community ontology development
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
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Community Ontology DevelopmentLessons from the Gene Ontology
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Ontology:
Sets of classes (terms) with relationships between them that
describe a given domain
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Annotation
Associating some object (e.g. protein, gene, experiment) with ontology
terms with some evidence
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Gene Ontology Consortium
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OBO Foundryhttp://www.obofoundry.org/
“a suite of orthogonal interoperable reference ontologies in the
biomedical domain”
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Overview1. Scope2. Users3. Development mechanism4. Standards5. Community input6. Publicize7. Feedback cycle8. Document
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1. Define your scope
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• Related efforts• Make contact• Know what’s out there
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2. Have a user community
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3. Decide on a mechanism for development
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Editors
• Who can edit the ontology?
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How
• Versioning system or database• Critical that you know what others
are working on
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• Remember – no system is a replacement for communication between developers!
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Meet regularly
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Developing GO• Core editors– 5-10 editors– Communicate extensively– Distributed globally– Only these people are direct editors
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Developing GO• Per term requests• Major overhauls• Systematic changes
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4. Define and use standards
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Naming conventions
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Relationships• Use standard where possible• Define where not
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Good ontology design • rubbish in = rubbish out• modularity• pragmatism v/s perfectionism
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5. Use your community
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Community input to GO• Public tracker, email discussion lists• Involvement in specific development
projects• Direct term submission• Community annotation tools
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6. Publicize
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• Make sure people know you’re there• OBO Foundry, Ontology Lookup
Service, BioPortal• Publish• Advertise
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7. Development cycle
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• 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
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8. Document
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• 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
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9. Other considerationspost- v/s pre-composition
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Adding logical constraints to terms
• Adds valuable reasoning power• Automatic term placement, definition
generation etc.• Requires more thought per term