447818880105247092"
creationDate="2023-03-22T15:52:24">
-
+
@@ -43,7 +43,7 @@
-
+
@@ -76,7 +76,7 @@
KNTEGTQKQK
-
+
@@ -110,7 +110,7 @@
-
+
@@ -621,7 +621,7 @@
-
+
@@ -673,7 +673,7 @@
-
+
diff --git a/src/tests/topp/OpenPepXL_output.mzid b/src/tests/topp/OpenPepXL_output.mzid
index 49fb24b6f0f..6a9ac540fce 100644
--- a/src/tests/topp/OpenPepXL_output.mzid
+++ b/src/tests/topp/OpenPepXL_output.mzid
@@ -6,7 +6,7 @@
id="OpenMS_5634796270667792442"
creationDate="2023-03-22T14:19:34">
-
+
@@ -43,20 +43,20 @@
FIVKASSGPR
-
+
KELLK
-
+
FIVKASSGPR
-
+
@@ -72,13 +72,13 @@
LEGTIDYQKL
-
+
SAVIKTSTR
-
+
@@ -88,25 +88,25 @@
-
+
KELLK
-
+
KELLK
-
+
SAVIKTSTR
-
+
@@ -116,7 +116,7 @@
-
+
@@ -126,13 +126,13 @@
-
+
SAVIKTSTR
-
+
@@ -142,14 +142,14 @@
-
+
FIVKASSGPR
-
+
@@ -159,7 +159,7 @@
-
+
@@ -169,7 +169,7 @@
-
+
@@ -200,19 +200,19 @@
FIVKASSGPR
-
+
SAVIKTSTR
-
+
KELLK
-
+
@@ -224,19 +224,19 @@
KELLK
-
+
LKPLIEK
-
+
SAVIKTSTR
-
+
@@ -246,13 +246,13 @@
-
+
KELLK
-
+
@@ -268,13 +268,13 @@
FIVKASSGPR
-
+
KELLK
-
+
@@ -287,7 +287,7 @@
FIVKASSGPR
-
+
@@ -297,45 +297,45 @@
-
+
FIVKASSGPR
-
+
SAVIKTSTR
-
+
SAVIKTSTR
-
+
FIVKASSGPR
-
+
SAVIKTSTR
-
+
KELLK
-
+
@@ -393,7 +393,7 @@
-
+
@@ -513,7 +513,7 @@
-
+
@@ -596,7 +596,7 @@
-
+
@@ -688,7 +688,7 @@
-
+
@@ -778,7 +778,7 @@
-
+
@@ -831,7 +831,7 @@
-
+
@@ -884,7 +884,7 @@
-
+
@@ -976,7 +976,7 @@
-
+
@@ -1066,7 +1066,7 @@
-
+
@@ -1119,7 +1119,7 @@
-
+
@@ -1172,7 +1172,7 @@
-
+
@@ -1269,7 +1269,7 @@
-
+
@@ -1366,7 +1366,7 @@
-
+
@@ -1419,7 +1419,7 @@
-
+
@@ -1472,7 +1472,7 @@
-
+
@@ -1569,7 +1569,7 @@
-
+
@@ -1666,7 +1666,7 @@
-
+
@@ -1719,7 +1719,7 @@
-
+
@@ -1772,7 +1772,7 @@
-
+
@@ -1855,7 +1855,7 @@
-
+
@@ -1938,7 +1938,7 @@
-
+
@@ -1991,7 +1991,7 @@
-
+
@@ -2044,7 +2044,7 @@
-
+
@@ -2129,7 +2129,7 @@
-
+
@@ -2212,7 +2212,7 @@
-
+
@@ -2265,7 +2265,7 @@
-
+
@@ -2318,7 +2318,7 @@
-
+
@@ -2387,7 +2387,7 @@
-
+
@@ -2456,7 +2456,7 @@
-
+
@@ -2509,7 +2509,7 @@
-
+
@@ -2562,7 +2562,7 @@
-
+
@@ -2647,7 +2647,7 @@
-
+
@@ -2730,7 +2730,7 @@
-
+
@@ -2783,7 +2783,7 @@
-
+
@@ -2836,7 +2836,7 @@
-
+
@@ -2907,7 +2907,7 @@
-
+
@@ -2976,7 +2976,7 @@
-
+
@@ -3045,7 +3045,7 @@
-
+
@@ -3114,7 +3114,7 @@
-
+
@@ -3199,7 +3199,7 @@
-
+
@@ -3282,7 +3282,7 @@
-
+
@@ -3365,7 +3365,7 @@
-
+
@@ -3448,7 +3448,7 @@
-
+
@@ -3533,7 +3533,7 @@
-
+
@@ -3616,7 +3616,7 @@
-
+
@@ -3699,7 +3699,7 @@
-
+
@@ -3782,7 +3782,7 @@
-
+
@@ -3881,7 +3881,7 @@
-
+
@@ -3978,7 +3978,7 @@
-
+
@@ -4031,7 +4031,7 @@
-
+
@@ -4084,7 +4084,7 @@
-
+
@@ -4181,7 +4181,7 @@
-
+
@@ -4278,7 +4278,7 @@
-
+
@@ -4331,7 +4331,7 @@
-
+
@@ -4384,7 +4384,7 @@
-
+
@@ -4481,7 +4481,7 @@
-
+
@@ -4578,7 +4578,7 @@
-
+
@@ -4631,7 +4631,7 @@
-
+
@@ -4684,7 +4684,7 @@
-
+
@@ -4776,7 +4776,7 @@
-
+
@@ -4866,7 +4866,7 @@
-
+
@@ -4919,7 +4919,7 @@
-
+
@@ -4972,7 +4972,7 @@
-
+
@@ -5057,7 +5057,7 @@
-
+
@@ -5140,7 +5140,7 @@
-
+
