Proteopedia:Guidelines for Ethical Writing

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

Content AttributionContent Attribution

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.

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.

• Example of attribution for re-use/adaptation of content from within Proteopedia: Helicase#Content Donators.

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.

• Example of attribution of molecular scenes created outside Proteopedia: Peptide#Content_Attribution.

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.

• Example of image used with permission from the publisher and the author: Mechanosensitive_channels:_opening_and_closing#Models_Available

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.

• Example of re-use of an image from Wikimedia Commons: Avian_Influenza_Neuraminidase,_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 WritingGuide To Ethical Writing

The following guidelines are 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

Cite All SourcesCite All Sources

• An ethical writer ALWAYS acknowledges the contributions of others and the sources of his/her ideas. See 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 <blockquote> and </blockquote>, which will make it look like this:

"Block-quoted text ..."

• 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 OthersRespect 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 . 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 . 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-PlagiarismAvoid 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 ReferencesVerify 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 WorkDistinguish Your Ideas from Previous Work

• 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.

Report Honestly and CompletelyReport Honestly and Completely

• 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.
• 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.

AuthorshipAuthorship

• 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.
• The office of research integrity states that "Only those individuals who have made substantitve contributions to a project merit authorship in a paper". 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."
• 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 AlsoSee Also

• Proteopedia:Copyrights