JMIR Publications has developed proprietary software (OrangeX) and a unique production process where, during copyediting, all references are extracted from the manuscript file, parsed, matched against various online databases (eg, PubMed and CrossRef), and automatically corrected.
In order for our system to recognize in-text citations and for our reference software, RefCheck, to complete its automated processes, specific formatting must be applied. Please review our guidelines below.
This article provides presubmission guidelines that can also be used shortly before revisions are submitted around the time of acceptance. If your paper is in copyediting, please consult What is the RefCheck process for authors? (copyediting step 2b).
In the manuscript
- Cite in-text references in square brackets in numerical order of their appearance in the manuscript (eg, , [1,3,18]).
- Separate consecutive citations using a hyphen (eg, [2-13]).
- List references in numerical order at the end of the manuscript using MS Word's numbered list function (1., 2., 3., ...). The numbering used must match the in-text citations.
- Only one publication can be listed for each reference number.
- Do not add unpublished materials (oral, written, or email-based personal communications or papers not yet accepted for publication).
- If references are added or removed during peer review, they will be automatically renumbered during typesetting. Authors should not manually renumber or fix citations after acceptance.
- See the Examples section below for our preferred reference formats.
Reference management system (ie, EndNote and Mendeley)
If you wish to use a bibliographic reference management system, please choose one that allows you to output the PMID (PubMed ID) after each journal reference (see below for information on database identifiers).
You can now download the EndNote output styles for all JMIR journals from the EndNote website.
Removal of field codes/hyperlinks
If you use a reference management system (eg, EndNote), in-text references (and the bibliography) may appear as field codes (can be recognized by a gray background). In this case, make sure to remove all field codes and hidden links from the manuscript.
- Before resubmitting your revised manuscript after acceptance:
- Open your document in Microsoft Word
- Select Tools
- Click EndNote (or Reference Manager)
- Click Remove Field Codes or Convert to Plain Text
- To remove hidden hyperlinks:
- Select all text (Ctrl+A or Cmd+A)
- Press Ctrl+Shift+F9 (or Cmd+6)
Using these methods, your in-text citations and bibliography will render as plain text without field codes or any hidden links. Save this version under a new file name and upload this as your final manuscript version.
- A reference can be formatted as a journal reference, book or book chapter, conference proceeding, or web reference.
- We recommend formatting references according to the AMA Manual of Style (11th edition; see examples below). Minor variation in reference format is acceptable as long as the correct digital identifier is provided for each reference (if available).
- For electronic journals that use electronic article IDs in lieu of page numbers, use the article ID as used in the journal (eg, "e123").
- The requirements for each type of reference are provided below.
Database digital identifiers for journal articles and books/book chapters
JMIR’s reference software, RefCheck, looks up references in online databases to correct them. Minor errors in references (eg, errors in author names, titles) can be automatically corrected using database identifiers like DOIs and PMIDs (eg, for journals, conference proceedings), if available.
PMID and DOI
Add the PMID or DOI at the end of each journal reference without brackets manually or using a reference management system that allows this.
Format as follows:
- PMID:1234567 or PMID: 1234567
- doi:10.1159/000398269 or doi: 10.1159/000398269
For books and book chapters, add the ISBN number at the end of the reference (eg, ISBN:12342345X).
- Cite preprints as you would journal references.
- Include the full date (eg, Sept 23, 2020) that the preprint was posted online.
- Your copyeditor will ensure the preprint reference is formatted correctly in the final typeset PDF.
- Add all web pages and URLs cited in the manuscript as a reference.
- Government reports, Pew Internet research reports, and other “gray” publications (eg, dissertations) are often freely available on the internet; add a URL linking directly to the PDF.
- Provide an access date.
- Avoid using URLs from a search result (eg, http://www.nature.com/search?journal=mp&q=A%20mega-analysis%20of%20genome-wide%20association%20&q_match=all&sp-a=sp1001702d&sp-m=0&sp-p-1=phrase&sp-sfvl-field=subject%7Cujournal&sp-x-1=ujournal&submit=go).
- Provide the direct link (eg, http://www.nature.com/mp/journal/v18/n4/full/mp201221a.html).
