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PubCrafts

Deposits

Depositing a journal in PubMed Central

PubMed Central is where a great deal of biomedical research is read, and for many journals being in it is the difference between being cited and being overlooked. It does not accept PDFs. It accepts structured full text, and that requirement is the reason most small biomedical journals first go looking for XML.

This is what the deposit involves, in the order you will meet it.

Being accepted as a journal first

Depositing is the second problem. The first is that the journal itself has to be accepted, and that is an editorial and scientific assessment rather than a technical one: scope, editorial board, peer review process, publication ethics, and a publishing history long enough to judge.

It is worth knowing that this assessment looks at the quality of the published articles as objects as well as as science. A journal whose articles have inconsistent metadata, missing dates, or reference lists that do not resolve is making its own case harder.

What a deposit consists of

For each article: the full text as structured XML, the figures as separate image files at usable resolution, any supplementary material, and usually the PDF as well. These are packaged together per article, with the files named so that the references to them inside the XML resolve.

The metadata requirements are stricter than many journals are used to. Expect to need, for every article and with no gaps:

  • The journal's own identifiers, including its ISSNs, print and electronic, correctly distinguished.
  • The article's DOI, and the volume, issue and page or article numbers.
  • Every author with their given and family names separated, and their affiliations linked to them individually rather than listed together.
  • The dates the article was received, revised and accepted, and the date it was published.
  • The licence under which it is published, stated in a machine-readable way and not only as a sentence.
  • The abstract as structured text, and keywords.
  • A reference list with each reference broken into its parts.

Where deposits get rejected

Almost never for the science, and almost always for one of a short list of avoidable things. In rough order of how often they happen: a figure referenced in the XML that is not in the package, or is named differently. An ISSN in the wrong field. An affiliation attached to the article rather than to an author. A missing accepted date. A licence stated only in prose. A reference with no year. An equation deposited as an image where mathematics was expected.

None of those is hard to fix. All of them are hard to find after the fact, which is why the useful place to catch them is before the article is published, not when the deposit bounces.

Doing it alongside publication rather than after it

The common pattern is that a journal publishes a PDF, and then months later commissions conversion for the deposit. By then the article is the version of record, the person who edited it has moved on, and any disagreement between the deposit and the published article is a correction rather than an edit.

If the structured file is produced from the same approved article as the galley, the deposit is ready on publication day and says exactly what the published article says. That is less work and a better result, and it is the main practical argument for producing the XML yourself.

Last reviewed

Questions

Can we deposit without being accepted as a journal?

Individual articles can reach PubMed Central by other routes - notably when a funder requires the accepted manuscript to be deposited - but that is deposit of a manuscript, not of your published article. Having the journal itself accepted is what gets the version of record in.

Does the PDF still matter?

Yes, and it is usually included. But it is the structured text that is indexed and searched, so it is the structured text that decides whether anyone finds the article.

How current do deposits have to be?

Expect to be asked to deposit on or close to publication, and to be asked about the back catalogue. A journal that deposits a year late is treated as a journal that may stop depositing.

Next step

Produce a deposit-ready article today.

Send us your journal's identifiers and licence with one accepted manuscript. We set the account up with them already in it, and you take that paper through to its structured files.