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 databases (e.g. PubMed and CrossRef), and automatically corrected. During step 2 of the copyediting process (see What are the steps during copyediting?), authors are asked to check/correct those references which were not matched against a database entry.
Only references which do not match (indicated by a red dash) need to be checked/corrected by the author. The author can enter a PMID or DOI in the form and retrieve the correct metadata elements, then save. Or change the reference type and enter the metadata in their respective fields manually.
The RefCheck process works best when authors include the PMID (Pubmed ID) to every journal reference in the format PMID:123456 behind every reference. In fact, when this is done, the actual formatting of the references do not matter, as long as they are a numbered list of references in any format (cited with ,  etc in the manuscript).
Note that references can not be added at this point (they should have been complete in the accepted version of the manuscript).
The references you see online cannot be deleted or rearranged, however, if an in-text citation in the manuscript file is removed, our typesetting scripts will later omit the non-cited references and renumber all subsequent in-text citations and references (see How do I delete a reference from RefCheck? and Why have my references been renumbered during typesetting?).
For example, if  is not cited in the manuscript at all, the online reference 1 ("ABS..." in the example below) will not appear in the final bibliography, and all references 2-n will be renumbered to be 1-m (where m=n-1), in both in-text citations and the bibliography. If you omit a citation from the manuscript, do not renumber subsequent in-text citations manually.
Similarly, you do not have to worry about rearranging in-text citations in the manuscript to bring them into a sequential order. If the order of cited references is not sequential (e.g. in the manuscript,  is cited before ), no manual rearrangement of the references in RefCheck or the manuscript file is required. During typesetting, our typesetting scripts would flip the order of reference 1 and 2 in both the manuscript (in-text citations to  are replaced with ) and the bibliography (ref 2 appears before ref 1 and is renumbered to be 1.). All this occurs after copyediting, when the final proofs are generated (see also Why have my references been renumbered during typesetting?).
- What do the different RefCheck icons mean?
- How should references be formatted in the manuscript?
- What are the steps during copyediting?
- How do I delete a reference from RefCheck?
- Why have my references been renumbered during typesetting?
- 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?