Tag: biorxiv pubmed

  • BioRxiv Preprint Server: NIH, Wellcome and Gates Compared

    Funder preprint requirements diverge sharply in 2026: the Gates Foundation and the Howard Hughes Medical Institute (HHMI) now mandate deposit on a recognised server such as the preprint server bioRxiv or its sister site medRxiv, the NIH indexes eligible preprints in PubMed Central without treating them as compliance, and Wellcome requires them only in defined public-health-emergency scenarios. Research administrators tracking multi-funder portfolios need a single reference for which rule applies where.

    A preprint server is an open-access repository — such as bioRxiv for biology or medRxiv for health sciences — where researchers post a complete but not-yet-peer-reviewed manuscript for immediate public access. Both platforms are operated by openRxiv, a nonprofit formed in 2025 specifically to run bioRxiv and medRxiv independently of their founding host institution.

    What Is a Preprint Server Like bioRxiv?

    A preprint server is a repository for manuscripts that have not yet completed formal peer review. bioRxiv, co-founded by John Inglis and Richard Sever, launched in November 2013 as a life-sciences equivalent to arXiv. Its companion site, medRxiv, covers health and clinical research and applies additional pre-posting screening because of the sensitivity of medical findings.

    Submissions to both platforms undergo basic scrutiny — plagiarism screening, an appropriateness check, and a safeguarding review — but not peer review itself. Roughly two-thirds of bioRxiv preprints are later published in a peer-reviewed journal, and by early 2026 bioRxiv was recording around four million article downloads a month, according to a Nature analysis of the server’s first 13 years.

    Which Funders Require Preprinting in 2026?

    Funder policy on preprints splits into three tiers: outright mandates, conditional requirements, and pure encouragement. The table below summarises the position of four major research funders as of 2026.

    Funder Preprint requirement Effective date Compliance role
    Gates Foundation Mandatory — deposit before or at journal submission, CC BY licence 1 January 2025 Core requirement of the Open Access Policy
    HHMI Mandatory for HHMI investigators, scholars and Janelia scientists 1 January 2026 Preprint required before journal submission
    Wellcome Trust Required only for research with significant public health implications; encouraged otherwise Ongoing Accepted as a fallback open access route if a fully OA journal or Europe PMC deposit is unavailable
    NIH Not required Preprint Pilot ongoing Discoverability only — does not satisfy the NIH Public Access Policy

    Two funders — Gates and HHMI — now treat preprinting as a compulsory step in the research lifecycle. NIH and Wellcome instead fold preprints into a wider menu of open access routes, which is the detail most other coverage of this topic omits.

    How Does the NIH Preprint Pilot Treat bioRxiv Deposits?

    The NIH Preprint Pilot makes eligible NIH-funded preprints — including bioRxiv and medRxiv deposits — discoverable in PubMed Central and PubMed, tagged clearly as preprints rather than peer-reviewed literature. This is a discoverability mechanism, not a compliance mechanism.

    Posting a preprint does not fulfil the NIH Public Access Policy. Grantees must still deposit the final, accepted peer-reviewed manuscript in PMC. NIH does, however, permit researchers to cite preprints in grant applications and progress reports, which gives early findings some formal standing without changing the underlying compliance obligation.

    Does Wellcome Require or Just Encourage Preprints?

    Wellcome strongly encourages preprinting across its funded portfolio and requires it specifically where a disease outbreak or comparable public health emergency makes rapid sharing a priority. Outside those defined scenarios, preprinting is not compulsory.

    Wellcome’s primary open access compliance routes are publication in a fully open access journal or deposit of the author’s accepted manuscript in Europe PMC. A CC BY-licensed preprint is accepted as a valid compliance route only if neither of those primary routes is available — a fallback position, not a default requirement.

    What Changed When bioRxiv and medRxiv Became openRxiv?

    bioRxiv and medRxiv were hosted by Cold Spring Harbor Laboratory (CSHL) from launch until 11 March 2025, when ownership transferred to openRxiv, a newly formed nonprofit dedicated solely to running the two preprint servers. This is a provenance detail funder-policy roundups routinely miss, and it matters for research administrators: openRxiv, not CSHL, is now the governing body whose terms of use and licensing options apply to deposits made under Gates, HHMI, Wellcome and NIH-linked research.

    The Chan Zuckerberg Initiative has funded platform development on both sites since 2017, part of a broader pattern of philanthropic infrastructure investment that runs parallel to — and distinct from — the funder mandates covered above.

    Common Questions About bioRxiv and Preprint Servers

    Is bioRxiv a preprint server?

    Yes. bioRxiv is an open-access preprint server for the biological sciences, hosting complete but not-yet-peer-reviewed manuscripts. It does not conduct peer review itself, though submissions undergo basic screening and reviews from journals or platforms such as Review Commons may be posted alongside preprints.

