ODK-ification

.github/workflows/docs.yml

@@ -0,0 +1,27 @@
+# Basic ODK workflow
+name: Docs
+
+# Controls when the action will run. 
+on:
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+  push:
+    branches:
+      - master
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  build:
+    name: Deploy docs
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v4
+
+      - name: Deploy docs
+        uses: mhausenblas/mkdocs-deploy-gh-pages@master
+        # Or use mhausenblas/mkdocs-deploy-gh-pages@nomaterial to build without the mkdocs-material theme
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          CONFIG_FILE: mkdocs.yaml
+

.github/workflows/qc.yml

@@ -0,0 +1,33 @@
+# Basic ODK workflow
+
+name: CI
+
+# Controls when the action will run. 
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "ontology_qc"
+  ontology_qc:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.6
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
+
+      - name: Run ontology QC checks
+        env:
+          DEFAULT_BRANCH: master
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false
+

.gitignore

@@ -1,45 +1,69 @@
-# Compiled class file
-*.class
-
-# Log file
-*.log
-
-# BlueJ files
-*.ctxt
-
-# Mobile Tools for Java (J2ME)
-.mtj.tmp/
+# ODK-managed rules, do not modify
+# If you need to add your own ignore rules, you may do so below
+# the "End ODK-managed rules" marker at the end of this file.
+.DS_Store
+semantic.cache
+bin/
 
-# Package Files #
-*.jar
-*.war
-*.ear
-*.zip
-*.tar.gz
-*.rar
+*.tmp
+*.tmp.obo
+*.tmp.owl
+*.tmp.json
+*-relation-graph.tsv.gz
+.template.db
 
-# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
-hs_err_pid*
+.github/token.txt
 
-.gradle
-/build/
+/msio.owl
+/msio.obo
+/msio.json
+/msio.db
+/msio-base.*
+/msio-basic.*
+/msio-full.*
+/msio-simple.*
+/msio-simple-non-classified.*
+/mappings/
+/patterns/
+/reports/
+/subsets/
 
-# Ignore Gradle GUI config
-gradle-app.setting
+src/ontology/mirror
+src/ontology/mirror/*
+src/ontology/reports/*
+!src/ontology/reports/release-diff.md
+src/ontology/msio.owl
+src/ontology/msio.obo
+src/ontology/msio.json
+src/ontology/msio.db
+src/ontology/msio-base.*
+src/ontology/msio-basic.*
+src/ontology/msio-full.*
+src/ontology/msio-simple.*
+src/ontology/msio-simple-non-classified.*
 
-# Avoid ignoring Gradle wrapper jar file (.jar files are usually ignored)
-!gradle-wrapper.jar
+src/ontology/seed.txt
+src/ontology/dosdp-tools.log
+src/ontology/ed_definitions_merged.owl
+src/ontology/ontologyterms.txt
+src/ontology/simple_seed.txt
+src/ontology/patterns
+src/ontology/merged-msio-edit.owl
+src/ontology/msio-edit.properties
 
-# Cache of project
-.gradletasknamecache
+src/ontology/target/
+src/ontology/tmp/*
+!src/ontology/tmp/.gitkeep
+!src/ontology/tmp/README.md
 
-# # Work around https://youtrack.jetbrains.com/issue/IDEA-116898
-# gradle/wrapper/gradle-wrapper.properties
+src/ontology/run.sh.conf
+src/ontology/run.sh.env
 
-#miscellaneous
-.DS_Store
-catalog-v001.xml
+src/ontology/imports/*_terms_combined.txt
 
+src/patterns/data/**/*.ofn
+src/patterns/data/**/*.txt
+src/patterns/pattern_owl_seed.txt
+src/patterns/all_pattern_terms.txt
 
