1 / 31

Community Ontology Development

Community Ontology Development. Lessons from the Gene Ontology. Ontology:. Sets of classes (terms) with relationships between them that describe a given domain. Annotation. Associating some object (e.g. protein, gene, experiment) with ontology terms with some evidence.

zandra
Télécharger la présentation

Community Ontology Development

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related