Pharos: collating protein information to shed light on the druggable genome
Open accessAbstract
The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental techniques and a Knowledge Management Center (KMC) that would collect and organize information about protein targets from four families, representing the most common druggable targets with an emphasis on understudied proteins. Here, we describe two resources developed by the KMC: the Target Central Resource Database (TCRD) which collates many heterogeneous gene/protein datasets and Pharos (https://pharos.nih.gov), a multimodal web interface that presents the data from TCRD. We briefly describe the types and sources of data considered by the KMC and then highlight features of the Pharos interface designed to enable intuitive access to the IDG knowledgebase. The aim of Pharos is to encourage 'serendipitous browsing', whereby related, relevant information is made easily discoverable. We conclude by describing two use cases that highlight the utility of Pharos and TCRD.
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The current version of DrugCentral reports 708 Tchem, 415 Tbio and 26 Tdark proteins, mapped onto TCRD and interfaced with Pharos.
“The current version of DrugCentral reports 708 Tchem, 415 Tbio and 26 Tdark proteins, mapped onto the Target Central Resource Database (TCRD) and interfaced with the TCRD portal, Pharos, respectively (39,40).”
From DrugCentral 2023 extends human clinical data and integrates veterinary drugs (2023) · cites this paper as [39]
Pharos and TCRD jointly serve as the knowledge hub for over 20 000 human protein targets.
“Pharos and the Target Central Resource Database (TCRD) are open-access resources developed as a part of the IDG program and jointly serve as the knowledge hub for over 20 000 human protein targets (2,3).”
From TCRD and pharos 2021: mining the human proteome for disease biology (2021) · cites this paper as [2]
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- Authors
- Nguyen, D.-T., Mathias, S., Bologa, C., Brunak, S., Fernandez, N., Gaulton, A., Hersey, A., Holmes, J., Jensen, L. J., Karlsson, A., Liu, G., Ma'ayan, A., Mandava, G., Mani, S., Mehta, S., Overington, J., Patel, J., Rouillard, A. D., Schürer, S., Sheils, T., Simeonov, A., Sklar, L. A., Southall, N., Ursu, O., Vidovic, D., Waller, A., Yang, J., Jadhav, A., Oprea, T. I., & Guha, R.
- Affiliations
- University of New Mexico (US)
- Icahn School of Medicine at Mount Sinai (US)
- European Bioinformatics Institute (GB)
- University of Copenhagen (DK)
- BenevolentAI (United Kingdom) (GB)
- East China University of Science and Technology (CN)
- National Center for Advancing Translational Sciences (US)
- University of Miami (US)
- Corresponding author
- Guha, Rajarshi
- ORCID
- Mathias, Stephen
- Bologa, Cristian
- Fernandez, Nicolas
- Gaulton, Anna
- Hersey, Anne
- Holmes, Jayme
- Jensen, Lars Juhl
- Karlsson, Anneli
- Liu, Guixia
- Mehta, Saurabh
- Overington, John
- Rouillard, Andrew D.
- Schürer, Stephan
- Sheils, Timothy
- Simeonov, Anton
- Sklar, Larry A.
- Southall, Noel
- Ursu, Oleg
- Waller, Anna
- Yang, Jeremy
- Jadhav, Ajit
- Oprea, Tudor I.
- Guha, Rajarshi
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-11-29
- Volume
- 45
- Issue
- D1
- Pages
- D995-D1002
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC5210555
- OpenAlex
- W2558366645
- Cited by
- 279
- References
- 22
- Citations by year
- 2026: 14 · 2025: 19 · 2024: 36 · 2023: 31 · 2022: 41 · 2021: 26 · 2020: 42 · 2019: 34 · 2018: 25 · 2017: 10 · 2016: 1
- FWCI
- 21.77
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Novo Nordisk (NNF14CC0001)
- Novo Nordisk Fonden (NNF 14CC0001)
- National Institutes of Health
- National Heart, Lung, and Blood Institute (T32HL007824)
- National Cancer Institute (U54CA189201, U54CA189205, P30CA118100)
- National Center for Advancing Translational Sciences
- Common Fund
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Keywords
- druggable genome, Pharo, protein targets, web interface, knowledge base
- MeSH terms
- Humans, Obesity, Pharmacogenetics, Software, Cluster Analysis, Computational Biology, Genomics, Databases, Genetic, Drug Discovery, Search Engine, Web Browser
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