-#  IntelliJ and Gradle
-.idea/*
+# End of ODK-managed rules

CONTRIBUTING.md

@@ -0,0 +1,86 @@
+# Contributing to Metabolomics Standards Initiative Ontology
+
+:+1: First of all: Thank you for taking the time to contribute!
+
+The following is a set of guidelines for contributing to MSIO. 
+These guidelines are not strict rules. Use your best judgment, and feel free to propose 
+changes to this document in a pull request.
+
+## Table Of Contents
+
+- [Guidelines for Contributions and Requests](#contributions)
+    * [Reporting problems with the ontology](#reporting-bugs)
+    * [Requesting new terms](#requesting-terms)
+    * [Adding new terms by yourself](#adding-terms)
+- [Best practices](#best-practices)
+    * [How to write a great issue?](#great-issues)
+    * [How to create a great pull/merge request?](#great-pulls)
+
+<a id="contributions"></a>
+
+## Guidelines for Contributions and Requests
+
+<a id="reporting-bugs"></a>
+
+### Reporting problems with the ontology
+
+Please use our [Issue Tracker](https://github.com/ISA-tools/MSIO - base - full/issues/) for reporting problems with the ontology. 
+To learn how to write a good issue [see here](#great-issues).
+
+<a id="requesting-terms"></a>
+
+### Requesting new terms
+
+Before you write a new request, please consider the following: 
+
+- **Does the term already exist?** Before submitting suggestions for new ontology terms, check whether the term exist, 
+either as a primary term or a synonym term. You can search for your term using [OLS](http://www.ebi.ac.uk/ols/ontologies/msio).
+- **Can you provide a definition for the term?** It should be very clear what the term means, and you should be
+able to provide a concise definition, ideally with a scientific reference.
+- **Is the ontology in scope for the term?** Sometimes, it is hard to tell whether a term "belongs" in
+and ontology. A rule of thumb is "if a similar term already exists, the new term is probably in scope."
+It can be very helpful to mention a very similar concept as part of the term request!
+
+#### Who can request a term?
+
+Anyone can request new terms. However, there is not guarantee that your term will be added automatically. Since this is a 
+community resource, it is often necessary to do at least some of the work of adding the term yourself, see below.
+
+#### How to write a new term request
+
+Request a new term _via_ the GitHub [Issue Tracker](https://github.com/ISA-tools/MSIO - base - full/issues/).
+
+It is important to remember that it takes a lot of time for curators to process issues submitted to the tracker.
+To make this work easier, please always use issue templates if they are available (https://github.com/ISA-tools/MSIO - base - full/issues/new/choose).
+
+For how to write a good term request, please read the [best practices carefully](#great-issues).
+
+<a id="adding-terms"></a>
+
+### How to add a new term
+
+If you have never editted this ontology before, first follow a [general tutorial](https://oboacademy.github.io/obook/lesson/contributing-to-obo-ontologies)
+
+**Process**:
+
+1. Clone the repository (In case you are not an offical team member, create a fork first)
+1. Create new branch in git, for example `git checkout -b issue123`
+1. Open src/ontology/msio-edit.owl in your favourite editor, i.e. [Protege](https://protege.stanford.edu/). **Careful:** double check you are editing the correct file. There are many ontology files in this repository, but only one _editors file_!
+1. Perform your edit and save your changes
+1. Commit changes to branch
+1. Push changes upstream
+1. Create pull request
+
+## Best Practices
+
+<a id="great-issues"></a>
+
+### How to write great issues?
+
+Please refer to the [OBO Academy term request guide](https://oboacademy.github.io/obook/howto/term-request/).
+
+<a id="great-pulls"></a>
+
+### How to create a great pull/merge request?
+
+Please refer to the [OBO Academy best practices](https://oboacademy.github.io/obook/howto/github-create-pull-request/)

Legacy/.gitignore

@@ -0,0 +1,45 @@
+# Compiled class file
+*.class
+
+# Log file
+*.log
+
+# BlueJ files
+*.ctxt
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.ear
+*.zip
+*.tar.gz
+*.rar
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+
+.gradle
+/build/
+
+# Ignore Gradle GUI config
+gradle-app.setting
+
+# Avoid ignoring Gradle wrapper jar file (.jar files are usually ignored)
+!gradle-wrapper.jar
+
+# Cache of project
+.gradletasknamecache
+
+# # Work around https://youtrack.jetbrains.com/issue/IDEA-116898
+# gradle/wrapper/gradle-wrapper.properties
+
+#miscellaneous
+.DS_Store
+catalog-v001.xml
+
+
+#  IntelliJ and Gradle
+.idea/*

