In situ migration of handcrafted ontologies to reason-able forms

A methodology for in situ migration of a handcrafted Directed Acyclic Graph (DAG), to a formal and expressive OWL version is presented. Well-known untangling methodologies recommend wholesale re-coding. Unable to do this, we have tackled portions of the DAG, lexically dissecting term names to property-based descriptions in OWL. The different levels of expressivity are presented in a model called the ''feature escalator'', where the user can choose the level needed for the application and the expressivity that delivers requirement. The results of applying the methodology to some areas of the gene ontology (GO) demonstrate the validity of the methodology.

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

[2]  Carole A. Goble,et al.  A short study on the success of the Gene Ontology , 2004, J. Web Semant..

[3]  G. A. Ringland,et al.  Approaches to knowledge representation: an introduction , 1988 .

[4]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[5]  Christopher J. Mungall,et al.  Obol: Integrating Language and Meaning in Bio-Ontologies , 2004, Comparative and functional genomics.

[6]  Sean Bechhofer,et al.  Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL , 2007, BMC Bioinformatics.

[7]  Robert Stevens,et al.  The Manchester OWL Syntax , 2006, OWLED.

[8]  Carol A. Bean,et al.  Relationships in the Organization of Knowledge , 2001, Information Science and Knowledge Management.

[9]  Thomas R. Gruber,et al.  A Translation Approach to Portable Ontologies , 1993 .

[10]  Steffen Staab,et al.  DILIGENT: Towards a fine-grained methodology for Distributed, Loosely-controlled and evolving Engineering of oNTologies , 2004, ECAI.

[11]  Carole A. Goble,et al.  A Methodology to Migrate the Gene Ontology to a Description Logic Environment Using DAML+OIL , 2002, Pacific Symposium on Biocomputing.

[12]  Betsy L. Humphreys,et al.  Relationships in Medical Subject Headings (MeSH) , 2001 .

[13]  Carole A. Goble,et al.  Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation , 2003, Bioinform..

[14]  Alan L. Rector,et al.  Web ontology segmentation: analysis, classification and use , 2006, WWW '06.

[15]  Alan L. Rector,et al.  Integrating existing drug formulation terminologies into an HL7 standard classification using OpenGALEN , 2001, AMIA.

[16]  J E Rogers,et al.  Rubrics to dissections to GRAIL to classifications. , 1997, Studies in health technology and informatics.

[17]  Christopher J. Mungall Obol: integrating language and meaning in bio-ontologies: Conference Papers , 2004 .

[18]  Michael Darsow,et al.  ChEBI: a database and ontology for chemical entities of biological interest , 2007, Nucleic Acids Res..

[19]  Ian Horrocks,et al.  A Logical Framework for Modular Integration of Ontologies , 2006 .

[20]  K. Bretonnel Cohen,et al.  The Compositional Structure of Gene Ontology Terms , 2003, Pacific Symposium on Biocomputing.

[21]  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.

[22]  Werner Ceusters,et al.  Reconciling users' needs and formal requirements: issues in developing a reusable ontology for medicine , 1998, IEEE Transactions on Information Technology in Biomedicine.

[23]  B Marshall,et al.  Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource , 2004, Nucleic Acids Res..

[24]  Mike Uschold,et al.  A Framework for Understanding and Classifying Ontology Applications , 1999 .

[25]  U. Hahn,et al.  The Semantics of Procedures and Diseases in SNOMED® CT , 2006, Methods of Information in Medicine.

[26]  Thomas R. Gruber,et al.  A translation approach to portable ontology specifications , 1993, Knowl. Acquis..

[27]  Ian Horrocks,et al.  OILing the way to machine understandable bioinformatics resources , 2002, IEEE Transactions on Information Technology in Biomedicine.

[28]  Diego Calvanese,et al.  The Description Logic Handbook: Theory, Implementation, and Applications , 2003, Description Logic Handbook.

[29]  Michael Uschold,et al.  Ontologies: principles, methods and applications , 1996, The Knowledge Engineering Review.

[30]  Ian Horrocks,et al.  A Logical Framework for Modularity of Ontologies , 2007, IJCAI.

[31]  Mark Fischetti,et al.  Weaving the web - the original design and ultimate destiny of the World Wide Web by its inventor , 1999 .

[32]  Alan L. Rector,et al.  Untangling taxonomies and relationships: personal and practical problems in loosely coupled development of large ontologies , 2001, K-CAP '01.

[33]  Ian Horrocks,et al.  Building a bioinformatics ontology using OIL , 2002, IEEE Transactions on Information Technology in Biomedicine.