Word sense disambiguation by selecting the best semantic type based on journal descriptor indexing: Preliminary experiment

Susanne M. Humphrey, Willie J. Rogers, Halil Kilicoglu, Dina Demner-Fushman, Thomas C. Rindflesch

Research output: Contribution to journalArticlepeer-review


An experiment was performed at the National Library of Medicine® (NLM®) in word sense disambiguation (WSD) using the Journal Descriptor Indexing (JDI) methodology. The motivation is the need to solve the ambiguity problem confronting NLM's MetaMap system, which maps free text to terms corresponding to concepts in NLM's Unified Medical Language System® (UMLS®) Metathesaurus®. If the text maps to more than one Metathesaurus concept at the same high confidence score, MetaMap has no way of knowing which concept is the correct mapping. We describe the JDI methodology, which is ultimately based on statistical associations between words in a training set of MEDLINE® citations and a small set of journal descriptors (assigned by humans to journals per se) assumed to be inherited by the citations. JDI is the basis for selecting the best meaning that is correlated to UMLS semantic types (STs) assigned to ambiguous concepts in the Metathesaurus. For example, the ambiguity transport has two meanings: "Biological Transport" assigned the ST Cell Function and "Patient transport" assigned the ST Health Care Activity. A JDI-based methodology can analyze text containing transport and determine which ST receives a higher score for that text, which then returns the associated meaning, presumed to apply to the ambiguity itself. We then present an experiment in which a baseline disambiguation method was compared to four versions of JDI in disambiguating 45 ambiguous strings from NLM's WSD Test Collection. Overall average precision for the highest-scoring JDI version was 0.7873 compared to 0.2492 for the baseline method, and average precision for individual ambiguities was greater than 0.90 for 23 of them (51%), greater than 0.85 for 24 (53%), and greater than 0.65 for 35 (79%). On the basis of these results, we hope to improve performance of JDI and test its use in applications.

Original languageEnglish (US)
Pages (from-to)96-113
Number of pages18
JournalJournal of the American Society for Information Science and Technology
Issue number1
StatePublished - Jan 1 2006
Externally publishedYes

ASJC Scopus subject areas

  • Software
  • Information Systems
  • Human-Computer Interaction
  • Computer Networks and Communications
  • Artificial Intelligence


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