Request for Information (RFI): Input on the Development of a Knowledge Management Center for the "Illuminating the Druggable Genome" Program
Release Date: May 20, 2013
Response Date: June 15, 2013
National Institutes of Health (NIH)
Office of Strategic Coordination (Common Fund)
This Request for Information (RFI) is to solicit comments and ideas for the development of an informatics resource leading to a public web portal that would illuminate the unannotated, or “dark matter,” portion of the “Druggable Genome”.
The human genome has revealed a great deal about the human proteome, though significant portions of the latter remain unannotated. The “Druggable Genome” has been described as “…the subset of the ~30,000 genes in the human genome that express proteins able to bind drug-like molecules.” (Hopkins, AL, and Groom, CR. The druggable genome. Nature Reviews/Drug Discovery 1:727, 2002). About 1000-6000 proteins are considered “druggable” due to their sequence similarity to established or putative drug targets (Ovington, JP, Al-Lazikani, B, and Hopkins, AL. Nature Reviews Drug Discovery 5:993, 2006). However, a sub-set of ~400 proteins within this category is still largely uncharacterized. Many proteins that comprise this ‘dark matter’ of the Druggable Genome are members of the G-protein coupled receptor (GPCR), nuclear receptor (NR), ion channel and protein kinase families. The presumed druggability of these proteins and their potential roles in disease warrant further investigation.
The NIH intends to develop a new program, “Illuminating the Druggable Genome” (IDG) to increase the understanding of the properties and functions of unannotated proteins within four of the most commonly drug-targeted protein families, the GPCRs, NRs, ion channels, and protein kinases. Towards this goal, the IDG program is planning to initiate a Knowledge Management Center (KMC). The role of the KMC is to develop an integrated informatics solution that enables data accrual, storage, catalog, analysis, and dissemination of standardized/annotated information related to unannotated proteins in the four gene families listed above. This effort will include appropriate summaries of the literature, usable links to relevant subsets of data available in large repositories, lists of reagents, assays, small molecules, etc. The aim is to create a community resource that would provide researchers access to relevant information on the Druggable Genome that enables investigations into (1) the biochemical functions and (2) potential role(s) in physiology and disease of unannotated GPCRs, NRs, ion channels, and protein kinases.
To enable users of the KMC to efficiently query and retrieve data from multiple data resources, a user-friendly web portal will be developed. The KMC is also going to have essential curatorial activities as needed for each data type including relevant standards and metadata that will be crucial for further analysis.
In order to maximize the impact of this valuable community resource, and facilitate its use by scientists with a broad range of expertise, we seek input on this proposed knowledgebase and public web portal for the "Illuminating the Druggable Genome" program:
- Please comment on the most essential data elements or types needed for such a resource
- Given the context of what is provided in the background of this RFI, please comment on essential metadata and curation activities that should be considered
- Comment on crucial computational challenges that should be addressed
- Comment on challenges faced when using other community web portals
- Comment on the issues faced and expertise needed when balancing building complex user interfaces versus providing an Application Programming Interface for the community to access data efficiently
- Describe the functionalities/query tools that would be desirable in a community-based web portal to be constructed and linked to the knowledgebase
- Describe the current state of the art standards for a linked research database
- Describe the kind of software tools that would allow investigators to better utilize or analyze the data
Submitting a Response
All responses must be submitted to IDG-KMC-RFI-Email@mail.nih.gov by June 15, 2013. Please include the Notice number NOT-RM-13-018 in the subject line. Response to this RFI is voluntary. Responders are free to address any or all of the categories listed above. The submitted information will be reviewed by the NIH staff. Submitted information will be considered confidential.
This request is for information and planning purposes only and should not be construed as a solicitation or as an obligation on the part of the Federal Government, the National Institutes of Health (NIH). The NIH does not intend to make any awards based on responses to this RFI or to otherwise pay for the preparation of any information submitted or for the Government's use of such information.
The NIH will use the information submitted in response to this RFI at its discretion and will not provide comments to any responder’s submission. However, responses to the RFI may be reflected in future solicitation(s). The information provided will be analyzed and may appear in reports. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s).
Please direct all inquiries to:
Veerasamy “Ravi” Ravichandran, Ph.D.
Health Scientist Administrator
Biomedical Technology, Bioinformatics and Computational Biology Division
National Institute of General Medical Sciences, NIH Building 45, Room 2As55B
45 Center Drive, MSC 6200
Bethesda, Maryland 20892-6200