@@ -5193,7 +5193,7 @@
-
+
@@ -5246,7 +5246,7 @@
-
+
@@ -5322,7 +5322,7 @@
-
+
@@ -5398,7 +5398,7 @@
-
+
@@ -5451,7 +5451,7 @@
-
+
@@ -5504,7 +5504,7 @@
-
+
@@ -5580,7 +5580,7 @@
-
+
@@ -5656,7 +5656,7 @@
-
+
@@ -5709,7 +5709,7 @@
-
+
@@ -5762,7 +5762,7 @@
-
+
@@ -5847,7 +5847,7 @@
-
+
@@ -5930,7 +5930,7 @@
-
+
@@ -5983,7 +5983,7 @@
-
+
@@ -6036,7 +6036,7 @@
-
+
@@ -6112,7 +6112,7 @@
-
+
@@ -6188,7 +6188,7 @@
-
+
@@ -6241,7 +6241,7 @@
-
+
@@ -6294,7 +6294,7 @@
-
+
diff --git a/src/tests/topp/PSMFeatureExtractor_2_out.mzid b/src/tests/topp/PSMFeatureExtractor_2_out.mzid
index 5cbe3c86ed4..d2325cf689c 100644
--- a/src/tests/topp/PSMFeatureExtractor_2_out.mzid
+++ b/src/tests/topp/PSMFeatureExtractor_2_out.mzid
@@ -6,7 +6,7 @@
id="OpenMS_10306100746905639127"
creationDate="2023-10-29T11:21:50">
-
+
diff --git a/src/tests/topp/QCCalculator_2_output.mzQC b/src/tests/topp/QCCalculator_2_output.mzQC
index 6e0764b41dc..03429e90413 100644
--- a/src/tests/topp/QCCalculator_2_output.mzQC
+++ b/src/tests/topp/QCCalculator_2_output.mzQC
@@ -192,8 +192,8 @@
},
{
"name": "Proteomics Standards Initiative Mass Spectrometry Ontology",
- "uri": "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo",
- "version": "4.1.56"
+ "uri": "http://purl.obolibrary.org/obo/ms/psi-ms.obo",
+ "version": "4.1.155"
}
]
}
diff --git a/src/tests/topp/THIRDPARTY/SageAdapter_1.mzML b/src/tests/topp/THIRDPARTY/SageAdapter_1.mzML
index 3dfb847a194..241b2c20dbb 100644
--- a/src/tests/topp/THIRDPARTY/SageAdapter_1.mzML
+++ b/src/tests/topp/THIRDPARTY/SageAdapter_1.mzML
@@ -1,7 +1,7 @@
-
+
diff --git a/src/tests/topp/THIRDPARTY/ginkgotoxin-ms-switching_out.mzML b/src/tests/topp/THIRDPARTY/ginkgotoxin-ms-switching_out.mzML
index ddb09738d98..e803d0ae5f0 100644
--- a/src/tests/topp/THIRDPARTY/ginkgotoxin-ms-switching_out.mzML
+++ b/src/tests/topp/THIRDPARTY/ginkgotoxin-ms-switching_out.mzML
@@ -2,7 +2,7 @@
-
+
diff --git a/src/tests/topp/XFDR_test_out1.mzid b/src/tests/topp/XFDR_test_out1.mzid
index 08800ca1806..5f52cb073f5 100644
--- a/src/tests/topp/XFDR_test_out1.mzid
+++ b/src/tests/topp/XFDR_test_out1.mzid
@@ -6,7 +6,7 @@
id="OpenMS_16250062551099875712"
creationDate="2019-07-31T13:23:40">
-
+
@@ -31,13 +31,13 @@
KNVPIEFPVIDR
-
+
LGCKALHVLFER
-
+
@@ -70,7 +70,7 @@
-
+
@@ -248,7 +248,7 @@
-
+
@@ -306,7 +306,7 @@
-
+
diff --git a/src/tests/topp/XFDR_test_out2.mzid b/src/tests/topp/XFDR_test_out2.mzid
index c8b9dae560e..964609fa0f6 100644
--- a/src/tests/topp/XFDR_test_out2.mzid
+++ b/src/tests/topp/XFDR_test_out2.mzid
@@ -6,7 +6,7 @@
id="OpenMS_16250062551099875712"
creationDate="2019-07-31T13:23:41">
-
+
@@ -31,13 +31,13 @@
KNVPIEFPVIDR
-
+
LGCKALHVLFER
-
+
@@ -70,7 +70,7 @@
-
+
@@ -248,7 +248,7 @@
-
+
@@ -306,7 +306,7 @@
-
+
diff --git a/src/tests/topp/XFDR_test_out3.mzid b/src/tests/topp/XFDR_test_out3.mzid
index 4c05ec28a17..4acf7ee0bbf 100644
