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


==Content Attribution==
==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 and conventional textbooks because they interweave text and interactive figures (through green links and widgets in the text). As an author of a Proteopedia page, it is your responsibility to create interactive figures and write the accompanying text. While you should use some or all of the sources above (and cite the sources you use), 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 some viewers).
 
==Citing Sources==
 
If you use literature references for your outline, to look for other sources, 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).
 
If you use other sources (Wikipedia, other electronic resources), you have to cite them as well.
 
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 <nowiki><blockquote> and </blockquote></nowiki>, which will make it look like this:
<blockquote>"Block-quoted text ..."<ref>Source of block-quoted text should be cited here.</ref></blockquote>
 
==Re-Use of Existing Content==


Online sources of content re-used or adapted into Proteopedia must be cited.
Online sources of content re-used or adapted into Proteopedia must be cited.
*Example of attribution of text re-used from outside Proteopedia: [[Isoelectric_point#Content_Attribution]].
*Example of attribution of text re-used from outside Proteopedia: [[Isoelectric_point#Content_Attribution]].


===Re-Use of Proteopedia Content===
====Re-Use of Proteopedia Content====


The contents of any page in Proteopedia (or [http://wikipedia.org 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'''.
The contents of any page in Proteopedia (or [http://wikipedia.org 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'''.
Line 13: Line 32:
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.
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===
====Molecular Scenes====


Re-use or adaptation of molecular scenes (green links) initially created by others should be attributed.
Re-use or adaptation of molecular scenes (green links) initially created by others should be attributed.
*Example of attribution of molecular scenes created outside Proteopedia: [[Peptide#Content_Attribution]].
*Example of attribution of molecular scenes created outside Proteopedia: [[Peptide#Content_Attribution]].


==Images==
====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.
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.


Line 33: Line 52:
*Example of re-use of an image from Wikimedia Commons: [[Avian_Influenza_Neuraminidase%2C_Tamiflu_and_Relenza#Influenza_Virus_Neuraminidase]]. Note the clear statement in the cited source that the image is in the public domain.
*Example of re-use of an image from Wikimedia Commons: [[Avian_Influenza_Neuraminidase%2C_Tamiflu_and_Relenza#Influenza_Virus_Neuraminidase]]. Note the clear statement in the cited source that the image is in the public domain.


==Guide To Ethical Writing==
== Use of Computer-generated Materials ==
The following guidelines are 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'']
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.
 
===Cite All Sources===
* An ethical writer ALWAYS acknowledges the contributions of others and the sources of his/her ideas. See [[Help:Editing#Citing_Literature_References|How to Cite Literature References]].
* Any verbatim text taken from another author must be enclosed in quotation marks. If it is a whole sentence or paragraph, it can be enclosed between <nowiki><blockquote> and </blockquote></nowiki>, which will make it look like this:
<blockquote>"Block-quoted text ..."<ref>Source of block-quoted text should be cited here.</ref></blockquote>
* We must always acknowledge every source that we use in our writing; whether we paraphrase it, summarize it, or enclose it quotations.
* When we summarize, we condense, in our own words, a substantial amount of material into a short paragraph or perhaps even into a sentence.
* Whether we are paraphrasing or summarizing we must always identify the source of our information.
 
===Respect Work of Others===
* When paraphrasing and/or summarizing others’ work we must reproduce the exact meaning of the other author’s ideas or facts using our words and sentence structure.
* In order to make substantial modifications to the original text that result in a proper paraphrase, the author must have a thorough understanding of the ideas and terminology being used.
* A responsible writer has an ethical responsibility to readers, and to the author/s from whom s/he is borrowing, to respect others’ ideas and words, to credit those from whom we borrow, and whenever possible, to use one’s own words when paraphrasing.
* When in doubt as to whether a concept or fact is common knowledge, provide a citation.
* Authors who submit a manuscript for publication containing data, reviews, conclusions, etc., that have already been disseminated in some significant manner (e.g., published as an article in another journal, presented at a conference, posted on the internet) must clearly indicate to the editors and readers the nature of the previous dissemination.
* Authors of complex studies should heed the advice previously put forth by Angell & Relman <ref>PMID: 2710194</ref>. If the results of a single complex study are best presented as a ‘cohesive’ single whole, they should not be partitioned into individual papers. Furthermore, if there is any doubt as to whether a paper submitted for publication represents fragmented data, authors should enclose other papers (published or unpublished) that might be part of the paper under consideration <ref>PMID: 7616995</ref>. Similarly old data that has been merely augmented with additional data points and that is subsequently presented as a new study is an equally serious ethical breach.
 
===Avoid Self-Plagiarism===
* Because some instances of plagiarism, self-plagiarism, and even some writing practices that might otherwise be acceptable (e.g., extensive paraphrasing or quoting of key elements of a book) can constitute copyright infringement, authors are strongly encouraged to become familiar with basic elements of copyright law.
* While there are some situations where text recycling is an acceptable practice, it may not be so in other situations. Authors are urged to adhere to the spirit of ethical writing and avoid reusing their own previously published text, unless it is done in a manner consistent with standard scholarly conventions (e.g., by using of quotations and proper paraphrasing).
 
