Drug Target Commons

A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions

Jing Tang, Zia-ur-Rehman Tanoli, Balaguru Ravikumar, Zaid Alam, Markus Vähä-Koskela, Gopal Peddinti, Arjan J. van Adrichem, Janica Wakkinen, Alok Jaiswal, Ella Karjalainen, Prson Gautam, Liye He, Elina Parri, Suleiman Khan, Abhishekh Gupta, Mehreen Ali, Laxman Yetukuri, Anna-Lena Gustavsson, Brinton Seashore-Ludlow, Anne Hersey & 5 others Andrew R. Leach, John P. Overington, Gretchen Repasky, Krister Wennerberg, Tero Aittokallio

Research output: Contribution to journalArticleScientificpeer-review

9 Citations (Scopus)

Abstract

Knowledge of the full target space of bioactive substances, approved and investigational drugs as well as chemical probes, provides important insights into therapeutic potential and possible adverse effects. The existing compound-target bioactivity data resources are often incomparable due to non-standardized and heterogeneous assay types and variability in endpoint measurements. To extract higher value from the existing and future compound target-profiling data, we implemented an open-data web platform, named Drug Target Commons (DTC), which features tools for crowd-sourced compound-target bioactivity data annotation, standardization, curation, and intra-resource integration. We demonstrate the unique value of DTC with several examples related to both drug discovery and drug repurposing applications and invite researchers to join this community effort to increase the reuse and extension of compound bioactivity data. Tang et al. launches a novel crowd-sourcing effort to standardize the collection, management, curation, and annotation of the notoriously heterogeneous compound-target bioactivity measurements. The web-based community platform aims to provide the most comprehensive, reproducible, and sustainable bioactivity knowledge base for the end users.

Original languageEnglish
Pages (from-to)224-229.e2
JournalCell Chemical Biology
Volume25
Issue number2
DOIs
Publication statusPublished - 15 Feb 2018
MoE publication typeA1 Journal article-refereed

Fingerprint

Knowledge Bases
Bioactivity
Drug Interactions
Crowdsourcing
Drug Repositioning
Investigational Drugs
Drug Discovery
Pharmaceutical Preparations
Research Personnel
Standardization
Assays
Therapeutics
Data Curation

Keywords

  • bioassay annotation
  • chemical biology
  • cheminformatics
  • community effort
  • crowd sourcing
  • data curation
  • drug discovery
  • drug repositioning
  • drug repurposing
  • open data

Cite this

Tang, Jing ; Tanoli, Zia-ur-Rehman ; Ravikumar, Balaguru ; Alam, Zaid ; Vähä-Koskela, Markus ; Peddinti, Gopal ; van Adrichem, Arjan J. ; Wakkinen, Janica ; Jaiswal, Alok ; Karjalainen, Ella ; Gautam, Prson ; He, Liye ; Parri, Elina ; Khan, Suleiman ; Gupta, Abhishekh ; Ali, Mehreen ; Yetukuri, Laxman ; Gustavsson, Anna-Lena ; Seashore-Ludlow, Brinton ; Hersey, Anne ; Leach, Andrew R. ; Overington, John P. ; Repasky, Gretchen ; Wennerberg, Krister ; Aittokallio, Tero. / Drug Target Commons : A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions. In: Cell Chemical Biology. 2018 ; Vol. 25, No. 2. pp. 224-229.e2.
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Tang, J, Tanoli, Z-R, Ravikumar, B, Alam, Z, Vähä-Koskela, M, Peddinti, G, van Adrichem, AJ, Wakkinen, J, Jaiswal, A, Karjalainen, E, Gautam, P, He, L, Parri, E, Khan, S, Gupta, A, Ali, M, Yetukuri, L, Gustavsson, A-L, Seashore-Ludlow, B, Hersey, A, Leach, AR, Overington, JP, Repasky, G, Wennerberg, K & Aittokallio, T 2018, 'Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions', Cell Chemical Biology, vol. 25, no. 2, pp. 224-229.e2. https://doi.org/10.1016/j.chembiol.2017.11.009

Drug Target Commons : A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions. / Tang, Jing; Tanoli, Zia-ur-Rehman; Ravikumar, Balaguru; Alam, Zaid; Vähä-Koskela, Markus; Peddinti, Gopal; van Adrichem, Arjan J.; Wakkinen, Janica; Jaiswal, Alok; Karjalainen, Ella; Gautam, Prson; He, Liye; Parri, Elina; Khan, Suleiman; Gupta, Abhishekh; Ali, Mehreen; Yetukuri, Laxman; Gustavsson, Anna-Lena; Seashore-Ludlow, Brinton; Hersey, Anne; Leach, Andrew R. ; Overington, John P.; Repasky, Gretchen; Wennerberg, Krister; Aittokallio, Tero.

In: Cell Chemical Biology, Vol. 25, No. 2, 15.02.2018, p. 224-229.e2.

Research output: Contribution to journalArticleScientificpeer-review

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T2 - A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions

AU - Tang, Jing

AU - Tanoli, Zia-ur-Rehman

AU - Ravikumar, Balaguru

AU - Alam, Zaid

AU - Vähä-Koskela, Markus

AU - Peddinti, Gopal

AU - van Adrichem, Arjan J.

AU - Wakkinen, Janica

AU - Jaiswal, Alok

AU - Karjalainen, Ella

AU - Gautam, Prson

AU - He, Liye

AU - Parri, Elina

AU - Khan, Suleiman

AU - Gupta, Abhishekh

AU - Ali, Mehreen

AU - Yetukuri, Laxman

AU - Gustavsson, Anna-Lena

AU - Seashore-Ludlow, Brinton

AU - Hersey, Anne

AU - Leach, Andrew R.

AU - Overington, John P.

AU - Repasky, Gretchen

AU - Wennerberg, Krister

AU - Aittokallio, Tero

PY - 2018/2/15

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KW - bioassay annotation

KW - chemical biology

KW - cheminformatics

KW - community effort

KW - crowd sourcing

KW - data curation

KW - drug discovery

KW - drug repositioning

KW - drug repurposing

KW - open data

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U2 - 10.1016/j.chembiol.2017.11.009

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