Validation of the OWL file for OLS (#295)

* MS2 MS3 dissociation method and mass analyzer * MS2 MS3 dissociation method and mass analyzer * Scout software added to the Ontology * update .gitignore * owl file validation * owl file validation * owl file validation * owl file validation * owl file validation * owl file validation * owl file validation * owl file validation * owl file validation * owl file validation * owl file validation * owl file validation * validate OWL for OLS * major changes in documentation * major changes in documentation * small change in the name of github action * small change in the name of github action * Update README.md --------- Co-authored-by: Joshua Klein <[email protected]>
HUPO-PSI · Jul 16, 2024 · fa3e11c · fa3e11c
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diff --git a/.github/workflows/validate-obo.yml b/.github/workflows/validate-obo.yml
@@ -1,6 +1,6 @@
 # This is a basic workflow to help you get started with Actions
 
-name: CI
+name: OBO file validation
 
 # Controls when the action will run. Triggers the workflow on push or pull request
 # events but only for the master branch

diff --git a/.github/workflows/validate-owl.yaml b/.github/workflows/validate-owl.yaml
@@ -0,0 +1,52 @@
+name: OWL file validation
+
+on:
+  push:
+    branches: [master, dev]
+
+  pull_request:
+    branches: [master, dev]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up JDK 11
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'temurin' # Install JDK from Eclipse Adoptium
+          java-version: '11'
+
+      - name: Cache Maven packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.m2
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: |
+            ${{ runner.os }}-maven-
+
+      - name: Set up Maven
+        run: mvn -v
+
+      - name: Build OLS dataload
+        run: |
+           git clone https://github.com/EBISPOT/ols4
+           cd ols4/dataload/rdf2json
+           mvn clean install
+
+      - name: Validate OWL File for OLS
+        run: |   
+           cd ols4/dataload/rdf2json/target
+           wget https://raw.githubusercontent.com/ypriverol/psi-ms-CV/dev/owl-config-ols/foundry.json
+           wget https://raw.githubusercontent.com/ypriverol/psi-ms-CV/dev/owl-config-ols/fail_owl.json
+           java -jar rdf2json-1.0-SNAPSHOT.jar --config foundry.json --output foundry_out.json
+           if diff foundry_out.json fail_owl.json > /dev/null; then
+              echo "The PSI-MS ontology has an error in the owl file and do not allow to import in OLS"
+              exit 1
+           else
+              echo "PSI-MS is valid"
+           fi
diff --git a/README.md b/README.md
@@ -1,17 +1,43 @@
-## psi-ms-CV - HUPO-PSI mass spectrometry CV
+## HUPO-PSI mass spectrometry controlled vocabulary (psi-ms)
+[![release-on-tag](https://github.com/HUPO-PSI/psi-ms-CV/actions/workflows/make-release-on-tag.yml/badge.svg)](https://github.com/HUPO-PSI/psi-ms-CV/actions/workflows/make-release-on-tag.yml)
+[![OBO validation](https://github.com/HUPO-PSI/psi-ms-CV/actions/workflows/validate-obo.yml/badge.svg)](https://github.com/HUPO-PSI/psi-ms-CV/actions/workflows/validate-obo.yml)
+[![Update OWL](https://github.com/HUPO-PSI/psi-ms-CV/actions/workflows/update-owl.yaml/badge.svg)](https://github.com/HUPO-PSI/psi-ms-CV/actions/workflows/update-owl.yaml)
 
-## General
+The [Human Proteome Organization (HUPO)–Proteomics Standards Initiative (PSI)](https://psidev.info/) extensively uses ontologies and controlled vocabularies (CVs) in their data formats. The PSI-Mass Spectrometry controlled vocabulary (PSI-MS) is the main ontology from PSI that store and control all terms for MS-based proteomics experiments. It encompasses terms for a complete MS analysis pipeline, including sample labeling, digestion enzymes, instrumentation, software for peptide/protein identification and quantification, and parameters for significance determination. This CV's development involved collaboration across PSI working groups, proteomics researchers, instrument manufacturers, and software vendors. This article outlines the CV's structure, development, maintenance, and dependencies on other ontologies.
 
-When you use psi-ms.obo, please cite the following publication:
+### OBO and OWL files
+
+The main files of this repository are the OBO and OWL files: 
+
+- **psi-ms.obo**: This file is the main source of the PSI-MS CV terms. All changes should be made in the psi-ms.obo file including addintions, changes, etc.  
+- **psi-ms.owl**: This is a read-only file generate from the **psi-ms.obo** file. This file is used by multiple services including OLS, The OBO Foundry, etc. 
 
-Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaíno JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M; HUPO-PSI Group. The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database (Oxford). 2013 Mar 12;2013:bat009. doi: 10.1093/database/bat009. Print 2013.  [pdf](http://database.oxfordjournals.org/content/2013/bat009.full.pdf+html)
+> The [robot.jar tool](https://github.com/ontodev/robot/) is used to convert from obo format to owl. 
 
-## Requesting a new term
+### Requesting a new term
 
 Anyone can request a new term be added to the controlled vocabulary by opening an issue or a pull
 request against this repository. We'd appreciate any help you can contribute when submitting a new
-term, from proposing the term name and description to defining its relationships and properties. Submitting
-the request already formatted as an OBO term is helpful too! Don't worry about finding an unused id string,
-that can be handled near the end.
+term, from proposing the term name and description to defining its relationships and properties. 
+
+### Submitting a new term 
+
+In order to submit a new term, please `fork` or make a new `branch` of this repository. Then, **you can add your CV term in the psi-ms.obo file**. Please do not modify the owl which will be auto-generate from the obo file. Finally, you can do a Pull Request to the main repo and a member of the HUPO-PSI CV group will review and merge the PR.  Alternatively, please open an issue and fill in whatever information you have and we will work with you to get it into the shape we need.
+
+> If you're requesting multiple related terms, you can submit them in a single issue/pull request.
+
+Please keep in mind that when you change the psi-ms.obo file you must increase the version of the file, change the `date` and `data-version` headers, and add your name to the list of contributors. 
+
+```obo
+format-version: 1.2
+data-version: 4.1.155
+date: 03:06:2024 13:22
+saved-by: Eric Deutsch
+```
+
+### How to cite
+
+When you use psi-ms.obo, please cite the following publication:
+
+>Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaíno JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M; HUPO-PSI Group. The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database (Oxford). 2013 Mar 12;2013:bat009. doi: 10.1093/database/bat009. Print 2013.  [pdf](http://database.oxfordjournals.org/content/2013/bat009.full.pdf+html)
 
