http://publicationethics.org/files/short_guide_to_ethical_editing_for_new_editors.pdf

A SHORT GUIDE TO ETHICAL EDITING FOR  NEW EDITORS

and 

Resources for journal editors and contributors

http://www.intellectbooks.co.uk/page/index,name=journalresources/

Specifically for medical editors:

Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals*

(Updated December 2013)

http://www.icmje.org/icmje-recommendations.pdf

As far as I know, there is no one standard style guide. I tend to use popular style guides, such as "The Chicago Manual of Style", for checking English grammar. For specific scientific terminology, "Scientific Style and Format: the CSE Manual for Authors, Editors and Publishers 8th ed." by the Council of Science Editors is highly recommended. But there are many others.

Thx to Gallicchio. What I meant was a special manual which all styles had an agreement on them that could be used by almost all branches of science..

There is no common approach to style that covers the various fields of science. Most initially follow an approach that represents the journals readership / application (i.e. international, USA etc.). WP gives a good coverage of this, with links to the various styles commonly adopted (http://en.wikipedia.org/wiki/Style_guide).

I edit papers for a living and find that most major journals follow the core guidelines of their parent publisher. Smaller journals/publishers are sometimes more flexible with their style requirements, and there are huge contrasts both within and between the sciences.

As for a book on how to edit a scientific journal: http://www.amazon.com/Scientific-Journal-Professional-Editing-Publishing/dp/0894950339 . I would also be interested in how people learn the structure & process of running a journal (before they take up the post).

The book I mention above is very dated, but there does not seem to be a great deal out there on that specific theme (but lots about writing for journals etc). Maybe a publishing opportunity if someone has experience in this field :-)

Yes, there is. One made by COPE

COPE Best Practice Guidelines for Journal Editors. Link to it is:

http://publicationethics.org/files/u2/Best_Practice.pdf

http://publicationethics.org/files/short_guide_to_ethical_editing_for_new_editors.pdf

A SHORT GUIDE TO ETHICAL EDITING FOR  NEW EDITORS

and 

Resources for journal editors and contributors

http://www.intellectbooks.co.uk/page/index,name=journalresources/

Specifically for medical editors:

Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals*

(Updated December 2013)

http://www.icmje.org/icmje-recommendations.pdf

As others have mentioned - unfortunately, there is no single protocol that has been widely accepted and/or standardized across the industry.  

Having said that, the list below covers styles that are most commonly referenced by editors and authors alike for academic publications:

Science, Technology, Engineering, and Math

• The Manual of Scientific Style: A Guide for Authors, Editors, and Researchers, Academic Press, 2009.
• American Medical Association (AMA) Manual of Style: http://www.amamanualofstyle.com/
• (American Psychological Association (APA) Manual of Style: http://www.apastyle.org/

Law

• ALWD Guide to Legal Citation, 5th ed., Wolters Kluwer Law & Business, 2014.
• The Bluebook: A Uniform System of Citation, 20th ed., The Harvard Law Review Association, 2015. See also: The Bluebook.

 Arts and Literature

The MLA Handbook for Writers of Research Papers, 7th ed., Modern Language Association of America, 2009.

MLA Style Manual and Guide to Scholarly Publishing, 3rd ed., Modern Language Association of America, 2008.

Business

• The Business Writer's Handbook, 11th ed., Bedford/St. Martin's, 2015.
• Franklin Covey Style Guide for Business and Technical Communication, 5th ed., Pearson FT Press, 2012. 

Lastly, if you're looking for help with professional editing of scholarly publications, I can recommend JournalEdit. Join the mailing list and get 20% off your first order.  Link: www.journaledit.com

https://www.journaledit.com

This book might also be helpful:

The EASE Science Editors’ Handbook (http://www.ease.org.uk/webshop/handbook/)

It is published by the The European Association of Science Editors (EASE) .

The article The Science of Scientific Writing by George Gopen and Judith Swan is also an excellent resource for authors looking for suggestions on how to improve writing style for clarity.

PDF copy attached for reference.

A book written by Jo Billingham " Editing and Revising Text" may be useful

there is a blog at https://www.journal-publishing.com/ which deals with paper writing and journal rejections and there is a book called Guide to Academic and Scientific Publication: How To Get Your Writing Published in Scholarly Journals at https://www.proof-reading-service.com/guide/