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Community-Driven Development of Biomedical Ontologies: Lessons from the Gene Ontology

This document outlines key lessons learned in developing the Gene Ontology (GO) and emphasizes a community-driven approach to ontology development. It covers essential aspects such as defining scope, involving user communities, establishing editing mechanisms, adhering to standards, and ensuring effective communication. The importance of documentation, iterative development, and community input in refining ontologies is stressed. It highlights the collaborative efforts of the Gene Ontology Consortium and offers practical advice for those involved in ontology creation in the biomedical field.

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Community-Driven Development of Biomedical Ontologies: Lessons from the Gene Ontology

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  1. Community Ontology Development Lessons from the Gene Ontology

  2. Ontology: Sets of classes (terms) with relationships between them that describe a given domain

  3. Annotation Associating some object (e.g. protein, gene, experiment) with ontology terms with some evidence

  4. Gene Ontology Consortium

  5. OBO Foundry http://www.obofoundry.org/ “a suite of orthogonal interoperable reference ontologies in the biomedical domain”

  6. Overview • Scope • Users • Development mechanism • Standards • Community input • Publicize • Feedback cycle • Document

  7. 1. Define your scope

  8. Related efforts • Make contact • Know what’s out there

  9. 2. Have a user community

  10. 3. Decide on a mechanism for development

  11. Editors • Who can edit the ontology?

  12. How • Versioning system or database • Critical that you know what others are working on

  13. Remember – no system is a replacement for communication between developers!

  14. Meet regularly

  15. Developing GO • Core editors • 5-10 editors • Communicate extensively • Distributed globally • Only these people are direct editors

  16. Developing GO • Per term requests • Major overhauls • Systematic changes

  17. 4. Define and use standards

  18. Naming conventions

  19. Relationships • Use standard where possible • Define where not

  20. Good ontology design • rubbish in = rubbish out • modularity • pragmatism v/s perfectionism

  21. 5. Use your community

  22. Community input to GO • Public tracker, email discussion lists • Involvement in specific development projects • Direct term submission • Community annotation tools

  23. 6. Publicize

  24. Make sure people know you’re there • OBO Foundry, Ontology Lookup Service, BioPortal • Publish • Advertise

  25. 7. Development cycle

  26. Ontologies should be developed interatively • need mechanism to communicate changes to users • Static ontologies are not useful • Don’t wait until it’s finished before you start using it

  27. 8. Document

  28. It’s boring, but you’ll thank yourself in the long run • Document how and why you made decisions, how you think terms should be used

  29. 9. Other considerations post- v/s pre-composition

  30. Adding logical constraints to terms • Adds valuable reasoning power • Automatic term placement, definition generation etc. • Requires more thought per term

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