Proteopedia:Guidelines for Ethical Writing

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Please keep in mind and follow this guide to ethical writing when creating your Proteopedia pages.

Contents

Authorship

When you edit (or create) a page, you become a co-author of it and are listed as such on the bottom of the page. This means you share responsibility for the accuracy and the integrity of the page, and you vouch for this integrity with your name and institutional affiliation. The history tab keeps a record of all the edits, so it is clear who wrote what. If you worked with others but they are not listed as authors, add their names to the acknowledgement section at the end of the page (for an example, see Thymidylate_synthase#Acknowledgements).

Proteopedia Pages are a Unique Genre

Proteopedia pages are different from the scientific literature, Wikipedia articles and printed books because they interweave text and interactive 3D figures (through green links and widgets in the text). As an author of a Proteopedia page, you are responsible for choosing structures to showcase, creating interactive figures, and writing the accompanying text. While you should use reputable sources to research your page, your job is to decide how to summarize this material and illustrate it with molecular scenes, choose your audience (e.g. layperson, biochemistry major, high school students), and create a concise and coherent story about your topic. You have to understand what you wrote and what the molecular scenes show, and make sure your readers can as well. Different from a review article, where there is an expectation that readers look at the cited sources if they are new to a topic, your Proteopedia pages should be comprehensible at the intended level without consulting the references (which might be behind a paywall for most viewers).

Citing Sources

When you use scientific literature for overall organization, for finding other literature, or in summarizing or paraphrasing information, you have to cite it (see How to Cite Literature References). In order to cite literature, you have to have full-text access to it (i.e. you should not cite a paper after just reading the abstract). Paraphrasing extended sections, while ethical, will not help in creating a great Proteopedia page because the genre (scope, audience, style) of your source will not match that of your page.

If you use other sources (Wikipedia, databases, electronic textbooks, or anything lacking an ISBN, ISSN, or DOI), you have to cite them as well, including the date when you accessed them. Here is an example how you could cite this page, generated by edubirdie:

Proteopedia:Guidelines for Ethical Writing - Proteopedia, Life in 3D. https://proteopedia.org/wiki/index.php/Proteopedia:Guidelines_for_Ethical_Writing. Accessed 27 June 2023.

For each molecular scene, clearly indicate which coordinates you are showing (typically by mentioning the PDB-ID in the caption). If you are using uploaded coordinates, include their provenance in the coordinates themselves (as a REMARK header comment) and in the meta-data, and include the filename of the coordinates in the caption of the scene.

In the rare cases where you copy text unchanged (verbatim), you have to mark it up as quotation and cite it. If it is a whole sentence or paragraph, it can be enclosed between <blockquote> and </blockquote>, which will make it look like this:

"Block-quoted text ..."[1]

Re-Use of Existing Content

Online sources of content re-used or adapted into Proteopedia must be cited.

Re-Use of Proteopedia Content

The contents of any page in Proteopedia (or Wikipedia) may be copied into other pages and adapted without explicit permission. Nevertheless the work of others, even when modified or adapted, must be attributed.

Every author in Proteopedia agrees to having their contributions copied, redistributed, and adapted. The licensing agreement for contributions to Proteopedia is displayed at the bottom of every page, and in more detail whenever you edit a page, beneath the wikitext editing box.

Molecular Scenes

Re-use or adaptation of molecular scenes (green links) initially created by others should be attributed.

Images

Images from published or online sources may not be used in Proteopedia articles without permission. Use without permission violates the intellectual property ownership of the author(s) of the image, and constitutes illegal copyright infringement.

Even if a journal article is open source, you have to check the license and often obtain permission to reuse figures. For example, you may use figures with a CC-BY license without contacting the author if you attribute the source. On the other hand, you may not use figures under a CC-BY-ND (no derivatives) license. Even when the work has no license or a restricted one for re-use, the copyright holder may always give you permission.

Permission must be requested from the author(s) or copyright holders via correspondence. The image should not be put into Proteopedia (uploaded) until after such permission is obtained, and the permission should be explicitly stated.

  • Examples of copyrighted images used with permission are in SARS-CoV-2 spike protein fusion transformation. Note the explicit mention of the publishers' licenses for each image, and naming the person who gave permission and the date permission was received for each figure.

If the image is accompanied by explicit permission for re-use, or is in the public domain, you do not need to request separate permission, but you should provide a link to the umbrella permission statement. And you must always cite the source of the image.

Use of Computer-generated Materials

Whenever you use text or coordinates generated by artificial intelligence (for example ChatGPT or AlphaFold), you should acknowledge it. Even when using these tools, you are responsible for the content of articles and edits. Remember that your name is associated with content that you post. Specific guidelines follow. As this is a rapidly evolving field, tools available to you might not be mentioned yet, Still, the general principles of acknowledging AI tools and personal responsibility for submitted content apply.

Generated Coordinates

If you use structure prediction tools (for example AlphaFold) to generate coordinates, you should make sure that the header section of the uploaded coordinate file states that the coordinates are not based on experimental data but are predictions, and states the methods used. As you create interactive Jmol figures based on these coordinates, make sure to mention that coordinates are predictions in the figure caption. Include at least one figure that shows an estimate of coordinate error, such as coloring the model by pLDDT.

Use of Text-generation Tools

If you use text-generation tools such as ChatGPT or machine translation, indicate this in the acknowledgments. If the first draft is created using these tools, include the prompt in the acknowledgement. If you use AI tools for researching the topic, planning the writing (outline, topic sentences, etc.) or to revise your own writing, acknowledge that as well. For example, say “Karsten Theis used ChatGPT to revise the section on Generated Coordinates”. This way, it is clear who used the tool, and what tool they used to what purpose.

Use of Image-generation Tools

It is unlikely that using an image-generation tool such as Dall-E would be appropriate for Proteopedia articles. In any case, if you upload AI-generated images, indicate it in the meta-data and in the figure caption.

See Also

Acknowledgements

Earlier versions of this guide reproduced, with permission from its author, from the work by Miguel Roig, Avoiding plagiarism, self-plagiarism, and other questionable writing practices: A guide to ethical writing, and it informed the current version.

References

  1. ↑ Source of block-quoted text should be cited here.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Karsten Theis, Jaime Prilusky, Wayne Decatur

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