Medical College of Wisconsin
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OntoMate: a text-mining tool aiding curation at the Rat Genome Database. Database (Oxford) 2015;2015 PMID: 25619558 PMCID: PMC4305386

Pubmed ID





The Rat Genome Database (RGD) is the premier repository of rat genomic, genetic and physiologic data. Converting data from free text in the scientific literature to a structured format is one of the main tasks of all model organism databases. RGD spends considerable effort manually curating gene, Quantitative Trait Locus (QTL) and strain information. The rapidly growing volume of biomedical literature and the active research in the biological natural language processing (bioNLP) community have given RGD the impetus to adopt text-mining tools to improve curation efficiency. Recently, RGD has initiated a project to use OntoMate, an ontology-driven, concept-based literature search engine developed at RGD, as a replacement for the PubMed ( search engine in the gene curation workflow. OntoMate tags abstracts with gene names, gene mutations, organism name and most of the 16 ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. All listed terms are linked both to data entry boxes and a term browser in the curation tool. OntoMate also provides user-activated filters for species, date and other parameters relevant to the literature search. Using the system for literature search and import has streamlined the process compared to using PubMed. The system was built with a scalable and open architecture, including features specifically designed to accelerate the RGD gene curation process. With the use of bioNLP tools, RGD has added more automation to its curation workflow. Database URL:

Author List

Liu W, Laulederkind SJ, Hayman GT, Wang SJ, Nigam R, Smith JR, De Pons J, Dwinell MR, Shimoyama M


Melinda R. Dwinell PhD Center Associate Director, Associate Professor in the Physiology department at Medical College of Wisconsin
Mary E. Shimoyama PhD Associate Professor in the Biomedical Engineering department at Medical College of Wisconsin


2-s2.0-85051605173   7 Citations

MESH terms used to index this publication - Major topics in bold

Data Mining
Databases, Nucleic Acid
Gene Ontology
Natural Language Processing
jenkins-FCD Prod-331 a335b1a6d1e9c32173c9534e6f6ff51494143916