--- a/src/tests/topp/XFDR_test_out3.mzid
+++ b/src/tests/topp/XFDR_test_out3.mzid
@@ -6,7 +6,7 @@
id="OpenMS_7619833075412535341"
creationDate="2019-07-31T12:12:08">
-
+
@@ -42,374 +42,374 @@
EEEKDEK
-
+
VEKVVVSNR
-
+
KQTNIASTLAR
-
+
TVSVLTKGEFEK
-
+
KNVPIEFPVIDR
-
+
EVTVKENK
-
+
IFSFSNDFTIQKLIETR
-
+
DQQFLNLCCKCFAK
-
+
MLVMELASKGSLDR
-
+
LFIEDVNFNDKASAECFR
-
+
EFEGKTLVSVTK
-
+
KILSSDDSLR
-
+
ENQKHIYYITGETK
-
+
GVGKTSLMER
-
+
GIGMTKADLINNLGTIAK
-
+
KYNEK
-
+
MGIKTSEGTPGFR
-
+
LSKIWDLPLDELHLNFDFK
-
+
LHLSHNKLK
-
+
SLTHLDLHSNKFTSFPSYLLK
-
+
NSVVVKEVK
-
+
MGTIQQAFKEGQQR
-
+
DIMKMWKPLDDFTEK
-
+
CLNEFKTK
-
+
ENQKHIYYITGETK
-
+
LEQLILEGNKISGICSPLR
-
+
EKEVFLTIPYGIFQSHK
-
+
EKYIDQEELNK
-
+
DILEKK
-
+
EELYETQDEKLHLIVK
-
+
VMMTAQLGSLKNVMLVLGYNR
-
+
NHISSLSENFLEACPKVESFSAR
-
+
DYHFVNATEESDALAKLR
-
+
AAYEGEEVAVKIFNK
-
+
KFYEQFSK
-
+
MLVMELASKGSLDR
-
+
DIMKMWKPLDDFTEK
-
+
LIKQCLK
-
+
IVEGLKFPNEFDELEIQGK
-
+
TWIPKTK
-
+
TIDYVLIIGKASR
-
+
TKNLEEQDIYK
-
+
GIGMTKADLINNLGTIAK
-
+
VMMTAQLGSLKNVMLVLGYNR
-
+
CLNEFKTK
-
+
VMMTAQLGSLKNVMLVLGYNR
-
+
VEPSWLGPLFPDKTSNLR
-
+
MNFLAAMPFLPPSMTILKLSQNK
-
+
GQAEVDAMKPWLFNIK
-
+
LNMVKK
-
+
EKEVFLTIPYGIFQSHK
-
+
GQAEVDAMKPWLFNIKAR
-
+
VAMDDYLKNVMLER
-
+
KAEEGDLLVNPDQPR
-
+
EYGCAPWPMVEKLIK
-
+
INNKK
-
+
KHLEINPDHSIIETLR
-
+
@@ -422,1060 +422,1060 @@
DEALETFLELCKK
-
+
KQTNIASTLAR
-
+
VEGCPKHPK
-
+
IVEGLKFPNEFDELEIQGK
-
+
HKMSYSGR
-
+
LSQNKFSCIPEAILNLPHLR
-
+
HIYYITGETKDQVANSAFVER
-
+
NLVKK
-
+
IVEGLKFPNEFDELEIQGK
-
+
KNVPIEFPVIDR
-
+
KVIEK
-
+
KVLNK
-
+
ENKESK
-
+
KALTISIGK
-
+
IFSFSNDFTIQKLIETR
-
+
EEEDEPLELGEKTVSVLTK
-
+
NVFIGTGHLLAKILVSSLYR
-
+
LFIEDVNFNDKASAECFR
-
+
QQGEKFAQQITGMR
-
+
ESSPKLVELLLNSGSR
-
+
IVEGLKFPNEFDELEIQGK
-
+
FENLCKIMK
-
+
FDAPRPPQKR
-
+
FIGNPGIQKCGLK
-
+
CYNIVVEAMKAFPMSER
-
+
MKLMIVGNTGSGK
-
+
YIDQEELNKTKPIWTR
-
+
GQAEVDAMKPWLFNIK
-
+
LEQLILEGNKISGICSPLR
-
+
VEPSWLGPLFPDKTSNLR
-
+
MWKPLDDFTEKK
-
+
DQQFLNLCCKCFAK
-
+
VIEKIR
-
+
KFYEQFSK
-
+
TVSVLTKGEFEK
-
+
ILTVMKR
-
+
IFNKHTSLR
-
+
YIDQEELNKTKPIWTR
-
+
NFLLVGTADGKLAIFEDK
-
+
VEKLHLSHNK
-
+
DTECDLKNGVLLLEADESAYK
-
+
ENKESK
-
+
KILSSDDSLR
-
+
MIKCLNEFK
-
+
HIYYITGETKDQVANSAFVER
-
+
HSNSLGPIFDHEDLLKR
-
+
EVFASNAVQDKTEGTIYYIHK
-
+
EGLELPEDEEEKK
-
+
EKYIDQEELNK
-
+
GQAEVDAMKPWLFNIK
-
+
FIGNPGIQKCGLK
-
+
DEKEEAEDDSVEK
-
+
QPPRPADFKLQVIIIGSR
-
+
WMKMIDK
-
+
ESKHK
-
+
KAEEGDLLVNPDQPR
-
+
EVTVKENK
-
+
YASEDAELLLVGNKLDCETDR
-
+
QSKQK
-
+
KILSSDDSLR
-
+
NTEGTQKQK
-
+
ILLDDLMKK
-
+
EELYETQDEKLHLIVK
-
+
KQTNIASTLAR
-
+
KDGDK
-
+
LQQVCYEDIPEIMYIVELGHKR
-
+
EEEKEK
-
+
KILSSDDSLR
-
+
EMLQQSKILK
-
+
EVFASNAVQDKTEGTIYYIHK
-
+
DIDALSQKCCISVHLEHLEK
-
+
HSNSLGPIFDHEDLLKR
-
+
DNFNVDEIFLKLVDDILK
-
+
YIDQEELNKTKPIWTR
-
+
LLQQDKASLTR
-
+
EMLQQSKILK
-
+
KAEEGDLLVNPDQPR
-
+
KNVPIEFPVIDR
-
+
VMMTAQLGSLKNVMLVLGYNR
-
+
HIYYITGETKDQVANSAFVER
-
+
QKAEADK
-
+
LSQNKFSCIPEAILNLPHLR
-
+
VEKLHLSHNK
-
+
KAEEGDLLVNPDQPR
-
+
