source_datasets.md

Source Datasets

Gene and Gene Products

• UniProt (Nucleic Acids Research 2004)

  • Apweiler, Rolf, Amos Bairoch, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger et al.
  • [Paper]
  • [Website]

• Ensembl (Nucleic Acids Research 2021)

  • Howe, Kevin L., Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M. Ridwan Amode, Irina M. Armean et al.
  • [Paper]
  • [Website]

• RNAcentral (Nucleic Acids Research 2021)

  • RNAcentral Consortium.
  • [Paper]
  • [Website]

• Entrez (Nucleic Acids Research 2021)

  • Brown, Garth R., Vichet Hem, Kenneth S. Katz, Michael Ovetsky, Craig Wallin, Olga Ermolaeva, Igor Tolstoy et al.
  • [Paper]
  • [Website]

Interactions, Pathways and Biological Processes

• STRING (Nucleic Acids Research 2019)

  • Szklarczyk, Damian, Annika L. Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic et al.
  • [Paper]
  • [Website]

• BioGRID (Nucleic Acids Research 2006)

  • Stark, Chris, Bobby-Joe Breitkreutz, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, and Mike Tyers.
  • [Paper]
  • [Website]

• IntAct (Nucleic Acids Research 2004)

  • Hermjakob, Henning, Luisa Montecchi‐Palazzi, Chris Lewington, Sugath Mudali, Samuel Kerrien, Sandra Orchard, Martin Vingron et al.
  • [Paper]
  • [Website]

• OmniPath (Nature Methods 2016)

  • Türei, Dénes, Tamás Korcsmáros, and Julio Saez-Rodriguez.
  • [Paper]
  • [Website]

• Reactome (Nucleic Acids Research 2005)

  • Joshi-Tope, G., Marc Gillespie, Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Bernard de Bono, Bijay Jassal et al.
  • [Paper]
  • [Website]

• WikiPathways (Nucleic Acids Research 2016)

  • Slenter, Denise N., Martina Kutmon, Kristina Hanspers, Anders Riutta, Jacob Windsor, Nuno Nunes, Jonathan Mélius et al.
  • [Paper]
  • [Website]

• KEGG Pathways (Nucleic Acids Research 1999)

  • Ogata, Hiroyuki, Susumu Goto, Kazushige Sato, Wataru Fujibuchi, Hidemasa Bono, and Minoru Kanehisa.
  • [Paper]
  • [Website]

Disease

• KEGG Disease (Nucleic Acids Research 2007)

  • Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T. and Yamanishi, Y
  • [Paper]
  • [Website]

• DISEASES (Methods 2015)

  • Pletscher-Frankild, Sune, Albert Pallejà, Kalliopi Tsafou, Janos X. Binder, and Lars Juhl Jensen.
  • [Paper]
  • [Website]

• DisGeNET (Nucleic Acids Research 2016)

  • Piñero, Janet, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, and Laura I. Furlong.
  • [Paper]
  • [Website]

• OMIM (Nucleic Acids Research 2005)

  • Hamosh, Ada, Alan F. Scott, Joanna S. Amberger, Carol A. Bocchini, and Victor A. McKusick.
  • [Paper]
  • [Website]

• GWAS Catalog (Nucleic Acids Research 2019)

  • Buniello, Annalisa, Jacqueline A. L. MacArthur, Maria Cerezo, Laura W. Harris, James Hayhurst, Cinzia Malangone, Aoife McMahon et al.
  • [Paper]
  • [Website]

Drugs & Compounds

• ChEMBL (Nucleic Acids Research 2012)

  • Gaulton, Anna, Louisa J. Bellis, A. Patricia Bento, Jon Chambers, Mark Davies, Anne Hersey, Yvonne Light et al.
  • [Paper]
  • [Website]

• PubChem (Nucleic Acids Research 2016)

  • Kim, Sunghwan, Paul A. Thiessen, Evan E. Bolton, Jie Chen, Gang Fu, Asta Gindulyte, Lianyi Han et al.
  • [Paper]
  • [Website]

• DrugBank (Nucleic Acids Research 2008)

  • Wishart, David S., Craig Knox, An Chi Guo, Dean Cheng, Savita Shrivastava, Dan Tzur, Bijaya Gautam, and Murtaza Hassanali.
  • [Paper]
  • [Website]

• DrugCentral(Nucleic Acids Research 2017)

  • Ursu, Oleg, Jayme Holmes, Jeffrey Knockel, Cristian G. Bologa, Jeremy J. Yang, Stephen L. Mathias, Stuart J. Nelson, and Tudor I. Oprea.
  • [Paper]
  • [Website]

• Binding DB (Combinatorial Chemistry & High Throughput Screening 2001)

  • Chen, Xi, Ming Liu, and Michael K. Gilson.
  • [Paper]
  • [Website]

• RepoDB (Scientific Data 2017)

  • Brown, Adam S., and Chirag J. Patel.
  • [Paper]
  • [Website]