- Software is cited as a web reference only if it is the subject of the paper. If the software is just mentioned in passing, it can be mentioned in the Methods section without a citation.
- If possible, provide a reference to the manufacturer’s URL or a product description/manual/feature sheet on the developer’s website.
- Do not provide Webcite IDs for web references, as these are now defunct.
- References of social media posts will vary depending on the platform (see Examples section below for our preferred reference format)
In press/forthcoming references
Submitted or under peer review
- Do not include submitted papers or papers in preparation in your reference list. Instead, cite these as unpublished data in the text parenthetically (eg, HE Marman, MD, unpublished data, January 2015).
- Note that citing unpublished data does not conform to best practices. You may want to cite these as personal communications instead (see below, under “Unpublished materials”).
- If, from the time of submission to acceptance of your article in a JMIR journal, the submitted manuscript cited in your article is accepted for publication, inform your copyeditor during the copyediting stage of production (ie, during Step 2 of copyediting).
- Cite as “forthcoming” in the reference list by adding the term "forthcoming" after the journal name in parentheses
- Update references previously cited as “forthcoming” if they are published before your paper enters copyediting (add the PMID or DOI if known).
- To cite JMIR papers that are in press, see As an author, how can I cite my accepted but not yet published article (in press/forthcoming JMIR article)?
- If you did not cite a paper as “forthcoming” before copyediting, your copyeditor can add a new reference during copyediting. It is not desirable to have a statement such as, “As the companion paper in this issue of the journal shows...” without citing it properly.
Author surname, first name initial(s). Article title. Abbreviated journal name. Year;volume(issue):pages. PMID:XXX doi: XXX
Westberg EE, Miller RA. The basis for using the Internet to support the information needs of primary care. J Am Med Inform Assoc. 1999 Jan-Feb;6(1):6-25. PMID:9925225
Kourou K, Exarchos TP, Exarchos KP, Karamouzis MV, Fotiadis DI. Machine learning applications in cancer prognosis and prediction. Comput Struct Biotechnol J. 2015; 13:8-17. doi: 10.1016/j.csbj.2014.11.005
International Committee of Medical Journal Editors. Uniform requirements for manuscripts submitted to biomedical journals. JAMA. 1997;277:927-934. PMID:9062335
Non–English-language titles may be provided without translation: Rubbert-Roth A. Differenzialdiagnostik der frühen Polyarthritis. Dtsch Med Wochenschr. 2015;140(15):1125-1130. doi:10.1055/s-0041-103627
Journal article in electronic format: Morse SS. Factors in the emergence of infectious diseases. Emerg Infect Dis. 1995 Jan-Mar; 1(1). http://www.cdc.gov/ncidod/EID/eid.htm
Supplemental content: Meeker D, Linder JA, Fox CR, et al. Effect of behavioral interventions on inappropriate antibiotic prescribing among primary care practices: a randomized clinical trial. Supplement 1. Study protocol and changes to analysis plan. JAMA. 2016;315(6):562-570. https://www.jamanetwork.com/journals/jama/fullarticle/2488307 [access June 18, 2019]
Bloss CS, Wineinger NE, Peters M. A prospective randomized trial examining health care utilization in individuals using multiple smartphone-enabled biosensors. bioRxiv. Preprint posted online October 28, 2015. doi:10.1101/029983
Author surname, first name initial(s). Book Title. Edition number (if it is the second edition or later). Publisher location: publisher’s name; copyright year. ISBN: XXX
Iverson CL, Flanagin A, Fontanarosa PB. American Medical Association Manual of Style: A Guide for Authors and Editors. 9th edition. Baltimore, MD: Williams & Wilkins; 1998. ISBN:0195176332
Chapter in a book: Phillips SJ, Whisnant JP. Hypertension and stroke. In: Laragh JH, Brenner BM, editors. Hypertension: Pathophysiology, Diagnosis, and Management. 2nd ed. New York, NY: Raven Press; 1995:465-78. ISBN: 0781701570
eBook: Guyatt G, Rennie D, Meade MO, Cook DJ. Users’ Guides to the Medical Literature: A Manual for Evidence-Based Clinical Practice. 3rd ed. New York, NY: McGraw-Hill; 2015. https://jamaevidence.mhmedical.com/book.aspx?bookID=847 [accessed Aug 15, 2016]
Author surname, first initial(s). Editor surname, first initials (if applicable). Title. Name of proceedings. Date of conference; location of conference. Publisher location: publisher name (if available); year. URL (if available). DOI (if available).
