Modeling a description logic vocabulary for cancer research

The National Cancer Institute has developed the NCI Thesaurus, a biomedical vocabulary for cancer research, covering terminology across a wide range of cancer research domains. A major design goal of the NCI Thesaurus is to facilitate translational research. We describe: the features of Ontylog, a description logic used to build NCI Thesaurus; our methodology for enhancing the terminology through collaboration between ontologists and domain experts, and for addressing certain real world challenges arising in modeling the Thesaurus; and finally, we describe the conversion of NCI Thesaurus from Ontylog into Web Ontology Language Lite. Ontylog has proven well suited for constructing big biomedical vocabularies. We have capitalized on the Ontylog constructs Kind and Role in the collaboration process described in this paper to facilitate communication between ontologists and domain experts. The artifacts and processes developed by NCI for collaboration may be useful in other biomedical terminology development efforts.

[1]  Scott Sanner.  Towards practical taxonomic classification for description logics on the Semantic Web , 2003 .

[2]  K. Lambert.  Philosophical Problems in Logic , 1970 .

[3]  Daniel G. Bobrow,et al.  On Overview of KRL, a Knowledge Representation Language , 1976, Cogn. Sci..

[4]  M S Tuttle,et al.  From meaning to term: semantic locality in the UMLS Metathesaurus. , 1991, Proceedings. Symposium on Computer Applications in Medical Care.

[5]  Diego Calvanese,et al.  The Description Logic Handbook , 2007 .

[6]  Eric Mays,et al.  K-Rep system overview , 1991, SGAR.

[7]  Alan L. Rector,et al.  Modularisation of domain ontologies implemented in description logics and related formalisms including OWL , 2003, K-CAP '03.

[8]  Patrick Henry Winston,et al.  The psychology of computer vision , 1976, Pattern Recognit..

[9]  Peter F. Patel-Schneider,et al.  Living wiht Classic: When and How to Use a KL-ONE-Like Language , 1991, Principles of Semantic Networks.

[10]  Deborah L. McGuinness,et al.  Ontologies Come of Age , 2003, Spinning the Semantic Web.

[11]  Marvin Minsky,et al.  A framework for representing knowledge , 1974 .

[12]  Franz Baader.  Appendix: description logic terminology , 2003 .

[13]  Mark S. Tuttle,et al.  NCI Thesaurus: Using Science-Based Terminology to Integrate Cancer Research Results , 2004, MedInfo.

[14]  Jules J. Berman.  Cancer Informatics: Essential Technologies for Clinical Trials , 2002 .

[15]  Scott Gustafson,et al.  caCORE: A common infrastructure for cancer informatics , 2003, Bioinform..

[16]  Alan L. Rector,et al.  Scale and context: issues in ontologies to link health- and bio-informatics , 2002, AMIA.

[17]  L. Ohno-Machado.  Journal of Biomedical Informatics , 2001 .

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

[19]  Dana S. Scott,et al.  Advice on Modal Logic , 1970 .

[20]  R. Goldblatt.  Topoi, the Categorial Analysis of Logic , 1979 .

[21]  Daniele Nardi,et al.  An Introduction to Description Logics , 2003, Description Logic Handbook.

[22]  Werner Nutt,et al.  Basic Description Logics , 2003, Description Logic Handbook.

[23]  Franz Baader,et al.  KRIS: Knowledge Representation and Inference System , 1991, SGAR.

[24]  James A. Hendler,et al.  The National Cancer Institute's Thésaurus and Ontology , 2003, J. Web Semant..

[25]  Gilberto Fragoso,et al.  Enhancing Quality of Retrieval Through Concept Edit History , 2003, AMIA.

[26]  Robert M. MacGregor,et al.  Inside the LOOM description classifier , 1991, SGAR.

[27]  Kent A. Spackman,et al.  Role grouping as an extension to the description logic of Ontylog, motivated by concept modeling in SNOMED , 2002, AMIA.

[28]  Ralf Küsters,et al.  Computing the Least Common Subsumer and the Most Specific Concept in the Presence of Cyclic ALN-Concept Descriptions , 1998, KI.

[29]  Frank J. Oles,et al.  Scalable and expressive medical terminologies. , 1996, Proceedings : a conference of the American Medical Informatics Association. AMIA Fall Symposium.