Pharos is the user interface to the Knowledge Management Center (KMC) for the Illuminating the Druggable Genome (IDG) program funded by the National Institutes of Health (NIH) Common Fund. (Grant No. 5U54CA189205-02). The goal of KMC is to develop a comprehensive, integrated knowledge-base for the Druggable Genome (DG) to illuminate the uncharacterized and/or poorly annotated portion of the DG, focusing on four of the most commonly drug-targeted protein families: G-protein-coupled receptors (GPCRs); nuclear receptors (NRs); ion channels (ICs); and kinases. For more information on opportunities in the druggable human genome see this poster
Based on modern web design principles the interface provides facile access to all data types collected by the KMC. Given the complexity of the data surrounding any target, efficient and intuitive visualization has been a high priority, to enable users to quickly navigate & summarize search results and rapidly identify patterns. A critical feature of the interface is the ability to perform flexible search and subsequent drill down of search results. Underlying the interface is a RESTful API that provides programmatic access to all KMC data, allowing for easy consumption in user applications.
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Pharos is developed at NCATS, together with collaborators from the University of New Mexico, Icahn School of Medicine, Mount Sinai, EMBL-EBI, the Novo Nordisk Foundation Center for Protein Research (U. Copenhagen) and the University of Miami.
The IDG TechDev network is the experimental side of IDG. TechDev research aims to develop and utilize technologies and streamlined experimental workflows for functional studies of poorly characterized and/or un-annotated genes and proteins, thereby providing high value data and knowledge for KMC. KMC in turn is tasked with providing guidance as to research priorities based on knowledge gaps and druggability likelihood analyses.
To find more details on our collaborators visit http://targetcentral.ws/
What data is available?
The data available in Pharos is obtained from the Target Central Resource Database which integrates data from a variey of data sources including the Harmonizome, Jensen Lab datasets, EBI data sets (such as ChEMBL) and the Drug Target Ontology (DTO) from U. Miami. TCRD integration methodology involves importation by value or by reference to external sources, as informed by performance, provenance, and other design criteria. See here for a full listing of datasets incorporated in to TCRD.
The key data types represented in Pharos are listed below:
Small molecule dataincluding approved drug data, bioassay data
Protein dataincluding protein-protein interaction data
Disease datafrom OMIM and Disease Ontology
Genomic dataincluding expression (protein, RNA), transcription factors and epigenomic associations
Phenotypic dataincluding mouse phenotypes, mouse/human orthologs and GWAS results
Funding datavia NIH RePORTER
Text dataincluding GeneRIF's and text-mined publications
Ontologiesincluding the Drug Target Ontology, Disease Ontology, PANTHER and GO.
What license does Pharos use?
All data accessed from Pharos is made available under the CC BY-SA 4.0 license.
Where can I get the code?
How can I cite Pharos?
If you use Pharos, please consider citing it as
Nguyen, D.-T., Mathias, S. et al, "Pharos: Collating Protein Information to Shed Light on the Druggable Genome", Nucl. Acids Res.i>, 2017, 45(D1), D995-D1002. DOI: 10.1093/nar/gkw1072