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How should references be formatted? Which journal style should I choose when using EndNote or other reference management software?

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JMIR Copyediting Team
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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

In-text citations

  • Cite in-text references in square brackets in numerical order of their appearance in the manuscript (eg, [1], [1,3,18]).
  • Separate consecutive citations using a hyphen (eg, [2-13]).

Reference list

  • 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  • Do not add unpublished materials (oral, written, or email-based personal communications or papers not yet accepted for publication).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.

 

Reference formatting

General information

  • 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

ISBN

For books and book chapters, add the ISBN number at the end of the reference (eg, ISBN:12342345X).

Preprints

  • 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.

Web references

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).

Accepted

 

Examples

Journal articles

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]

 

Preprints

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

 

Books

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]

 

Conference proceedings

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.

 

 
 

 

Web references

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].

Social Media 

  • 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]
  • 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]

Unpublished materials

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).
doi:10.2196/10000. http://dx.doi.org/10.2196/10000

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 [43] and by JA Wilson, PhD (email, August 15, 2015)

 

 

External links

 

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