Experiences from the NCBO OBO-to-OWL Mapping Effort Dilvan A. Moreira, University of São Paulo Mark A. Musen, Stanford University

OBO Format Evolved from DAG representation initially created for Gene Ontology Adopted by dozens of biomedical ontologies stored in the OBO repository Used by most GO-based data analysis tools Designed for human readability extensibility minimal redundancy

OWL – Web Ontology Language W3C recommendation Offers important advantages A well defined, standardized syntax and semantics Interoperability with ontologies created in other domains of science Growing support from open-source and commercial tools Editors Parsers Classifiers Reasoning systems

The NCI Thesaurus in Protégé-OWL

Why map from OBO to OWL? Many Bio-Ontologies are modeled in OWL (e.g., NCI Thesaurus, BioPAX, SNOMED-CT) OBO format has not been adopted outside the Bio-ontology community, where OWL is the recognized standard Bio-Ontologies need to interoperate with other ontologies used throughout e-science The standardization of OWL is leading to many commercial ontology-oriented tools that biologists might wish to use

Requirements for mapping OBO to OWL Map all OBO format constructs in use to OWL Make no assumptions other than those written in the OBO format specification itself Ensure no loss of information Enable round trip conversion (OBO to OWL and back again)

Mapping clarifies the OBO specification OBO syntax is not uniformly documented No complete BNF exists to define the grammar Some new constructs lack clear definitions and have not yet been used by the community OBO Semantics sometimes need be clarified using textual style guides that do not adopt formal representations

Both languages support two types of elements Semantic information defines classes and relationships about which computers can reason automatically Textual properties offer the intended meanings of ontology elements for human consumption; such entries include names, textual definitions, descriptions, usage notes, and so on

Example of Mapping format-version: 1.0 date: 28:11: :22 saved-by: dilvan auto-generated-by: OBO-Edit default-namespace: test ontology remark: Modified snipet of the cell ontology [Term]id: CL: name: cell def: "Minute protoplasmic masses that make up organized tissue." [MESH:A.11] [Term]id: CL: name: cell in vivo is_a: CL: ! Cell [Term]id: CL: name: nurse cell related_synonym: "nurse cell" [] xref_analog: FBbt: is_a: CL: ! cell in vivo relationship: develops_from CL: ! Cell … [Typedef] id: develops_from name: develops_fromis_transitive: true Modified snipet of the cell ontology T23:22:00 dilvan test ontology cell Minute protoplasmic … tissue. MESH:A.11 cell in vivo … develops_from … OBO OWL

OWL Converter Tab for OBO-Edit

OBO Converter Tab for Protégé

Results We converted all 40 OBO Format files in the OBO repository (November 2006) to OWL with no errors detected by Protégé Of these 40 files, 30 were converted back to OBO Format without loss of information, as evidenced by running the obodiff tool Of the remaining 10 files that could not make the round trip Five had illegal characters in some of their OBO ids Three used new OBO 1.2 constructs that did not pass obodiff criteria for equality Two had syntax errors in their original form

Conclusions A translator enables interconversion of OBO format and standard OWL Underspecification of OBO format has made the development of OBO-to-OWL translators difficult in the past Even when the formal specification is incomplete, languages such as OBO format often have de facto specifications based on usage patterns in the community Work with the OBO community enabled us to clarify and document underspecified elements of OBO format, enabling implementation of a robust translation system

Acknowledgments Stuart Aitkin John Day-Richter Suzanna Lewis Chris Mungall Nigam Shah