semantic infrastructure to enable collaboration in ontology development
DESCRIPTION
This talk was presented at the 2011 International Conference on Collaboration Technologies and SystemsIn many scientific disciplines, and in biomedicine in particular, researchers rely on ontologies to enable them to annotate and inte- grate their data. These ontologies are living and constantly evolving artifacts and the ontology authors must rely on their user community to ensure that the coverage of the ontologies is sufficient for annotations and other tasks for which users deploy the ontologies.We have developed a distributed collaborative mechanism to enable users to provide feedback to ontology authors, to request new terms, and to use provisional terms in their applications. The ontology authors can use the same infrastructure to explore this feedback in their ontology-editing environment, to update the ontology, to record their decisions on the users’ requests, and to publish both the updated ontology and the information on how they acted on the requested changes.Specifically, we present the Notes ontology that we use to rep- resent the different types of user feedback and change requests, the service-oriented Notes API to access the information that con- forms to this ontology, and the two ontology editing and publishing environments—WebProtégé and NCBO BioPortal—that use this API to provide services for their users.TRANSCRIPT
Semantic Infrastructure to Enable Collaboration in Ontology DevelopmentPresenter: Paul R. AlexanderAuthors: Paul R. Alexander, Csongor Nyulas, Tania Tudorache,Patricia L. Whetzel, Natalya F. Noy, Mark A. MusenStanford Center for Biomedical Informatics Research, Stanford University, US
2011 International Conference on Collaboration Technologies and SystemsSemantic Technologies for Information-Integrated CollaborationWednesday, May 25 2011
Notes Primer
Introduction
What is an ontology?
Ontology development and publication
Problems working together
Notes and provisional terms
Conclusion
What is an Ontology?
Ontology Development
Editing
Protégé, WebProtégé
Publishing
BioPortal
Biomedical Resource Ontology
MIAMExpress
Gene Ontology
Notes Use Cases
Consensus-building (BRO)
New term requests (MIAMExpress, Phenex)
Data annotation (GO)
Automated requests (ODIE)
Requirements for Notes
Comprised of structured information
Accessed via REST web service
Placed into an archived state
Extended via domain-specific notes types
Types of Notes
Notes APIs
Notes UsageComments/Requests
Notes UsageEditor Workflow
Notes UsageEditor Workflow
Provisional Terms
Requirements for Provisional Terms
Term creation
Query and filter
Get implemented term
Future Work
Further integration of BioPortal and WebProtégé
Automation support for editors
Full-fledged ‘Term Marketplace’
Conclusion
Ontology-based architecture to support collaboration and feedback
Service-oriented, RESTful architecture allows multiple systems to access a common store
Provisional terms enable immediate use
http://bioportal.bioontology.orghttp://protege.stanford.edu