The main goal of the Knowledge Management Center (KMC) for the Illuminating the Druggable Genome (IDG) program is to aggregate, update and articulate protein-centric data, information and knowledge for the entire human proteome with emphasis on understudied proteins from the 3 families that are the focus of the IDG (?IDG List?). The long-term objective of the KMC is to encourage and support biomedical research aimed at understudied proteins by providing an extensive resource of data, information, knowledge, methods and reagents for the entire human proteome, and to support the growing online community focused on understudied proteins. With focus on the IDG List and human proteins, the KMC will enable support for expanded coverage for non-human proteins of therapeutic interest and other associated human health data, in order to catalyze novel biomedical discoveries. To support the overall IDG objective, and to maintain, update and improve these integrated resources, the KMC draws upon expertise from multiple knowledge domains, specifically biology, chemistry and medicine, as well as computer science, graphic design and web programming. Specifically, for the Phase 2 of the IDG KMC we propose 4 Aims:1. Create an automated workflow that captures relevant public data for the entire proteome and manual annotations for the IDG list. The KMC knowledge management system will be built around knowledge graphs, focused on five major branches of the target knowledge tree, tkt: Genotype, Phenotype, Expression, Structure & Function, and Interactions & Pathways, respectively.
Aim 2 : Design, develop and implement a protein knowledgebase with Data Analytics support. Our protein-centric biomedical knowledge base, TCKB (Target Central Knowledgebase) will be comprised of the data, knowledge and information container, together with its codebase and software pipelines. TCKB will be the repository for experimental, processed and computed data and reagents originating from the IDG DRGCs (Data and Resource Generation Centers). We will provide informatics and modeling support for DRGC activities.
Aim 3 : We will expand, improve and maintain Pharos. Particularly ?knowledge packages,? support automated data summaries for Protein Dossiers, and actively seek feedback from our community.
Aim 4. Outreach to scientific community. We will support a series of activities that will leverage TCKB, Pharos and other IDG resources to increase adoption of IDG work, while observing FAIR (findable, accessible, interoperable, reusable) principles for our knowledgebase, portal and pipelines. The KMC will engage in community outreach by leading tutorials and feedback sessions and dissemination of the Pharos system. To meet its goals, the KMC will coordinate all core activities in close coordination with the IDG Steering Committee and IDG Project Scientists (PS), and include members of the IDG Consortium (IDG- C), other NIH Common Fund programs, NIH Commons, as well as other initiatives.
The Knowledge Management Center (KMC) for the Illuminating the Druggable Genome (IDG) program plans to aggregate, update and articulate protein-centric data, information and knowledge for the entire human proteome with emphasis on understudied proteins from the 3 families that are the focus of the IDG. The KMC long-term objective is to encourage and support biomedical research aimed at understudied proteins by providing an extensive resource of data, information, knowledge, methods and reagents for the entire human proteome, and to support the growing online community focused on understudied proteins.
| Oprea, Tudor I; Bologa, Cristian G; Brunak, Søren et al. (2018) Unexplored therapeutic opportunities in the human genome. Nat Rev Drug Discov 17:377 |
| Collins, Kyla A L; Stuhlmiller, Timothy J; Zawistowski, Jon S et al. (2018) Proteomic analysis defines kinase taxonomies specific for subtypes of breast cancer. Oncotarget 9:15480-15497 |
| Oprea, Tudor I; Bologa, Cristian G; Brunak, Søren et al. (2018) Unexplored therapeutic opportunities in the human genome. Nat Rev Drug Discov 17:317-332 |
| Sinha, Swati; Eisenhaber, Birgit; Jensen, Lars Juhl et al. (2018) Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000. Proteomics 18:e1800093 |
| Ursu, Oleg; Holmes, Jayme; Bologa, Cristian G et al. (2018) DrugCentral 2018: an update. Nucleic Acids Res : |
