presentationExtractingSynonymousGeneandProtein.pptVIP

ISMB 2003 presentation Extracting Synonymous Gene and Protein Terms from Biological Literature Hong Yu and Eugene Agichtein Significance and Introduction Genes and proteins are often associated with multiple names Apo3, DR3, TRAMP, LARD, and lymphocyte associated receptor of death Authors often use different synonyms Information extraction benefits from identifying those synonyms Synonym knowledge sources are not complete Developing automate approaches for identifying gene/protein synonyms from literature Background-synonym identification Semantically related words Distributional similarity [Lin 98][Li and Abe 98][Dagan et al 95] “beer” and “wine” “drink”, “people”, “bottle” and “make” Mapping abbreviations to full forms Map LARD to lymphocyte associated receptor of death [Bowden et al. 98] [Hisamitsu and Niwa 98] [Liu and Friedman 03] [Pakhomov 02] [Park and Byrd 01] [Schwartz and Hearst 03] [Yoshida et al. 00] [Yu et al. 02] Methods for detecting biomedical multiword synonyms Sharing a word(s) [Hole 00] cerebrospinal fluid? cerebrospinal fluid protein assay Information retrieval approach Trigram matching algorithm [Wilbur and Kim 01] Vector space model cerebrospinal fluid?cer, ere, …, uid cerebrospinal fluid protein assay?cer,ere, …, say Background-synonym identification GPE [Yu et al 02] A rule-based approach for detecting synonymous gene/protein terms Manually recognize patterns authors use to list synonyms Apo3/TRAMP/WSL/DR3/LARD Extract synonym candidates and heuristics to filter out those unrelated terms ng/kg/min Advantages and disadvantages High precision (90%) Recall might be low, expensive to build up Background—Machine-learning Machine-learning reduces manual effort by automatically acquiring rules from data Unsupervised and supervised Semi-supervised Bootstrapping [Hearst 92, Yarowsky 95] [Agichtein and Gravano 00] Hyponym detection [Hearst 92] The bow lute, such as the Bambara ndang, is plucked and has an individual curved neck for each stri