Preprint Deposition — Pick a Server, Prepare the Submission, Link the Published Version

The write/deposit side of preprinting. Given a finished manuscript, this skill turns "I want to post a preprint" into a concrete, server-specific plan: which server fits the field, what metadata and category to enter, which license to choose (and what it commits you to), how versioning and the preprint DOI work, whether the target journal even allows a preprint, and how to link the preprint to the article once it is published.

It is deliberately the deposit-side complement to the read-side connectors alterlab-arxiv and alterlab-biorxiv (which search and fetch preprints) and to alterlab-open-science (which chooses data repositories and writes DMPs). This skill does not reimplement their search/metadata code — it calls them.

Quick Start

I finished a CS paper — how do I post it to arXiv? Which category and license?
Should this biology manuscript go on bioRxiv or medRxiv?
Does Elsevier's journal X allow me to post a preprint before submission?
My preprint just got accepted — how do I link the published DOI to the arXiv version?
What license should I pick on arXiv if I might publish in a closed journal later?

→ Identify the field → route to a server (see the matrix) → assemble metadata → choose a license → run the journal-policy check before posting → after acceptance, link the published DOI back to the preprint.

When to Use This Skill

Use this skill when the user wants to act on a preprint — post it, choose where, prepare its metadata/license, or reconcile it with a journal or a published version. Core jobs:

1. Server selection — match field + manuscript type to arXiv, bioRxiv,

medRxiv, ChemRxiv, SSRN, Research Square, or OSF Preprints. See references/server_selection.md.

1. Submission metadata — title, authors + ORCID, abstract, **arXiv primary

+ cross-list categories** or bioRxiv/medRxiv subject collection, funding, declarations. See references/submission_metadata.md.

1. License choice — pick from each server's actual license set and explain

the downstream commitment (e.g. CC BY is irrevocable; a later journal may object to a permissive preprint license; a funder may require CC BY). See references/licensing.md.

1. Versioning & DOI — arXiv versions (v1, v2, …) are **immutable and

permanent*; a withdrawal is a new* version with a tombstone, never a deletion; every arXiv paper also gets a DataCite DOI (10.48550/arXiv.<id>). bioRxiv/medRxiv assign a Crossref DOI on posting (prefix 10.64898 since Dec 2025 under openRxiv, 10.1101 before) and accept revisions under the same DOI.

1. Journal preprint policy — query the Jisc Open Policy Finder API

(formerly Sherpa Romeo) for the target journal's prearchiving (preprint) policy before posting. See references/journal_policy.md.

1. Post-publication linking — connect the preprint to the published article

(publisher field on the server; the keyless api.biorxiv.org /details/ record carries a published DOI once bioRxiv/medRxiv detect the article).

Does NOT Trigger — route adjacent requests to the right sibling

This skill answers "how and where do I deposit this manuscript as a preprint, and is that compatible with my journal plans?" It makes no claim about manuscript quality, novelty, or whether the work should be published.

Server Matrix (summary — full detail in references/server_selection.md)

Category/license rows above name the option sets each server presents at submission, re-checked 2026-09-23. License implications (irrevocability, journal friction, funder mandates) are in references/licensing.md; never assert a "best" license without stating the trade-off.

Workflow

1. Determine the field and route to a server

Read the manuscript's domain. STEM-formal (physics/math/CS/stat/eess/econ/q-bio/ q-fin) → arXiv. Biology → bioRxiv. Clinical/health → medRxiv. Chemistry → ChemRxiv. Social science/law/economics → SSRN (or arXiv econ). Submitting to a Springer Nature / BMC journal that offers "In Review" → Research Square is the integrated option. Cross-disciplinary or a field-specific community server → OSF Preprints. Edge cases and the full decision tree live in references/server_selection.md.

Check the server's gatekeeping before promising a posting date: arXiv now needs either an institutional email plus a claimed paper in the same endorsement domain, or a personal endorsement (since 21 Jan 2026); arXiv CS posts review and position papers only with proof of prior peer review (since 31 Oct 2025); and bioRxiv/medRxiv will not post a manuscript that a journal has already accepted.

2. Run the journal-policy check FIRST (if a target journal is known)

Before posting, confirm the intended journal permits preprints. Use scripts/journal_policy.py to query the Jisc Open Policy Finder API (https://api.openpolicyfinder.jisc.ac.uk/retrieve, item-type=publication, key in an x-api-key header; the old v2.sherpa.ac.uk Sherpa Romeo API was switched off at the end of July 2026). Report the journal's prearchiving (preprint) permission, any conditions (embargo, version allowed, required statement), and link the source. If no key is available, fall back to WebFetch on the publisher's policy page and say so. Details: references/journal_policy.md.

