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