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1. Garten Y, Altman RB: Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text. BMC Bioinformatics; 2009 Feb 05;10 Suppl 2:S6
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text.
  • BACKGROUND: Pharmacogenomics studies the relationship between genetic variation and the variation in drug response phenotypes.
  • The field is rapidly gaining importance: it promises drugs targeted to particular subpopulations based on genetic background.
  • The pharmacogenomics literature has expanded rapidly, but is dispersed in many journals.
  • It is challenging, therefore, to identify important associations between drugs and molecular entities--particularly genes and gene variants, and thus these critical connections are often lost.
  • Text mining techniques can allow us to convert the free-style text to a computable, searchable format in which pharmacogenomic concepts (such as genes, drugs, polymorphisms, and diseases) are identified, and important links between these concepts are recorded.
  • Availability of full text articles as input into text mining engines is key, as literature abstracts often do not contain sufficient information to identify these pharmacogenomic associations.
  • RESULTS: Thus, building on a tool called Textpresso, we have created the Pharmspresso tool to assist in identifying important pharmacogenomic facts in full text articles.
  • Pharmspresso parses text to find references to human genes, polymorphisms, drugs and diseases and their relationships.
  • It presents these as a series of marked-up text fragments, in which key concepts are visually highlighted.
  • To evaluate Pharmspresso, we used a gold standard of 45 human-curated articles.
  • Pharmspresso identified 78%, 61%, and 74% of target gene, polymorphism, and drug concepts, respectively.
  • CONCLUSION: Pharmspresso is a text analysis tool that extracts pharmacogenomic concepts from the literature automatically and thus captures our current understanding of gene-drug interactions in a computable form.
  • We have made Pharmspresso available at http://pharmspresso.stanford.edu.

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  • (PMID = 19208194.001).
  • [ISSN] 1471-2105
  • [Journal-full-title] BMC bioinformatics
  • [ISO-abbreviation] BMC Bioinformatics
  • [Language] ENG
  • [Grant] United States / NIGMS NIH HHS / GM / R24 GM061374; United States / NIGMS NIH HHS / GM / GM61374; United States / NLM NIH HHS / LM / T15 LM007033; United States / NIGMS NIH HHS / GM / U01 GM061374; United States / NLM NIH HHS / LM / LM007033
  • [Publication-type] Journal Article; Research Support, N.I.H., Extramural
  • [Publication-country] England
  • [Other-IDs] NLM/ PMC2646239
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