June 1, 2001
Dear Editor:
The Pharmacogenetics Research Network and Knowledge Base is a consortium of investigators funded by NIH to study how human genetic variability contributes to observed variations in therapeutic drug responses. See http://www.nigms.nih.gov/Initiatives/PGRN/ for an overview of the initiative and a listing of the funded investigators and abstracts of their work (additional awards will be announced in mid-summer of 2001 at this site). Research conducted by the network includes identification of important genetic polymorphisms, functional studies of variant proteins, and studies that relate clinical drug responses to genetic variation.
A knowledge base is being developed (PharmGKB, http://www.pharmgkb.org) to which network investigators, as well as other scientists who study pharmacogenetics, will regularly submit their findings. PharmGKB will contain data sets that document genotypic and phenotypic variability within the context of pharmacogenetics and pharmacogenomics. Curators of PharmGKB will remove all personal identifiers from the data. PharmGKB is envisioned as one of the next generation of databases that explicitly links phenotype to genotype. It will be available to all researchers to enable future hypothesis-driven research.
To increase awareness of PharmGKB in the scientific community, the network would like to establish a relationship with one or more journals to publish summaries of submissions to PharmGKB. We anticipate that deposits to PharmGKB will include a range of types of information, such as: 1) observed variability in a gene of pharmacologic interest, 2) a range of phenotypic variability (at a molecular, cellular, or clinical level of investigation), or 3) combinations of these. A standard report format would be useful in order to routinely alert the scientific community to the availability of new data sets. It could contain a limited amount of free text description, a summary of the elements in a data set (highlighting the special features), and a pointer to the PharmGKB database with the detailed data.
This function would be a service for all in the research community, as well as point to an electronic archival reference. Although analysis and interpretation of some data will become parts of more complete journal articles, brief reports of PharmGKB submissions will focus simply on data elements. One example of this mode of publication is the presentation of data in a standard format by the journal Acta Crystallographica. This journal reports the structures of small molecules (see http://journals.iucr.org/c/issues/2001/01/00/me0110/me0110.pdf and ftp://ftp.iucr.org/pub/form.cif), which are always associated with deposits into the small molecule structure database.
The network would like to work with an interested journal to define a standard format for the three submission types listed above. If your journal wants to consider publishing regular summaries of new deposits, we ask that you submit a proposal of two pages (recommended) maximum length, exclusive of the list of editors. The proposal should include the following information:
- List of editors and associate editors of the journal
- Mission statement of the journal
- Circulation of the journal
- Impact factor of the journal
- Proposed times for publication of submissions (e.g., monthly, bimonthly)
- Format for publication (propose the characteristics of a format that can be generated automatically by the knowledge base)
- Companion pieces (will submissions be accompanied by commentaries or other articles?)
- Other unique strengths provided by the journal
Please send your proposal (electronic submission preferred) by July 20, 2001, to:
Rochelle M. Long, Ph.D.
National Institute of General Medical Sciences
National Institutes of Health
45 Center Drive MSC 6200
Room 2AS.49G
Bethesda, MD 20892-6200
Tel: 301-594-1826
Fax: 301-480-2802
longr@nigms.nih.gov
Proposals will be considered by the Steering Committee of the Pharmacogenetics Research Network and Knowledge Base. It is anticipated that selections will be made by late summer 2001. Feel free to call either one of us if you have any questions.
Sincerely,
Rochelle M. Long, Ph.D.
NIH Program Director
Pharmacogenetics Research Network
Chief, Pharmacology and Physiology Branch
National Institute of General Medical Sciences, NIH |
Kathleen M. Giacomini, Ph.D.
Chair, Communications Subcommittee
Pharmacogenetics Research Network
Professor and Chair, Department of
Biopharmaceutical Sciences
University of California, San Francisco |
