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; 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, 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 HerseyAndrew R. Leach, John P. Overington, Gretchen Repasky, Krister Wennerberg, Tero Aittokallio

Not published at VTT

University of Helsinki

Research output: Contribution to journal › Article › Scientific › peer-review

117 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
Pages (from-to)	224-229.e2
Journal	Cell Chemical Biology
Volume	25
Issue number	2
DOIs	https://doi.org/10.1016/j.chembiol.2017.11.009
Publication status	Published - 15 Feb 2018
MoE publication type	A1 Journal article-refereed

Funding

The authors thank all the parties that have made their compound-target bioactivity data publicly available, Dr. Ola Engkvist (AstraZeneca R&D Gothenburg) for his help with the BAO assay annotations, and Kyösti Sutinen and Olle Hansson (FIMM) for their help with the DTC interface and server. This work was supported by funding from the European Union's Horizon 2020 research and innovation program 2014–2020 under grant agreement no. 634143 (MedBioinformatics to T.A.), the European Research Council (ERC) starting grant agreement no. 716063 (DrugComb to J.T.), the Academy of Finland (grants 292611 , 269862 , 272437 , 279163 , 295504 , 310507 to T.A.; 272577 , 277293 to K.W.; and 296516 to S.K.), The Sigrid Jusélius Foundation (K.W.), Cancer Society of Finland (T.A and K.W.). J.P.O. and A.H. were funded by EMBL member nation states and Wellcome Trust Strategic Awards ( WT086151/Z/08/Z and WT104104/Z/14/Z ).

Keywords

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

Access to Document

10.1016/j.chembiol.2017.11.009

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5814751/

Cite this

Tang, J., Tanoli, Z.-R., Ravikumar, B., Alam, Z., 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., Seashore-Ludlow, B., ... 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

@article{a3e5857c0c944ad5bf8eb45554477852,

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.",

keywords = "bioassay annotation, chemical biology, cheminformatics, community effort, crowd sourcing, data curation, drug discovery, drug repositioning, drug repurposing, open data",

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

year = "2018",

month = feb,

day = "15",

doi = "10.1016/j.chembiol.2017.11.009",

language = "English",

volume = "25",

pages = "224--229.e2",

journal = "Cell Chemical Biology",

issn = "2451-9456",

publisher = "Elsevier",

number = "2",

}

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

TY - JOUR

T1 - Drug Target Commons

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

Y1 - 2018/2/15

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.

AB - 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.

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

UR - http://www.scopus.com/inward/record.url?scp=85038839435&partnerID=8YFLogxK

U2 - 10.1016/j.chembiol.2017.11.009

DO - 10.1016/j.chembiol.2017.11.009

M3 - Article

C2 - 29276046

SN - 2451-9456

VL - 25

SP - 224-229.e2

JO - Cell Chemical Biology

JF - Cell Chemical Biology

IS - 2

ER -

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

Abstract

Funding

Keywords

Access to Document

Other files and links

Fingerprint

Cite this