Resources
Resources from KEGG,
Reactome,
WikiPathways, and
MSigDB
have been used to build this package and application.
KEGG
License
KEGG KGML files are downloaded via the KEGG API for
academic purposes (Terms and
conditions). More info at Bio2BEL KEGG.
References
- Kanehisa, Furumichi, M., Tanabe, M., Sato, Y., and Morishima, K.; KEGG: new
perspectives
on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353-D361
(2017).
- Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; KEGG as a
reference resource for gene and protein annotation. Nucleic Acids Res. 44,
D457-D462
(2016).
- Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes.
Nucleic Acids
Res. 28, 27-30 (2000).
Reactome
License
Reactome RDF files are downloaded via the Reactome
API for academic purposes (Terms and
conditions).
References
- Fabregat, Antonio et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids
Research 44.Database issue (2016): D481–D487. PMC. Web. 6 Oct. 2017.
- Croft, David et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research
42.Database issue (2014): D472–D477. PMC. Web. 6 Oct. 2017.
WikiPathways
License
WikiPathways RDF files are downloaded via WikiPathways for academic purposes (Terms and
conditions).
References
- Slenter DN, Kutmon M, Hanspers K, Riutta A, Windsor J, Nunes N, Mélius J, Cirillo E,
Coort SL, Digles D, Ehrhart F, Giesbertz P, Kalafati M, Martens M, Miller R, Nishida
K,
Rieswijk L, Waagmeester A, Eijssen LMT, Evelo CT, Pico AR, Willighagen EL.
WikiPathways:
a multifaceted pathway database bridging metabolomics to other omics research
Nucleic
Acids Research, (2017)doi.org/10.1093/nar/gkx1064
- Kutmon M, Riutta A, Nunes N, Hanspers K, Willighagen EL, Bohler A, Mélius J,
Waagmeester
A, Sinha SR, Miller R, Coort SL, Cirillo E, Smeets B, Evelo CT, Pico AR.
WikiPathways:
capturing the full diversity of pathway knowledge Nucl. Acids Res., 44, D488-D494
(2016)
doi:10.1093/nar/gkv1024
- Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo C, Pico AR.
WikiPathways: building research communities on biological pathways. Nucleic Acids
Res.
2012 Jan;40(Database issue):D1301-7