Pharos: Collating protein information to shed light on the druggable genome

Dac-Trung Nguyen; Stephen Mathias; Cristian Bologa; Soren Brunak; Nicolas Fernandez; Anna Gaulton; Anne Hersey; Jayme Holmes; Lars Juhl Jensen; Anneli Karlsson; Guixia Liu; Avi Ma'ayan; Geetha Mandava; Subramani Mani; Saurabh Mehta; John Overington; Juhee Patel; Andrew D Rouillard; Stephan Schürer; Timothy Sheils; Anton Simeonov; Larry A Sklar; Noel Southall; Oleg Ursu; Dusica Vidovic; Anna Waller; Jeremy Yang; Ajit Jadhav; Tudor I Oprea; Rajarshi Guha

doi:10.1093/nar/gkw1072

Pharos: Collating protein information to shed light on the druggable genome

Dac-Trung Nguyen, Stephen Mathias, Cristian Bologa, Soren Brunak, Nicolas Fernandez, Anna Gaulton, Anne Hersey, Jayme Holmes, Lars Juhl Jensen, Anneli Karlsson, Guixia Liu, Avi Ma'ayan, Geetha Mandava, Subramani Mani, Saurabh Mehta, John Overington, Juhee Patel, Andrew D Rouillard, Stephan Schürer, Timothy SheilsAnton Simeonov, Larry A Sklar, Noel Southall, Oleg Ursu, Dusica Vidovic, Anna Waller, Jeremy Yang, Ajit Jadhav, Tudor I Oprea, Rajarshi Guha

Disease Systems Biology Program

94 Citationer (Scopus)

Abstract

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.

Originalsprog	Engelsk
Tidsskrift	Nucleic Acids Research
Vol/bind	45
Udgave nummer	D1
Sider (fra-til)	D995–D1002
ISSN	0305-1048
DOI	https://doi.org/10.1093/nar/gkw1072
Status	Udgivet - 1 jan. 2017

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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., ... Guha, R. (2017). Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Research, 45(D1), D995–D1002. https://doi.org/10.1093/nar/gkw1072

Nguyen, D-T, 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 2017, 'Pharos: Collating protein information to shed light on the druggable genome', Nucleic Acids Research, bind 45, nr. D1, s. D995–D1002. https://doi.org/10.1093/nar/gkw1072

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title = "Pharos: Collating protein information to shed light on the druggable genome",

abstract = "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.",

author = "Dac-Trung Nguyen and Stephen Mathias and Cristian Bologa and Soren Brunak and Nicolas Fernandez and Anna Gaulton and Anne Hersey and Jayme Holmes and Jensen, {Lars Juhl} and Anneli Karlsson and Guixia Liu and Avi Ma'ayan and Geetha Mandava and Subramani Mani and Saurabh Mehta and John Overington and Juhee Patel and Rouillard, {Andrew D} and Stephan Sch{\"u}rer and Timothy Sheils and Anton Simeonov and Sklar, {Larry A} and Noel Southall and Oleg Ursu and Dusica Vidovic and Anna Waller and Jeremy Yang and Ajit Jadhav and Oprea, {Tudor I} and Rajarshi Guha",

note = "Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.",

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T2 - Collating protein information to shed light on the druggable genome

AU - Nguyen, Dac-Trung

AU - Mathias, Stephen

AU - Bologa, Cristian

AU - Brunak, Soren

AU - Fernandez, Nicolas

AU - Gaulton, Anna

AU - Hersey, Anne

AU - Holmes, Jayme

AU - Jensen, Lars Juhl

AU - Karlsson, Anneli

AU - Liu, Guixia

AU - Ma'ayan, Avi

AU - Mandava, Geetha

AU - Mani, Subramani

AU - Mehta, Saurabh

AU - Overington, John

AU - Patel, Juhee

AU - Rouillard, Andrew D

AU - Schürer, Stephan

AU - Sheils, Timothy

AU - Simeonov, Anton

AU - Sklar, Larry A

AU - Southall, Noel

AU - Ursu, Oleg

AU - Vidovic, Dusica

AU - Waller, Anna

AU - Yang, Jeremy

AU - Jadhav, Ajit

AU - Oprea, Tudor I

AU - Guha, Rajarshi

N1 - Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

PY - 2017/1/1

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N2 - 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.

AB - 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.

U2 - 10.1093/nar/gkw1072

DO - 10.1093/nar/gkw1072

M3 - Journal article

C2 - 27903890

SN - 0305-1048

VL - 45

SP - D995–D1002

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -

Pharos: Collating protein information to shed light on the druggable genome

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