Disambiguation in the biomedical domain: the role of ambiguity type

Word Sense Disambiguation (WSD), the automatic identification of the meanings of ambiguous terms in a document, is an important stage in text processing. We describe a WSD system that has been developed specifically for the types of ambiguities found in biomedical documents. This system uses a range of knowledge sources. It employs both linguistic features, such as local collocations, and features derived from domain-specific knowledge sources, the Unified Medical Language System (UMLS) and Medical Subject Headings (MeSH). This system is applied to three types of ambiguities found in Medline abstracts: ambiguous terms, abbreviations with multiple expansions and names that are ambiguous between genes. The WSD system is applied to the standard NLM-WSD data set, which consists of ambiguous terms from Medline abstracts, and was found to perform well in comparison with previously reported results. The system's performance and the contribution of each knowledge source depends upon the type of lexical ambiguity. 87.9% of the ambiguous terms are correctly disambiguated using a combination of linguistic features and MeSH terms, 99% of abbreviations are disambiguated by combining all knowledge sources, while 97.2% of ambiguous gene names are disambiguated using the MeSH terms alone. Analysis reveals that these differences are caused by the nature of each ambiguity type. These results should be taken into account when deciding which information to use for WSD and the level of performance that can be expected.