MSIO-edit.owl → Legacy/MSIO-edit.owl

@@ -17,13 +17,7 @@
      xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/msio.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/msio/2020-02-20/msio.owl"/>
-        <owl:imports rdf:resource="http://nmrML.org/nmrCV"/>
-        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/MSIO_CHMO_import.owl"/>
-        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/MSIO_ChEBI_import.owl"/>
-        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/MSIO_OBI_import.owl"/>
-        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/MSIO_PSIMS_import.owl"/>
-        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/MSIO_UO_import.owl"/>
+        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/msio/imports/merged_import.owl"/>
         <dc:contributor xml:lang="en">Alejandra Gonzalez-Beltran</dc:contributor>
         <dc:contributor xml:lang="en">Andrew Lane</dc:contributor>
         <dc:contributor xml:lang="en">Hunter Moseley</dc:contributor>
@@ -34,7 +28,6 @@
         <dc:contributor>Vitaly Selivanov</dc:contributor>
         <dc:creator>Philippe Rocca-Serra</dc:creator>
         <dc:description xml:lang="en">an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.</dc:description>
-        <dc:format>OWL</dc:format>
         <dc:license>http://creativecommons.org/licenses/by/3.0/</dc:license>
         <dc:title xml:lang="en">Metabolomics Standards Initiative Ontology (MSIO)</dc:title>
         <doap:bug-database>https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO/issues</doap:bug-database>
@@ -1566,7 +1559,7 @@ last accessed: 2018-01-11</obo:IAO_0000119>
     <!-- http://purl.obolibrary.org/obo/MSIO_0000015 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/MSIO_0000015">
-        <owl:equivalentClass>
+       <owl:equivalentClass>
             <owl:Class>
                 <owl:intersectionOf rdf:parseType="Collection">
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>

Legacy/README.md

@@ -0,0 +1,40 @@
+# Metabolomics Standards Initiative Ontology (MSIO)
+
+MSIO aims to provide a single point of entry to support semantic markup of experiments making use of NMR and MS techniques to identify, measure and quantify small molecules known as metabolites. MSIO covers metabolite profiling, targeted or undertargeted, tracer based applications. MSIO reuses a number of resources such as [CHEBI](https://www.ebi.ac.uk/ols/ontologies/chebi), [DUO](https://www.ebi.ac.uk/ols/ontologies/duo), [NMRCV](https://www.ebi.ac.uk/ols/ontologies/nmrcv), [OBI](https://www.ebi.ac.uk/ols/ontologies/obi),  and [STATO](https://www.ebi.ac.uk/ols/ontologies/stato).
+
+It is compatible with OBI and can be imported in it but also can be used as is for users working solely on Metabolomics.
+
+MSIO is now available from EMBL EBI Ontology Lookup System, [here.](https://www.ebi.ac.uk/ols/ontologies/msio)
+
+Log term requests [here.](https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO/issues)
+
+The following screenshots allow for a sneak peak at the resource to gauge its coverage.
+_________
+Material Processing:
+
+![alt text](https://github.com/ISA-tools/MSIO/blob/master/docs/img/msio-material-processing.png "Logo Title Text 1")
+
+_________
+Data Transformation:
+
+![alt text](https://github.com/ISA-tools/MSIO/blob/master/docs/img/msio-data-transformation.png "Logo Title Text 2")
+
+_________
+Material Entities:
+
+![alt text](https://github.com/ISA-tools/MSIO/blob/master/docs/img/msio-material-entities.png "Logo Title Text 3")
+
+_________
+Material Entities:
+
+![alt text](https://github.com/ISA-tools/MSIO/blob/master/docs/img/msio-material-entities-chebi-imports.png "Logo Title Text 4")
+
+_________
+Information Entities:
+
+![alt text](https://github.com/ISA-tools/MSIO/blob/master/docs/img/msio-information-entities.png "Logo Title Text 5")
+
+## Versions
+
+The development version of the ontology is at: [MSIO-edit.owl](https://raw.githubusercontent.com/ISA-tools/MSIO/master/MSIO-edit.owl)
+