CASRAI Dictionary

Tag: how to cite biorxiv in endnote

  • How bioRxiv Versioning Works (v1, v2, v3)

    bioRxiv versioning works by assigning every preprint a version number starting at v1 on first posting; authors can submit revisions at any time before journal acceptance, each becoming v2, v3 and so on under the same DOI, with every prior version preserved and independently citable via the “Info/History” tab. Unlike a journal correction process, there is no editor gatekeeping a revision, and nothing is ever deleted from the record.

    A bioRxiv version is a distinct, permanently archived snapshot of a preprint’s PDF, HTML and XML files, numbered sequentially (v1, v2, v3…) and linked to one persistent DOI that never changes across revisions. Understanding this versioning system — what triggers a new version, what stays fixed, and how to cite a specific one — matters for authors tracking revision history and readers who need to know exactly which version of a claim they are reading.

    What happens when a preprint first posts as v1?

    When a manuscript clears bioRxiv’s screening process — typically within 72 hours of submission, according to bioRxiv’s own FAQ — it is posted as version 1 (v1). The PDF appears first; full-text HTML and XML conversion follows 24–48 hours later.

    Each version, from v1 onward, is independently available in PDF, HTML and XML — the XML format exists for text-mining and machine-readable indexing, a detail most competing explainers omit. Once v1 is live, it is immediately assigned a DOI (via Crossref) and indexed by Google Scholar, Europe PubMed Central and the Preprint Citation Index connected to Web of Science: v1 is citable and part of the permanent scientific record from the moment it posts, not a provisional draft.

    How do authors submit a v2 or later revision?

    Authors submit revisions through the “Submit a Revision” option in their bioRxiv Author Area, locating their existing submission ID and selecting “Submit a revised manuscript.” bioRxiv’s policy states a manuscript “can be revised at any time until it is published in a journal” — there is no fixed revision window and no limit on the number of versions.

    The revision mechanism is intended for substantive changes: new datasets, re-analyses, expanded discussion, or additional supplemental information. A revision is posted under the same DOI, and — critically — the prior version is not overwritten. It remains permanently accessible through the article’s Info/History tab, so a reader can always compare what changed between v1 and v2, or v2 and v3.

    One detail rarely covered elsewhere: if a preprint was originally submitted indirectly via a journal’s own pipeline (journal-to-bioRxiv, or “J2B”), the corresponding author must first register a bioRxiv account using the same email address used at journal submission before they can access the Author Area to file a revision.

    Does the DOI change between versions, and how do you cite one?

    The DOI stays fixed across every version of a bioRxiv preprint. v1, v2 and v3 of the same manuscript all resolve through one DOI — a reader following an older citation lands on whatever version is current, with the option to step back through history.

    To cite a specific version rather than “whatever is current,” bioRxiv appends a version-specific URL to the DOI. Its FAQ gives this exact pattern:

    Element Format Example
    Standard DOI citation doi: 10.1101/[identifier] doi: 10.1101/2019.12.11.123456
    Version-specific citation DOI + version-specific URL doi: 10.1101/2019.12.11.123456 version 2, https://www.biorxiv.org/content/10.1101/2019.12.11.123456v2

    This matters for reference managers such as EndNote: the DOI field should carry the persistent identifier, while the version number belongs in the URL or a note field if the citing author wants to pin the exact revision read, rather than whichever version happens to be live later.

    One exception: if a revision alters the manuscript so substantially that bioRxiv considers it a genuinely different article, the author must submit it as a new manuscript — which receives its own, separate DOI rather than becoming v2 of the original.

    What does NOT require a new version?

    Three specific cases are worth flagging because they trip up first-time bioRxiv authors and are absent from most general explainers:

    • Metadata typos. If the title, author names, affiliations or abstract in the submission form contain an error but the PDF is correct, bioRxiv auto-replaces the site metadata with text extracted from the PDF within roughly 48 hours — authors are told not to submit a full revision solely to fix this.
    • Author name changes. bioRxiv permits a “silent” first/last name update — for example after a legal name change — by direct email request, without a new version or correction notice. This excludes author removal or reordering, which need a standard revision.
    • Supplemental-file-only changes. If only supplemental files change, bioRxiv still requires them submitted together with the article file as part of a new version; a supplemental-only upload cannot be filed alone.

    What happens if an author withdraws a preprint?

    bioRxiv preprints cannot be deleted once posted, because each version carries a DOI and is indexed externally by Google Scholar and Crossref, creating a permanent footprint independent of bioRxiv’s own servers. If authors no longer stand behind their findings, the remedy is a formal withdrawal, not removal.

    To withdraw, the corresponding author uses “Submit a Withdrawal Statement” inside the same Author Area used for revisions. A withdrawal adds a “Withdrawn” watermark to the PDF of every version ever posted and posts an explanatory statement on the article page — but the original manuscript remains viewable via the Info/History tab. It is a labelled correction, not an erasure. bioRxiv notes outright removal happens only in “extremely rare cases,” for legal or safety reasons.

