Open Access Publishing in Medicine: The Complete Guide

Open access is no longer only a choice of journal. Funders now set the licence, the repository and the deadline, and their rules differ more than most authors expect.

Guide · 19 min read · Directive Publications Editorial Team

What open access means, and what it does not

A widely quoted definition comes from the Budapest Open Access Initiative of 2002. It describes open access as free availability on the public internet, permitting any user to read, download, copy, distribute, print, search or link to the full text, crawl it for indexing, pass it as data to software, or use it for any other lawful purpose. The only constraint it leaves in place is the author's control over the integrity of the work and the right to be properly acknowledged and cited.

That definition has two parts, and they are easy to separate by accident:

1. Free to read. Anyone can open the full text without paying or logging in.
2. Free to reuse. A licence tells readers what else they may do: translate it, adapt a figure for teaching, include it in a text-mining project, or redistribute it.

An article that is free on a journal website with no licence meets the first part only. In medicine, that gap matters to people who need to build on your work rather than simply read it, such as educators, translators and review teams.

Open access also leaves three things undecided. It says nothing about how carefully the paper was peer reviewed, whether anyone paid a fee, or how often the paper will be cited. When someone offers you an "open access" option, ask three questions instead of relying on the label:

• Where will the article be free to read, and from what date?
• Under which licence?
• Who pays, if anyone?

The main routes to open access

Sources define the colour labels for open access routes slightly differently. The table uses the common meanings; the three questions above settle whether a route works for you.

cOAlition S, the group of funders behind Plan S, describes diamond open access as a model in which journals and platforms charge fees to neither authors nor readers. Bronze is a term from bibliometric research for articles that are free to read on a publisher's site without an identifiable licence.

Two decision rules follow from the table. If your funder requires immediate open access under an open licence, bronze never satisfies it. And the repository route satisfies it only if you can apply the required licence to your accepted manuscript without waiting out an embargo, which is what rights retention statements, covered below, are designed to secure.

Licences: what readers may do with your paper

The licences you are most likely to be offered are the Creative Commons licences. The six licences all require attribution and differ on commercial use and adaptation; CC0 is a public domain dedication and does not require attribution.

The licence is not a matter of taste when a funder is involved. Plan S states a preference for CC BY. UKRI and Wellcome require CC BY, with CC BY-ND only by exception, and the Gates Foundation requires CC BY 4.0 or an equivalent licence. If a journal offers a licence menu at acceptance, the funder's requirement decides the answer; the usual worries about CC BY are addressed in open access myths that still mislead research offices.

Treat the licence as part of the shortlist, because it constrains the shortlist. A journal publishing clinical research only under CC BY-NC-ND cannot take a UKRI-funded paper through its own website, leaving the repository route and a rights retention statement at first submission.

Two licence issues specific to medical papers

Patient images and case details. A CC BY licence lets anyone copy and adapt your article, including commercially. The ICMJE Recommendations say identifying information should not be published unless it is essential for scientific purposes and the patient, parent or guardian gives written informed consent for publication. An identifiable patient should be shown the manuscript, and authors should tell patients whether identifiable material might be available on the internet as well as in print. Before you submit a case report or clinical image, make sure the consent form the patient signed covers free online availability, use the journal's own consent form if it has one, and remove any identifying detail that is not essential.

Material you do not own. A figure adapted from another publication, or a copyrighted assessment instrument, is not yours to license. UKRI notes that its licensing requirement does not apply to third-party material, which can appear under a more restrictive licence. Get permission, and label that material clearly so readers do not assume the article's licence covers it.

Copyright and author rights

Open access articles are published under one of three broad arrangements:

• Copyright transfer. You assign copyright to the publisher, which then licenses the article.
• Exclusive licence to publish. You keep nominal copyright but grant the publisher exclusive rights.
• Author keeps copyright. You grant the publisher a non-exclusive licence, and the article is released under an open licence.

Plan S states that authors or their institutions should retain copyright. The Principles of Transparency and Best Practice in Scholarly Publishing, published jointly by COPE, DOAJ, OASPA and WAME, say journals should state copyright and licensing terms clearly on their websites, name the copyright holder on the full text of every article, and state their policies on posting author manuscripts in repositories.

Rights retention. Several funders ask you to declare the licence for your accepted manuscript when you first submit. UKRI, for example, asks authors using its repository route to put a statement in the acknowledgements and in any cover letter saying that a CC BY licence has been applied to any author accepted manuscript version arising. The Gates Foundation provides its own acknowledgement wording. Use your funder's exact wording, at first submission. If a publisher then rejects the submission, tells you that you must pay for open access, or changes its terms, UKRI advises contacting your research organisation for advice.

Before you sign any publishing agreement, check three things and keep a copy of what you signed: who holds copyright, which licence applies to the version of record, and what you may do with the accepted manuscript and when.

Funder open access policies in medicine

For many medical researchers, the funder decides most of the route. The table summarises the current requirements of five large funders of health research. Read the full policy before you rely on it, because details change.

