OBO and OWL: Leveraging Semantic Web Technologies for the Life Sciences

OBO is an ontology language that has often been used for modeling ontologies in the life sciences. Its definition is relatively informal, so, in this paper, we provide a clear specification for OBO syntax and semantics via a mapping to OWL. This mapping also allows us to apply existing Semantic Web tools and techniques to OBO. We show that Semantic Web reasoners can be used to efficiently reason with OBO ontologies. Furthermore, we show that grounding the OBO language in formal semantics is useful for the ontology development process: using an OWL reasoner, we detected a likely modeling error in one OBO ontology.

[1]  H. Chertkow,et al.  Semantic memory , 2002, Current neurology and neuroscience reports.

[2]  Boris Motik,et al.  A Comparison of Reasoning Techniques for Querying Large Description Logic ABoxes , 2006, LPAR.

[3]  Ian Horrocks,et al.  Framework for an Automated Comparison of Description Logic Reasoners , 2006, SEMWEB.

[4]  Alan Ruttenberg,et al.  Experience Using OWL DL for the Exchange of Biological Pathway Information , 2005, OWLED.

[5]  Marvin Minsky,et al.  Semantic Information Processing , 1968 .

[6]  Frehiwot Fisseha,et al.  Reengineering Thesauri for New Applications: The AGROVOC Example , 2006, J. Digit. Inf..

[7]  Alice M. Mulvehill,et al.  Experiences Using OWL in Military Applications , 2005, OWLED.

[8]  Larry Wos,et al.  What Is Automated Reasoning? , 1987, J. Autom. Reason..

[9]  John Goodwin Experiences of Using OWL at the Ordnance Survey , 2005, OWLED.

[10]  Ian Horrocks,et al.  Automated Benchmarking of Description Logic Reasoners , 2006, Description Logics.

[11]  Frank Wolter,et al.  Monodic fragments of first-order temporal logics: 2000-2001 A.D , 2001, LPAR.

[12]  Jennifer Golbeck,et al.  Modeling a description logic vocabulary for cancer research , 2005, J. Biomed. Informatics.

[13]  Alan L. Rector,et al.  Ontological and Practical Issues in Using a Description Logic to Represent Medical Concept Systems: Experience from GALEN , 2006, Reasoning Web.

[14]  Andrea Preite-Martinez,et al.  An ontology of sstronomical object types for the Virtual Observatory , 2006 .

[15]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[16]  Peter F. Patel-Schneider,et al.  DLP System Description , 1998, Description Logics.

[17]  Tharam S. Dillon,et al.  Protein Ontology Development using OWL , 2005, OWLED.

[18]  Jeffrey M. Bradshaw,et al.  Applying KAoS Services to Ensure Policy Compliance for Semantic Web Services Workflow Composition and Enactment , 2004, SEMWEB.

[19]  Francesco M. Donini,et al.  Description logics of minimal knowledge and negation as failure , 2002, TOCL.

[20]  Sean Bechhofer,et al.  Igniting the OWL 1.1 Touch Paper: The OWL API , 2007, OWLED.

[21]  Boris Motik,et al.  Optimized Reasoning in Description Logics Using Hypertableaux , 2007, CADE.

[22]  James A. Hendler,et al.  A Tool for Working with Web Ontologies , 2005, Int. J. Semantic Web Inf. Syst..

[23]  Ian Horrocks,et al.  Just the right amount: extracting modules from ontologies , 2007, WWW '07.

[24]  Volker Haarslev,et al.  RACER System Description , 2001, IJCAR.

[25]  Holger Knublauch,et al.  The Protégé OWL Plugin: An Open Development Environment for Semantic Web Applications , 2004, SEMWEB.

[26]  Boris Motik,et al.  Bridging the gap between OWL and relational databases , 2007, WWW '07.

[27]  Christine Golbreich,et al.  The Foundational Model of Anatomy in OWL: Experience and Perspectives , 2006, OWLED.

[28]  Ian Horrocks,et al.  FaCT++ Description Logic Reasoner: System Description , 2006, IJCAR.

[29]  James A. Hendler,et al.  Debugging unsatisfiable classes in OWL ontologies , 2005, J. Web Semant..

[30]  Bijan Parsia,et al.  Pellet: An OWL DL Reasoner , 2004, Description Logics.