From b0c1790fa3163dfcfd295f6f5b19d8a1855ca365 Mon Sep 17 00:00:00 2001 From: Chris Bielow Date: Thu, 22 Aug 2024 09:44:42 +0200 Subject: [PATCH 1/2] some menu cleanup -- not final --- docs/_data/menu.yml | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/docs/_data/menu.yml b/docs/_data/menu.yml index 26a1c49..5198154 100644 --- a/docs/_data/menu.yml +++ b/docs/_data/menu.yml @@ -4,41 +4,41 @@ # LINKS ARE UNBROKEN AND ALL CONTENT IS REACHABLE!!! - title: Home url: / -- title: The Format +- title: mzQC for Users url: /mzQC-intro/ submenu: - - title: Specification - url: /spec-doc/ - - title: '*omics' + - title: Introduction + url: /mzQC-intro/ + - title: 'Use cases' url: /use-cases/ + - title: QC Software with mzQC + url: /resource-guide/#qc-software - title: Examples url: /examples/ - - title: Metrics - url: /metrics/ - - title: The Format - url: /mzQC-intro/ -- title: Validator - url: /validator/ - submenu: - - title: Validation Process - url: /validator/validation - - title: Local Validation - url: /validator/validation/#offline-validation - - title: Online Validator - url: /validator/ -- title: mzQC Resources +- title: mzQC for Developers url: /resource-guide/ submenu: + - title: Specification + url: /spec-doc/ + - title: Metrics + url: /metrics/ - title: mzQC Frameworks url: /resource-guide/#core-libraries - title: Tutorials url: /tutorials/ - - title: QC Software with mzQC - url: /resource-guide/#qc-software - title: JSON Primer url: /tutorials/#json - title: Ontology Primer url: /tutorials/#ontologies +- title: Validator + url: /validator/ + submenu: + - title: Validation Process + url: /validator/validation + - title: Offline Validation + url: /validator/validation/#offline-validation + - title: Online Validator + url: /validator/ - title: About url: /about/ submenu: From ce927b1078018960e8b934ee90575a4812231157 Mon Sep 17 00:00:00 2001 From: Chris Bielow Date: Thu, 22 Aug 2024 09:45:00 +0200 Subject: [PATCH 2/2] fix broken links --- docs/index.md | 3 +-- docs/pages/contribs.md | 2 +- docs/pages/tutorials.md | 2 +- docs/pages/use-cases.md | 16 +++++++++++----- docs/pages/worked-examples/adv_mzqc_in_mzml.md | 2 +- 5 files changed, 15 insertions(+), 10 deletions(-) diff --git a/docs/index.md b/docs/index.md index 62b8851..9973c8f 100644 --- a/docs/index.md +++ b/docs/index.md @@ -33,8 +33,7 @@ and analysts wanting a better insight to the data they analyse. * If you are familiar with JSON or have an understanding of PSI file formats, are however pressed for time, [mzQC at a glance](use-cases/at-a-glance/) will give you a brief overview of the essentials. -* A in a nutshell exlanation is [here](mzQC-in-a-nutshell/) -* Find out more about the format in general [here](mzQC-intro/)! +* Find out more about the format in general [in our Introduction](mzQC-intro/)! ### Specification Document For the technical details on the mzQC format see either the [latest release static version](spec-doc/), or diff --git a/docs/pages/contribs.md b/docs/pages/contribs.md index e93b7dd..a6a755d 100644 --- a/docs/pages/contribs.md +++ b/docs/pages/contribs.md @@ -26,7 +26,7 @@ If you spot a problem, [search if an issue already exists](https://docs.github.c #### Request a new metric -If you miss a specific metric, you can request it's addition via the issue system. It might be good if you'd familiarise yourself with [mzQC](https://hupo-psi.github.io/mzqc/) and [CV metric representation](https://hupo-psi.github.io/mzqc/metrics/) in particular. We have a dedicated issue template for the request of new QC terms in the PSI-MS-CV repository. +If you miss a specific metric, you can request it's addition via the issue system. It might be good if you'd familiarise yourself with [mzQC](https://hupo-psi.github.io/mzQC/) and [CV metric representation](https://hupo-psi.github.io/mzQC/metrics/) in particular. We have a dedicated issue template for the request of new QC terms in the PSI-MS-CV repository. #### Solve an issue diff --git a/docs/pages/tutorials.md b/docs/pages/tutorials.md index 51de3cf..57c5082 100644 --- a/docs/pages/tutorials.md +++ b/docs/pages/tutorials.md @@ -35,7 +35,7 @@ Here is a list of links and documents that should help you out in case you want * Ontologies are powerful tools, we mostly use them as [controlled vocabularies](https://en.wikipedia.org/w/index.php?title=Controlled_vocabulary&oldid=1092198296) * The W3C has a bit broader explanation of [ontologies](https://www.w3.org/standards/semanticweb/ontology) * Visit the [HUPO-PSI webpage](https://www.psidev.info/groups/controlled-vocabularies) for more information on CV use in different settings. -* __Browse our controlled vocabulary terms on [OLS](https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_4000000&lang=en&viewMode=All&siblings=false)__ +* __Browse our controlled vocabulary terms on [OLS](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_4000000?