    Once a preprint is published in a peer-reviewed journal, no further author action is usually needed: bioRxiv automatically adds a link to the published version within approximately two weeks, and all preprint versions — v1 through the final revision — remain live alongside it.

    Common questions about bioRxiv versioning

    Can I upload a new version or replace a bioRxiv preprint?

    Authors cannot replace or delete a posted version, but they can add a new one. Using “Submit a Revision” in the Author Area at any point before journal acceptance creates the next sequential version (v2, v3…) while every earlier version stays permanently visible in the Info/History tab.

    Why does bioRxiv take so long to post a new version?

    Both initial posting and revisions go through the same screening step, which usually completes within 72 hours. Delays typically occur over weekends or holidays, or when a submission needs extra scrutiny for scope, plagiarism or safety-related content before the new version is approved.

    Does bioRxiv count as published once it has multiple versions?

    No. Additional versions do not confer peer-reviewed status. bioRxiv is explicit that it “is not a journal” and has no Impact Factor; every version, however many revisions deep, carries the standard disclaimer that the content has not been certified by peer review.

    Are previous bioRxiv versions still readable after a revision posts?

    Yes. Every prior version remains permanently accessible through the Info/History tab on the preprint’s landing page after a new version is submitted, so readers can compare v1 against later revisions rather than losing access to earlier text.

    Implications for research administrators and institutions

    For institutions tracking preprint outputs in repository or CRIS systems, the persistent-DOI-plus-version model means a single DOI can legitimately correspond to several distinct texts over time. Metadata harvesting workflows that snapshot “the” abstract or author list at ingestion risk becoming stale if a later version changes those fields — administrators should record which version number was harvested, not just the DOI.

    For funders, the NIH has stated it “encourages investigators to use interim research products, such as preprints, to speed the dissemination and enhance the rigor of their work,” and preprints of NIH-funded studies are indexed in PubMed regardless of version count. Citing the version actually reviewed — using the version-specific URL pattern above — gives reviewers an unambiguous audit trail rather than a moving target.

    As preprint volume grows, the version history itself is becoming part of the evidentiary record: it documents how a finding evolved in response to community comment before formal peer review.

  • How to Cite bioRxiv: APA, Vancouver, EndNote

    How to cite bioRxiv in a reference list is straightforward once you know the rule: cite the preprint’s DOI, not a URL alone, mark it explicitly as unreviewed, and — if the content you consulted may differ from the current version — reference the specific version number. bioRxiv preprints receive a DOI (prefix 10.1101/) on posting and are, in the platform’s own words, “citable and part of the scientific record”, but they are not equivalent to a peer-reviewed journal article and most style guides require a disclaimer to say so.

    A preprint is a complete but not-yet-peer-reviewed manuscript posted to an open server — bioRxiv for biology, medRxiv for health sciences — so that findings can be shared, discussed and built upon before formal journal certification. This guide sets out the exact APA and Vancouver formats, how to handle multiple versions, journal-specific quirks, and how to configure EndNote and Zotero so the “not peer reviewed” flag survives into your final manuscript.

    What counts as a citable bioRxiv or medRxiv preprint?

    Every manuscript accepted onto bioRxiv or medRxiv is assigned a DOI at the point of posting, and, per bioRxiv’s own FAQ, “preprints deposited in bioRxiv should be cited using their digital object identifier (DOI)”. The platform is explicit that manuscripts “cannot be removed” once posted, because the DOI is indexed by Crossref, Google Scholar, Europe PMC and the Preprint Citation Index in Web of Science — meaning the preprint is a permanent, citable object regardless of whether it is later published in a journal.

    DOI structure changed part-way through bioRxiv’s history: DOIs assigned before 11 December 2019 use a short six-digit suffix (e.g. 10.1101/123456), while DOIs assigned from that date onward use a longer, date-based suffix (e.g. 10.1101/2023.07.03.123456). medRxiv, co-managed with bioRxiv by the non-profit openRxiv, uses the same 10.1101/ DOI prefix. Neither platform has an Impact Factor, because neither is a journal.

    How do you cite bioRxiv in APA style?

    APA 7th edition treats a preprint as an informally published work, so the citation must name the repository and flag the manuscript’s status in square brackets. There is no separate APA “preprint” reference category — you build it from the general work template.

    Element APA 7th edition rule
    Author Surname, Initials — as listed on the preprint
    Year Year of posting, in parentheses
    Title Italicised, sentence case
    Status flag [Preprint] in square brackets after the title
    Source Repository name (bioRxiv or medRxiv)
    Locator https://doi.org/10.1101/...

    Worked example, adapted from bioRxiv’s official citation model:

    Author, A. N., & Author, B. T. (2013). My article title [Preprint]. bioRxiv. https://doi.org/10.1101/2019.12.11.123456

    In-text citation follows the standard author-date form: (Author & Author, 2013). Do not cite the preprint’s landing-page URL in place of the DOI — the DOI is the stable, version-agnostic locator that Crossref and journal reference-checkers expect.