EKYIDQEELNK
-
+
MIDKYASEDAELLLVGNK
-
+
INKSFQEYFK
-
+
ESKHK
-
+
TEGTIYYIHKQNEK
-
+
NDIGPSVVLDPTVKCPTLK
-
+
DIMKMWKPLDDFTEK
-
+
FDAPRPPQKR
-
+
LSQNKFSCIPEAILNLPHLR
-
+
VEKVVVSNR
-
+
IFNKHTSLR
-
+
KWALYSFNDGEEHQK
-
+
ELAEKMR
-
+
HTLEKMTDSVTCLYCNSFSK
-
+
LLQQDKASLTR
-
+
EFEGKTLVSVTK
-
+
ILLSKGIHLNVLELMQK
-
+
KNVPIEFPVIDR
-
+
DVEKFLSK
-
+
HSNSLGPIFDHEDLLKR
-
+
DLKPHNVLLFTLYPNAAIIAK
-
+
LEQLILEGNKISGICSPLR
-
+
KMPLDILR
-
+
LSQNKFSCIPEAILNLPHLR
-
+
NVMWGGCGTKIFSFSNDFTIQK
-
+
TVKLK
-
+
FDVGVTSKCAECFTDDTFR
-
+
QNEKMR
-
+
ENKESK
-
+
GVGKTSLMER
-
+
ASSSPVILVGTHLDVSDEKQR
-
+
FPKNYMSQYFK
-
+
GQAEVDAMKPWLFNIK
-
+
KSNSISVGEFYR
-
+
SGIIIVQLKFDAPRPPQK
-
+
KYNEK
-
+
KNVPIEFPVIDR
-
+
FPNEFDELEIQGKLPDPVK
-
+
CYNIVVEAMKAFPMSER
-
+
QCFKNDIHK
-
+
ESKHK
-
+
NVMWGGCGTKIFSFSNDFTIQK
-
+
WMKMIDK
-
+
KWALYSFNDGEEHQK
-
+
KYNEK
-
+
MWKPLDDFTEKK
-
+
VAMDDYLKNVMLER
-
+
LIKQCLK
-
+
DILEKK
-
+
KTIINESLNFK
-
+
AEADKNDK
-
+
KMPLDILR
-
+
FTDDTFCEACKSTVGVDFK
-
+
AITGLNNILDAKTMGIG
-
+
DKEVSDDEAEEK
-
+
KHGLEVIYMIEPIDEYCVQQLK
-
+
NHISSLSENFLEACPKVESFSAR
-
+
ILNLSKNHISSLSENFLEACPK
-
+
IVEGLKFPNEFDELEIQGK
-
+
KALTISIGK
-
+
AAYEGEEVAVKIFNK
-
+
AITGLNNILDAKTMGIG
-
+
KVLNK
-
+
DEALETFLELCKK
-
+
IWDLPLDELHLNFDFKHIGCK
-
+
FCEASAKDNFNVDEIFLK
-
+
EMLSTKGVGR
-
+
LTEIISHDPNIELHKK
-
+
ILLDDLMKK
-
+
LEQLILEGNKISGICSPLR
-
+
FCEASAKDNFNVDEIFLK
-
+
LKELK
-
+
YASEDAELLLVGNKLDCETDR
-
+
VEPSWLGPLFPDKTSNLR
-
+
FTSFPSYLLKMSCIANLDVSR
-
+
MWKPLDDFTEKK
-
+
TTLLQQLMKTK
-
+
KILSSDDSLR
-
+
SFPNEMGKLSK
-
+
@@ -1488,3858 +1488,3858 @@
GFQTILAILKLSASFSK
-
+
IMKDILEK
-
+
EDKEEEK
-
+
NNIKLYVR
-
+
DNSTMGYMAAKK
-
+
KILSSDDSLR
-
+
VAMDDYLKNVMLER
-
+
TLVSVTKEGLELPEDEEEK
-
+
DVEKFLSK
-
+
YASEDAELLLVGNKLDCETDR
-
+
EMLSTKGVGR
-
+
KLSELLR
-
+
KAEEGDLLVNPDQPR
-
+
WLCKIMAQILTVK
-
+
QNSPVVEVWDKK
-
+
QNEKMR
-
+
QNSPVVEVWDKK
-
+
CYNIVVEAMKAFPMSER
-
+
NVMWGGCGTKIFSFSNDFTIQK
-
+
GQAEVDAMKPWLFNIK
-
+
WLCKIMAQILTVK
-
+
FTSFPSYLLKMSCIANLDVSR
-
+
DYHFVNATEESDALAKLR
-
+
KNTEGTQK
-
+
KNVPIEFPVIDR
-
+
VEKLHLSHNK
-
+
KILSSDDSLR
-
+
TEGTIYYIHKQNEK
-
+
KYNEK
-
+
QKNFLLVGTADGK
-
+
LKEIPPEIGCLENLTSLDVSYNLELR
-
+
KSDLGMQSATVGIDVK
-
+
IVKLIK
-
+
VEPSWLGPLFPDKTSNLR
-
+
FPKNYMSQYFK
-
+
ENQKHIYYITGETK
-
+
EEEKDEK
-
+
DNFNVDEIFLKLVDDILK
-
+
VLNKR
-
+
FPKNYMSQYFK
-
+
YIDQEELNKTKPIWTR
-
+
FENLCKIMK
-
+
TLVSVTKEGLELPEDEEEK
-
+
MKLMIVGNTGSGK
-
+
ELIDKMIK
-
+
KHSQFIGYPITLFVEK
-
+
VIEKIR
-
+
IKTVELR
-
+
EYGCAPWPMVEKLIK
-
+
EEEKDEK
-
+
HSNSLGPIFDHEDLLKR
-
+
DIMKMWKPLDDFTEK
-
+
LLQQDKASLTR
-
+
EKEEK
-
+
LLQQDKASLTR
-
+
KTIINESLNFK
-
+
ESSPKLVELLLNSGSR
-
+
LEVTKIK
-
+
ASSSPVILVGTHLDVSDEKQR
-
+
FIGNPGIQKCGLK
-
+
QNSPVVEVWDKK
-
+
MWKPLDDFTEK
-
+
MNFLAAMPFLPPSMTILKLSQNK
-
+
LHLSHNKLK
-
+
VEKLHLSHNK
-
+
SLTNDWEDHLAVKHFSVEGQLEFR
-
+
SLTNDWEDHLAVKHFSVEGQLEFR
-
+
LPDPVKEYGCAPWPMVEK
-
+
NHISSLSENFLEACPKVESFSAR
-
+
NLEEQDIYKEK
-
+
ENKESK
-
+
CYNIVVEAMKAFPMSER
-
+
KSDLGMQSATVGIDVK
-
+
NQSDEHIGLKINK
-
+
KILSSDDSLR
