Ontology Contributor Pathway¶
Description: These are guidelines are developed for anyone interested in contributing to ontologies to provide guidance on how to contribute to OBO Foundry ontologies.
Why you should contribute to ontology development efforts?¶
Ontologies are routinely used for data standardization and in the analytical analysis, but the ontologies themselves are under constant revisions and iterative development. Building ontologies is a community effort and we need expertise from different areas:
- Technical expertise
- Domain expertise
- User experiences
The OBO foundry ontologies are open, which means anyone can access them, and anyone can contribute to them. The types of contributions may include reporting issues, identifying bugs, making requests for new terms or changes, and you can also contribute directly to the ontology itself- if you are familiar with ontology editing workflows, you can download our ontologies and make edits on a branch and do a pull request in GitHub.
Providing Feedback to an Ontology¶
- The preferred mechanism for feedback for almost all OBO Foundry ontologies is via the ontology's GitHub issue tracker.
- To find the correct GitHub issue tracker, go to the OBO Foundry website website and search for a particular ontology.
- For example, click on go (Gene Ontology) and you should see a link to the tracker (https://github.com/geneontology/go-ontology/issues/)
- The OBO Metadata also has a link to a contact but this is generally for OBO administrative purposes, and should not be used for general questions, new term requests, or general feedback
- Some ontologies may have other means of engaging their use community, and these should all be listed in a standard way on the OBO page. This includes mailing lists, slack groups, and Twitter or other social media accounts.
Getting Started with GitHub¶
- Open a free account at https://github.com/.
- GitHub Fundamentals for OBO Engineers. Provides an introduction to GitHub including:
- how to get started
- an overview of the organization of GitHub
- an introduction to Markdown (the simple markup language used in GitHub to do format text, like bold or italics)
- types of content that can be added to GitHub (e.g. you can attach a screenshot to an issue)
- Intro to managing and tracking issues in GitHub. This tutorial walks you through creating issues in GitHub.
Using Ontologies and Ontology Terms¶
- Why ontologies are useful
- Finding good ontologies
- Ontology repositories
- Assessing ontologies for use
Contributing to Ontologies¶
Community feedback is welcome for all open, OBO Foundry ontologies. Feedback is often provided in the form of:
- New terms requests
- Add/revise synonyms, definitions
- Reclassify a term
- Report a bug
Ways to provide feedback¶
- Create a new issue on a GitHub issue tracker
- See lesson on Identifying missing terms
- See lesson on Making term requests to existing ontologies
- Join the discussion: Comment on tickets or discussion board
- Join the conversation: Attend ontology calls (many ontology developer groups have recurring calls that are open to the community. Contact the ontology owner to request information about calls.)
- Edit the ontology file: make changes on a branch and do a pull request (more advanced)
- See lesson on Contributing to OBO ontologies
- Using ontologies to standardize rare disease data collection - By Nicole Vasilevsky, Presentation on June 15, 2022
- RDCA-DAP: Searchability and Standardized Ontologies- By Ramona Walls, Recording from October 13, 2020