WikiPathways:License Terms

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Overview

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. A more detailed version of what CC-O entails can be found below.
  • EU General Data Protection Regulation - we value your privacy and commit ourselves full to the European GDPR, which requires, among other things, that we are 100% transparent in how we use your data. When you visit this website, there are various ways we "get" data. For example, by design, we learn your IP address. In order to create an account, you have to provide us with some basic information to register your account (this information is displayed when you click on your user name in the top right corner of a page, which guides you to your "User Page"). When providing this information, you are agreeing to allow us to share that (the wiki concept). You can view which profile information you entered into our system, by clicking the "my preferences" button (top right corner). We do not share your data with third parties, other than the data files we provide as download and on our web pages. You can view all your contributions to the WikiPathways data, by clicking the "my contributions" button from within your "User Page". We use Google Analytics as a third party service to help us develop this project. Questions about the above are most welcome via email.
  • Terms of Use - these are our own terms for how we expect WikiPathways content to be used. This is not a legally-binding code, but rather an explicit declaration of our expectations. If you find someone violating the terms of use, let us know and we'll let the community know that they are not playing fair. We believe this approach will be less costly than legal action and, at the same time, more effective at discouraging unfair use. A more detailed version of our terms of use can be found below.
  • Trademark - Anyone using or redistributing WikiPathways content under the terms of our license and terms of use can proudly display the WikiPathways trademark as evidence of being a trusted member of the community. Our logo can be downloaded below.


The License/Waiver

WikiPathways content is covered by the Creative Commons CC0 Waiver, which states that you are free to share (copy, distribute and transmit) and remix (adapt) the work. Refer to the original announcement for additional history and context. Our terms of use covers the ethical and social norms for attribution that we expect from research communities. For any reuse or distribution, we would appreciate that you make clear to others the CC0 terms for the work. The best way to do this is with a link to this web page. Again, this license is fairly permissive, so you shouldn't feel paralyzed by legalese if you are interested in using or redistributing WikiPathways content. Just be sure to read the terms of use and if you have any questions about fair use, don't hesitate to contact us. A detailed FAQ on CC0 can be found here, which was written by the Wikimedia community.


Terms of Use

Contributing

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 manually transcribe content from the following resources with appropriate attribution:

  • text books
  • research articles and reviews
  • public databases and pathway resources
  • 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 should also not create content from other content in an automated way, unless that content is CC0 too.

Downloading

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.

Using

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. We appreciate it if you cite or give appropriate attribution to WikiPathways, since we believe this to be in accordance with community and professional norms and standards of all science domains. See Attribution below

Redistributing

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 we would be very disappointed if you would charge users for the content it self, since the content is freely available on WikiPathways. 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, however we would appreciate that you make 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, but we sincerely hope that you make 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, and we would love you to make clear that the content is free and freely available from WikiPathways.org. We think you get the idea: we would not be happy if you are making money of content, which other users freely donated to the community. So please, be a good person and do not charge for the content as provided by WikiPathways and if you do associate the content with something you are are selling, add a statement to make clear that the content is free and freely available from WikiPathways.org. See Attribution below

Adapting, Dissecting, Augmenting

You are free to download, use and redistribute any part of a given pathway at WikiPathways according to the Terms of Use. You are free to augment, extend and build upon the content outside of WikiPathways and then use or redistribute according to the Terms of Use. You are free to edit, subtract from and change the content outside of WikiPathways and then use or redistribute according to the Terms of Use. Of course, we believe it is better to make edits directly to the content within WikiPathways itself, to grow the content and share alike, but this is not strictly required. If there is a feature or function you require in order to perform an edit to the content, do not hesitate to contact us and participate in the design and implementation of the new feature yourself. This is an open source project, after all!

Attribution

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, doi.org/10.1093/nar/gkaa1024 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) doi.org/10.1093/nar/gkx1064 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: www.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


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

Trademark

The WikiPathways trademark (our logo) can be reproduced with any use and redistribution of WikiPathways content. You do not necessarily have to ask permission before using the logo, if you are confident that you satisfy the license and Terms of Use. However, we always appreciate hearing about related efforts, so please drop us a line. We have a wiki page dedicated to listing such efforts here, and we would love to add your tool.

If you do not satisfy the license or Terms of Use (they're really quite leanient) our first measure will be to contact you and request that you change your behavior. Failing that, we will require that you remove the WikiPathways trademark from your site or resource. Please see this FAQ on Trademarks and CC0.

Logos can be downloaded or linked to from WikiMedia:

150px-Wplogo_with_text_500.png

100px-Wplogo_500.png

And here are some SVG versions:

References

Definitions

Content 
The pathway information (in part or in whole) represented in data and image formats at WikiPathways.
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