1. State of the Art for Ontology Repositories Frank Olken National Science Foundation CISE/IIS/III folken@nsf.gov Presentation to Ontology Summit NIST Gaithersburg, MD v05 April 28, 2008

2. F. Olken, Ontology Summit 20082 Disclaimer Opinions expressed in this talk are solely those of the author, and do not reflect the positions of either the National Science Foundation, CISE, IIS or Lawrence Berkeley National Laboratory.

3. April 28, 2008F. Olken, Ontology Summit 20083 This talk: I will address key issues in the design and implementation of ontology repositories and some of the major technologies being used to address these issues.

4. April 28, 2008F. Olken, Ontology Summit 20084 Outline What is an ontology repository? Why doe one want one? Macro vs. Micro Issues Implementation Issues

5. April 28, 2008F. Olken, Ontology Summit 20085 Implementation Issues Ontology acquisition, ingestion Macro vs. micro issues Centralized vs. Decentralized Ontology representation Ontology search, query Ontology Integration Auxiliary tools SOA, etc.

6. April 28, 2008F. Olken, Ontology Summit 20086 What is an Ontology Repository? System for storing, searching, retrieving multiple ontologies Support for ontology integration Variously: Tools for ontology creation, editing, visualization Tools for ontology annotation, curation,....

7. April 28, 2008F. Olken, Ontology Summit 20087 Multiple Ontologies This is the source of the hardest problems in building ontology repositories: Scale Diverse ontology representations Ontology integration (mapping) Namespace issues Complex provenance issues

8. April 28, 2008F. Olken, Ontology Summit 20088 Why would you want an OR? You need to deal with multiple ontologies Usual reasons for ontologies: Natural Language Processing support Data Integration, Exchange Data semantics Support for DB queries DB, application design Classification / Indexing of documents, etc. Creation / maintenance /use of controlled vocabularies

9. April 28, 2008F. Olken, Ontology Summit 20089 Ontology Acquisition Manual acquisition and loading e.g. XMDR Useful if ontology representations are very diverse. Spidering the web to find ontologies (e.g., Nutch) Google (etc.) search to find ontologies How does one recognize an ontology? Use of OWL, RDF, CL, etc. Lots of is-a, part-of relations... Comments that assert file is an ontology

10. April 28, 2008F. Olken, Ontology Summit 200810 Ontology Ingestion Parsing ontology, syntactic validation Consistency checking (no cycles in partial orders: taxonomies, partonomies) Conversion to common representation (?) Syntactic translation Semantic translation e.g., CWA vs. OWA Indexing, transitive closure computations,...

11. April 28, 2008F. Olken, Ontology Summit 200811 Centralized vs. Federated Architectures Centralized: collect ontologies into one place High startup, maintenance costs Fast retrieval, facilitates integration Federated: ontologies stay put Low startup, maintenance costs Less performance, reliability More requirements on ontology sites Hybrid Centralize ontology level metadata, indices Leave individual ontologies in place

12. April 28, 2008F. Olken, Ontology Summit 200812 Macro vs. Micro-level Issues Macro-level Searching across a collection of ontologies and their metadata Micro-level Searching, inferencing, within individual ontologies

13. April 28, 2008F. Olken, Ontology Summit 200813 Macro & Micro similarities Most (not all) macro and micro level issues are essentially the same and can use the same technologies for implementation.

14. April 28, 2008F. Olken, Ontology Summit 200814 Macro-level Support Over collections of ontologies Use an ontology of ontologies e.g., taxonomy of subject matter Ontology of ontology metadata

15. April 28, 2008F. Olken, Ontology Summit 200815 Ontology Search Text-based search Natural language definitions Symbols E.g., Lucene, UIMA Semantic Search Over ontology representation (RDF, OWL, CL) e.g., SPARQL, etc. e.g., faceted search (e.g., Siderean) e.g., navigation over taxonomies, etc.

