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J Bioinform Comput Biol. 2005 Jun;3(3):743-70.

Suregene, a scalable system for automated term disambiguation of gene and protein names.

Author information

1
Karolinska Institutet, SE-171 77 Stockholm, Sweden. rpodowski@cmmt.ubc.ca

Abstract

Researchers, hindered by a lack of standard gene and protein-naming conventions, endure long, sometimes fruitless, literature searches. A system that is able to automatically assign gene names to their LocusLink ID (LLID) in previously unseen MEDLINE abstracts is described. The system is based on supervised learning and builds a model for each LLID. The training sets for all LLIDs are extracted automatically from MEDLINE references in the LocusLink and SwissProt databases. A validation was done of the performance for all 20,546 human genes with LLIDs. Of these, 7344 produced good quality models (F-measure >0.7, nearly 60% of which were >0.9) and 13,202 did not, mainly due to insufficient numbers of known document references. A hand validation of MEDLINE documents for a set of 66 genes agreed well with the system's internal accuracy assessment. It is concluded that it is possible to achieve high quality gene disambiguation using scaleable automated techniques.

PMID:
16108092
[Indexed for MEDLINE]

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