-If you're requesting multiple related terms, you can submit them in a single issue/pull request.
diff --git a/...evelopment_of_controlled_vocabularies.pdf → ...evelopment_of_controlled_vocabularies.pdf b/...evelopment_of_controlled_vocabularies.pdf → ...evelopment_of_controlled_vocabularies.pdf
diff --git a/...e in OBO Foundry ontology development.pdf → ...e in OBO Foundry ontology development.pdf b/...e in OBO Foundry ontology development.pdf → ...e in OBO Foundry ontology development.pdf
diff --git a/...ss_Spectrometry_Controlled_Vocabulary.pdf → ...ss_Spectrometry_Controlled_Vocabulary.pdf b/...ss_Spectrometry_Controlled_Vocabulary.pdf → ...ss_Spectrometry_Controlled_Vocabulary.pdf
diff --git a/...ng to MS (IUPAC recommendations 2013).pdf → ...ng to MS (IUPAC recommendations 2013).pdf b/...ng to MS (IUPAC recommendations 2013).pdf → ...ng to MS (IUPAC recommendations 2013).pdf
diff --git a/...sed in PSIMSI supported XML standards.pdf → ...sed in PSIMSI supported XML standards.pdf b/...sed in PSIMSI supported XML standards.pdf → ...sed in PSIMSI supported XML standards.pdf
diff --git a/...mats with controlled vocabulary terms.pdf → ...mats with controlled vocabulary terms.pdf b/...mats with controlled vocabulary terms.pdf → ...mats with controlled vocabulary terms.pdf
diff --git a/...tes_guide_for_requesting_new_CV_terms.pdf → ...tes_guide_for_requesting_new_CV_terms.pdf b/...tes_guide_for_requesting_new_CV_terms.pdf → ...tes_guide_for_requesting_new_CV_terms.pdf
diff --git a/owl-config-ols/fail_owl.json b/owl-config-ols/fail_owl.json
@@ -0,0 +1,3 @@
+{
+  "ontologies": []
+}
diff --git a/owl-config-ols/foundry.json b/owl-config-ols/foundry.json
@@ -0,0 +1,159 @@
+{
+  "name": "OBO Foundry",
+  "title": "The OBO Foundry",
+  "markdown": "kramdown",
+  "highlighter": "rouge",
+  "baseurl": "/",
+  "imgurl": "/images",
+  "repo": "https://github.com/OBOFoundry/OBOFoundry.github.io/",
+  "repo_src": "https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/",
+  "author": {
+    "name": "OBO Technical WG"
+  },
+  "plugins": [
+    "jekyll-sitemap"
+  ],
+  "ontologies": [
+    {
+      "activity_status": "active",
+      "build": {
+        "method": "obo2owl",
+        "source_url": "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"
+      },
+      "contact": {
+        "email": "[email protected]",
+        "github": "germa",
+        "label": "Gerhard Mayer",
+        "orcid": "0000-0002-1767-2343"
+      },
+      "dependencies": [
+        {
+          "id": "pato"
+        },
+        {
+          "id": "uo"
+        }
+      ],
+      "description": "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.",
+      "domain": "investigations",
+      "homepage": "http://www.psidev.info/groups/controlled-vocabularies",
+      "id": "ms",
+      "integration_server": "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master",
+      "label": "MS",
+      "layout": "ontology_detail",
+      "license": {
+        "label": "CC BY 3.0",
+        "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
+        "url": "https://creativecommons.org/licenses/by/3.0/"
+      },
+      "mailing_list": "[email protected]",
+      "ontology_purl": "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.owl",
+      "page": "http://www.psidev.info/groups/controlled-vocabularies",
+      "preferredPrefix": "MS",
+      "products": [
+        {
+          "id": "ms.obo",
+          "ontology_purl": "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"
+        },
+        {
+          "id": "ms.owl",
+          "ontology_purl": "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.owl"
+        }
+      ],
+      "publications": [
+        {
+          "id": "https://www.ncbi.nlm.nih.gov/pubmed/23482073",
+          "title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary."
+        }
+      ],
+      "repository": "https://github.com/HUPO-PSI/psi-ms-CV",
+      "tags": [
+        "MS experiments"
+      ],
+      "title": "Mass spectrometry ontology",
+      "tracker": "https://github.com/HUPO-PSI/psi-ms-CV/issues"
+    }
+  ],
+  "principles": [
+    {
+      "id": "fp-000-summary",
+      "layout": "principle",
+      "title": "Overview"
+    },
+    {
+      "id": "fp-001-open",
+      "layout": "principle",
+      "title": "Open (principle 1)"
+    },
+    {
+      "id": "fp-002-format",
+      "layout": "principle",
+      "title": "Common Format (principle 2)"
+    },
+    {
+      "id": "fp-003-uris",
+      "layout": "principle",
+      "title": "URI/Identifier Space (principle 3)"
+    },
+    {
+      "id": "fp-004-versioning",
+      "layout": "principle",
+      "title": "Versioning (principle 4)"
+    },
+    {
+      "id": "fp-005-delineated-content",
+      "layout": "principle",
+      "title": "Scope (principle 5)"
+    },
+    {
+      "id": "fp-006-textual-definitions",
+      "layout": "principle",
+      "title": "Textual Definitions (principle 6)"
+    },
+    {
+      "id": "fp-007-relations",
+      "layout": "principle",
+      "title": "Relations (principle 7)"
+    },
+    {
+      "id": "fp-008-documented",
+      "layout": "principle",
+      "title": "Documentation (principle 8)"
+    },
+    {
+      "id": "fp-009-users",
+      "layout": "principle",
+      "title": "Documented Plurality of Users (principle 9)"
+    },
+    {
+      "id": "fp-010-collaboration",
+      "layout": "principle",
+      "title": "Commitment To Collaboration (principle 10)"
+    },
+    {
+      "id": "fp-011-locus-of-authority",
+      "layout": "principle",
+      "title": "Locus of Authority (principle 11)"
+    },
+    {
+      "id": "fp-012-naming-conventions",
+      "layout": "principle",
+      "title": "Naming Conventions (principle 12)"
+    },
+    {
+      "id": "fp-013-notification",
+      "layout": "principle",
+      "title": "Notification of Changes (principle 13)"
+    },
+    {
+      "id": "fp-016-maintenance",
+      "layout": "principle",
+      "title": "Maintenance (principle 16)"
+    },
+    {
+      "id": "fp-020-responsiveness",
+      "layout": "principle",
+      "title": "Responsiveness (principle 20)"
+    }
+  ]
+}