If you are like us, issues about licensing, copyrights and trademarks are boring at best and quickly become frustratingly opaque. At the same time, we recognize that they are important issues, especially when it comes to promoting and protecting data sharing in scientific domains. So, we have done our homework here at WikiPathways and have decided to adopt the Creative Commons CC0 waiver for our content. We are going to do our best to explain the strategy in clear terms below. Please feel free to give us feedback on these issues and voice your opinions and questions on the WikiPathways discussion mailing list.
- The License/Waiver - this is the legal code applicable to the content at WikiPathways. In our continuing effort to make pathway knowledge as widely accessible as possible, WikiPathways has adopted the Creative Commons CC0 waiver. More details below...
When editing an existing pathway or creating a new pathway, your contributions to WikiPathways content should reflect your best understanding of the biology you are representing. Whenever possible, contributions should be referenced by published, peer-reviewed literature. You can transcribe content from the following resources with appropriate attribution:
- text books
- research articles and reviews
- public databases and pathway resources: KEGG and Reactome
- trusted online resources, including wikipedia
- your own research and hypotheses (reasonably tested)
You should not make contributions based on work presented by other researchers yet to be published or based on proprietary sources (purchased databases, company secrets, etc).
You can download WikiPathways content in any of the available data and image formats we provide, including but not limited to: gpml, mapp, text, eu.gene, html, png, svg, jpeg.
You are free to use the pathway images in presentations, documents, websites and publications. You are free to use the pathway data in analyses, qualitative or quantitative. But you must cite or give appropriate attribution. See Attribution below
You are free to redistribute WikiPathways content on your website, as part of your own resource, with your own software application. You are free to charge for services associated with WikiPathways content, but you are not allowed to charge for the content it self. This does not prevent you from redistributing the content on a CD or as a digital download along with software that you are charging for as long as it is made clear that the content is free and freely available from WikiPathways.org. This does not prevent you from charging for services including additional curation, modification or analysis of the content as long as it is made clear that the content is free and freely available from WikiPathways.org. You may even sell modified versions of the images of the pathway content, e.g., as art, on your website as long as it is made clear that the content is free and freely available from WikiPathways.org. We think you get the idea: do not charge for the content as provided by WikiPathways and if you do associate the content with something you are are selling, make it clear that the content is free and freely available from WikiPathways.org. See Attribution below
Adapting, Dissecting, Augmenting
When referring to the latest website or content, please cite the most recent update 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, (2017) doi.org/10.1093/nar/gkx1064 PMC5753270
When referring to specific issues described in previous update papers, please cite the respective paper:
- 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 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: wikipathways.org/instance/WP254
- 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: wikipathways.org/instance/WP254_r93003. 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). wikipathways.org/instance/WP706_r92921
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- Full legal code for CC0 - frankly, not that much fun to read.
- How CC0 works - including why it is good for scientific data and databases.
- Who else is using CC0 - list of other resources that have adopted this approach.
- The pathway information (in part or in whole) represented in data and image formats at WikiPathways.