Most major publishers permit preprints, but conditions vary (some bar posting the accepted version, some require a DOI link or a specific notice). Never assert a policy from memory — verify it per journal.

3. Assemble submission metadata

Build the metadata block the server needs: title, all authors with ORCID and affiliations, abstract, arXiv primary category + optional cross-lists (or bioRxiv/medRxiv subject collection), declarations (competing interests, funding, data/code availability, ethics/IRB for medRxiv), and the manuscript files. For arXiv, upload the TeX/LaTeX source when the paper was written in TeX — arXiv typically rejects a PDF generated from TeX — and include a full English version if the paper is in another language. The canonical field-by-field checklist is in references/submission_metadata.md. To look up an existing arXiv/bioRxiv record's metadata for reuse, defer to alterlab-arxiv / alterlab-biorxiv rather than re-querying here.

4. Choose the license deliberately

Present the actual license set for the chosen server (see the matrix), then explain the commitment:

• CC BY 4.0 — maximum reuse; irrevocable; some closed-access journals

dislike a permissive preprint and may ask you to change it (you cannot revoke CC BY on already-posted versions).

• arXiv non-exclusive license 1.0 — arXiv-specific; you keep copyright,

grant arXiv a distribution license; the least journal-friction option on arXiv.

• *CC BY-NC-/-ND** — narrower reuse; check it against any funder open-access

mandate (e.g. cOAlition S Plan S generally requires CC BY).

• CC0 — public-domain dedication; broadest, also irrevocable.

arXiv states that the license chosen is irrevocable and cannot be changed, though a later version may carry a different license. Confirm whether a funder mandate forces a specific license before recommending — e.g. the Gates Foundation (policy effective 1 Jan 2025) expects funded manuscripts to be shared as a preprint under CC BY 4.0, and Plan S funders want CC BY. The NIH (from 1 July 2025) and NSF (awards from 22 Jan 2026) zero-embargo policies cover the peer-reviewed accepted manuscript, not the preprint. Full table + funder-mandate notes: references/licensing.md.

5. Post, then manage versions

After posting: record the arXiv ID / preprint DOI and the version. Revisions are replacements (arXiv) or new versions (bioRxiv/medRxiv) — the old version stays public and immutable. Do not advise "deleting" an announced arXiv paper; that is impossible — only a withdrawal-version with a tombstone.

6. Link the published article after acceptance

When the paper is published, link the DOI back to the preprint (arXiv's journal-ref/DOI fields; bioRxiv/medRxiv auto-detect many links). On the api.biorxiv.org content API the /details/{server}/{doi} record carries a published field with the article DOI once detected; the per-DOI /pubs/{server}/{doi} lookup currently returns nothing for 10.64898 DOIs, so read published first. This makes the version of record discoverable from the preprint and vice versa.

Scripts

• scripts/journal_policy.py — query the Jisc Open Policy Finder API for a

journal's preprint/self-archiving policy by ISSN or title (needs a free key via --api-key or the OPEN_POLICY_FINDER_API_KEY environment variable; prints a structured summary incl. embargo and locations; degrades to a manual-check instruction offline).

• scripts/server_recommender.py — given a few flags (--field, --needs-doi,

--target-journal-known, --funder-requires-cc-by), prints a recommended server + license shortlist with the trade-offs and gatekeeping notes, from the rules in references/server_selection.md.

• scripts/preprint_link_check.py — query the keyless api.biorxiv.org

/details/ (and, for journal name/date, /pubs/) endpoints to confirm a bioRxiv/medRxiv DOI exists and surface any detected preprint→published-article link; works for both 10.1101 and 10.64898 DOIs.

All scripts are stdlib-first (use requests if present, else urllib), run in a bare uv run python, and never require a key except the Open Policy Finder lookup.

Self-Check Before Reporting

• Did I verify the journal's preprint policy (Open Policy Finder or the live

publisher page), or did I assert it from memory? Only the former is allowed, because publisher policies change and a wrong "yes" can cost the submission.

• Did I name the server's real license options and state the irrevocability

/ journal-friction trade-off, not a bare "use CC BY"?

• Did I route a search/fetch request to alterlab-arxiv/alterlab-biorxiv,

and a data-repository/DMP request to alterlab-open-science, and a TÜBİTAK request to alterlab-aperta, instead of handling it here?

• Did I avoid telling the user to "delete" an already-announced arXiv preprint?

References

• references/server_selection.md — full server decision tree, field-by-field.
• references/submission_metadata.md — per-server metadata field checklist.
• references/licensing.md — license option sets, irrevocability, funder mandates.
• references/journal_policy.md — Open Policy Finder API usage and policy reading.

Part of the AlterLab Academic Skills suite.