    Is it free to publish on bioRxiv?

    Yes. Authors register without charge and there is no fee to deposit a manuscript on bioRxiv or medRxiv. This zero-cost deposit model is one reason funders increasingly treat preprinting as a low-friction first step toward full open access compliance.

    What is a preprint server?

    A preprint server is an online repository where researchers post manuscripts before or during formal peer review, giving the wider research community immediate access to findings. bioRxiv and medRxiv are the leading discipline-specific examples in the life and health sciences.

    What are the disadvantages of preprints?

    Preprints add an extra step to the publishing process, are not peer-reviewed at the point of posting, and can attract premature media coverage or public comment before findings are validated. Some journals and funders still weigh these risks against the benefit of faster dissemination.

    What This Means for Institutions and Researchers

    Research administrators managing grants across multiple funders now need to track preprint policy at the individual-funder level rather than assuming a single institutional rule applies. A grantee funded jointly by Gates and NIH, for example, must preprint to satisfy Gates while still separately depositing the accepted manuscript in PMC for NIH.

    • Confirm licence requirements before deposit — Gates and HHMI specify CC BY, which is not the default licence offered on every server.
    • Do not treat NIH Preprint Pilot indexing as equivalent to Public Access Policy compliance — the two are separate obligations.
    • Check Wellcome’s public-health-emergency criteria before assuming preprinting is optional on a given grant.
    • Record the openRxiv terms of use in grant files, since bioRxiv and medRxiv are no longer governed by Cold Spring Harbor Laboratory.

    The Direction of Travel for Funder Preprint Policy

    The trend across 2025 and 2026 runs firmly toward mandatory preprinting among the largest philanthropic funders, while NIH and Wellcome hold a more conditional position rooted in their existing open access frameworks. Institutions should expect more funders to follow the Gates and HHMI model as preprint infrastructure matures under openRxiv’s independent stewardship. Research administration teams that build funder-specific preprint checklists now, rather than applying a single blanket policy, will be better placed as more mandates convert from encouragement to requirement.

    For related definitions and terminology used across research administration and open access compliance, see the CASRAI Dictionary and the research administration resource hub.

  • BioRxiv PubMed Indexing: How the NIH Pilot Works

    BioRxiv PubMed indexing is not automatic. Preprints reach PubMed through a single federal mechanism — the NIH Preprint Pilot, run by the U.S. National Library of Medicine (NLM) — which pulls in preprints that acknowledge direct NIH funding or carry an NIH-affiliated author, provided they were posted from 1 January 2023 onward under the pilot’s current phase.

    The NIH Preprint Pilot is an NLM programme that makes NIH-funded preprints from eligible servers — bioRxiv, medRxiv, arXiv, and Research Square — discoverable through PubMed Central (PMC) and PubMed ahead of formal peer review, with a corresponding citation added on a weekly cycle.

    What is the NIH Preprint Pilot?

    The NIH Preprint Pilot began in June 2020 as a narrow, COVID-19-only initiative. NLM made more than 3,300 preprints reporting NIH-supported SARS-CoV-2 research discoverable in PMC and PubMed between June 2020 and June 2022, testing whether preprint records could accelerate discovery during a public-health emergency.

    Phase 2 launched on 30 January 2023 and dropped the COVID-only restriction. It now covers any preprint that acknowledges direct NIH support and/or lists an NIH-affiliated author, posted to an eligible server on or after 1 January 2023. Eligible preprints are added to PMC on a weekly basis and receive a corresponding PubMed citation automatically — authors do not submit anything separately.

    How a preprint moves from bioRxiv to PubMed

    The pipeline is largely invisible to authors and runs on a fixed weekly cadence. NLM does not wait for a submission; it identifies eligible content and pulls it in automatically, then layers PubMed on top of the PMC record.

    • Identification: NLM text-mines new bioRxiv and medRxiv postings for NIH-support acknowledgements and cross-checks the NIH Office of Portfolio Analysis tool for NIH-affiliated authors.
    • PMC ingestion: Citation and abstract metadata are pulled from the preprint server’s machine-readable feed to build an “article header” record, and a PMCID is assigned immediately to enable rapid discovery.
    • PubMed record creation: Once the PMC record exists, NLM generates the corresponding PubMed citation the same week, tagged with publication type “Preprint.”
    • Full-text conversion: Preprints posted under a Creative Commons licence enter a separate workflow to produce archival full-text XML, a process NLM says takes a few days and enables full-text search within PMC.

    Every record carries a prominent yellow information panel confirming the work has not been peer-reviewed, and NLM runs weekly checks — against the bioRxiv API, the Crossref API, and the Europe PMC API — to link a preprint to its eventual journal version, updating the PubMed status to “Updated” once that link is confirmed.

