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‎.github/workflows/docs.yml‎

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

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

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# ODK-managed rules, do not modify
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# If you need to add your own ignore rules, you may do so below
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# the "End ODK-managed rules" marker at the end of this file.
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.DS_Store
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semantic.cache
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bin/
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*.tmp
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*.tmp.obo
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*.tmp.owl
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*.tmp.json
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*-relation-graph.tsv.gz
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.template.db
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.github/token.txt
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/idpo.owl
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/idpo.obo
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/idpo.json
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/idpo.db
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/idpo-base.*
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/idpo-basic.*
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/idpo-full.*
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/idpo-simple.*
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/idpo-simple-non-classified.*
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/mappings/
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/patterns/
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/reports/
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/subsets/
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src/ontology/mirror
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src/ontology/mirror/*
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src/ontology/reports/*
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!src/ontology/reports/release-diff.md
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src/ontology/idpo.owl
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src/ontology/idpo.obo
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src/ontology/idpo.json
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src/ontology/idpo.db
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src/ontology/idpo-base.*
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src/ontology/idpo-basic.*
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src/ontology/idpo-full.*
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src/ontology/idpo-simple.*
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src/ontology/idpo-simple-non-classified.*
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src/ontology/seed.txt
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src/ontology/dosdp-tools.log
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src/ontology/ed_definitions_merged.owl
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src/ontology/ontologyterms.txt
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src/ontology/simple_seed.txt
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src/ontology/patterns
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src/ontology/merged-idpo-edit.owl
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src/ontology/idpo-edit.properties
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src/ontology/target/
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src/ontology/tmp/*
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!src/ontology/tmp/.gitkeep
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!src/ontology/tmp/README.md
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src/ontology/run.sh.conf
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src/ontology/run.sh.env
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src/ontology/imports/*_terms_combined.txt
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src/patterns/data/**/*.ofn
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src/patterns/data/**/*.txt
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src/patterns/pattern_owl_seed.txt
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src/patterns/all_pattern_terms.txt
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# End of ODK-managed rules

‎CONTRIBUTING.md‎

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# Contributing to Intrinsically Disordered Proteins Ontology
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:+1: First of all: Thank you for taking the time to contribute!
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The following is a set of guidelines for contributing to IDPO.
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These guidelines are not strict rules. Use your best judgment, and feel free to propose
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changes to this document in a pull request.
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## Table Of Contents
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- [Guidelines for Contributions and Requests](#contributions)
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* [Reporting problems with the ontology](#reporting-bugs)
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* [Requesting new terms](#requesting-terms)
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* [Adding new terms by yourself](#adding-terms)
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- [Best practices](#best-practices)
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* [How to write a great issue?](#great-issues)
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* [How to create a great pull/merge request?](#great-pulls)
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<a id="contributions"></a>
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## Guidelines for Contributions and Requests
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<a id="reporting-bugs"></a>
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### Reporting problems with the ontology
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Please use our [Issue Tracker](https://github.com/BioComputingUP/idpo/issues/) for reporting problems with the ontology.
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To learn how to write a good issue [see here](#great-issues).
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<a id="requesting-terms"></a>
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### Requesting new terms
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Before you write a new request, please consider the following:
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- **Does the term already exist?** Before submitting suggestions for new ontology terms, check whether the term exist,
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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).
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- **Can you provide a definition for the term?** It should be very clear what the term means, and you should be
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able to provide a concise definition, ideally with a scientific reference.
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- **Is the ontology in scope for the term?** Sometimes, it is hard to tell whether a term "belongs" in
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and ontology. A rule of thumb is "if a similar term already exists, the new term is probably in scope."
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It can be very helpful to mention a very similar concept as part of the term request!
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#### Who can request a term?
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Anyone can request new terms. However, there is not guarantee that your term will be added automatically. Since this is a
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community resource, it is often necessary to do at least some of the work of adding the term yourself, see below.
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#### How to write a new term request
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Request a new term _via_ the GitHub [Issue Tracker](https://github.com/BioComputingUP/idpo/issues/).
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It is important to remember that it takes a lot of time for curators to process issues submitted to the tracker.
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To make this work easier, please always use issue templates if they are available (https://github.com/BioComputingUP/idpo/issues/new/choose).
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For how to write a good term request, please read the [best practices carefully](#great-issues).
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<a id="adding-terms"></a>
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### How to add a new term
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If you have never editted this ontology before, first follow a [general tutorial](https://oboacademy.github.io/obook/lesson/contributing-to-obo-ontologies)
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**Process**:
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1. Clone the repository (In case you are not an offical team member, create a fork first)
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1. Create new branch in git, for example `git checkout -b issue123`
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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_!
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1. Perform your edit and save your changes
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1. Commit changes to branch
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1. Push changes upstream
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1. Create pull request
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## Best Practices
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<a id="great-issues"></a>
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### How to write great issues?
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Please refer to the [OBO Academy term request guide](https://oboacademy.github.io/obook/howto/term-request/).
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<a id="great-pulls"></a>
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### How to create a great pull/merge request?
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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)
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# Intrinsically Disordered Proteins Ontology
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Description: None
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More information can be found at http://obofoundry.org/ontology/idpo
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## Versions
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### Stable release versions
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The latest version of the ontology can always be found at:
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http://purl.obolibrary.org/obo/idpo.owl
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(note this will not show up until the request has been approved by obofoundry.org)
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### Editors' version
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Editors of this ontology should use the edit version, [src/ontology/idpo-edit.owl](src/ontology/idpo-edit.owl)
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## Contact
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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.
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## Acknowledgements
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This ontology repository was created using the [Ontology Development Kit (ODK)](https://github.com/INCATools/ontology-development-kit).

