JMIR Publications has developed a proprietary software (OrangeX) and unique production process where, during copyediting, all references are extracted from the manuscript file, parsed, and 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:
In-text citations (manuscript body)
- In-text references are cited in square brackets (eg, )
- Multiple citations are separated by a comma, without a space (eg, [1,2,3])
- Inclusive citations are separated by a hyphen (eg, [1-3])
- Citations should appear in numerical order in the manuscript throughout the manuscript
The references at the end of the manuscript need to be numbered sequentially using MS Word's numbered list function (1., 2. , 3., ...). This helps eliminate extra line breaks which will register as a separate reference in our system.
If a reference has to be added or removed during copyediting (resulting in in-text citations that are out of order), our system will renumber these automatically during XML conversion. For example, if  is cited before , or if a citation is removed from the text during copyediting, our system will renumber and omit references as necessary.
At JMIR Publications we use a sophisticated RefCheck process after acceptance where the references are looked up in bibliographic databases and cleaned up. Thus, while we prefer AMA-Style, the actual minutia of reference formatting (e.g. where a semicolon should go etc) are not so relevant - let us do the work after acceptance!
Ideally, include PMIDs in your references, so the reference lookup can be optimized.
Do not use "pg" or "p" in front of page numbers.
However, for electronic journals that use electronic ArticleIDs in lieu of page numbers, use the ArticleID as used in the journal (e.g. "e123").
Reference management system (ie, Endnote and Mendeley)
Our journals follow the AMA Manual of Style (11th edition). Remember to use a bibliographic reference management system that allows you to output the PMID (Pubmed ID) after each journal reference (see below for information on database identifiers).
Importantly, you can now download the EndNote output styles for all JMIR journals from the EndNote website.
JMIR uses a reference software (RefCheck) to check for references in online databases and correct them. Minor errors in references (such as errors in authors, titles, etc) will be automatically corrected using information from other databases.
PubMed Identifier (PMID)
For best results, simply add the PubMed Identifier (PMID) behind each reference without brackets manually or with a reference management system that allows this (eg, PMID:12345). Alternatively, a Medline link can be appended (the link contains the PMID as well).
Use a reference management system which allows you to output the PMID (PubMed Identifier) after each journal reference. The PMID allows the RefCheck system to pull references from various databases and automatically correct any formatting errors.
Correct format of identifiers in Word document:
- "PMID:1234567" or "PMID: 1234567"
- Medline link contains the PMID (ie, http://pubmed.gov/1234567 or http://www.ncbi.nlm.nih.gov/pubmed/1234567). There are some hyperlinks to a PubMed abstract which contain something like “cmd=Search” which will not result in a successful search.
If a reference contains a PMID or Medline link but a red minus is displayed, check that they are correct and in the correct format. You can also manually search PubMed for the PMID, enter it in the lookup field, and press save.
DOIs should be found in PubMed or CrossRef. If they are not recognized, have the author confirm that the DOI is correct or search at http://crossref.org/. It is possible that the DOI is correct but is not indexed in the databases we search.
For books, add the ISBN number after the reference, eg, ISBN:12342345X.
Removal of field codes
If authors used a reference management system (like Endnote), in-text references (and the bibliography) may appear as field codes (can be recognized by a grey background). In this case, make sure to remove all field codes and hidden links from the manuscript.
Before re-submitting your revised manuscript after acceptance, open your document in Microsoft Word, select Tools -> Endnote (or Reference Manager) -> Remove Field Codes or convert to Plain Text -> save the manuscript under a new name. Then resubmit that version.
To remove hidden links, select all text (Ctrl+A or Cmd+A), then press Ctrl+Shift+F9 or Cmd+6 to unlink all fields.
Using these methods, your in-text citations and bibliography should become regular text, without field codes or any hidden links. Save under a new file name and upload this as your final manuscript version.
References “In Press”/"Forthcoming"
Submitted or under peer-review
- These do not belong in the references section.
- These must be deleted unless they have been accepted in the time since submission (in which case you must cite them as "forthcoming").
- Cited as “forthcoming” in the reference list.
- Make sure to update references previously cited as "forthcoming" if they are published in the time after submission before copyediting (add the PMID or DOI if known).
- For citing JMIR papers that are in press, see As 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, copyeditors can follow 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.
Please cite preprints as you would journal references. Your copyeditor and production editor will ensure the preprint reference is formatted correctly in the final typeset PDF.
A reference can be formatted as a journal reference, web reference, book or book chapter, or conference proceeding in our reference management system, RefCheck.
Notes on web references
- All Webpages and URLs cited in the manuscript should be added as a reference
- Government reports, Pew Internet Research reports, and other "gray" publications such as dissertations are often freely available on the Web, and we prefer that you add a URL linking directly to the PDF
- 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 referred to in the Methods section
- If possible, reference is to the manufacturer’s URL or, even better, a product description/manual/feature sheet on the developers website.
Preferred format since 12/2010 (including the PMID leads to better results as during production our RefCheck script will clean up and autocorrect the references):
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
International Committee of Medical Journal Editors. Uniform requirements for manuscripts submitted to biomedical journals. JAMA 1997;277:927-934. PMID:9062335
(old format with link to Pubmed handing over the PMID, now discouraged)
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. [Medline]
International Committee of Medical Journal Editors. Uniform requirements for manuscripts submitted to biomedical journals. JAMA 1997;277:927-934. [Medline]
Iverson CL, Flanagin A, Fontanarosa PB, et al. American Medical Association Manual of Style: A Guide for Authors and Editors. 9th edition. Baltimore, Md: Williams & Wilkins; 1998. ISBN:0195176332
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.
Note: If conference proceedings are available through Medline, please use the Medline citation rather than the style above - for example in case of AMIA proceedings or IMIA proceedings (=Medinfo) the citation is as follows:
Mandl KD, Kohane IS. Healthconnect: clinical grade patient-physician communication. Proc AMIA Symp 1999;(1-2):849-53. PMID: 10566480
Hachem F, Bellet J, Flory A, Leverve X. A generic model for Internet-accessed databases in epidemiology: a nutritional application. Medinfo 1998;9 Pt 2:1310-3.
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: Raven Press; 1995. p. 465-78.
Web references (webpages, grey/government reports available on the web as PDFs, etc.)
JMIR authors citing webpages, PDF reports available online, and other web-based references used to be asked to add a WebCite link to their references; however, since December 2018 this is no longer mandatory due to WebCite phasing out its service to the community.
Please ensure you include the original URL in the reference. If you cite reports (such as Pew Internet reports, government reports, etc.), try to locate a free PDF on the web and cite the PDF version.
Journal article in electronic format:
Morse SS. Factors in the emergence of infectious diseases. Emerg Infect Dis 1995 Jan-Mar; 1(1):[24 screens]. http://www.cdc.gov/ncidod/EID/eid.htm
- Endnote style for all JMIR journals
- Official Zotero style (untested)
- Mendeley style hacked by Robin Kok (untested)