NCBO Webinar Series - Parsa Mirhaji, Dec. 2 Print
Written by Virginia Gonzalez   
Wednesday, 02 December 2009 13:27
The next NCBO Webinar will be held TOMORROW, December 2 at 10am PT. Please note there will not be a VOIP option and attendees must call into the teleconference.

The Webinar will be presented by Dr. Parsa Mirhaji, from The School of Health Information Sciences at the University of Texas at Houston. The title of the presentation will be “UMLS-SKOS: A Semantic Web Framework for Representation of Biomedical Terminological Knowledge using Simple Knowledge Organization System (SKOS)”. Below is information on how to join the online meeting and accompanying teleconference. For a schedule of the 2009-2010 presentations or for more information about the NCBO Seminar series, see:

UMLS-SKOS: A Semantic Web Framework for Representation of Biomedical Terminological Knowledge using Simple Knowledge Organization System (SKOS)  


 SKOS is a Semantic Web framework for representing thesauri, classification schemes, subject heading systems, controlled vocabularies, and taxonomies. It enables novel ways of representing terminological knowledge and its linkage with domain knowledge in unambiguous, reusable, and encapsulated fashion within computer applications. According to the National Library of Medicine, the UMLS Knowledge Source (UMLS-KS) integrates and distributes key terminology, classification and coding standards, and associated resources to promote creation of more effective and interoperable biomedical information systems and services “that behave as if they ‘understand’ the meaning of the language of biomedicine and health”. However the current information representation model utilized by UMLS-KS itself is not conducive to computer programs effectively retrieving and automatically and unambiguously interpreting the ‘meaning’ of the biomedical terms and concepts and their relationships.  

In this presentation we propose using Simple Knowledge Organization System (SKOS) as an alternative to represent the body of knowledge incorporated within the UMLS-KS within the framework of the Semantic Web technologies. We also introduce our conceptualization of a transformation algorithm to produce an SKOS representation of the UMLS-KS that integrates UMLS-Semantic Network, the UMLS-Metathesaurus complete with all its source vocabularies as a unified body of knowledge along with appropriate information to trace or segregate information based on provenance and governance information. Our proposal and method is based on the idea that formal and explicit representation of any body of knowledge enables its unambiguous, and precise interpretation by automated computer programs. The consequences of such undertaking would be at least three fold: 1) ability to automatically check inconsistencies and errors within a large and complex body of knowledge, 2) automated information interpretation, integration, and discovery, and 3) better information sharing, repurposing and reusing (adoption), and extending the knowledgebase within a distributed and collaborative community of researchers. We submit that UMLS-KS is no exception to this and may benefit from all those advantages if represented fully using a formal representation language. Using SKOS in combination with the transformation algorithm introduced in this presentation are our first steps in that direction. We explain our conceptualization of the algorithms, problems we encountered and how we addressed them with a brief gap analysis to outline the road ahead of us. At the end we also present several use cases from our laboratories at the School of Health information Sciences utilizing this artifact.


Topic: NCBO Seminar Series 
Date: Wednesday, December 2, 2009  
Time: 10:00 am, Pacific Standard Time (San Francisco, GMT-08:00) 
Meeting Number: 926 719 478 
Meeting Password: ncbomeeting 

To join the online meeting (Now from iPhones too!) 
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Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
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Last Updated on Wednesday, 02 December 2009 13:35