From 1c5a78f161ca30adce8196c772879ca06c7b77ab Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Mon, 12 Feb 2018 15:29:55 -0500 Subject: [PATCH] Add new release candidate 2018-02-12 --- obi.owl | 347 +++++++++++++++++++++++++++++++++++++++++++++++---- obi_core.owl | 41 ++++-- 2 files changed, 355 insertions(+), 33 deletions(-) diff --git a/obi.owl b/obi.owl index c8aaee8f..2e4a5c9a 100755 --- a/obi.owl +++ b/obi.owl @@ -12,7 +12,7 @@ xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:dc="http://purl.org/dc/elements/1.1/"> - + Pierre Grenon Bjoern Peters Matthew Pocock @@ -21,7 +21,6 @@ Chris Taylor Chris Stoeckert Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2017-11-07 Tina Hernandez-Boussard Jessica Turner Allyson Lister @@ -40,6 +39,7 @@ James Malone Kevin Clancy Susanna-Assunta Sansone + 2018-02-12 Norman Morrison Daniel Rubin Cristian Cocos @@ -5842,7 +5842,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ adaptive immune response - An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory). + An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). adaptive immune response @@ -5938,7 +5938,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ molecular_function - Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. + The actions of a single gene product or complex at the molecular level consisting of a single biochemical activity or multiple causally linked biochemical activities. A given gene product may exhibit one or more molecular functions. molecular_function @@ -5986,7 +5986,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ ion channel activity - Catalysis of facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. + Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). ion channel activity @@ -5998,7 +5998,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ cellular_component - The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. + The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. cellular_component @@ -6203,7 +6203,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ gene expression - The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. + The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. gene expression @@ -6378,6 +6378,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + interferon-alpha production + The appearance of interferon-alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interferon-alpha production + + + + @@ -7098,7 +7110,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ protein complex A ribosome is a protein complex - Any macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. + A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. protein complex @@ -12315,7 +12327,7 @@ editor = PRS - + @@ -14468,7 +14480,7 @@ for now. - + @@ -14491,7 +14503,7 @@ for now. analyte role Glucose in blood (measured in an assay to determine the concentration of glucose). - A role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role + A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role. interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested. qualities such as weight, color are not assayed but measured, so they do not fall into this category. @@ -20499,6 +20511,7 @@ Genome Res. 2008 Mar;18(3):469-76. Epub 2008 Jan 24. PMID: 18218979Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device + There is some question of whether 'device setting' is really best modelled as a quality. To be revisited after assay terms have been worked through. See https://github.com/obi-ontology/obi/issues/133 PERSON: Frank Gibson device setting @@ -40921,9 +40934,10 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) proteomic profiling by array design - A study design in which proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology - Person: Chris Stoeckert, Jie Zheng + A study design in which proteins in a sample are detected, quantified or otherwise analysed, through an array-based technology. + Person: Chris Stoeckert, Jie Zheng, Dan Berrios Group: ArrayExpress production team + https://github.com/obi-ontology/obi/issues/854 proteomic profiling by array design @@ -57823,7 +57837,7 @@ https://sourceforge.net/p/obi/obi-terms/766/ - + @@ -57848,13 +57862,13 @@ https://sourceforge.net/p/obi/obi-terms/766/ - hydrogen/deuterium exchange assay + hydrogen/deuterium exchange footprinting assay Performing deuterium exchange on a protein by itself and in the presence of a binding partner, degrading the protein into peptide segments and identifying where deuterium exchange occurred by detecting the peptides in Mass Spectrometry. Peptides that have a modified deuteration pattern when the protein was bound to a partner are expected to be part of the binding interface. - An assay that uses a chemical reaction whereby a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa in order to gather information about the solvent accessibility of parts of a molecule and thus its tertiary structure. + A footprinting assay that uses a chemical reaction whereby a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa in order to gather information about the solvent accessibility of parts of a molecule and thus its tertiary structure. IEDB IEDB - hydrogen/deuterium exchange assay + hydrogen/deuterium exchange footprinting assay @@ -58563,7 +58577,7 @@ https://sourceforge.net/p/obi/obi-terms/766/ - + @@ -58571,10 +58585,10 @@ https://sourceforge.net/p/obi/obi-terms/766/ - + hydrogen/deuterium exchange assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses a hydrogen/deuterium exchange assay. + A footprinting assay that uses hydrogen/deuterium exchange to measure B cell epitope qualitative binding to antibody. IEDB IEDB qualitative binding|hydrogen/deuterium exchange @@ -62960,9 +62974,9 @@ https://www.doi.org/ footprinting assay - An assay that identifies binding interactions between molecular entities by detecting changes in biochemical properties of the binding site (the footprint) which is protected from, for example, enzymatic cleavage. + An assay that measures ligand binding and conformational changes by the solvent accessibility of the backbone, bases, or side-chain structures of macromolecules through their sensitivity to chemical or enzymatic cleavage or modification reactions. Bjoern Peters - PERSON: Bjoern Peters + DOI: 10.1002/3527600906.mcb.200300025 footprinting assay @@ -65595,7 +65609,7 @@ https://www.doi.org/ - + @@ -65606,7 +65620,7 @@ https://www.doi.org/ - + @@ -65644,9 +65658,9 @@ https://www.doi.org/ hydroxyl-radical footprinting assay - A footprinting assay that determines protein-binding sites on DNA by identifying bound fragments that are protected from hydroxyl radicals which cleave DNA by abstracting a hydrogen atom from C4 of the sugar in the minor groove. + A footprinting assay that uses the reaction of hydroxyl radicals with side-chain sites in molecules (proteins, DNA, etc) with the resultant mass shift demonstrating the site of modification, used to to asses the accessibility of that site. Jie Zheng - url:http://cshprotocols.cshlp.org/content/2007/12/pdb.prot4810.abstract + PMID:21770468 hydroxyl-radical footprinting assay @@ -65733,6 +65747,287 @@ https://www.doi.org/ + + + + + + + + + + + measurand role + + A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role. + Person: Alan Ruttenberg, Jie Zheng + https://en.wiktionary.org/wiki/measurand + https://github.com/obi-ontology/obi/issues/778 + measurand role + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + transcription start site mapping by primer extension assay + + A transcription profiling assay in which the transcription start site for a gene is determined by identifying the 5' end of mRNA. A radio-labeled primer is annealed to a complementary mRNA sequence near the 3' end, then cDNA is synthesized until the 5' end is reached. + Rebecca Tauber + PMID:23378648 + url:https://en.wikipedia.org/wiki/Primer_extension + transcription start site mapping by primer extension assay + + + + + + + + + proteomic profiling design + + A study design in which proteins in a sample are detected, quantified or otherwise analysed. + Dan Berrios + OBI:0001441 + proteomic profiling design + + + + + + + + + suppression subtractive hybridization + + An artificially induced nucleic acid hybridization that is performed to compare gene expression in different cell or tissue types based on normalization and suppression, which creates a subtracted cDNA or genomic DNA library. + Rebecca Tauber + SSH + subtractive hybridization + PMID:14970460 + suppression subtractive hybridization + + + + + + + + + differential screening hybridization + + An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes. + Rebecca Tauber + DSH + differential screening + PMID:25472628 + differential screening hybridization + + + + + + + + + + + + + + + footprinting assay measuring binding of a B cell epitope:antibody complex + + A B cell epitope qualitative binding to antibody assay that uses a footprinting assay. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + qualitative binding|footprinting assay + footprinting assay measuring binding of a B cell epitope:antibody complex + + + + + + + + + + + + + + + + + + + + hydroxyl-radical footprinting assay measuring binding of a B cell epitope:antibody complex + + A footprinting assay that uses hydroxyl-radical footprinting to measure B cell epitope qualitative binding to antibody. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + qualitative binding|hydroxyl-radical footprinting assay + hydroxyl-radical footprinting assay measuring binding of a B cell epitope:antibody complex + + + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interferon-alpha production by T cells + + An assay of epitope specific interferon-alpha production by T cells that uses an ELISA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNa release|ELISA + ELISA measuring epitope specific interferon-alpha production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + biological activity assay measuring epitope specific interferon-alpha production by T cells + + A T cell epitope specific cytokine production assay that detects interferon-alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNa release|biological activity + biological activity assay measuring epitope specific interferon-alpha production by T cells + + + + + + + + + health status inclusion criterion + ‘diagnosed with Type 2 diabetes mellitus’, ‘E11.4’, ’not finding of hypertension' + + An inclusion criterion that defines and states one or more clinically significant bodily components, dispositions, and/or bodily processes of an entity that are inferred from relevant clinical findings or self-reported, which, if met, makes the entity suitable for a given task or participation in a given process. + Mathias Brochhausen + MIABIS2.0 + health status inclusion criterion + + + + + + + + + clinically relevant lifestyle inclusion criterion + 'smoking behavior’ + + An inclusion criterion that defines and states one or more clinically relevant planned processes that a human being actively participates in , which, if met, makes the human being suitable for a given task or participation in a given process. + Mathias Brochhausen + MIABIS2.0 + clinically relevant lifestyle inclusion criterion + + + + + + + + + clinically relevant exposure inclusion criterion + 'exposure to cigarette smoke’, ‘exposure to lead through drinking water' + + An inclusion criterion that defines and states one or more clinically relevant histories of exposure of an entity, which, if met, makes the entity suitable for a given task or participation in a given process. + Mathias Brochhausen + MIABIS2.0 + clinically relevant exposure inclusion criterion + + + + + + + + + gravidity inclusion criterion + 'pregnant’, ‘not pregnant' + + An inclusion criterion that defines and states one or more gravidity statuses of an organism, which, if met, makes the entity suitable for a given task or participation in a given process. + Mathias Brochhausen + MIABIS2.0 + gravidity inclusion criterion + + + + diff --git a/obi_core.owl b/obi_core.owl index 719fff43..9638aad0 100755 --- a/obi_core.owl +++ b/obi_core.owl @@ -11,7 +11,7 @@ xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:dc="http://purl.org/dc/elements/1.1/"> - + en Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg @@ -77,7 +77,7 @@ An ontology for the annotation of biomedical and functional genomics experiments. Ontology for Biomedical Investigation Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2017-11-07 + 2018-02-12 @@ -277,6 +277,12 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + @@ -1867,7 +1873,7 @@ every c that is a concretization of g specifically denotes r molecular_function - Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. + The actions of a single gene product or complex at the molecular level consisting of a single biochemical activity or multiple causally linked biochemical activities. A given gene product may exhibit one or more molecular functions. molecular_function @@ -1879,7 +1885,7 @@ every c that is a concretization of g specifically denotes r cellular_component - The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. + The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. cellular_component @@ -2773,7 +2779,7 @@ editor = PRS - + @@ -3100,7 +3106,7 @@ for now. - + @@ -3123,7 +3129,7 @@ for now. analyte role Glucose in blood (measured in an assay to determine the concentration of glucose). - A role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role + A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role. interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested. qualities such as weight, color are not assayed but measured, so they do not fall into this category. @@ -3863,6 +3869,27 @@ The following are NOT conclusions based on data: data themselves; results from p + + + + + + + + + + + measurand role + + A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role. + Person: Alan Ruttenberg, Jie Zheng + https://en.wiktionary.org/wiki/measurand + https://github.com/obi-ontology/obi/issues/778 + measurand role + + + +