OntoMate: a text-mining tool aiding curation at the Rat Genome Database.

Journal: Database : the journal of biological databases and curation
Published Date: Jan 25, 2015

Abstract

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 (http://www.ncbi.nlm.nih.gov/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: http://rgd.mcw.edu.

Authors

  • Weisong Liu
    Human and Molecular Genetics Center, Medical College of Wisconsin, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI53226, USA.
  • Stanley J F Laulederkind
    Human and Molecular Genetics Center, Medical College of Wisconsin, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI53226, USA.
  • G Thomas Hayman
    Human and Molecular Genetics Center, Medical College of Wisconsin, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI53226, USA.
  • Shur-Jen Wang
    Human and Molecular Genetics Center, Medical College of Wisconsin, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI53226, USA sjwang@mcw.edu.
  • Rajni Nigam
    Human and Molecular Genetics Center, Medical College of Wisconsin, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI53226, USA.
  • Jennifer R Smith
    Human and Molecular Genetics Center, Medical College of Wisconsin, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI53226, USA.
  • Jeff De Pons
    Human and Molecular Genetics Center, Medical College of Wisconsin, Department of Quantitative Health Sciences, University of Massachusetts Medical School, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA.
  • Melinda R Dwinell
    Human and Molecular Genetics Center, Medical College of Wisconsin, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI53226, USA.
  • Mary Shimoyama
    Human and Molecular Genetics Center, Medical College of Wisconsin, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI53226, USA Human and Molecular Genetics Center, Medical College of Wisconsin, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI53226, USA.

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