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_4000000&lang=en&viewMode=All&siblings=false)__ * If you want to start with the foundations and get ambitious here are the resources [from protege for ontology development](https://protege.stanford.edu/publications/ontology_development/ontology101.pdf) * Luckily, we have all the relevant metrics and terms in [PSI-MS CV](https://github.com/HUPO-PSI/psi-ms-CV) (so no [Ontology Dowsing](https://www.w3.org/wiki/Ontology_Dowsing) necessary) diff --git a/docs/pages/use-cases.md b/docs/pages/use-cases.md index ce59b19..7106197 100644 --- a/docs/pages/use-cases.md +++ b/docs/pages/use-cases.md @@ -6,19 +6,25 @@ permalink: /use-cases/ This page should give you a (non-exclusive) overview over the use cases covered by mzQC: ## Handover Format -It is easy with **mzQC** to get relevant QC info, easy to put your data into context (of measurement realities). That makes it a preferred medium to handover quality information. Read more about it in [mzQC at a glance](at-a-glance/) and explore [a small mzQC example](../examples/intro_run/). +It is easy with **mzQC** to get relevant QC info, easy to put your data into context (of measurement realities). That makes it a preferred medium to handover quality information. +Read more about it in [mzQC at a glance](at-a-glance/) and explore [a small mzQC example](../examples/intro_run/). ## Quality Reports -With JSON at its core, mzQC follows a '_works online, works everywhere_' approach. Even for single spectra, as we show with the [universal spectrum identifier example](../examples/USI-example/). +With JSON at its core, mzQC follows a '_works online, works everywhere_' approach. Even for single spectra, as we show with the [universal spectrum identifier example](../examples/adv_mzqc_usi/). ## Archival -The format is an optimal QC tool for the analytical chemist and instrument operators keeping track (and archive) instrument performance. Read on with an [introduction to mzQC for anlytical chemists](analytical-chemists/) or explore our [QC sample example](../examples/QC2-sample-example/). You can even embed mzQC in mzML, should you choose to. [View an example here](../examples/mzml-mzqc-example/). +The format is an optimal QC tool for the analytical chemist and instrument operators keeping track (and archive) instrument performance. +Read on with an [introduction to mzQC for anlytical chemists](analytical-chemists/) or explore our [QC sample example](../examples/intro_qc2/). +You can even embed mzQC in mzML, should you choose to. [View an example here](../examples/adv_mzqc_in_mzml/). ## Common currency With mzQC for archival, quality reports, and as handover format, [mzQC can serve as a common currency](mzQC-common-currency/) for data repositories, journals, and collaborators. ## Bridge the *omics Gap: Metabolomics -A technology agnostic design makes QC with mzQC easy in other fields as well! Assuming you make per sample measurements (runs in mzQC parlance) and multiple groups of runs in a study (sets), then all you need is to define your metrics to open up the mzQC 'ecosystem' to your field. Explore in [this example](../examples/metabo-batches/), how easy you can include QC data from quite different instruments, employ advanced QC concepts like batch correction, and use metrics on expansive datasets. +A technology agnostic design makes QC with mzQC easy in other fields as well! Assuming you make per sample measurements (runs in mzQC parlance) and multiple groups of runs in a study (sets), +then all you need is to define your metrics to open up the mzQC 'ecosystem' to your field. Explore in [this example](../examples/metabo-batches/), +how easy you can include QC data from quite different instruments, employ advanced QC concepts like batch correction, and use metrics on expansive datasets. ## Keep track of your study's runs as a whole -With mzQC you can keep track of the quality of all your study's runs. We show in [this example](../examples/set-of-runs/) how you can apply metrics to a whole set of runs. There are of course more scenarios in which you want to consider the quality of multiple runs, and you can read [more here](mzqc-multi/). +With mzQC you can keep track of the quality of all your study's runs. We show in [this example](../examples/intro_set/) how you can apply metrics to a whole set of runs. +There are of course more scenarios in which you want to consider the quality of multiple runs, and you can read [more here](mzqc-multi/). diff --git a/docs/pages/worked-examples/adv_mzqc_in_mzml.md b/docs/pages/worked-examples/adv_mzqc_in_mzml.md index 1a13614..7849e7e 100644 --- a/docs/pages/worked-examples/adv_mzqc_in_mzml.md +++ b/docs/pages/worked-examples/adv_mzqc_in_mzml.md @@ -7,7 +7,7 @@ permalink: /examples/adv_mzqc_in_mzml/ While QC metrics in the PSI-MS controlled vocabulary are primarily intended for use in mzQC files, they can also be embedded directly within other file formats developed by the Proteomics Standards Initiative, such as [mzML](https://github.com/HUPO-PSI/mzML) and [mzIdentML](https://github.com/HUPO-PSI/mzIdentML) files. This integration is particularly useful when it's preferred to store a limited set of QC metrics alongside the data they describe, thereby enhancing data integrity and accessibility. -You can view a comprehensive example of an mzML file incorporating QC metrics [here](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/adv_mzqc_in_mzml.mzml). +You can view a comprehensive example of an mzML file incorporating QC metrics [here](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/adv_mzqc_in_mzml.mzML). Below, we detail the steps and elements involved in this process. 1. **Source file specification**