===Verify References===
* Authors are strongly urged to double-check their citations.  Specifically, authors should always ensure that each reference notation appearing in the body of the manuscript corresponds to the correct citation listed in the reference section and vice versa and that each source listed in the reference section has been cited at some point in the manuscript. In addition, authors should also ensure that all elements of a citation (e.g., spelling of authors’ names, volume number of journal, pagination) are derived directly from the original paper, rather than from a citation that appears on a secondary source.  Finally, authors should ensure that credit is given to those authors who first reported the phenomenon being studied.
* The references used in a paper should only be those that are directly related to its contents. The intentional inclusion of references of questionable relevance for purposes of manipulating a journal’s or a paper’s impact factor or a paper’s chances of acceptance is an unacceptable practice. 
* Authors should follow a simple rule: Strive to obtain the actual published paper.  When the published paper cannot be obtained, cite the specific version of the material being used, whether it is conference presentation, abstract, or an unpublished manuscript.
* Generally, when describing others’ work, do not rely on a secondary summary of that work. It is a deceptive practice, reflects poor scholarly standards, and can lead to a flawed description of the work described. Always consult the primary literature.
* If an author must rely on a secondary source (e.g., textbook) to describe the contents of a primary source (e.g., an empirical journal article), s/he should consult writing manuals used in her discipline to follow the proper convention to do so. Above all, always indicate the actual source of the information being reported.  


===Distinguish Your Ideas from Previous Work===
==== Generated Coordinates ====
* When borrowing heavily from a source, authors should always craft their writing in a way that makes clear to readers, which ideas are their own and which are derived from the source being consulted.
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]].


===Report Honestly and Completely===
==== Use of Text Generation Tools ====
* When appropriate, authors have an ethical responsibility to report evidence that runs contrary to their point of view. In addition, evidence that we use in support of our position must be methodologically sound. When citing supporting studies that suffer from methodological, statistical, or other types of shortcomings, such flaws must be pointed out to the reader.
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.
* Authors have an ethical obligation to report all aspects of the study that may impact the independent replicability of their research.
* Researchers have an ethical responsibility to report the results of their studies according to their a priori plans. Any post hoc manipulations that may alter the results initially obtained, such as the elimination of outliers or the use of alternative statistical techniques, must be clearly described along with an acceptable rationale for using such techniques.


===Authorship===
==== Use of Image Generation Tools ====
* Authorship determination should be discussed prior to commencing a research collaboration and should be based on established guidelines, such as those of the International Committee of Medical Journal Editors.
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.
* The office of research integrity states that "Only those individuals who have made substantitve contributions to a project merit authorship in a paper"<ref>https://ori.hhs.gov/establishing-authorship</ref>. In Proteopedia, anyone who makes an edit is included in the automatically maintained list of authors. If you copy and paste material, or if a group of authors writes a piece that is posted by a single individual, attribution should be included in a different manner. If possible, include a paragraph summarizing the contributions of each author.
* "Faculty-student collaborations should follow the same criteria to establish authorship. Mentors must exercise great care to neither award authorship to students whose contributions do not merit it, nor to deny authorship and due credit to the work of students." <ref>https://ori.hhs.gov/authorship-faculty-student-collaborations</ref>
* Academic or professional ghost authorship in the sciences is ethically unacceptable.
* Authors must become aware of possible conflicts of interest in their own research and to make every effort to disclose those situations (e.g., stock ownership, consulting agreements to the sponsoring organization) that may pose actual or potential conflicts of interest.


==See Also==
==See Also==
* [[Proteopedia:Copyrights]]
* [[Proteopedia:Copyrights]]
==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.


== References ==
== References ==
<references/>
<references/>

Revision as of 17:38, 27 June 2023

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

AuthorshipAuthorship

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 GenreProteopedia Pages are a Unique Genre

Proteopedia pages are different from the scientific literature, Wikipedia and conventional textbooks because they interweave text and interactive figures (through green links and widgets in the text). As an author of a Proteopedia page, it is your responsibility to create interactive figures and write the accompanying text. While you should use some or all of the sources above (and cite the sources you use), 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 some viewers).

Citing SourcesCiting Sources

If you use literature references for your outline, to look for other sources, 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).

If you use other sources (Wikipedia, other electronic resources), you have to cite them as well.

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 ContentRe-Use of Existing Content

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

Re-Use of Proteopedia ContentRe-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 ScenesMolecular Scenes

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

ImagesImages

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 MaterialsUse 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 CoordinatesGenerated 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 ToolsUse 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 ToolsUse 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 AlsoSee Also

AcknowledgementsAcknowledgements

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.

ReferencesReferences

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

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Jaime Prilusky, Eric Martz, Wayne Decatur, Karsten Theis
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