About

PathMe is developed and maintained in an academic capacity by Daniel Domingo-Fernández at the Fraunhofer SCAI Department of Bioinformatics.

References

If you use PathMe in your work, please cite:

Domingo-Fernandez et al., 2019. PathMe: Merging and exploring mechanistic pathway knowledge. bioRxiv 451625.

References

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

Application Metadata

Python Version

3.6.5 (default, Jun 27 2018, 08:15:56) [GCC 6.3.0 20170516]

Deployed

2020-06-23 07:41:13.404535

KEGG Version

2019-01-17 15:16:49.049917

Reactome Version

2019-01-17 15:18:06.287321

WikiPathways Version

2019-01-17 15:17:28.428295