-
+
MWKPLDDFTEK
-
+
GQAEVDAMKPWLFNIKAR
-
+
KELIDK
-
+
STVGVDFKIK
-
+
EVTVKENK
-
+
LEQLILEGNKISGICSPLR
-
+
VILHLKEDQTEYLEER
-
+
EDKEEEK
-
+
TVSVLTKGEFEK
-
+
VEPSWLGPLFPDKTSNLR
-
+
QQGEKFAQQITGMR
-
+
DVAEIQTKGFQTILAILK
-
+
VEPSWLGPLFPDKTSNLR
-
+
KNVPIEFPVIDR
-
+
FDAPRPPQKR
-
+
ITKELLNK
-
+
SFQEYFKK
-
+
FIGNPGIQKCGLK
-
+
ESSPKLVELLLNSGSR
-
+
DEALETFLELCKK
-
+
DYHFVNATEESDALAKLR
-
+
FCEASAKDNFNVDEIFLK
-
+
CYNIVVEAMKAFPMSER
-
+
FKDVAEIQTK
-
+
DEALETFLELCKK
-
+
KHSQFIGYPITLFVEK
-
+
LHLSHNKLK
-
+
TKNLEEQDIYK
-
+
DTECDLKNGVLLLEADESAYK
-
+
ILTVMKR
-
+
TEKLCGLIDCVHFLR
-
+
LSQNKFSCIPEAILNLPHLR
-
+
SFQEYFKK
-
+
KTIINESLNFK
-
+
DEALETFLELCKK
-
+
TTLLQQLMKTK
-
+
LEQLILEGNKISGICSPLR
-
+
TTLLQQLMKTK
-
+
KNVFIGTGHLLAK
-
+
IVEGLKFPNEFDELEIQGK
-
+
TIINESLNFKIR
-
+
CYNIVVEAMKAFPMSER
-
+
DYHFVNATEESDALAKLR
-
+
ILKVIR
-
+
LIDDVLKLFIEDVNFNDK
-
+
YIDQEELNKTKPIWTR
-
+
SDLGMQSATVGIDVKDWPIQIR
-
+
NDIGPSVVLDPTVKCPTLK
-
+
NDIGPSVVLDPTVKCPTLK
-
+
LPDPVKEYGCAPWPMVEK
-
+
NLVKK
-
+
DNFNVDEIFLKLVDDILK
-
+
ESSPKLVELLLNSGSR
-
+
TVSVLTKGEFEK
-
+
HSQFIGYPITLFVEKER
-
+
KILSSDDSLR
-
+
LHLIVKTGR
-
+
EFEGKTLVSVTK
-
+
VEKLHLSHNK
-
+
EEEDEPLELGEKTVSVLTK
-
+
AKDIIR
-
+
KVLNK
-
+
AAYEGEEVAVKIFNK
-
+
ENYKK
-
+
TVSVLTKGEFEK
-
+
ESEDKPEIEDVGSDEEEEKK
-
+
LEQLILEGNKISGICSPLR
-
+
LLQQDKASLTR
-
+
YASEDAELLLVGNKLDCETDR
-
+
HSNSLGPIFDHEDLLKR
-
+
LHLSHNKLK
-
+
KHLEINPDHSIIETLR
-
+
GIGMTKADLINNLGTIAK
-
+
TEKLCGLIDCVHFLR
-
+
NDIHKLVLAALNR
-
+
CYNIVVEAMKAFPMSER
-
+
MGTIQQAFKEGQQR
-
+
CYNIVVEAMKAFPMSER
-
+
HIYYITGETKDQVANSAFVER
-
+
TKFENLCK
-
+
EKEVFLTIPYGIFQSHK
-
+
MKLMIVGNTGSGK
-
+
NFLLVGTADGKLAIFEDK
-
+
LLQQDKASLTR
-
+
FPNEFDELEIQGKLPDPVK
-
+
IFNKHTSLR
-
+
FYEQFSKNIK
-
+
EEKESEDKPEIEDVGSDEEEEK
-
+
EDTEFHHKLNMVK
-
+
NFLLVGTADGKLAIFEDK
-
+
KEEEDEPLELGEK
-
+
GIGMTKADLINNLGTIAK
-
+
LTEIISHDPNIELHKK
-
+
KHSQFIGYPITLFVEK
-
+
DTECDLKNGVLLLEADESAYK
-
+
EEEKEK
-
+
ESSPKLVELLLNSGSR
-
+
FPNEFDELEIQGKLPDPVK
-
+
VSKDNK
-
+
ELAEKMR
-
+
LEQLILEGNKISGICSPLR
-
+
EYGCAPWPMVEKLIK
-
+
NHISSLSENFLEACPKVESFSAR
-
+
VIEKIR
-
+
DYHFVNATEESDALAKLR
-
+
KHLEINPDHSIIETLR
-
+
LIKQCLK
-
+
LTEIISHDPNIELHKK
-
+
TCYDKLSVMEDGSASTYYR
-
+
VEPSWLGPLFPDKTSNLR
-
+
IFNKHTSLR
-
+
EELYETQDEKLHLIVK
-
+
KSDLGMQSATVGIDVK
-
+
HSQFIGYPITLFVEKER
-
+
VILHLKEDQTEYLEER
-
+
FLSKK
-
+
MKLMIVGNTGSGK
-
+
ESSPKLVELLLNSGSR
-
+
NQSDEHIGLKINK
-
+
KQTNIASTLAR
-
+
VEKLHLSHNK
-
+
HIYYITGETKDQVANSAFVER
-
+
DIMKMWKPLDDFTEK
-
+
ELAEKMR
-
+
HIGCKAK
-
+
FTSFPSYLLKMSCIANLDVSR
-
+
WMKMIDK
-
+
EYGCAPWPMVEKLIK
-
+
MGIKTSEGTPGFR
-
+
DNKDAEAK
-
+
KELIDK
-
+
NNIKLYVR
-
+
LLQQDKASLTR
-
+
ENKESK
-
+
EFEGKTLVSVTK
-
+
LKGAAPLK
-
+
KYNEK
-
+
IFNKHTSLR
-
+
EKEEEK
-
+
FTSFPSYLLKMSCIANLDVSR
-
+
KAEEGDLLVNPDQPR
-
+
DEALETFLELCKK
-
+
NGVLLLEADESAYKDIMK
-
+
WLCKIMAQILTVK
-
+
IKTVELR
-
+
KILSSDDSLR
-
+
MWKPLDDFTEKK
-
+
TWIPKTK
-
+
VEGCPKHPK
-
+
MGIKTSEGTPGFR
-
+
SDLGMQSATVGIDVKDWPIQIR
-
+
LEQLILEGNKISGICSPLR
-
+
DIMKMWKPLDDFTEK
