Paper: TX Task: Automatic Detection of Focus Organisms in Biomedical Publications

ACL ID W09-1310
Title TX Task: Automatic Detection of Focus Organisms in Biomedical Publications
Venue Workshop on Biomedical Natural Language Processing
Session
Year 2009
Authors

In biomedical information extraction (IE), a central problem is the disambiguation of am- biguous names for domain specific entities, such as proteins, genes, etc. One important dimension of ambiguity is the organism to which the entities belong: in order to disam- biguate an ambiguous entity name (e.g. a pro- tein), it is often necessary to identify the spe- cific organism to which it refers. In this paper we present an approach to the detection and disambiguation of the focus or- ganism(s), i.e. the organism(s) which are the subject of the research described in scientific papers, which can then be used for the disam- biguation of other entities. The results are evaluated against a gold stan- dard derived from IntAct annotations. The evaluation suggests that the results may al- ready be u...