How to Cite
Depending on how you use WikiPathways, please consider citing one or more of the following articles:
Citing the WikiPathways project
- In general, we recommend citing either our latest NAR database article or the original 2008 PLoS Biology article:
- Potentially-relevant topics are highlighted in our other project articles:
- Miller RA, et al. (2022) Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions. PLoS ONE. [topics: biological interactions]
- Slenter DN, et al. (2018) WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. NAR. [topics: Metabolomics, QA, WikiPathways Academy]
- Kutmon M, et al. (2016) WikiPathways: capturing the full diversity of pathway knowledge. NAR. [topics: Growth, Reactome, Pathway Widget]
- Waagmeester A, et al. (2016) Using the semantic web for rapid integration of WikiPathways with other biological online data resources. PLoS Comput Biol. [topics: RDF, SPARQL, vocabularies, nanopublications]
- Kelder T, et al. (2012) WikiPathways: building research communities on biological pathways. NAR. [topics: Communities, Ontologies, Linkouts]
- Kelder T, et al. (2009) Mining Biological Pathways Using WikiPathways Web Services. PLoS One. [topics: Web service]
Citing individual pathways
- To cite a specific pathway, use its permalink, for example: https://www.wikipathways.org/instance/WP254. The permalink for each pathway is available in the "options" menu. When citing the live version of a pathway, attribution of individual contributors is not necessary since it is continuously tracked and displayed on each pathway page.
- To cite a specific version of a pathway, we recommend downloading the pathway as PDF (see "options" menu) and uploading it to Zenodo to generate a DOI that you can then reference in your paper. Alternatively, your can upload and image file or figure that you have made using WikPathways content. An example Zenodo record can be found here. Follow these steps:
- Once your paper is published, Add a citation to the corresponding pathway page(s):
- To complete these steps, first make sure you are logged in to your GitHub account.
- Find the corresponding pathway on WikiPathways, for example WP4629.
- In the Cited In section, click the pencil icon to edit the list. This will open a new browser tab with the "citedin_lookup.yaml" file open in edit mode.
- Click anywhere in the editable area and use Ctrl+F to search for the WPID, for example "WP4629".
- If the PMCID or DOI for the publication has not already been added, add an entry under the relevant WPID in the following format:
- link: PMC9603647.
- Enter a commit message ("added citation for WP4629") and click "Commit changes".