-
+
LQQVCYEDIPEIMYIVELGHKR
-
+
FPKNYMSQYFK
-
+
LMIVGNTGSGKTTLLQQLMK
-
+
ESSPKLVELLLNSGSR
-
+
DEALETFLELCKK
-
+
KEEEDEPLELGEK
-
+
IKEIVK
-
+
LLQQDKASLTR
-
+
KNNIK
-
+
KILSSDDSLR
-
+
AAYEGEEVAVKIFNK
-
+
QSKQK
-
+
NHISSLSENFLEACPKVESFSAR
-
+
KTIINESLNFK
-
+
TKPIWTR
-
+
MIKCLNEFK
-
+
SAKGIILVYDITK
-
+
LPDPVKEYGCAPWPMVEK
-
+
DQLVVGQLIPDCYVELEKIILSER
-
+
NVFIGTGHLLAKILVSSLYR
-
+
LGCKALHVLFER
-
+
DIMKMWKPLDDFTEK
-
+
ENKESK
-
+
MWKPLDDFTEKK
-
+
ELIDKMIK
-
+
EKYIDQEELNK
-
+
VEKLHLSHNK
-
+
MNFLAAMPFLPPSMTILKLSQNK
-
+
IVEGLKFPNEFDELEIQGK
-
+
DIDALSQKCCISVHLEHLEK
-
+
SDLGMQSATVGIDVKDWPIQIR
-
+
EGSSLICQVCEKESSPK
-
+
AKDIIR
-
+
EYGCAPWPMVEKLIK
-
+
MKENQK
-
+
KNVPIEFPVIDR
-
+
VMMTAQLGSLKNVMLVLGYNR
-
+
KNVPIEFPVIDR
-
+
FYEQFSKNIK
-
+
AEADKNDK
-
+
AITGLNNILDAKTMGIG
-
+
NVFIGTGHLLAKILVSSLYR
-
+
SLDMSSNDIQYLPGPAHWKSLNLR
-
+
HSNSLGPIFDHEDLLKR
-
+
WLCKIMAQILTVK
-
+
FTSFPSYLLKMSCIANLDVSR
-
+
WLCKIMAQILTVK
-
+
CYNIVVEAMKAFPMSER
-
+
KILSSDDSLR
-
+
FELQGEVSFHKVALHDEWDNTLSK
-
+
QQGEKFAQQITGMR
-
+
KNVPIEFPVIDR
-
+
KELAEK
-
+
LSQNKFSCIPEAILNLPHLR
-
+
STVGVDFKIK
-
+
NLEEQDIYKEK
-
+
EGSSLICQVCEKESSPK
-
+
MGIKTSEGTPGFR
-
+
NHISSLSENFLEACPKVESFSAR
-
+
EVFASNAVQDKTEGTIYYIHK
-
+
TKPIWTRNPDDITNEEYGEFYK
-
+
TTLLQQLMKTK
-
+
CYNIVVEAMKAFPMSER
-
+
KALTISIGK
-
+
EVFASNAVQDKTEGTIYYIHK
-
+
FYEQFSKNIK
-
+
NFLLVGTADGKLAIFEDK
-
+
EYGCAPWPMVEKLIK
-
+
LEQLILEGNKISGICSPLR
-
+
KALTISIGK
-
+
LIKQCLK
-
+
GIGMTKADLINNLGTIAK
-
+
DIMKMWKPLDDFTEK
-
+
IFNKHTSLR
-
+
AITGLNNILDAKTMGIG
-
+
INKSFQEYFK
-
+
ENYKK
-
+
NLEEQDIYKEK
-
+
NLEEQDIYKEK
-
+
EKEVFLTIPYGIFQSHK
-
+
YIDQEELNKTKPIWTR
-
+
FTSFPSYLLKMSCIANLDVSR
-
+
HSNSLGPIFDHEDLLKR
-
+
DTECDLKNGVLLLEADESAYK
-
+
KLIVR
-
+
HIYYITGETKDQVANSAFVER
-
+
IFNKHTSLR
-
+
LHLIVKTGR
-
+
VILHLKEDQTEYLEER
-
+
MGIKTSEGTPGFR
-
+
TLVSVTKEGLELPEDEEEK
-
+
KQTNIASTLAR
-
+
KQTNIASTLAR
-
+
HKMSYSGR
-
+
DAEAKQR
-
+
GQAEVDAMKPWLFNIKAR
-
+
MWKPLDDFTEKK
-
+
EEKESEDKPEIEDVGSDEEEEK
-
+
LEQLILEGNKISGICSPLR
-
+
ENKESK
-
+
VEKVVVSNR
-
+
KAEEGDLLVNPDQPR
-
+
VSKDNK
-
+
KILSSDDSLR
-
+
NDIHKLVLAALNR
-
+
LSQNKFSCIPEAILNLPHLR
-
+
TTLLQQLMKTK
-
+
NHISSLSENFLEACPKVESFSAR
-
+
VEGCPKHPK
-
+
INNKK
-
+
EDKEEEK
-
+
MKLMIVGNTGSGK
-
+
KNVPIEFPVIDR
-
+
FPKNYMSQYFK
-
+
NLVKK
-
+
HIYYITGETKDQVANSAFVER
-
+
LIDLPMKK
-
+
HPKGIISR
-
+
LIKQCLK
-
+
KNVFIGTGHLLAK
-
+
VEKLHLSHNK
-
+
LLQQDKASLTR
-
+
TLVSVTKEGLELPEDEEEK
-
+
LKELK
-
+
EGLELPEDEEEKK
-
+
WLCKIMAQILTVK
-
+
EVTVKENK
-
+
TTLLQQLMKTK
-
+
KILSSDDSLR
-
+
KNVPIEFPVIDR
-
+
ILNLSKNHISSLSENFLEACPK
-
+
QKAEADK
-
+
QKNFLLVGTADGK
-
+
LLQQDKASLTR
-
+
FDAPRPPQKR
-
+
VEKLHLSHNK
-
+
FPNEFDELEIQGKLPDPVK
-
+
HSNSLGPIFDHEDLLKR
-
+
GQAEVDAMKPWLFNIKAR
-
+
VILHLKEDQTEYLEER
-
+
EEEDEPLELGEKTVSVLTK
-
+
AKDIIR
-
+
KHLEINPDHSIIETLR
-
+
LSQNKFSCIPEAILNLPHLR
-
+
KELAEK
-
+
ENKESK
-
+
ENKESK
-
+
KNVPIEFPVIDR
-
+
KILSSDDSLR
-
+
ASSSPVILVGTHLDVSDEKQR
-
+
FPNEFDELEIQGKLPDPVK
-
+
TIINESLNFKIR
-
+
QSKQK
-
+
FCEASAKDNFNVDEIFLK
