Structural methodologies for auditing SNOMED

SNOMED is one of the leading health care terminologies being used worldwide. As such, quality assurance is an important part of its maintenance cycle. Methodologies for auditing SNOMED based on structural aspects of its organization are presented. In particular, automated techniques for partitioning SNOMED into smaller groups of concepts based primarily on relationships patterns are defined. Two abstraction networks, the area taxonomy and p-area taxonomy, are derived from the partitions. The high-level views afforded by these abstraction networks form the basis for systematic auditing. The networks tend to highlight errors that manifest themselves as irregularities at the abstract level. They also support group-based auditing, where sets of purportedly similar concepts are focused on for review. The auditing methodologies are demonstrated on one of SNOMED's top-level hierarchies. Errors discovered during the auditing process are reported.

[1]  Olivier Bodenreider,et al.  Aggregating UMLS Semantic Types for Reducing Conceptual Complexity , 2001, MedInfo.

[2]  Adam Pease,et al.  Origins of The IEEE Standard Upper Ontology , 2004 .

[3]  Li Zhang,et al.  Auditing concept categorizations in the UMLS , 2004, Artif. Intell. Medicine.

[4]  Olivier Bodenreider,et al.  Circular hierarchical relationships in the UMLS: etiology, diagnosis, treatment, complications and prevention , 2001, AMIA.

[5]  James Geller,et al.  Representing the UMLS as an OODB: Modeling Issues and Advantages , 2000 .

[6]  Adam Pease,et al.  Linking Lixicons and Ontologies: Mapping WordNet to the Suggested Upper Merged Ontology , 2003, IKE.

[7]  William T. Hole,et al.  Discovering missed synonymy in a large concept-oriented Metathesaurus , 2000, AMIA.

[8]  Adam Pease,et al.  Towards a standard upper ontology , 2001, FOIS.

[9]  Naomi C. Broering,et al.  High performance medical libraries: Advances in information management for the virtual era , 1993 .

[10]  Olivier Bodenreider,et al.  Exploring semantic groups through visual approaches , 2003, J. Biomed. Informatics.

[11]  James J. Cimino,et al.  Research Paper: Auditing the Unified Medical Language System with Semantic Methods , 1998, J. Am. Medical Informatics Assoc..

[12]  James Geller,et al.  Research on structural issues of the UMLS - past, present, and future , 2003, J. Biomed. Informatics.

[13]  George Hripcsak,et al.  Research Paper: Knowledge-based Approaches to the Maintenance of a Large Controlled Medical Terminology , 1994, J. Am. Medical Informatics Assoc..

[14]  James Geller,et al.  Auditing the UMLS for redundant classifications , 2002, AMIA.

[15]  James Geller,et al.  The cohesive metaschema: a higher-level abstraction of the UMLS Semantic Network , 2002, J. Biomed. Informatics.

[16]  P J Haug,et al.  Designing a controlled medical vocabulary server: the VOSER project. , 1994, Computers and biomedical research, an international journal.

[17]  James Geller,et al.  Research Paper: Representing the UMLS as an Object-oriented Database: Modeling Issues and Advantages , 2000, J. Am. Medical Informatics Assoc..

[18]  Douglas B. Lenat,et al.  CYC: a large-scale investment in knowledge infrastructure , 1995, CACM.

[19]  M S Tuttle,et al.  Adding your terms and relationships to the UMLS Metathesaurus. , 1991, Proceedings. Symposium on Computer Applications in Medical Care.

[20]  Kent A. Spackman,et al.  SNOMED clinical terms: overview of the development process and project status , 2001, AMIA.

[21]  Ramanathan V. Guha,et al.  Cyc: toward programs with common sense , 1990, CACM.

[22]  James J. Cimino Battling Scylla and Charybdis: the search for redundancy and ambiguity in the 2001 UMLS metathesaurus , 2001, AMIA.

[23]  Olivier Bodenreider,et al.  An Object-oriented Model for Representing Semantic Locality in the UMLS , 2001, MedInfo.

[24]  John E. Mattison,et al.  Kaiser Permanente's Convergent Medical Terminology , 2004, MedInfo.

[25]  Alexa T. McCray,et al.  Representing biomedical knowledge in the UMLS semantic network , 1993 .

[26]  Werner Ceusters,et al.  Ontology-Based Error Detection in SNOMED-CT® , 2004, MedInfo.

[27]  James Geller,et al.  Model Formulation: Benefits of an Object-oriented Database Representation for Controlled Medical Terminologies , 1999, J. Am. Medical Informatics Assoc..

[28]  Betsy L. Humphreys,et al.  Technical Milestone: The Unified Medical Language System: An Informatics Research Collaboration , 1998, J. Am. Medical Informatics Assoc..

[29]  James Geller,et al.  Controlled Vocabularies in OODBs: Modeling Issues and Implementation , 2004, Distributed and Parallel Databases.

[30]  Werner Ceusters,et al.  Mistakes in medical ontologies: where do they come from and how can they be detected? , 2004, Studies in health technology and informatics.

[31]  Steven H. Brown,et al.  U.S. Department of Veterans Affairs Enterprise Reference Terminology Strategic Overview , 2004, MedInfo.

[32]  Carole D. Hafner,et al.  The State of the Art in Ontology Design: A Survey and Comparative Review , 1997, AI Mag..

[33]  H Gu,et al.  Partitioning an Object-Oriented Terminology Schema , 2001, Methods of Information in Medicine.

[34]  Hua Min,et al.  Consistency across the hierarchies of the UMLS Semantic Network and Metathesaurus , 2003, J. Biomed. Informatics.

[35]  John Mylopoulos,et al.  Ontologies for Knowledge Management: An Information Systems Perspective , 2004, Knowledge and Information Systems.

[36]  James Geller,et al.  Using OODB Modeling to Partition a Vocabulary in Structurally and Semantically Uniform Concept Groups , 2002, IEEE Trans. Knowl. Data Eng..

[37]  Moses Maimonides,et al.  A Guide for the Perplexed , 1954 .

[38]  Alexa T. McCray,et al.  Mapping the Gene Ontology Into the Unified Medical Language System , 2004, Comparative and functional genomics.

[39]  Christiane Fellbaum,et al.  Book Reviews: WordNet: An Electronic Lexical Database , 1999, CL.

[40]  P L Schuyler,et al.  The UMLS Metathesaurus: representing different views of biomedical concepts. , 1993, Bulletin of the Medical Library Association.

[41]  José L. V. Mejino,et al.  A reference ontology for biomedical informatics: the Foundational Model of Anatomy , 2003, J. Biomed. Informatics.

[42]  Yue Wang,et al.  Research Paper: Auditing as Part of the Terminology Design Life Cycle , 2006, J. Am. Medical Informatics Assoc..

[43]  George Hripcsak,et al.  A lexical metaschema for the UMLS semantic network , 2005, Artif. Intell. Medicine.

[44]  Alexa T. McCray,et al.  Concepts, Issues, and Standards. Current Status of the NLM's Umls Project: The Scope and Structure of the First Version of the UMLS Seoantic Network , 1990 .

[45]  David S. Johnson,et al.  Computers and Intractability: A Guide to the Theory of NP-Completeness , 1978 .