CASRAI Dictionary

Tag: preprint indexing

  • BioRxiv ISSN Explained: Why It’s Not a Journal

    BioRxiv holds ISSN 2692-8205, but an ISSN is a serial-registration number, not proof of peer review. BioRxiv is a preprint repository, not a peer-reviewed journal: it has no Scimago Journal Rank, no Scopus record and no impact factor, because those metrics apply only to indexed journals, and bioRxiv does not perform peer review.

    BioRxiv is an open-access preprint repository for the biological sciences, launched in November 2013 by John Inglis and Richard Sever and now operated by the nonprofit openRxiv. Confusion about its status is common because bioRxiv looks and behaves like a journal platform — it has a citable DOI, a formal ISSN and a Wikipedia entry — while lacking the editorial infrastructure that “indexing” actually measures.

    Does bioRxiv have an ISSN, and what does that prove?

    BioRxiv is registered with ISSN 2692-8205, listed in the ISSN Portal and cross-referenced in the NLM Catalog under record ID 101680187, where the U.S. National Library of Medicine lists its electronic ISSN and title abbreviation “bioRxiv: the preprint server for biology”. An ISSN is issued by the ISSN International Centre to any continuing resource — journals, newspapers, monograph series, and repositories that publish serially.

    Holding an ISSN confirms only that a publication is a recognised, ongoing serial with a stable identity. It carries no implication about peer review, editorial oversight, or scholarly indexing. Many predatory journals and informal newsletters also carry valid ISSNs, which is precisely why the number is frequently mistaken for a quality signal.

    Is bioRxiv indexed in Scimago or Scopus?

    No. Scimago Journal & Country Rank derives its rankings exclusively from the Scopus citation database, which indexes peer-reviewed journals, conference proceedings and book series — not preprint servers. Because bioRxiv preprints are not peer-reviewed at the point of posting, they fall outside Scopus’s inclusion criteria, and bioRxiv correspondingly has no Scimago Journal Rank (SJR) or quartile ranking.

    Search results that appear to show “bioRxiv” scientometric profiles, such as third-party aggregator pages listing publication and citation counts, are counting citations to the individual preprints hosted on the platform, not a journal-level metric assigned to bioRxiv itself. This distinction matters for anyone assessing where a piece of research sits in the scholarly record.

    ISSN record vs. Scimago-indexed journal
    Attribute bioRxiv (ISSN 2692-8205) Typical Scimago/Scopus-indexed journal
    Peer review before posting No — basic screening only Yes — mandatory
    ISSN Yes Yes
    Scopus/Scimago listing No Yes (if indexed)
    Impact factor / SJR None Assigned annually
    Editorial board with reject/accept decisions No Yes
    DOI registration Yes, via Crossref (prefix 10.1101) Yes, via Crossref or DataCite

    What does bioRxiv’s Wikipedia entry actually describe?

    The Wikipedia article for bioRxiv describes it plainly as “an open access preprint repository for the biological sciences”, founded by John Inglis and Richard Sever in November 2013 and inspired by arXiv, the physics and mathematics preprint server launched by Paul Ginsparg in 1991. The entry documents bioRxiv’s ownership history in detail: it was hosted by Cold Spring Harbor Laboratory (CSHL) until 11 March 2025, when ownership transferred to openRxiv, a newly formed nonprofit created to run bioRxiv and its clinical-sciences counterpart, medRxiv.

    Nowhere does the entry describe bioRxiv as a peer-reviewed journal. It explicitly notes that submissions “undergo a basic scrutinisation process, which includes safeguarding checks, an automated plagiarism screening and an assessment of appropriateness” — a moderation gate, not editorial peer review. The article also cites a 2019 eLife meta-research study (Abdill and Blekhman) finding that roughly two-thirds of bioRxiv preprints are subsequently published in peer-reviewed journals, underscoring that bioRxiv functions as a pre-publication staging ground rather than a publication venue in its own right.

    Is bioRxiv a journal, and what does “indexing” really mean?

    BioRxiv is not a journal. In scholarly-communication terms, “indexing” means a database such as Scopus, Web of Science, PubMed or the Directory of Open Access Journals has evaluated a title against inclusion criteria — regular publication schedule, peer review, editorial governance, ethical standards — and added its articles to a searchable, citation-tracked index. bioRxiv preprints are discoverable and citable via Google Scholar, PubMed Central (in some cases) and their own DOIs, but that is discovery, not journal indexing.

    • ISSN registration confirms serial identity only.
    • DOI registration (via Crossref) confirms a persistent, citable identifier for a specific preprint version.
    • Scopus/Web of Science indexing confirms a journal has passed a database’s editorial and peer-review vetting process.
    • Scimago/impact factor are journal-level citation metrics computed only for indexed journals — bioRxiv has neither.

    The bioRxiv-to-Journals (B2J) initiative, which by May 2020 allowed authors at 177 participating journals to submit a posted preprint directly into a journal’s manuscript system, illustrates the actual relationship: bioRxiv is a feeder and archive that sits upstream of formal, indexed publication, not a substitute for it. For definitions of related scholarly-communication terms, see the CASRAI Dictionary.

    Answer-first Q&A

    Does bioRxiv have an ISSN?

    Yes. BioRxiv holds ISSN 2692-8205, registered with the ISSN International Centre and cross-listed in the NLM Catalog (record 101680187). An ISSN is a serial-identification number confirming bioRxiv is a continuing publication series — it does not certify that content has passed peer review or editorial vetting.

    Is bioRxiv considered a journal?

    No. BioRxiv is a preprint repository, not a peer-reviewed journal. Submissions undergo only basic screening for plagiarism, safeguarding and appropriateness, not scientific peer review. A 2019 eLife study found roughly two-thirds of bioRxiv preprints are later published in peer-reviewed journals.

    Is bioRxiv a publisher?

    BioRxiv describes itself as an archive and distribution service, operated by the nonprofit openRxiv since March 2025 (previously hosted by Cold Spring Harbor Laboratory). It distributes manuscripts rather than publishing them editorially — authors remain free to submit the same work to a journal afterwards.

    How do you cite bioRxiv?

    Cite bioRxiv preprints using their DOI (prefix 10.1101, registered via Crossref), per bioRxiv’s own FAQ guidance. If multiple versions exist, cite the version-specific URL. ICMJE-aligned journals typically require the citation to flag the work explicitly as a preprint, unlike a peer-reviewed indexed article.

    What this means for authors and institutions

    For research administrators and institutional leaders verifying publication records, the practical takeaway is definitive: a bioRxiv deposit is not equivalent to a peer-reviewed, indexed publication for the purposes of research assessment exercises, promotion dossiers, or funder reporting, regardless of how citable or ISSN-bearing the platform is. Research administration teams verifying publication records for compliance purposes should treat a bioRxiv ISSN or DOI as evidence of deposit and discoverability, not as evidence of peer review or journal-level standing.

    Authors should continue citing bioRxiv preprints by DOI, clearly labelled as preprints, and should track whether a peer-reviewed version has since appeared in an indexed journal — since roughly two-thirds eventually do. Terminology precision matters here: conflating “has an ISSN” with “is indexed” or “is a journal” produces avoidable errors in CVs, grant reports and library catalogues. As preprint servers proliferate across disciplines, the ISSN-versus-indexing distinction bioRxiv illustrates will only become more relevant to how research administrators, publishers and funders classify the scholarly record.

  • 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.