-
+
MGIKTSEGTPGFR
-
+
FKDVAEIQTK
-
+
KAEEGDLLVNPDQPR
-
+
YASEDAELLLVGNKLDCETDR
-
+
KHGLEVIYMIEPIDEYCVQQLK
-
+
FCEASAKDNFNVDEIFLK
-
+
LGCKALHVLFER
-
+
MWKPLDDFTEKK
-
+
NDIGPSVVLDPTVKCPTLK
-
+
TIINESLNFKIR
-
+
STVGVDFKIK
-
+
EYGCAPWPMVEKLIK
-
+
IVEGLKFPNEFDELEIQGK
-
+
FIGNPGIQKCGLK
-
+
MNFLAAMPFLPPSMTILKLSQNK
-
+
FTSFPSYLLKMSCIANLDVSR
-
+
CYNIVVEAMKAFPMSER
-
+
MLVMELASKGSLDR
-
+
KELAEK
-
+
HPKGIISR
-
+
IVEGLKFPNEFDELEIQGK
-
+
ELAEKMR
-
+
CYNIVVEAMKAFPMSER
-
+
LPDPVKEYGCAPWPMVEK
-
+
LEQLILEGNKISGICSPLR
-
+
SSKLQSHMR
-
+
NQSDEHIGLKINK
-
+
NVMWGGCGTKIFSFSNDFTIQK
-
+
LLESLKK
-
+
MKLMIVGNTGSGK
-
+
MNFLAAMPFLPPSMTILKLSQNK
-
+
KILSSDDSLR
-
+
KILSSDDSLR
-
+
LKELK
-
+
KSNSISVGEFYR
-
+
DQQFLNLCCKCFAK
-
+
KLSELLR
-
+
TTLLQQLMKTK
-
+
KVLNK
-
+
NFLLVGTADGKLAIFEDK
-
+
SLDMSSNDIQYLPGPAHWKSLNLR
-
+
DNFNVDEIFLKLVDDILK
-
+
QKNFLLVGTADGK
-
+
EEEDEPLELGEKTVSVLTK
-
+
AAYEGEEVAVKIFNK
-
+
QSKQK
-
+
LIDDVLKLFIEDVNFNDK
-
+
FPKNYMSQYFK
-
+
KFYEQFSK
-
+
NTEGTQKQK
-
+
CYNIVVEAMKAFPMSER
-
+
GQAEVDAMKPWLFNIKAR
-
+
MIKCLNEFK
-
+
LNMVKK
-
+
HKMSYSGR
-
+
LLQQDKASLTR
-
+
HSNSLGPIFDHEDLLKR
-
+
ACMSKITK
-
+
DGDKK
-
+
MNFLAAMPFLPPSMTILKLSQNK
-
+
KNVFIGTGHLLAK
-
+
NDIGPSVVLDPTVKCPTLK
-
+
GQAEVDAMKPWLFNIKAR
-
+
CYNIVVEAMKAFPMSER
-
+
EKYIDQEELNK
-
+
LIDDVLKLFIEDVNFNDK
-
+
NLVKK
-
+
DIMKMWKPLDDFTEK
-
+
NFLLVGTADGKLAIFEDK
-
+
DGDKK
-
+
VEPSWLGPLFPDKTSNLR
-
+
LLQQDKASLTR
-
+
LPDPVKEYGCAPWPMVEK
-
+
TTLLQQLMKTK
-
+
EEEEDSGVDEIEPKDESEK
-
+
EFEGKTLVSVTK
-
+
DVEKFLSK
-
+
VEPSWLGPLFPDKTSNLR
-
+
EFEGKTLVSVTK
-
+
ESEDKPEIEDVGSDEEEEK
-
+
KLSELLR
-
+
CYNIVVEAMKAFPMSER
-
+
INNKK
-
+
KNVPIEFPVIDR
-
+
MWKPLDDFTEKK
-
+
TEGTIYYIHKQNEK
-
+
DVAEIQTKGFQTILAILK
-
+
NHISSLSENFLEACPKVESFSAR
-
+
CYNIVVEAMKAFPMSER
-
+
TVSVLTKGEFEK
-
+
KSNSISVGEFYR
-
+
LLQQDKASLTR
-
+
DQQFLNLCCKCFAK
-
+
MIKCLNEFK
-
+
TIINESLNFKIR
-
+
HSNSLGPIFDHEDLLKR
-
+
HSNSLGPIFDHEDLLKR
-
+
KSNSISVGEFYR
-
+
FPNEFDELEIQGKLPDPVK
-
+
TKNLEEQDIYK
-
+
KMPLDILR
-
+
KCLELFTELAEDK
-
+
NDIGPSVVLDPTVKCPTLK
-
+
KETFDDLPK
-
+
EVFASNAVQDKTEGTIYYIHK
-
+
KVLNK
-
+
KNVPIEFPVIDR
-
+
IVEGLKFPNEFDELEIQGK
-
+
DAEAKQR
-
+
LQQVCYEDIPEIMYIVELGHKR
-
+
EDTEFHHKLNMVK
-
+
TEGTIYYIHKQNEK
-
+
MGTIQQAFKEGQQR
-
+
DIDALSQKCCISVHLEHLEK
-
+
KNVPIEFPVIDR
-
+
NVMWGGCGTKIFSFSNDFTIQK
-
+
FPNEFDELEIQGKLPDPVK
-
+
KLSELLR
-
+
VYLKINNK
-
+
AEADKNDK
-
+
KNVPIEFPVIDR
-
+
LTEIISHDPNIELHKK
-
+
MGTIQQAFKEGQQR
-
+
FKDVAEIQTK
-
+
TKNLEEQDIYK
-
+
FDAPRPPQKR
-
+
VEGCPKHPK
-
+
EYGCAPWPMVEKLIK
-
+
KACMSK
-
+
LKGAAPLK
-
+
TIINESLNFKIR
-
+
HIYYITGETKDQVANSAFVER
-
+
ENQKHIYYITGETK
-
+
KCLELFTELAEDK
-
+
KILSSDDSLR
-
+
EKEVFLTIPYGIFQSHK
-
+
VEPSWLGPLFPDKTSNLR
-
+
MKENQK
-
+
MKLMIVGNTGSGK
-
+
MWKPLDDFTEKK
-
+
QCFKNDIHK
-
+
SLTHLDLHSNKFTSFPSYLLK
-
+
LQQVCYEDIPEIMYIVELGHKR
-
+
VIEKIR
-
+
NHISSLSENFLEACPKVESFSAR
-
+
QKNFLLVGTADGK
-
+
DIMKMWKPLDDFTEK
-
+
LLQQDKASLTR
-
+
DIMKMWKPLDDFTEK
-
+
ESWIVSGTQSGTLLVINTEDGKK
-
+
ACMSKITK
-
+
LEQLILEGNKISGICSPLR
