From an accepted Word file to a PubMed Central–ready article.
Colophon builds the complete production package your journal needs to publish and get indexed — structured XML, verified and linked references, production-ready figures and a typeset PDF — and checks it against PubMed Central’s own rules before you ever see it. In hours, not weeks. No XML vendor, no XML expertise.
Works with OJS, from the web, or with your own systems. Your editors keep the final say on every decision.
The problem
Indexing needs XML. XML has been slow, expensive, and impossible to check.
You pay for every article
Every issue goes to an outside vendor, and every manuscript costs money — whether or not the result is any good.
You wait for weeks
Publication stalls while files travel back and forth. Every correction starts the clock again.
You find out too late
Errors surface when PubMed Central rejects the deposit — after you have already paid, and already published.
How it works
Four steps from a Word file to a finished article
01
Upload
Drop the accepted Word manuscript into the web app — or send it straight from your OJS workflow with one click.
02
Colophon builds the package
It reads the real structure of the document: sections, tables, figures, funding, ethics, affiliations. References are matched against Crossref and PubMed and linked to every citation in the text — superscript numbers included.
03
You review what it flags
Anything Colophon cannot settle on its own — a missing page range, a reference it cannot verify — comes to you as a clear item to resolve. Nothing is guessed silently. Optional AI copy editing arrives as suggestions your editors accept or reject.
04
Download or attach
Get a deposit-ready ZIP checked against PubMed Central’s own style rules, plus a typeset PDF. From OJS, the finished galley attaches itself.
Tested on a real issue
15 articles. Checked by PubMed Central’s own tool. Zero errors.
We took a complete, already-published issue of a medical journal — fifteen research articles — and ran every one through Colophon. Then we validated the results with the National Library of Medicine’s official PMC style checker, not our own judgement.
15/15
articles passed PMC’s official style checker with zero errors
653
citations linked to the right reference — none left broken
0
lines of the final XML written by AI. Generation is rule-based: the same input always gives the same output.
100%
of references linked. The paid vendor’s version of the same issue linked none of them.
What the manuscript looked like
<!-- Word, flattened to text --> Survival improved markedly in the treated cohort.³ Similar gains were reported in 2019.⁷ References 3. Ahmadi R, et al. Outcomes after adjuvant therapy. Arch Breast Cancer. 2019;6(2):41-8.
What Colophon produced
<p>Survival improved markedly in the treated cohort.<xref ref-type="bibr" rid="B3">3</xref> …</p> <ref id="B3"><element-citation publication-type="journal"> <article-title>Outcomes after adjuvant therapy</article-title> <pub-id pub-id-type="doi">10.32...
For the technical reader: the same paragraph, before and after. Every citation becomes a live link to its reference entry.
Works where you work
Three ways in, one production engine
Use the web app, connect your Open Journal Systems, or plug into our API. They all run the same pipeline — so a fix made once holds everywhere.
Web app
Upload and go
Drop a Word file, choose the journal and issue, and watch each stage complete. Anything that needs your attention stays on the page, and Resume picks up exactly where it stopped.
OJS plugin
Send from inside OJS
Connect your journal once — no keys to copy. From then on, send an accepted manuscript to Colophon from the editorial workflow; the finished package returns to your production files, and the galley attaches at publication. Status and credits stay visible inside OJS.
API
For automated publishers
Submit manuscripts and metadata programmatically, poll for status, and receive results by webhook — the same pipeline as the web app, for hosts that already automate their intake.
You stay in control
Nothing ships without a person deciding
The XML is predictable
Your production XML is built by fixed rules from reviewed data — not written by an AI. The same article always produces the same package, and any problem can be reproduced and fixed.
Your editors have the final word
Once an editor approves a field, a reference or a figure, it stays approved until a person changes it. Nothing automated can quietly overwrite a decision your team already made.
AI suggests. It never overwrites.
Extraction, cleanup and copy editing arrive as suggestions with a visible before-and-after. Accepting is a deliberate act — and any edit that would invent a number, a citation or an identifier is refused automatically.
Your manuscripts stay yours
Access is controlled per journal and per role. Nothing is published, deposited or sent anywhere unless someone on your team decides it should be.
Try it on your next issue
Connect your journal and start with welcome credits — enough to see Colophon work on your own articles. After that, you pay per issue, only for what you produce. Your current vendor stays optional.