Open Targets Platform: new developments and updates two years on

被引:301
作者
Carvalho-Silva, Denise [1 ,2 ]
Pierleoni, Andrea [1 ,2 ]
Pignatelli, Miguel [1 ,2 ]
Ong, ChuangKee [1 ,2 ]
Fumis, Luca [1 ,2 ]
Karamanis, Nikiforos [1 ,2 ]
Carmona, Miguel [1 ,2 ]
Faulconbridge, Adam [1 ,2 ]
Hercules, Andrew [1 ,2 ]
McAuley, Elaine [1 ,2 ]
Miranda, Alfredo [1 ,2 ]
Peat, Gareth [1 ,2 ]
Spitzer, Michaela [1 ,2 ]
Barrett, Jeffrey [2 ,3 ]
Hulcoop, David G. [2 ,4 ]
Papa, Eliseo [2 ,5 ]
Koscielny, Gautier [2 ,4 ]
Dunham, Ian [1 ,2 ]
机构
[1] EBI, EMBL, Wellcome Genome Campus, Hinxton CB10 1SD, Cambs, England
[2] Open Targets, Wellcome Genome Campus, Hinxton CB10 1SD, Cambs, England
[3] Wellcome Sanger Inst, Wellcome Genome Campus, Cambridge CB10 1SA, England
[4] Med Res Ctr, GSK, Gunnels Wood Rd, Stevenage SG1 2NY, Herts, England
[5] Biogen, Cambridge, MA 02142 USA
关键词
GENOME-WIDE ASSOCIATION; CANCER; INFORMATION; HALLMARKS; DATABASE; ATLAS;
D O I
10.1093/nar/gky1133
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The Open Targets Platform integrates evidence from genetics, genomics, transcriptomics, drugs, animal models and scientific literature to score and rank target-disease associations for drug target identification. The associations are displayed in an intuitive user interface (https://www.targetvalidation.org), and are available through a REST-API (https://api.opentargets.io/v3/platform/docs/swagger-ui) and a bulk download (https://www.targetvalidation.org/downloads/data). In addition to target-disease associations, we also aggregate and display data at the target and disease levels to aid target prioritisation. Since our first publication two years ago, we have made eight releases, added new data sources for target-disease associations, started including causal genetic variants from non genome-wide targeted arrays, added new target and disease annotations, launched new visualisations and improved existing ones and released a new web tool for batch search of up to 200 targets. We have a new URL for the Open Targets Platform REST-API, new REST endpoints and also removed the need for authorisation for API fair use. Here, we present the latest developments of the Open Targets Platform, expanding the evidence and target-disease associations with new and improved data sources, refining data quality, enhancing website usability, and increasing our user base with our training workshops, user support, social media and bioinformatics forum engagement.
引用
收藏
页码:D1056 / D1065
页数:10
相关论文
共 40 条
  • [31] DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes
    Pinero, Janet
    Queralt-Rosinach, Nuria
    Bravo, Alex
    Deu-Pons, Jordi
    Bauer-Mehren, Anna
    Baron, Martin
    Sanz, Ferran
    Furlong, Laura I.
    [J]. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2015,
  • [32] Samet Hanan, 2006, Foundations of multidimensional and metric data structures
  • [33] Perturbation-response genes reveal signaling footprints in cancer gene expression
    Schubert, Michael
    Klinger, Bertram
    Kluenemann, Martina
    Sieber, Anja
    Uhlitz, Florian
    Sauer, Sascha
    Garnett, Mathew J.
    Bluethgen, Nils
    Saez-Rodriguez, Julio
    [J]. NATURE COMMUNICATIONS, 2018, 9
  • [34] Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse
    Smith, Cynthia L.
    Blake, Judith A.
    Kadin, James A.
    Richardson, Joel E.
    Bult, Carol J.
    [J]. NUCLEIC ACIDS RESEARCH, 2018, 46 (D1) : D836 - D842
  • [35] The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers
    Sondka, Zbyslaw
    Bamford, Sally
    Cole, Charlotte G.
    Ward, Sari A.
    Dunham, Ian
    Forbes, Simon A.
