initial commit

Author: XimeAixa

.github/workflows/docs.yml

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+# 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:
+      - main
+
+# 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

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+# 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 main branch
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+  # 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: main
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false
+

.gitignore

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+# 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/
+
+*.tmp
+*.tmp.obo
+*.tmp.owl
+*.tmp.json
+*-relation-graph.tsv.gz
+.template.db
+
+.github/token.txt
+
+/idpo.owl
+/idpo.obo
+/idpo.json
+/idpo.db
+/idpo-base.*
+/idpo-basic.*
+/idpo-full.*
+/idpo-simple.*
+/idpo-simple-non-classified.*
+/mappings/
+/patterns/
+/reports/
+/subsets/
+
+src/ontology/mirror
+src/ontology/mirror/*
+src/ontology/reports/*
+!src/ontology/reports/release-diff.md
+src/ontology/idpo.owl
+src/ontology/idpo.obo
+src/ontology/idpo.json
+src/ontology/idpo.db
+src/ontology/idpo-base.*
+src/ontology/idpo-basic.*
+src/ontology/idpo-full.*
+src/ontology/idpo-simple.*
+src/ontology/idpo-simple-non-classified.*
+
+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-idpo-edit.owl
+src/ontology/idpo-edit.properties
+
+src/ontology/target/
+src/ontology/tmp/*
+!src/ontology/tmp/.gitkeep
+!src/ontology/tmp/README.md
+
+src/ontology/run.sh.conf
+src/ontology/run.sh.env
+
+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
+
+# End of ODK-managed rules

CONTRIBUTING.md

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+# Contributing to Intrinsically Disordered Proteins Ontology
+
+:+1: First of all: Thank you for taking the time to contribute!
+
+The following is a set of guidelines for contributing to IDPO. 
+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/BioComputingUP/idpo/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/idpo).
+- **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/BioComputingUP/idpo/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/BioComputingUP/idpo/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/idpo-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/)

README.md

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+
+![Build Status](https://github.com/BioComputingUP/idpo/actions/workflows/qc.yml/badge.svg)
+# Intrinsically Disordered Proteins Ontology
+
+Description: None
+
+More information can be found at http://obofoundry.org/ontology/idpo
+
+## Versions
+
+### Stable release versions
+
+The latest version of the ontology can always be found at:
+
+http://purl.obolibrary.org/obo/idpo.owl
+
+(note this will not show up until the request has been approved by obofoundry.org)
+
+### Editors' version
+
+Editors of this ontology should use the edit version, [src/ontology/idpo-edit.owl](src/ontology/idpo-edit.owl)
+
+## Contact
+
+Please use this GitHub repository's [Issue tracker](https://github.com/BioComputingUP/idpo/issues) to request new terms/classes or report errors or specific concerns related to the ontology.
+
+## Acknowledgements
+
+This ontology repository was created using the [Ontology Development Kit (ODK)](https://github.com/INCATools/ontology-development-kit).

docs/cite.md

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+# How to cite IDPO

docs/contributing.md

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+# How to contribute to IDPO

docs/index.md

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+# IDPO Ontology Documentation
+
+[//]: # "This file is meant to be edited by the ontology maintainer."
+
+Welcome to the IDPO documentation!
+
+You can find descriptions of the standard ontology engineering workflows [here](odk-workflows/index.md).

docs/odk-workflows/ContinuousIntegration.md

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+# Introduction to Continuous Integration Workflows with ODK
+
+Historically, most repos have been using Travis CI for continuous integration testing and building, but due to
+runtime restrictions, we recently switched a lot of our repos to GitHub actions. You can set up your repo with CI by adding 
+this to your configuration file (src/ontology/idpo-odk.yaml):
+
+```
+ci:
+  - github_actions
+```
+
+When [updateing your repo](RepoManagement.md), you will notice a new file being added: `.github/workflows/qc.yml`.
+
+This file contains your CI logic, so if you need to change, or add anything, this is the place!
+
+Alternatively, if your repo is in GitLab instead of GitHub, you can set up your repo with GitLab CI by adding 
+this to your configuration file (src/ontology/idpo-odk.yaml):
+
+```
+ci:
+  - gitlab-ci
+```
+
+This will add a file called `.gitlab-ci.yml` in the root of your repo.
+