A few details change what you do in practice:

• NIH deposit. PMC's guidance on submission methods explains that some journals deposit the final article directly, with no author action needed. Otherwise the accepted manuscript goes in through the NIH Manuscript Submission system, and you should start at acceptance because processing can take up to four weeks when volumes are high.
• UKRI. Biomedical research articles acknowledging MRC or BBSRC funding must also be archived in Europe PMC, whichever route you use. UKRI open access funds cannot pay for a hybrid journal outside a Jisc-approved transitional arrangement.
• Plan S funders. The Plan S principles say its funders do not support the hybrid model except as part of transformative arrangements. cOAlition S members, who include Wellcome, the Gates Foundation, HHMI, UKRI, the European Commission and WHO, confirmed that they would stop financially supporting transformative arrangements after 2024, though individual funders may still take part in agreements under national strategies.

When a paper acknowledges more than one funder, meet every requirement: the strictest licence, the earliest deadline, each named repository, and a payment route that none of the funders prohibits. Several policies cover work funded "in whole or in part", so a co-author's grant counts.

A worked example: your paper acknowledges a Wellcome award and a Gates Foundation grant. Both require CC BY with no embargo, so a noncommercial licence is out. Wellcome requires the article to be free in Europe PMC on publication, and the Gates policy requires deposit in PMC or another open repository, so confirm where the journal deposits or plan to deposit yourself. The Gates Foundation pays no APCs, and Wellcome pays only at fully open access journals indexed in DOAJ, so a hybrid fee would have to come from somewhere else that permits it. A preprint is also expected under the Gates policy.

Who pays: fees, agreements and free routes

Open access is free to read, not free to produce. How the costs are covered depends on the journal and your funders.

• Article processing charges. Charged by many fully open access journals and for the hybrid option. Amounts vary by journal and article type.
• Library and consortium agreements. Transitional or read-and-publish agreements can cover fees for eligible authors, often depending on the corresponding author's affiliation. UK authors can use Jisc's transitional agreement look-up.
• Grant and block grant funds. Allowed by some funders, restricted by others, and ruled out entirely by the Gates Foundation.
• Waivers and discounts. The Principles of Transparency say journals should state who is eligible for a waiver, which author in the group must qualify, and when and how to apply. Our guide to APC waivers and funding language covers how to ask.
• No-fee routes. Diamond journals, Open Research Europe for Horizon Europe beneficiaries, and repository deposit.

Whatever the route, the same principles say fees should be stated on the journal website as early as possible, and that author fees or waiver status should not influence editorial decisions.

The order in which to check no-fee routes, institutional agreements, grant funds and waivers is set out in open access myths that still mislead research offices. Two parts behave differently for a funded medical paper.

The first is eligibility, which usually turns on the corresponding author. Read-and-publish agreements and many waiver schemes are keyed to that author's affiliation, not the first author's. On a multi-centre study the role is often assigned for convenience, and moving it between co-authors can decide whether a fee is covered at all, so settle it while choosing the journal.

The second is that a compliant route and a paid route are separate questions. A funder willing to pay at a journal has not confirmed that its licence and deposit arrangements satisfy the policy. Confirm both by email before submission.

Repositories and self-archiving

Repository deposit is the route most often misunderstood, because the rules come from two directions: the publisher's sharing policy and the funder's requirement.

PubMed Central (PMC) is the National Library of Medicine's full-text repository of life sciences journal literature, established in 2000. It is the designated repository for the NIH Public Access Policy, and it also holds papers under the policies of other funders, including the Gates Foundation and HHMI. Author review and approval is required for every accepted manuscript deposited.

Europe PMC is a partner in the PMC International network and is supported by a group of international science funders as their repository. It runs Europe PMC plus, a manuscript submission system for those funders.

Institutional and subject repositories meet UKRI's repository route and many institutional policies. UKRI points authors to OpenDOAR to find one.

Three rules prevent most repository problems:

• Deposit the right version. Funder policies usually ask for the accepted manuscript: the final text after peer review, before publisher typesetting. If the difference between versions is unclear, see preprint, accepted manuscript and version of record.
• Resolve embargo conflicts before submission. If a journal's sharing policy imposes an embargo and your funder requires none, you need rights retention, a paid open option your funder accepts, or a different journal. Jisc's Open Policy Finder lets you look up a journal's policies and check them against a funder's requirements.
• Save the accepted manuscript on the day of acceptance. Keep the final accepted text, tables, figures and supplementary files together, labelled by version. Rebuilding it months later from email attachments is how the wrong file gets deposited.

The policies above name specific destinations, such as PMC, Europe PMC or an institutional or subject repository. A copy on a personal website or an academic networking profile does not meet those requirements.

Preprints in medical research

A preprint is a complete manuscript shared publicly before peer review. medRxiv, a preprint server for the health sciences, states that its preprints are not certified by peer review, edited or typeset. It screens every submission for plagiarism, non-scientific content, inappropriate article types, and material that could endanger the health of individual patients or the public. It also checks for ethical oversight, clinical trial registration, and information that could identify a patient or participant.

