Proteopedia:Guidelines for Ethical Writing: Difference between revisions
No edit summary |
|||
| (5 intermediate revisions by the same user not shown) | |||
| Line 11: | Line 11: | ||
==Citing Sources== | ==Citing Sources== | ||
When you use literature | When you use scientific literature for overall organization, for finding other literature, or in summarizing or paraphrasing information, you have to cite it (see [[Help:Editing#Citing_Literature_References|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, | If you use other sources (Wikipedia, databases, electronic textbooks, or anything lacking an [https://isbn.org/ ISBN], [https://www.issn.org/understanding-the-issn/what-is-an-issn/ ISSN], or [https://www.doi.org/ 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 [https://edubirdie.com/citation/mla/cite-a-webpage/ edubirdie]: | ||
<blockquote>''Proteopedia:Guidelines for Ethical Writing - Proteopedia, Life in 3D.'' https://proteopedia.org/wiki/index.php/Proteopedia:Guidelines_for_Ethical_Writing. Accessed 27 June 2023. | |||
</blockquote> | |||
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. | 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. | ||
| Line 58: | Line 61: | ||
If you use structure prediction tools (for example [[AlphaFold]]) to generate coordinates, you should make sure that the [[Header of PDB file|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 [[AlphaFold pLDDT and expected distance error|pLDDT]]. | If you use structure prediction tools (for example [[AlphaFold]]) to generate coordinates, you should make sure that the [[Header of PDB file|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 [[AlphaFold pLDDT and expected distance error|pLDDT]]. | ||
==== Use of Text | ==== 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. | 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 | ==== 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. | 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== | ==See Also== | ||
* [[Proteopedia:Copyrights]] | * [[Proteopedia:Copyrights]] | ||
* [[Proteopedia:Terms_of_Service]] | |||
* [https://en.wikipedia.org/wiki/Wikipedia:Large_language_models Wikipedia working on a policy re: LLMs] | |||
* [https://meta.wikimedia.org/wiki/Wikilegal/Copyright_Analysis_of_ChatGPT Wikimedia legal analysis on LLMs] | |||
==Acknowledgements== | ==Acknowledgements== | ||
Earlier versions of this guide reproduced, with permission from its author, from the work by Miguel Roig, [http://facpub.stjohns.edu/~roigm/plagiarism/ ''Avoiding plagiarism, self-plagiarism, and other questionable writing practices: A guide to ethical writing''], and it informed the current version. | Earlier versions of this guide reproduced, with permission from its author, from the work by Miguel Roig, [http://facpub.stjohns.edu/~roigm/plagiarism/ ''Avoiding plagiarism, self-plagiarism, and other questionable writing practices: A guide to ethical writing''], and it informed the current version. | ||