Spotlight on Pharmacogenomics Knowledge Base (PharmGKB)

This week, we profile thePharmacogenomics Knowledge Base (PharmGKB) a knowledge base professional scientists and developers at Stanford University. Dr. Michelle Whirl-Carrillo, the Associate Director of PharmGKB, kindly answered our questions.

  1. In one tweet or less, introduce us to your tool/database/website.
    PharmGKB is the premier resource of knowledge in pharmacogenomics, the study of how individual genetic variation influences drug response.
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  3. Why is your knowledge base unique and special?
  4. PharmGKB is the largest publicly-available pharmacogenomics knowledge resource, encompassing genotype-phenotype relationships from primary literature as well as clinical-level information including dosing guidelines, approved drug labels and potentially clinically actionable gene-drug associations. PharmGKB collects, curates and disseminates knowledge about the impact of human genetic variation on drug responses through the following activities:

    • Annotate genetic variants and gene-drug-disease relationships via literature reviews.
    • Summarize important pharmacogenomic genes, associations between genetic variants and drugs, and drug pathways.
    • Curate FDA drug labels containing pharmacogenomic information.
    • Enable consortia examining important questions in pharmacogenomics.
    • Curate and participate in writing pharmacogenomic-based drug dosing guidelines.
    • Contribute to clinical implementation projects for pharmacogenomics through collaborations.
    • Publish pharmacogenomic-based drug dosing guidelines, very important pharmacogene summaries and drug-centered pathways.
    • Display all information on the website and provide comprehensive downloads.
  5. Who is your target audience?
    PharmGKB has a broad audience that includes primary pharmacogenomic researchers, students ranging from graduate school to high school or younger, clinicians (medical doctors, pharmacists, genetics counselors, etc.) who are interested in implementing pharmacogenomics in the clinic, and bioinformaticians and data/text miners.
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  7. Why did you create your knowledge base?
    PharmGKB aims to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs by providing a central repository of pharmacogenomic knowledge.
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  9. What is your greatest success story so far?
    It is difficult to point to one greatest success story, but PharmGKB receives much positive feedback, including many emails about how users have used PharmGKB information and images in their lectures, conference presentations, grant applications and papers.
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  11. What improvements are coming in the future?
    We hope to provide several new interfaces to PharmGKB in the future that will provide specialized entry points to the knowledge for targeted audiences. For example, a network-based viewer may be valuable to a researcher investigating all known genetic associations for a particular therapy, while a clinician may want a mobile, easy-to-query system that provides drug dosing guidelines for a specific patient genotype. A bioinformatician may prefer a way to directly query the knowledge base and download large amounts of information without using a browser interface. PharmGKB hopes to provide these methods and more for accessing knowledge in the coming year or so.
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  13. Who is the team behind your knowledge base?
    PharmGKB is run by an excellent team of professional scientists and developers at Stanford University. The project PIs are Dr. Russ Altman and Dr. Teri Klein. A listing of team members, their positions and background information can be found on the PharmGKB website at: http://www.pharmgkb.org/aboutUs.jsp

Thanks to Dr. Michelle Whirl-Carrillo, for guiding us through their extremely useful and FREE knowledge base. Be sure to check out their plugin in the plugin library.


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