    [J]. NATURE REVIEWS CANCER, 2018, 18 (11) : 696 - 705
  • [36] Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations
    Tamborero, David
    Rubio-Perez, Carlota
    Deu-Pons, Jordi
    Schroeder, Michael P.
    Vivancos, Ana
    Rovira, Ana
    Tusquets, Ignasi
    Albanell, Joan
    Rodon, Jordi
    Tabernero, Josep
    de Torres, Carmen
    Dienstmann, Rodrigo
    Gonzalez-Perez, Abel
    Lopez-Bigas, Nuria
    [J]. GENOME MEDICINE, 2018, 10
  • [37] OmniPath: guidelines and gateway for literature-curated signaling pathway resources
    Turei, Denes
    Korcsmaros, Tamas
    Saez-Rodriguez, Julio
    [J]. NATURE METHODS, 2016, 13 (12) : 965 - 967
  • [38] A human protein atlas for normal and cancer tissues based on antibody proteomics
    Uhlén, M
    Björling, E
    Agaton, C
    Szigyarto, CA
    Amini, B
    Andersen, E
    Andersson, AC
    Angelidou, P
    Asplund, A
    Asplund, C
    Berglund, L
    Bergström, K
    Brumer, H
    Cerjan, D
    Ekström, M
    Elobeid, A
    Eriksson, C
    Fagerberg, L
    Falk, R
    Fall, J
    Forsberg, M
    Björklund, MG
    Gumbel, K
    Halimi, A
    Hallin, I
    Hamsten, C
    Hansson, M
    Hedhammar, M
    Hercules, G
    Kampf, C
    Larsson, K
    Linskog, M
    Lodewyckx, W
    Lund, J
    Lundeberg, J
    Magnusson, K
    Malm, E
    Nilsson, P
    Ödling, J
    Oksvold, P
    Olsson, I
    Öster, E
    Ottosson, J
    Paavilainen, L
    Persson, A
    Rimini, R
    Rockberg, J
    Runeson, M
    Sivertsson, Å
    Sköllermo, A
    [J]. MOLECULAR & CELLULAR PROTEOMICS, 2005, 4 (12) : 1920 - 1932
  • [39] The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits
    Voight, Benjamin F.
    Kang, Hyun Min
    Ding, Jun
    Palmer, Cameron D.
    Sidore, Carlo
    Chines, Peter S.
    Burtt, Noel P.
    Fuchsberger, Christian
    Li, Yanming
    Erdmann, Jeanette
    Frayling, Timothy M.
    Heid, Iris M.
    Jackson, Anne U.
    Johnson, Toby
    Kilpelaeinen, Tuomas O.
    Lindgren, Cecilia M.
    Morris, Andrew P.
    Prokopenko, Inga
    Randall, Joshua C.
    Saxena, Richa
    Soranzo, Nicole
    Speliotes, Elizabeth K.
    Teslovich, Tanya M.
    Wheeler, Eleanor
    Maguire, Jared
    Parkin, Melissa
    Potter, Simon
    Rayner, N. William
    Robertson, Neil
    Stirrups, Kathleen
    Winckler, Wendy
    Sanna, Serena
    Mulas, Antonella
    Nagaraja, Ramaiah
    Cucca, Francesco
    Barroso, Ines
    Deloukas, Panos
    Loos, Ruth J. F.
    Kathiresan, Sekar
    Munroe, Patricia B.
    Newton-Cheh, Christopher
    Pfeufer, Arne
    Samani, Nilesh J.
    Schunkert, Heribert
    Hirschhorn, Joel N.
    Altshuler, David
    McCarthy, Mark I.
    Abecasis, Goncalo R.
    Boehnke, Michael
    [J]. PLOS GENETICS, 2012, 8 (08):
  • [40] Computational resources associating diseases with genotypes, phenotypes and exposures
    Zhang, Wenliang
    Zhang, Haiyue
    Yang, Huan
    Li, Miaoxin
    Xie, Zhi
    Li, Weizhong
    [J]. BRIEFINGS IN BIOINFORMATICS, 2019, 20 (06) : 2098 - 2115