About

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

Database Version

This table shows the last update in the database plugins.

WikiPathways

Empty

Reactome

Empty

KEGG

Empty

NeuroMMSig AD

Empty

NeuroMMSig PD

Empty

References

Resources

Resources from KEGG, Reactome, WikiPathways, and MSigDB have been used to build this package and application.


KEGG

License

KEGG gene sets 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 gene sets are downloaded via the Reactome API for academic purposes (Terms and conditions). More info at Bio2BEL Reactome.

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 gene sets are downloaded via the WikiPathways API for academic purposes (Terms and conditions). More info at Bio2BEL WikiPathways.

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

MSigDB

License

Only MSig gene sets with (CC BY 4.0) are used in ComPath (Terms and conditions). More info at Bio2BEL MSig.

References

  • Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., ... & Mesirov, J. P. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545-15550.

Visualization Tools

This application makes use of other dedicated bioinformatics software such as Clustergrammer and Cytoscape JS.

References

  • Fernandez, N. F. et al. Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data. Sci. Data 4:170151 doi: 10.1038/sdata.2017.151 (2017).
  • Franz, M., Lopes, C. T., Huck, G., Dong, Y., Sumer, O., & Bader, G. D. (2015). Cytoscape. js: a graph theory library for visualisation and analysis. Bioinformatics, 32(2), 309-311.

Links and Cards

API

Our RESTful service is documented with the OpenAPI specification. In the future, we will also provide a GraphQL API using graphene.

Swagger UI OpenAPI Spec

Legal

ComPath is hosted in Germany, and has an imprint dictating disclaimers, etc.

Imprint

Artwork

The ComPath logo is derived from Road by Lorc and Compact Disc by Delapouite, used under CC BY 3.0. The ComPath logo is licensed under CC BY 3.0 by Daniel Domingo Fernández.

Dependencies

Application Metadata

Python Version

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

Deployed

2020-08-17 11:45:14.897191