1. Supporting Collaborative Ontology Development in Protégé International Semantic Web Conference 2008 Tania Tudorache, Natalya F. Noy, Mark A. Musen Stanford University 28.. October 2008 Karlsruhe, Germany

2. Ontology development becomes collaborative Ontologies are developed collaboratively by a large groups of domain experts Ontologies are becoming larger Users are familiar to user-contributed content (Web 2.0)‏

3. Requirements Analysis Analysis of the collaboration processes in projects developing biomedical ontologies The CKC Challenge at WWW’08 in Banff:  get users to try the tools for collaborative construction of structured knowledge  collect feedback and provide forum for discussion  It was not a competition between the tools, most tools are not mature enough for that  Competition between users to encourage participation

4. Use cases of collaborative development in biomedical domain Gene Ontology (GO)‏ NCI Thesaurus BiomedGT OBI, BIRNLex, RadLex Open Biomedical Ontologies (OBO)‏ International Classification of Diseases (ICD-10)‏

5. The NCI Thesaurus collaborative development process Simultaneous editing in Protégé clients Custom UI for restricting user input and enforcing business rules Development cycle begins after baseline ~20 full-time editors making changes; 1 “lead editor” who approves the changes, and assigns new tasks Reference ontology for cancer biology, translational science, and clinical oncology

6. Tool Requirements Tools for discussion and reaching consensus  annotate components and, maybe, changes  have as an integral part of the development process Context for discussions on modeling decisions Record of changes and associated discussions and controversies Provenance and trust  support concept histories  have ways establish trust and credibility Personalized views of an ontology based on:  user’s role and tasks  user’s level of expertise  user’s trust network

7. Tool Requirements (cont.)‏ User roles and access control  fine-grained control for editing and viewing rights Flexible workflow support  configurable workflows  workflow-execution coupled with ontology development Support for different levels of expressiveness Scalability, reliability and robustness

8. The Protégé ontology editor Free, open source ontology editor and knowledge-base framework Protégé 3 (OWL 1.0, RDF(S), Frames, DB backend)‏ Protégé 4 (OWL 2.0, import/export to several formats)‏ Java-based, plug-in architecture Strong community: over 100.000 users

9. Collaborative Protégé Features Extension of existing Protégé system Support for:  annotating ontology components and changes in the ontology  discussion threads  proposals and voting  searching and filtering  defining users, groups, policies Works in Protégé 3.x OWL and Frames Available in multi-user and stand-alone modes Distributed with Protégé installation http://protege.stanford.edu/doc/collab-protege/

10. Collaborative Protégé GUI has annotations Annotations Annotation details Collaborative Tabs

11. Basic collaborative mechanism in Protégé Ontology editor component:  basic ontology editing functionalities Annotation component:  user ontology is annotated with annotation instances from the Annotation ontology Change tracking component:  changes are stored as instance of the Annotation ontology

12. Ontologies for supporting the collaborative development process We used ontologies for representing: Ontology components (e.g., classes, properties, individuals)‏ Changes (e.g., Domain changed for a property)‏ Roles (e.g., Manager, Editor, SME, etc.)‏ Annotations (e.g., comments on classes, or changes)‏

13. The Changes & Annotation Ontology (ChAO)‏

14. Changes API Annotations API Workflow API Policy Manager... Ontology Access API NCI Thesaurus Guidelines Ontology Gene Ontology... Ontologies supporting the collaboration process API access Ontology repository The Collaboration Framework

15. The Collaborative Framework + Clients Collaborative Protégé WebProtégé Collaborative Framework

16. Annotations and Discussion Threads Annotations are linked to a specific ontology component Different types of annotations Annotations types can be extended with no extra coding Users may annotate:  classes  properties  individuals  the ontology as a whole Annotations may be filtered and searched based on different criteria

17. Changes Tab See the history of a concept Users may comment on changes; for example on a class rename operation or on a change of a domain property Browse the change details (e.g. author, creation date, sub- changes, etc.)

18. Chat Tab Exchange live messages between users connected to the same Protégé server Supports HTML formatting (hyperlinks, bold, italics, etc.)‏ Internal links to ontology entities (e.g., @'Gene')‏ Chat available also as a Tab plug-in

19. WebProtégé – an alternative client for Collaborative Protégé WebProtégé is an open source light-weight ontology editor for the Web It is a Collaborative Protégé client Main features of WebProtégé:  Browsing of ontologies on the Web  Lightweight ontology editing  Designed using a portal metaphor: The user interface is composed of reusable components, called portlets  Customizable UI by drag-n-drop and by showing or hiding different ontology tabs  Extensible: Developers may easily implement their own tabs and portlets

20. WebProtégé GUI – showing the NCI Thesaurus

21. Evaluation Performed formative evaluation in the ATHENA-DSS project – a clinical decision support system that generates guideline-based recommendations 3 editors evaluated the tool for one month without prior training Results:  Used mostly comments on instances  Used discussions to ask questions (e.g., modeling questions)‏

22. Evaluation (cont.)‏ Used annotations to document the narrative description of a guideline and a set of qualitative parameters  need to create custom annotation type: GuidelineComment  Need to link one annotation to multiple ontology components involved in the guideline description Other uses:  record the design rationale  explain a modeling approach  educate new users

23. Future directions Flexible workflow support integrated in the ontology development environment:  Proof of concept implementation is already available, but still needs to be done Supporting synchronous and asynchronous editing modes Usability study and subsequent improvements Integration with current work environment:  Issue trackers, RSS feeds, Calendar Porting the collaborative framework and the rich clients to Protégé 4

24. Supporting Collaborative Ontology Development in Protégé International Semantic Web Conference 2008 Tania Tudorache, Natalya F. Noy, Mark A. Musen Stanford University 28.. October 2008 Karlsruhe, Germany