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; Anni Rebane; 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; Andrew R Leach; John P Overington; Gretchen Repasky; Krister Wennerberg; Tero Aittokallio

doi:10.1016/j.chembiol.2017.11.009

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, Anni Rebane, 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-LudlowAnne Hersey, Andrew R Leach, John P Overington, Gretchen Repasky, Krister Wennerberg, Tero Aittokallio

34 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 language	English
Journal	Cell Chemical Biology
Volume	25
Issue number	2
Pages (from-to)	224-229.e2
ISSN	2451-9448
DOIs	https://doi.org/10.1016/j.chembiol.2017.11.009
Publication status	Published - 15 Feb 2018
Externally published	Yes

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Tang, J., Tanoli, Z.-U.-R., Ravikumar, B., Alam, Z., Rebane, A., Vähä-Koskela, M., Peddinti, G., van Adrichem, A. J., Wakkinen, J., Jaiswal, A., Karjalainen, E., Gautam, P., He, L., Parri, E., Khan, S., Gupta, A., Ali, M., Yetukuri, L., Gustavsson, A.-L., ... Aittokallio, T. (2018). Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions. Cell Chemical Biology, 25(2), 224-229.e2. https://doi.org/10.1016/j.chembiol.2017.11.009

Tang, J, Tanoli, Z-U-R, Ravikumar, B, Alam, Z, Rebane, A, 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

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title = "Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions",

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.",

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AU - Rebane, Anni

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

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N2 - 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.

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

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