-
+
MGIKTSEGTPGFR
-
+
ENYKK
-
+
IFSFSNDFTIQKLIETR
-
+
TKFENLCK
-
+
DILEKK
-
+
MIKCLNEFK
-
+
MIDKYASEDAELLLVGNK
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KAAMYGMTSNDR
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DNKDAEAK
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ITKELLNK
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TLVSVTKEGLELPEDEEEK
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ENKESK
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HKMSYSGR
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DIMKMWKPLDDFTEK
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+
FIGNPGIQKCGLK
-
+
NHISSLSENFLEACPKVESFSAR
-
+
HSQFIGYPITLFVEKER
-
+
EKEEEK
-
+
VEPSWLGPLFPDKTSNLR
-
+
VEKLHLSHNK
-
+
MGIKTSEGTPGFR
-
+
DESEKEEK
-
+
FCEASAKDNFNVDEIFLK
-
+
HIGCKAK
-
+
HKMSYSGR
-
+
GVGKTSLMER
-
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NFLLVGTADGKLAIFEDK
-
+
MNFLAAMPFLPPSMTILKLSQNK
-
+
DVEKFLSK
-
+
LIDLPMKK
-
+
TKPIWTR
-
+
QNSPVVEVWDKK
-
+
HSQFIGYPITLFVEKER
-
+
TLVSVTKEGLELPEDEEEK
-
+
TCYDKLSVMEDGSASTYYR
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IFSFSNDFTIQKLIETR
-
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QNEKMR
-
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FELQGEVSFHKVALHDEWDNTLSK
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VAMDDYLKNVMLER
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IKTVELR
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INKSFQEYFK
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FTSFPSYLLKMSCIANLDVSR
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MGTIQQAFKEGQQR
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HSNSLGPIFDHEDLLKR
-
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MWKPLDDFTEKK
-
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AITGLNNILDAKTMGIG
-
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KACMSK
-
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AAYEGEEVAVKIFNK
-
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ESSPKLVELLLNSGSR
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NHISSLSENFLEACPKVESFSAR
-
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LEQLILEGNKISGICSPLR
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EEEKEK
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NGVLLLEADESAYKDIMK
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HIYYITGETKDQVANSAFVER
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LEVTKIK
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DEALETFLELCKK
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HSNSLGPIFDHEDLLKR
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HTLEKMTDSVTCLYCNSFSK
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KELAEK
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TKNLEEQDIYK
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