‎issue_template.md‎

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For new term requests, please provide the following information:
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## Preferred term label
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(e.g., Asplenia)
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## Synonyms
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(e.g., Absent spleen)
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## Textual definition
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the definition should be understandable even for non-specialists. Include a PubMed ID to refer to any relevant article that provides additional information about the suggested term.
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## Suggested parent term
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Please look in the hierarchy in a browser such as [OLS](http://www.ebi.ac.uk/ols/ontologies/idpo)
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## Attribution
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If you would like a nanoattribution, please indicate your ORCID id

‎src/metadata/README.md‎

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Metadata files for the OBO Library
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* [idpo.yml](idpo.yml)
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* Determines how your purl.obolibrary.org/obo/idpo/ redirects will be handled
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* Go here: https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config
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* Click [New File](https://github.com/OBOFoundry/purl.obolibrary.org/new/master/config)
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* Paste in the contents of [idpo.yml](idpo.yml)
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* Click "Commit new file"
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* IMPORTANT: remember to make a pull request
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* An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library*
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* [idpo.md](idpo.md)
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* Determines how your metadata is shown on OBO Library, OLS and AberOWL
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* Go here: https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology
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* Click [New File](https://github.com/OBOFoundry/OBOFoundry.github.io/new/master/ontology)
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* Paste in the contents of [idpo.md](idpo.md)
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* Click "Commit new file"
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* IMPORTANT: remember to make a pull request
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* An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library*
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For more background see:
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* http://obofoundry.org/
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* http://obofoundry.org/faq/how-do-i-edit-metadata.html
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‎src/metadata/idpo.md‎

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---
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layout: ontology_detail
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id: idpo
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title: Intrinsically Disordered Proteins Ontology
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jobs:
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- id: https://travis-ci.org/BioComputingUP/idpo
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type: travis-ci
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build:
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checkout: git clone https://github.com/BioComputingUP/idpo.git
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system: git
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path: "."
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contact:
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email:
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label:
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github:
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description: Intrinsically Disordered Proteins Ontology is an ontology...
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domain: stuff
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homepage: https://github.com/BioComputingUP/idpo
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products:
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- id: idpo.owl
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name: "Intrinsically Disordered Proteins Ontology main release in OWL format"
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- id: idpo.obo
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name: "Intrinsically Disordered Proteins Ontology additional release in OBO format"
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- id: idpo.json
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name: "Intrinsically Disordered Proteins Ontology additional release in OBOJSon format"
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- id: idpo/idpo-base.owl
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name: "Intrinsically Disordered Proteins Ontology main release in OWL format"
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- id: idpo/idpo-base.obo
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name: "Intrinsically Disordered Proteins Ontology additional release in OBO format"
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- id: idpo/idpo-base.json
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name: "Intrinsically Disordered Proteins Ontology additional release in OBOJSon format"
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dependencies:
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- id: ro
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- id: go
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- id: omo
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tracker: https://github.com/BioComputingUP/idpo/issues
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license:
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url: http://creativecommons.org/licenses/by/3.0/
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label: CC-BY
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activity_status: active
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---
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Enter a detailed description of your ontology here. You can use arbitrary markdown and HTML.
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You can also embed images too.
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‎src/metadata/idpo.yml‎

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# PURL configuration for http://purl.obolibrary.org/obo/idpo
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idspace: IDPO
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base_url: /obo/idpo
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products:
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- idpo.owl: https://raw.githubusercontent.com/BioComputingUP/idpo/main/idpo.owl
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- idpo.obo: https://raw.githubusercontent.com/BioComputingUP/idpo/main/idpo.obo
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term_browser: ontobee
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example_terms:
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- IDPO_0000000
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entries:
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- prefix: /releases/
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replacement: https://raw.githubusercontent.com/BioComputingUP/idpo/v
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- prefix: /tracker/
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replacement: https://github.com/BioComputingUP/idpo/issues
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- prefix: /about/
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replacement: http://www.ontobee.org/ontology/IDPO?iri=http://purl.obolibrary.org/obo/
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## generic fall-through, serve direct from github by default
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- prefix: /
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replacement: https://raw.githubusercontent.com/BioComputingUP/idpo/main/
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