    How do you cite bioRxiv in Vancouver style?

    Vancouver style, the dominant convention in biomedical journals, follows National Library of Medicine (NLM) guidance for citing preprints, which explicitly reserves a field for the version number and a bracketed “[Preprint]” tag immediately after the title.

    Author FM, Author SM. Title of preprint. Version 2. bioRxiv [Preprint]. 2023 Jul 3 [cited 2026 Jul 3]. Available from: https://doi.org/10.1101/2023.07.03.123456

    In-text citation is numeric, in order of first appearance in the text — for example (1) or a superscript ¹. Journals that follow ICMJE’s Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work permit preprints in the reference list on the same condition APA and NLM apply: the entry must make unambiguous that the work has not been peer-reviewed.

    How do you cite a specific preprint version?

    Unlike a journal article, a preprint can be revised multiple times under one unchanging DOI. If the substance of your citation depends on data, figures or conclusions that changed between versions, cite the version you actually used, not just the DOI.

    • bioRxiv’s own convention: append the version-specific URL — e.g. doi: 10.1101/2019.12.11.123456 version 2, https://www.biorxiv.org/content/10.1101/2019.12.11.123456v2.
    • APA: add (Version 2) after the title, before the [Preprint] tag.
    • Vancouver/NLM: insert Version 2. as its own sentence element between the title and the repository name.
    • New manuscript vs revision: a genuine revision keeps the same DOI; a substantially different follow-up manuscript is assigned a new DOI and must be treated as a separate reference.

    If a preprint has since been formally published, cite the published version of record wherever possible — bioRxiv automatically links the published article to the preprint page within roughly two weeks of publication, and most journals require you to switch the citation once that link exists.

    How do you handle bioRxiv and medRxiv in EndNote and Zotero?

    Reference managers diverge sharply on preprint support, which is the step most researchers get wrong even after they have the correct written format.

    Zotero has offered a dedicated Preprint item type since 2019, with discrete fields for Repository, DOI and Archive ID — importing a bioRxiv record via its DOI or the browser connector populates these automatically, and the “not peer reviewed” status is preserved in the item type itself rather than relying on free text.

    EndNote has no equivalent native preprint type in most current libraries. The practical workaround is:

    1. Create the reference as Unpublished Work or Journal Article, whichever your output style maps most cleanly to a preprint field set.
    2. Enter “bioRxiv” or “medRxiv” as the publisher/journal field, and paste the full DOI (not the landing-page URL) into the DOI field.
    3. Add “Preprint, not peer reviewed” to the Notes or Type of Work field so it survives into any custom output style you build.
    4. If you cite a specific version, record it in the Edition or Notes field, since EndNote has no dedicated version field for preprints.

    Whichever manager you use, verify the exported reference against the APA or Vancouver template above before submission — auto-generated preprint references are the most common source of missing DOIs and dropped “[Preprint]” tags in manuscript reference lists.

    Frequently asked questions

    Is it okay to cite bioRxiv?

    Yes. bioRxiv states that manuscripts posted to the server “receive DOIs and thus are citable and part of the scientific record.” Citing is acceptable across most disciplines and funders, provided the reference clearly discloses that the work is a preprint and has not completed peer review.

    Does bioRxiv have a DOI?

    Yes. Every preprint deposited on bioRxiv is assigned a DOI under the 10.1101/ prefix at the point of posting, and this DOI remains stable across revisions of the same manuscript, resolving by default to the latest version.

    Is bioRxiv considered published?

    No. bioRxiv preprints are not formally “published” in the peer-reviewed sense — they have not been certified, edited or typeset by a journal. They are nonetheless a permanent, indexed part of the scientific record and cannot be withdrawn from the server once posted, only marked as withdrawn.

    Can I cite a preprint in my paper?

    Yes, in most journals and grant applications. Guidance aligned with ICMJE recommendations and publisher policy (e.g. Springer Nature) requires the reference to carry a “[Preprint]” note, the DOI, and standard bibliographic details, so readers cannot mistake it for a peer-reviewed source.

    What this means for authors, editors and institutions

    Funders have moved from tolerating preprint citation to actively encouraging it: the US National Institutes of Health states that it “encourages investigators to use interim research products, such as preprints, to speed the dissemination and enhance the rigor of their work,” and NIH-funded preprints are indexed directly in PubMed. That policy signal, combined with Crossref and Europe PMC indexing, means a correctly formatted preprint citation is no longer a stylistic afterthought — it is a discoverability and compliance requirement.

    Research offices, editors and reference-management teams should standardise on three checks before submission: the DOI (not a bare URL) is present, the cited version matches the version consulted, and the “[Preprint]” disclaimer appears in the visible reference text, not only in a database field. As preprint volume grows, these checks keep a reference list accurate and consistent with the style guide a target journal enforces.