Some practical limits catch medical authors:

• Not every article type fits. medRxiv does not post case reports or case series, narrative reviews, editorials, letters or opinion pieces.
• Acceptance is the cutoff. medRxiv's submission rules say a manuscript will not be posted if it has already been accepted for publication, published or posted elsewhere, though its FAQ is looser and refers to publication. Work to the stricter rule: post before acceptance, ideally at first journal submission.
• Journal policies differ. medRxiv notes that many journals consider manuscripts previously posted as preprints, and advises authors to check the policy of the journal they intend to submit to, and to contact it if in doubt.

Funders are pushing in the same direction. The Gates Foundation expects funded manuscripts to be shared as preprints unless there are ethical, safety or other legitimate concerns. Wellcome strongly encourages preprints and requires them where rapid sharing has a significant public health benefit, such as during a disease outbreak.

Preprints carry a particular responsibility in medicine. medRxiv urges journalists to stress that preprint findings have not yet been evaluated by the medical community and may be wrong. When you post one, describe the findings as preliminary in any press release or social media post. Once the paper appears, check that the server has linked the published version. medRxiv says it usually adds that link automatically within about two weeks and emails the corresponding author to confirm it, so answer that email and contact the server if the link is still missing.

Judging the quality of an open access journal

A journal's business model says nothing about how its papers are reviewed, so judge each journal on evidence that it has publicly committed to a process it can be held to.

The Principles of Transparency give you a checklist. A journal should state on its website:

1. Whether content is peer reviewed, who reviews it, which review model it uses, and how final decisions are made
2. All author fees, or a clear statement that there are none, plus its waiver policy
3. Copyright and licensing terms, shown on every article
4. Its plan for long-term digital preservation if the journal stops operating
5. Its publication ethics policies, including corrections and retractions

The same document says journals should not guarantee acceptance of initial submissions. For a fully open access journal, a listing in DOAJ is a useful further check, and it is also a condition of Wellcome paying the fee. For the warning signs that should end your evaluation, see the 12 red flags of predatory journals.

Open access benefits: what the evidence supports

Some benefits follow directly from the definition. An open article can be read by clinicians without institutional subscriptions, by patients and carers, by policy makers, and by researchers at institutions that cannot afford every journal. An open licence adds the right to translate, teach with and computationally analyse the work. For a funded paper, open access is also a condition of the grant.

The citation benefit is less certain than it is often presented. A systematic review published in PLOS ONE in 2021 included 134 studies comparing citations to open access and non-open access articles. Of these, 64 found a citation advantage, 37 found none, 32 found one only in subsets of their sample, and one was inconclusive. Only three studies had a low overall risk of bias, and they split three ways. The authors concluded that the quality and heterogeneity of the studies make generalisation difficult.

The honest message to authors is this: choose open access because it widens who can read and use your work, and because your funder may require it. Do not promise a department or a promotion committee that it will raise citation counts.

What research offices should put in place

Institutions carry much of the compliance burden, because authors meet these rules only a few times a year. The standing resources every office needs, including the dated one-page funder summary and an advance agreement with communications on unreviewed postings, are in open access myths that still mislead research offices. This list adds what a medical portfolio needs:

1. Per-funder summaries in that form, extended with the named repository and any extra biomedical deposit requirement
2. Rights retention and data availability wording in submission templates and cover letter guidance
3. A deposit workflow triggered by acceptance, with a named person responsible for NIHMS, Europe PMC plus or the institutional repository
4. Fund rules that match funder rules, so the institution never pays a fee a funder would not accept as compliant
5. A current list of publisher agreements, showing which authors and article types are covered
6. Guidance on checking journals against the Principles of Transparency
7. Consent form templates for case reports and clinical images that mention free online availability and reuse
8. A post-publication check that the licence appears on the article and the repository record is live
9. A rule that trial and public health preprints reach the communications team before posting, not after

One resource matters most: a named person who answers journal questions while the paper is still being written. Most compliance failures are questions nobody asked in time.

From grant to publication: a compliance workflow

Open access decisions are cheapest when they are made early. This sequence works for most funded medical papers:

1. At grant award. Record each funder's open access requirements and budget for any fees the funder allows.
2. Before choosing a journal. List every funder acknowledged by every author. For each shortlisted journal, confirm a compliant route, the licence and the cost.
3. At submission. Add the funder's rights retention wording, the data availability statement and grant numbers. Disclose any preprint, and confirm patient consent covers open publication.
4. At acceptance. Save the accepted manuscript, start any required deposit, and confirm the licence and any fee in writing.
5. At publication. Check that the article shows the correct licence, that the repository record is live, and that the preprint links to the published version.
6. Afterwards. Record compliance for grant reports, and make sure any later correction reaches the repository copy as well.

Directive Publications brings its author guidance, open access and licensing, copyright, fee and waiver policies together on its For Authors page, so you can check them against your funders' requirements before you submit. Its peer review process is set out in full on a separate page.