    Which preprint servers qualify

    Only four servers currently feed the pilot. NLM evaluates candidate servers against a published checklist — clear non-peer-review labelling, transparent versioning, open licensing information, machine-readable metadata, and a public archiving policy — modelled on NIH’s 2017 interim-research-products guidance (NOT-OD-17-050) and COPE’s preprint discussion document.

    Server Subject scope Operator DOI registration
    bioRxiv Life sciences openRxiv (independent nonprofit, formerly a Cold Spring Harbor Laboratory service) Crossref
    medRxiv Health and clinical sciences openRxiv, with Yale University and BMJ as founding partners Crossref
    arXiv Physics, mathematics, computer science, quantitative biology Cornell University Crossref
    Research Square Multidisciplinary Research Square Company Crossref

    bioRxiv and medRxiv are the two servers most relevant to biomedical research administrators, since both fall under openRxiv, the independent nonprofit that took over operation of both platforms from Cold Spring Harbor Laboratory. openRxiv’s separation from a single host institution was framed explicitly around long-term sustainability for the two servers NIH now indexes directly — a governance detail that matters for anyone assessing the pilot’s durability, since NLM’s own eligibility criteria require a “publicly stated archiving strategy to ensure long-term access.”

    What this means for discoverability, DOIs, and citation

    PubMed indexing changes where a preprint can be found, not whether it can be cited. Every bioRxiv preprint already receives a DOI registered through Crossref at posting, which is what makes it part of the citable scientific record regardless of NIH eligibility.

    According to bioRxiv’s own FAQ, preprints are indexed by “Google, all other search engines, Google Scholar, Crossref, Semantic Scholar, Europe PubMed Central, and Preprint Citation Index (connected to the Web of Science)” independent of the NIH pilot — PubMed indexing is an additional, funder-gated channel layered on top of that baseline discoverability.

    One clarification worth making explicitly: bioRxiv and medRxiv do not carry a Scimago Journal Rank or an impact factor. Both metrics are journal-level indicators computed from peer-reviewed citation data; a preprint server is a distribution platform, not a journal, so no SJR score exists for bioRxiv as a whole, and any figure circulating under “bioRxiv impact factor” searches is not an NLM, Crossref, or Scimago-sourced metric.

    Indexing also does not substitute for compliance. NLM is explicit that even when a preprint sits in PMC under the pilot, the NIH Public Access Policy still requires the peer-reviewed, accepted author manuscript to be separately deposited via NIHMS, with its own PMCID reported as proof of compliance.

    Answer-first questions about bioRxiv and PubMed

    Does bioRxiv show up in PubMed?

    Yes, but only conditionally. A bioRxiv preprint appears in PubMed only if it acknowledges direct NIH funding or lists an NIH-affiliated author and was posted under Phase 2 of the NIH Preprint Pilot (from 1 January 2023). Non-NIH preprints stay discoverable via Google Scholar, Crossref, and Europe PMC instead.

    What is a preprint in PubMed?

    In PubMed, a preprint is a record carrying the publication type “Preprint,” which separates it from peer-reviewed literature in search filters. It displays a yellow information panel stating the work has not undergone peer review, and PubMed links it automatically to the journal version once one is published.

    Does bioRxiv count as published?

    No. bioRxiv distributes complete but unpublished manuscripts, so posting there is not equivalent to journal publication. A preprint carries a DOI and is part of the citable record, but it lacks the peer-review certification that ICMJE and COPE norms attach to a published article.

    Is it okay to cite bioRxiv?

    Yes. bioRxiv preprints receive a DOI through Crossref, making them formally citable, and are indexed by Google Scholar, Crossref, Semantic Scholar, and Europe PMC. Authors citing them should flag that the underlying findings have not yet completed peer review.

    Why other funders are watching the pilot

    NIH’s approach is unusual because it is infrastructural rather than a mandate: it does not require authors to preprint, it simply makes eligible preprints easier to find once posted. That distinction is why other funders are studying it rather than replicating it wholesale.

    cOAlition S, the funder coalition behind Plan S, already treats preprints as an acceptable route to satisfying immediate open-access requirements, but no cOAlition S member currently operates an equivalent centralised indexing pipeline into a national biomedical database. UKRI’s open access policy similarly recognises preprints as compliant interim outputs without building comparable PMC-style ingestion.

    For research administrators, the practical takeaway is that discoverability infrastructure and funder mandates remain two separate policy levers. NIH has built the first at meaningful scale; whether other national funders follow with their own PMC-equivalent indexing pipeline — rather than policy language alone — is the open question institutions tracking preprint compliance should watch through 2026 and beyond.