Knowledge Management Center for Illuminating the Druggable Genome

Contacts

• PHAROS (user interface for KMC): https://pharos.nih.gov
• Docker: https://hub.docker.com/r/ncats/pharos
• Spotlite: https://spotlite.nih.gov/pharos
• Emails: pharos@nih.gov

Pharos: @idg_pharos

Overview

As a partner with the KMC, NCATS is developing and implementing PHAROS as the User Interface Portal to access all the integrated data, metadata and annotation collected into TCRD and via tools from ISMMS. Queries across all human proteins can be carried out based on Target Development Levels stages of knowledge for protein targets from most known (Tclin) to least known (Tdark), tissue expression, chemical tools, Novelty score, etc.

NIH grant number: 1U24 CA224370-01 and ZIA TR000057

KMC-NCATS publications:

1. Pharos 2023: an integrated resource for the understudied human proteome.
   Kelleher KJ, Sheils TK, Mathias SL, Yang JJ, Metzger VT, Siramshetty VB, Nguyen DT, Jensen LJ, Vidović D, Schürer SC, Holmes J, Sharma KR, Pillai A, Bologa CG, Edwards JS, Mathé EA, Oprea TI. Nucleic Acids Res. 2023 Jan 6;51(D1):D1405-D1416. doi: 10.1093/nar/gkac1033. Erratum in: Nucleic Acids Res. 2023 Feb 28;51(4):1999. PMID: 36624666; PMCID: PMC9825581.
2. Getting Started with the IDG KMC Datasets and Tools.
   Kropiwnicki E, Binder JL, Yang JJ, Holmes J, Lachmann A, Clarke DJB, Sheils T, Kelleher KJ, Metzger VT, Bologa CG, Oprea TI, Ma'ayan A. Curr Protoc. 2022 Jan;2(1):e355. doi: 10.1002/cpz1.355. PMID: 35085427; PMCID: PMC10789444.
3. TCRD and Pharos 2021: mining the human proteome for disease biology.
   Sheils TK, Mathias SL, Kelleher KJ, Siramshetty VB, Nguyen DT, Bologa CG, Jensen LJ, Vidović D, Koleti A, Schürer SC, Waller A, Yang JJ, Holmes J, Bocci G, Southall N, Dharkar P, Mathé E, Simeonov A, Oprea TI. Nucleic Acids Res. 2021 Jan 8;49(D1):D1334-D1346. doi: 10.1093/nar/gkaa993. PMID: 33156327; PMCID: PMC7778974.
4. How to Illuminate the Druggable Genome Using Pharos.
   Sheils T, Mathias SL, Siramshetty VB, Bocci G, Bologa CG, Yang JJ, Waller A, Southall N, Nguyen DT, Oprea TI. Curr Protoc Bioinformatics. 2020 Mar;69(1):e92. doi: 10.1002/cpbi.92. PMID: 31898878
5. DrugCentral 2018: an update. Nucleic Acids Res.
   Ursu O, Holmes J, Bologa CG, Yang JJ, Mathias SL, Stathias V, Nguyen DT, Schürer S, Oprea T. 2019 Jan 8;47(D1):D963-D970. doi: 10.1093/nar/gky963. PMID: 30371892; PMCID: PMC6323925.
6. Pharos: Collating protein information to shed light on the druggable genome.
   Nguyen DT, Mathias S, Bologa C, Brunak S, Fernandez N, Gaulton A, Hersey A, Holmes J, Jensen LJ, Karlsson A, Liu G, Ma'ayan A, Mandava G, Mani S, Mehta S, Overington J, Patel J, Rouillard AD, Schürer S, Sheils T, Simeonov A, Sklar LA, Southall N, Ursu O, Vidovic D, Waller A, Yang J, Jadhav A, Oprea TI, Guha R. Nucleic Acids Res. 2017 Jan 4;45(D1):D995-D1002. doi: 10.1093/nar/gkw1072. Epub 2016 Nov 29. PMID: 27903890, PMCID: PMC5210555  
7. Unexplored therapeutic opportunities in the human genome.
   Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, Ma'ayan A, Malovannaya A, Mani S, Mathias SL, McManus MT, Meehan TF, von Mering C, Muthas D, Nguyen DT, Overington JP, Papadatos G, Qin J, Reich C, Roth BL, Schürer SC, Simeonov A, Sklar LA, Southall N, Tomita S, Tudose I, Ursu O, Vidovic D, Waller A, Westergaard D, Yang JJ, Zahoránszky-Köhalmi G. Nat Rev Drug Discov. 2018 May;17(5):377. doi: 10.1038/nrd.2018.52. Epub 2018 Mar 23. Erratum for: Nat Rev Drug Discov. 2018 May;17 (5):317-332. PMID: 29567993.
8. Drug target ontology to classify and integrate drug discovery data.
   Lin Y, Mehta S, Küçük-McGinty H, Turner JP, Vidovic D, Forlin M, Koleti A, Nguyen DT, Jensen LJ, Guha R, Mathias SL, Ursu O, Stathias V, Duan J, Nabizadeh N, Chung C, Mader C, Visser U, Yang JJ, Bologa CG, Oprea TI, Schürer SC. J Biomed Semantics. 2017 Nov 9;8(1):50. doi: 10.1186/s13326-017-0161-x. PMID: 29122012, PMCID: PMC5679337

Page reviewed March 11, 2024