Collaborative ontology development

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Natasha Noy's presentation at the SSSW 2013 summer school

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Collaborative ontology development

  1. 1. Collaborative Ontology Development Natasha Noy Stanford University Monday, July 15, 13
  2. 2. The ontology development that we grew up with Courtesy of Mark Musen Monday, July 15, 13
  3. 3. Lots of databases and sources The data is in different silos Need to integrate them Considerable benefit if you can integrate the data Ontologies are essential to science Monday, July 15, 13
  4. 4. Many ontologies today are large and there are lots of them • Gene ontology: 28K classes • Foundational Model of Anatomy: >80K classes • NCI Thesaurus: 80K classes • SNOMED CT: >300K classes Monday, July 15, 13
  5. 5. There are lots of ontologies and more to come BioPortal has more than 350 ontologies only in the field of biomedicine Users uploaded more than 230 ontologies to WebProtégé in the first two months after its release Monday, July 15, 13
  6. 6. To provide canonical representation of scientific knowledge To annotate experimental data to enable interpretation, comparison, and discovery across databases To facilitate knowledge-based applications for decision support, natural language-processing, data integration and other applications Scientists have adopted ontologies Monday, July 15, 13
  7. 7. Ontology development has changed, too or to any number of users anywhere in the world from a lone knowledge engineer to a few distributed users Monday, July 15, 13
  8. 8. Courtesy of Mark Musen Monday, July 15, 13
  9. 9. Collaborative Ontology Development • Collaborative • Several users contribute to a single developing ontology • There are mechanisms to carry out discussions and to reach consensus • Ontologies • From simple taxonomies • To expressive OWL ontologies Monday, July 15, 13
  10. 10. Ontologies That Are Being Developed Collaboratively Monday, July 15, 13
  11. 11. Gene Ontology (GO) • Developed by the Gene Ontology Consortium • Goal: create a single terminological resource for annotating genes and gene function from different model organisms: • drosophilla, mouse, e.coli, homo sapiens, ... • GO: 38,000 classes Monday, July 15, 13
  12. 12. Monday, July 15, 13
  13. 13. Key Resource: GO Annotations Manually curated over the past 10 years Publicly available 345,000 annotations for homo sapiens TP53 Gene product GO:0007569 cell aging GO Term PubMed article Manual GO Annotation Monday, July 15, 13
  14. 14. Monday, July 15, 13
  15. 15. The Gene Ontology Terminology for consistent description of gene products Issue Tracker Curators of biomedical databases GO Curators 3 full-time curators have access to edit GO Anyone in the community can submit an issue or request Monday, July 15, 13
  16. 16. Monday, July 15, 13
  17. 17. The NCI Thesaurus A reference ontology for cancer biology, translational science, and clinical oncology ~20 full-time editors making changes Changes are not immediately visible A “lead editor” who approves the changes, and assigns new tasks Monday, July 15, 13
  18. 18. International Classification of Diseases (ICD) Have you looked at your medical insurance bill lately? Monday, July 15, 13
  19. 19. International Classification of Diseases Monday, July 15, 13
  20. 20. ICD – Why should you care? Certificate of death Policy making Medical bills Monday, July 15, 13
  21. 21. Developing ICD-10: Revision process in the 20th century 8 Annual Revision Conferences (1982 - 89) 17 – 58 Countries participated 1- 5 person delegations Mainly Health Statisticians Manual curation List exchange Index was done later "Decibel” Method of discussion Output: Paper Copy Work in English only Limited testing in the field Monday, July 15, 13
  22. 22. ICD-11: the 21st century • ICD-11 is being developed as an OWL ontology • Being developed collaboratively, in an open editing process • Links to other ontologies, such as SNOMED CT • 33,000 classes Monday, July 15, 13
  23. 23. Over 250 domain experts from around the world Organized in groups, which edit different parts of the ontology T. Tudorache, S. Falconer, C. Nyulas, N. F. Noy and M. A. Musen Will Semantic Web Technologies Work for the Development of ICD-11? International Semantic Web Conference (ISWC 2010), In-Use Track, Shanghai, China Monday, July 15, 13
  24. 24. ICD-11 development process • Each night a snapshot of the commonly edited ontology is published in a public platform to encourage feedback from the larger community http://apps.who.int/classifications/ icd11/browse/f/en • Editorial workflow • Centrally overseen by WHO • Peer-reviewed process for the content and structure • Experts may add change proposals • WebProtégé used as the collaborative ontology development platform Monday, July 15, 13
  25. 25. Modeling ICD-11: Different views Monday, July 15, 13
  26. 26. Linearization Foundation: ICD categories with Definitions, synonyms Clinical descriptions Diagnostic criteria Causal mechanism Functional impact Primary care Morbidity Mortality Monday, July 15, 13
  27. 27. Multi-Linguality Monday, July 15, 13
  28. 28. Links to Other Terminologies Search in BioPortal Monday, July 15, 13
  29. 29. All properties are reified Multi-linguality External references Metadata Evidence Monday, July 15, 13
  30. 30. related to linguisticEntity : LinguisticEntity LanguageTerm id : xsd:string linearizationSpecification* : LinearizationSpecification definition : DefinitionTerm synonym* : LanguageTerm bodyPart* : BodyPartTerm ... ICDCategory source : xsd:string label : LinguisticEntity ... ReferenceTerm label : xsd:string language : xsd:string LinguisticEntity linearizationView : LinearizationValueSet linearizationParent : ICDCategoryType ... LinearizationSpecification id : xsd:string Term DomainConcept subclass of Courtesy of Tania Tudorache Monday, July 15, 13
  31. 31. Monday, July 15, 13
  32. 32. Ontology Development as a Collaborative Process • Ontology development is an inherently collaborative process • It is also inherently modular, so “stepping on someone else’s toes” is not a big issue • Users expect Web 2.0-style interaction: • feeds, emails • watched entities • Web interface • social-networking features Monday, July 15, 13
  33. 33. Dimensions of Collaborative Workflows •Ontology size • from 100s to 10,000s of concepts •Size of the community • Contributors (in some form): from 2-3 to dozens • Editors: from 1-2 to 20 •Control mechanisms • Variety of roles • Gatekeepers, etc. • Client-server editing •Discussion tools • mailing lists, message boards • face-to-face meetings, telecons • Synchronization and editing mechanisms • CVS, SVN Monday, July 15, 13
  34. 34. WebProtégé Monday, July 15, 13
  35. 35. “Google docs” for ontologies Monday, July 15, 13
  36. 36. Collaboration Features • Simultaneous editing • Change tracking • Threaded discussions for ontology entities and changes (notes, discussions, proposals, reviews) • Watching ontology entities and branches and notifications • Upload and sharing of ontologies • Download any revision of the ontology • Access policies • User interface customization for domain experts • Change analysis and statistics Monday, July 15, 13
  37. 37. Monday, July 15, 13
  38. 38. Notes and discussions Monday, July 15, 13
  39. 39. Monday, July 15, 13
  40. 40. Change tracking Monday, July 15, 13
  41. 41. Watching entities and branches Monday, July 15, 13
  42. 42. Download any snapshot in time Monday, July 15, 13
  43. 43. Research Challenges • Human-Computer Interaction: • How do we enable domain experts to contribute effectively? • What are the minimal sets of constructs necessary? • Change analysis: • Are there patterns in how users edit ontologies? • Can we use these patterns to guide user interfaces? • Community dynamics: • What are the dynamics in groups that develop ontologies collaboratively? • Are there explicit or implicit roles? • Do roles change over time? Monday, July 15, 13

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