The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies

Gautam K. Parai (1) , Clement Jonquet (1) , Rong Xu (1) , Mark A. Musen (1) , Nigam H. Shah (1)

1 BMIR - Stanford Center for BioMedical Informatics Research

Domain specific biomedical lexicons are extensively used by researchers for natural language processing tasks. Currently these lexicons are created manually by expert curators and there is a pressing need for automated methods to compile such lexicons. The Lexicon Builder Web service addresses this need and reduces the investment of time and effort involved in lexicon maintenance. The service has three components: Inclusion – selects one or several ontologies (or its branches) and includes preferred names and synonym terms; Exclusion – filters terms based on the term's Medline frequency, syntactic type, UMLS semantic type and match with stopwords; Output – aggregates information, handles compression and output formats. Evaluation demonstrates that the service has high accuracy and runtime performance. It is currently being evaluated for several use cases to establish its utility in biomedical information processing tasks. The Lexicon Builder promotes collaboration, sharing and standardization of lexicons amongst researchers by automating the creation, maintainence and cross referencing of custom lexicons.

Mots clés: biomedical lexicons; biomedical ontologies; natural language processing

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Traitement du texte et du document

Gautam K. Parai, Clement Jonquet, Rong Xu, Mark A. Musen, Nigam H. Shah. The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies. American Medical Informatics Association Annual Symposium, AMIA'10, Nov 2010, Washington, DC, United States. pp.6. ⟨hal-00558033⟩