16. April 28, 2008F. Olken, Ontology Summit 200816 Ontology Representations Text Frames (OBO) Graphs (RDF) Logics (OWL-DL, OWL Full, CL)

17. April 28, 2008F. Olken, Ontology Summit 200817 Text Representation Obvious candidate for ontology representation of informal ontologies, with natural language definitions, etc..... A lowest common denominator representation for more formal ontology representations Readily supports handling diverse ontology representations (must add tags for underlying ontology representation language) Only supports text search directly

18. April 28, 2008F. Olken, Ontology Summit 200818 Frame Representations Each frame is a collection of: (slot, value) pairs or (slot, value list) Originally deployed in Lisp Secondary Storage Each frame is a BLOB Or, decompose into finer grained DB entries Current uses: OBO (open biological ontology) format

19. April 28, 2008F. Olken, Ontology Summit 200819 Graph Representations a.k.a. Semantic networks, semantic graphs Examples: RDF, RDF schemas, XLinks List of edges, each edge: Subject Predicate (relation name, attribute name) Object (or attribute value) Very flexible Only support binary relations directly

20. April 28, 2008F. Olken, Ontology Summit 200820 Types of Graphs Trees Simple Taxonomies (isa), Partonomies (partof) Multi-faceted Classifications Taxonomies with multiple facets e.g.., Vehicles: purpose, propulsion, wheels, axles, color Directed acyclic graphs Multiple inheritance Partial orders

21. April 28, 2008F. Olken, Ontology Summit 200821 Types of graphs Arbitrary directed graphs Allows arbitrary binary relationships Named graphs Allows separate inclusion hierarchy Allow edges to point to/from subgraphs

22. April 28, 2008F. Olken, Ontology Summit 200822 Partial Orders Many ontologies are Partial Orders (i.e, directed acyclic graphs), e.g., taxonomies, partonomies,... Mappings among partial ordered ontologies should be order preserving See work of Cliff Joslyn (PNNL)

23. April 28, 2008F. Olken, Ontology Summit 200823 Note: RDF are collections of edges (triples) No naked nodes allowed

24. April 28, 2008F. Olken, Ontology Summit 200824 Graph Implementations Represent graph as: Triple store (as on previous slide) Quad store (support named graphs) Standalone system, relational DBMS, column store

25. April 28, 2008F. Olken, Ontology Summit 200825 Quad stores & Named graphs Quad stores allow named graphs (named graph, subject, predicate, object) Named graphs (quads) allow one to name subgraphs (collections of edges) and to refer to them by name Hence, subjects and objects are no longer just nodes, but may be subgraphs (collections of edges)

26. April 28, 2008F. Olken, Ontology Summit 200826 Secondary storage of graphs Long skinny relations Triples or quads Column stores (Monet DB, Vertica) Multiple indices sorted by: subject, predicate, object, combinations,... Clusters of edges (Cogito)

27. April 28, 2008F. Olken, Ontology Summit 200827 Semantic graph query languages SPARQL is now the primary candidate Undergoing W3C standardization

28. April 28, 2008F. Olken, Ontology Summit 200828 Logic-based Ontology Representations Description Logic (e.g., OWL-DL) Restricted to make it decidable and computationally tractable Typically, lacks cardinality constraints, arithmetic Datalog (Horn clause logic + recursion) Prolog based First Order Logic (e.g., Common Logic) IKL (FOL + name propositions)

29. April 28, 2008F. Olken, Ontology Summit 200829 Logic-based representations Precise, formal semantics Expressiveness (esp. FOL) Issues of scaling, decidability, computational tractability Esp. for FOL Description Logics growing usage DL + rules languages to approx. FOL

30. April 28, 2008F. Olken, Ontology Summit 200830 Ontology Integration Construct mappings between entities (concepts) in pairs of ontologies Mapping relations: same_as, is_a, part_of units_conversion Specify mappings via: frames, graphs,or logic Graph-based mappings (C. Joslyn, PNNL) Logic-based mappings (PROMPT, N. Noy)

31. April 28, 2008F. Olken, Ontology Summit 200831 Partial Orders Many ontologies are Partial Orders (i.e, directed acyclic graphs), e.g., taxonomies, partonomies,... Mappings among partial ordered ontologies should be order preserving See work of Cliff Joslyn (PNNL)

