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Gene annotation from scientific literature using mappings between keyword systems

Item Type:Article
Title:Gene annotation from scientific literature using mappings between keyword systems
Creators Name:Perez, A.J. and Perez-Iratxeta, C. and Bork, P. and Thode, G. and Andrade-Navarro, M.A.
Abstract:Motivation: The description of genes in databases by keywords helps the non-specialist to quickly grasp the properties of a gene and increases the efficiency of computational tools that are applied to gene data (e.g. searching a gene database for sequences related to a particular biological process). However, the association of keywords to genes or protein sequences is a difficult process that ultimately implies examination of the literature related to a gene. Results: To support this task, we present a procedure to derive keywords from the set of scientific abstracts related to a gene. Our system is based on the automated extraction of mappings between related terms from different databases using a model of fuzzy associations that can be applied with all generality to any pair of linked databases. We tested the system by annotating genes of the SWISS-PROT database with keywords derived from the abstracts linked to their entries (stored in the MEDLINE database of scientific references). The performance of the annotation procedure was much better for SWISS-PROT keywords (recall of 47%, precision of 68%) than for Gene Ontology terms (recall of 8%, precision of 67%).
Keywords:Abstracting and Indexing, Algorithms, Documentation, Gene Expression Profiling, Natural Language Processing, Periodicals, Protein Databases, Proteins, Protein Sequence Analysis, Terminology
Source:Bioinformatics
ISSN:1367-4803
Publisher:Oxford Univ Press (England)
Volume:20
Number:13
Page Range:2084-2091
Date:1 January 2004
Official Publication:https://doi.org/10.1093/bioinformatics/bth207
PubMed:View item in PubMed

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