How to cite WikiPathways

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When referring to the latest website or content, please cite the most recent update paper:

  • Martens M, Ammar A, Riutta A, Waagmeester A, Slenter DN, Hanspers K, Miller RA, Digles D, Lopes EN, Ehrhart F, Dupuis LJ, Winckers LA, Coort SL, Willighagen EL, Evelo CT, Pico AR, Kutmon M. WikiPathways: connecting communities Nucleic Acids Research, (2021), Volume 49, Issue D1, 8 January 2021, Pages D613–D621, PMID:33211851.

When referring to specific issues described in previous update papers, please cite the respective paper:

  • 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, (2018) PMC5753270
  • 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 PMC4702772
  • 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 (link to article)

When referring to the web services, please cite:

  • Kelder T, Pico AR, Hanspers K, van Iersel MP, Evelo C, Conklin BR. (2009) Mining Biological Pathways Using WikiPathways Web Services. PLoS ONE 4(7): (link to article)

When referring to or using the semantic web (RDF) version, please cite:

  • Waagmeester A, Kutmon M. Riutta A, Miller R, Willighagen E, Evelo CT, Pico AR. (2016) Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PLoS Comput Bio 12(6): (link to article)

When referring to the origins of WikiPathways, please cite:

  • Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. (2008) WikiPathways: Pathway Editing for the People. PLoS Biol 6(7): (link to article)

When using or referencing WikiPathways in general, please cite the main page:

When using, referencing or redistributing particular pathways, please cite the specific pathway, for example:

  • When citing the live version of a pathway, attribution to individual contributors is not necessary. WikiPathways will track and display contributions from individual authors and curators to each pathway on each pathway page. So as long as hyperlinks are provided to WikiPathways, the evolving list of contributors will be indirectly referenced.
  • However, if you are referencing a specific version of a pathway (even including the current version), then it is important to include a URL of the form: This approach is useful if you want to maintain a link to a snapshot of the pathway and not have future changes obscure your original points. Use the "r" argument in the URL to refer to particular revision ID numbers, which you can find in the History section of each pathway page.
  • Also, when referencing a specific version, it is appropriate to list the individual contributors, since future contributors are not an issue. Thus, the reference might look like this:

Salomonis N, Pico A, Hanspers K: SIDS Susceptibility Pathways (Homo sapiens).

When referring to the use of Adverse Outcome Pathways (AOPs) and WikiPathways, please cite the respective paper:

  • Martens M, Verbruggen T, Nymark P, Grafström R, Burgoon LD, Aladjov H, Torres Andón T, Evelo CT, Willighagen EL. Introducing WikiPathways as a data-source to support Adverse Outcome Pathways for regulatory risk assessment of chemicals and nanomaterials. Front. Genet. , (2018) doi:10.3389/fgene.2018.00661


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