32. April 28, 2008F. Olken, Ontology Summit 200832 Materialization of Partial Orders Partial orders = taxonomies, partonomies Typically specified as direct edges Immediate is-a, or part-of relations Naïve implementation requires repeated traversal of the partial order graph. Materialization of the transitive closure of the partial order (e.g., taxonomy) can reduce query times However, initialization and maintenance are expensive in time and storage

33. April 28, 2008F. Olken, Ontology Summit 200833 Ontology Constraints Type constraints Range, domain constraints Cardinality constraints on relations DB Integrity constraints Functional dependencies Inclusion dependencies (foreign key constraints) Invertibility Disjointedness (of subclasses)

34. April 28, 2008F. Olken, Ontology Summit 200834 Need for Provenance Fiction: Ontologists write definitions ab initio Reality: Most definitions are written by: Administrators (e.g., Code of Federal Regulations) Legislatures (legislation) Judges (court decisions) Professional bodies (accounting regulations)

35. April 28, 2008F. Olken, Ontology Summit 200835 Implications for Provenance We need to track the provenance of definitions Typically this requires citations to external documents May also require tracking of individual definition decisions.... Varying granularity requirements Individual definitions Collections of axioms, definitions Examples: see ISO 11179, XMDR

36. April 28, 2008F. Olken, Ontology Summit 200836 Other Tools Ontology Creation tools Ontology Editors Ontology Differencing tools Ontology modularization tools (clustering, etc.) Ontology Export Ontology Visualization (e.g., graph visualization) Version management Access control

37. April 28, 2008F. Olken, Ontology Summit 200837 SOA: Service Oriented Architecture Very popular Permit distributed implementations Two major alternatives: REST (Representational State Transfer) Built on HTTP (get, put, delete, post operators) URL/URI addresses for all objects SOAP/WSDL Based on XML Remote Procedure Calls

38. April 28, 2008F. Olken, Ontology Summit 200838 REST vs SOAP REST Simple to implement Requires little more than: HTTP server XML parsers SOAP Much more software complexity Lots of software tooling from commercial vendors Better security ?

39. April 28, 2008F. Olken, Ontology Summit 200839 My advice on REST vs. SOAP: Use REST.

40. April 28, 2008F. Olken, Ontology Summit 200840 Ontology Repository Related Standards ISO/IEC 11179 Metadata Registries version 3.0 of Part 3) OMG ODM Ontology Definition Metamodel ISO 13250 Topic Maps XML Topic Maps Specification (topicmaps.org) W3C OWL recommendations W3C RDF recommendations

41. April 28, 2008F. Olken, Ontology Summit 200841 Ontology Related Standards ISO/IEC 24707 Common Logic ISO TC 37 Terminology Services Standards W3C SKOS Simple Knowledge Organization System Reference ISO/IEC 19763 Metamodel Framework for Interoperability (Ontology metadata)

42. April 28, 2008F. Olken, Ontology Summit 200842 Recapitulation Ontology Repositories support storage, search, retrieval of multiple ontologies and ontology integration Macro-level & Micro-level support and search pose similar problems A common ontology representation is desirable, but difficult Multiple ontology representations and ontology integration are the most difficult issues aspects.

43. April 28, 2008F. Olken, Ontology Summit 200843 Acknowledgements This work was supported by NSF IPA agreement with LBNL, IRD support. My earlier work on ontology repositories at LBNL was supported by EPA and DOD. The author would like to thank Joel Sachs, Mark Musen, Natasha Noy, Eric Neumann, Bob MacGregor, Cliff Joslyn, Kevin Keck, Elise Kendall, Mala Mehrotra, Dan Abadi, Deb McGuiness, et al. for their remarks to me about knowledge representation, ontology repositories and ontology mappings.

44. April 28, 2008F. Olken, Ontology Summit 200844 Contact Information Frank Olken National Science Foundation 4201 Wilson Blvd., Suite 1125 Arlington, VA 22230 Email: folken@nsf.govfolken@nsf.gov Tel: 703-292-8930 (receptionist) Tel: 703-292-7350 (direct)