DIN Profile (Alumni, 2000-2003)

Design and Implementation of Pharmacogenetic Network

Abstract (September, 2003 Update)

Goals

To support individual PGRN research groups with respect to various informatics needs. These include:

• Assistance in development of Web sites, local data management, and assistance in preparation of data for submission to PharmGKB
• Provision of a Web-accessible database system, TrialDB, for the support of institutional as well as multi-centric clinical studies.
• Creation of a Web-accessible database for managing information about resources (available to the entire scientific community, or restricted to use within the PGRN) that individual PGRN research groups choose to make available. A "resource" may be: software, expertise, biospecimens such as DNA or tissue samples, or a service (such as a drug assay).

Progress

• Web site development, Data Preparation:
  • We originally worked with the Relling group to create a liver biospecimens database that captures inventory information, genotyping data, and microsomal assay data. This database continues to be used in the Relling lab. We have subsequently developed a similar inventory database for the Ratain group for their lymphocyte specimens, and worked with the O'Connor lab to teach them how to build laboratory databases for various purposes.
  • We continue to collaborate with the Weinshilboum, Flockhart, Licinio and O'Connor groups. Working with Mathieu Wiepert of the Weinshilboum group, we have created a standalone Microsoft Access application that supports interactive data entry and, among other things, generates output that can be submitted to PharmGKB. This application can be deployed within a local-area-network, and assists individual groups in their local data management needs.
  • We have also developed a tool that merges data from dbSNP and other sources with locally generated laboratory data to display a diagram of a gene of interest, the SNPs at various positions along its length, and laboratory-specific data associated with each SNP, such as allele frequencies and associated phenotyping data.

• Provision of TrialDB:
  This is being used by the Licinio group for their study of depression in Mexican-American subjects. TrialDB itself is open-source freeware that is distributed under the GNU General Public License: its URL is at http://ycmi.med.yale.edu/TrialDB, from here access to the source code, the demonstration system, and the online help and documentation is provided.
• The Resources database:
  The current Web site, which is fully operational, is available at http://custard.med.yale.edu/PGRN_res/resources_list.aspx.
  This site will be hyperlinked from PharmGKB. More features will be added based on feedback from the
  PGRN members. Among these will be the ability for members of individual PGRN research groups to edit
  their own submissions online, as well as create new submissions via the Web.

DIPN Team