A chemical specialty semantic network for the unified medical language system

C. Paul Morrey, Yehoshua Perl, Michael Halper, Ling Chen, Huanying Gu

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


Background: Terms representing chemical concepts found the Unified Medical Language System (UMLS) are used to derive an expanded semantic network with mutually exclusive semantic types. The UMLS Semantic Network (SN) is composed of a collection of broad categories called semantic types (STs) that are assigned to concepts. Within the UMLS's coverage of the chemical domain, we find a great deal of concepts being assigned more than one ST. This leads to the situation where the extent of a given ST may contain concepts elaborating variegated semantics. A methodology for expanding the chemical subhierarchy of the SN into a finer-grained categorization of mutually exclusive types with semantically uniform extents is presented. We call this network a Chemical Specialty Semantic Network (CSSN). A CSSN is derived automatically from the existing chemical STs and their assignments. The methodology incorporates a threshold value governing the minimum size of a type's extent needed for inclusion in the CSSN. Thus, different CSSNs can be created by choosing different threshold values based on varying requirements. Results: A complete CSSN is derived using a threshold value of 300 and having 68 STs. It is used effectively to provide high-level categorizations for a random sample of compounds from the "Chemical Entities of Biological Interest" (ChEBI) ontology. The effect on the size of the CSSN using various threshold parameter values between one and 500 is shown. Conclusions: The methodology has several potential applications, including its use to derive a pre-coordinated guide for ST assignments to new UMLS chemical concepts, as a tool for auditing existing concepts, inter-terminology mapping, and to serve as an upper-level network for ChEBI.

Original languageEnglish (US)
Article number9
JournalJournal of Cheminformatics
Issue number5
StatePublished - May 2012

All Science Journal Classification (ASJC) codes

  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Computer Graphics and Computer-Aided Design
  • Library and Information Sciences


  • Chemical
  • Chemical Entities of Biological Interest
  • Chemical characterization
  • Controlled
  • Models
  • Semantic network
  • Semantics
  • Unified Medical Language System
  • Vocabulary


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