Kimura J, Shibasaki H, editors. Recent advances in clinical neurophysiology. Proceedings of the 10th International Congress of EMG and Clinical Neurophysiology; 1995 Oct 15-19; Kyoto, Japan. Amsterdam: Elsevier; 1996.
Author surname, first name initial(s) (or organization name). Title (if available). Name of the website. Published year/date (if available). URL. [access date]
Website: PatientsLikeMe. Available from: https://www.patientslikeme.com/ [accessed Nov 5, 2020].
Government/agency report: World Health Organization. World Health Report 2013: Research for Universal Health Coverage. 2013. https://www.afro.who.int/publications/world-health-report-2013-research-universal-health-coverage [accessed Apr 16, 2021].
Theses and dissertations: Ghanbari S. Integration of the Arts in STEM: A Collective Case Study of Two Interdisciplinary University Programs. Dissertation. University of California; 2014. http://escholarship.org/uc/item/9wp9x8sj [accessed Oct 14, 2016].
News publication: Anthes, E. What the coronavirus variants mean for testing. New York Times. April 14, 2021. https://www.nytimes.com/2021/04/14/health/coronavirus-testing-variants.html [accessed Apr 16, 2021].
- Facebook (limit the post content to the first meaningful stand-alone sentence or phrase and follow it with an ellipsis; see Facebook post example followed by the correct reference format):
Mayo Clinic Sports Medicine Facebook page. #RotatorCuff tears are among the most common shoulder injuries... March 4, 2019. URL: https://www.facebook.com/mayoclinicsportsmedicine [Accessed 2019-05-04]
Gray T. Advice after mischief is like medicine after death. AMA Style Insider blog. February 11, 2019. URL: https://amastyleinsider.com/2019/02/11/advice-after-mischief-is-like-medicine-after-death/ [Accessed 2019-03-10]
- YouTube channel:
Khan Academy Health and Medicine YouTube page. URL: https://www.youtube.com/user/khanacademymedicine [Accessed 2016-02-10]
- YouTube video:
SciComm teaser: patient-led mass screening for atrial fibrillation in seniors using handheld ECGs. JMIR Publications YouTube page. April 11, 2022. URL: https://www.youtube.com/watch?v=l3PeFOS7awE [accessed 2022-08-10]
- YouTube channel:
- Twitter (the whole post content should be included in the reference; see Twitter post example followed by the correct reference format):
@AMAManual. Double negatives can be used to express a positive, but this yields a weaker affirmative than the simpler positive and may be confusing. “Our results are not inconsistent with the prior hypothesis.” “That won’t do you no good.” And the classic: “I can’t get no satisfaction.” March 7, 2019. URL: https://twitter.com/AMAManual/status/1103678998327017483 [Accessed 2019-03-10]
Materials accepted for publication: Shelley, N. Health Care in Canada. Oxford, UK: Oxford University Press. Forthcoming 2021.
Lobban, F. Assessing Feasibility and Acceptability of Web-Based Enhanced Relapse Prevention for Bipolar Disorder (ERPonline): A Randomized Controlled Trial. J Med Internet Res (forthcoming).
Materials submitted/under peer review (to be cited only in text): These findings were recently corroborated (JA Wilson, PhD, unpublished data, January 2020).
Personal communications (to be cited only in text): Similar findings have been noted by Firth et al  and by JA Wilson, PhD (email, August 15, 2015)
- EndNote style for all JMIR journals
- Official Zotero style (untested)
- Mendeley style hacked by Robin Kok (untested)
- What is the RefCheck process for authors? (copyediting step 2b)
- What do the different RefCheck icons mean?
- How do I add a reference to my paper (RefCheck) after it has been accepted?
- How do I delete a reference from RefCheck?
- How can I reorder references during copyediting?
- My paper has some material that is more appropriate for a Multimedia Appendix than the main manuscript. How do I make sure the sources are included in RefCheck?
- JMIR House Style and Editorial Guidelines