alterlab-preprint-deposition

name	alterlab-preprint-deposition
description	Drives preprint deposition across servers (arXiv, bioRxiv, medRxiv, SSRN, OSF Preprints): picks the right server by field, prepares submission metadata, sets the license (arXiv offers CC BY/BY-SA/BY-NC-SA/BY-NC-ND 4.0, the arXiv non-exclusive license, or CC0; bioRxiv/medRxiv offer CC BY/BY-NC/BY-ND/BY-NC-ND/CC0 or No-reuse), maps arXiv category taxonomy, handles immutable versioning and preprint DOIs, checks a journal's preprint/self-archiving policy via the Sherpa Romeo v2 API, and links the posted preprint to the published article. Reuses alterlab-arxiv and alterlab-biorxiv for metadata and alterlab-open-science for data-repository choice. Use when depositing a preprint, choosing a preprint server, preparing an arXiv or bioRxiv submission, setting a preprint license, or checking journal preprint policy; for Zenodo/Dryad/Figshare data deposition prefer alterlab-open-science, for TÜBİTAK Aperta prefer alterlab-aperta. Part of the AlterLab Academic Skills suite.
license	MIT
allowed-tools	Read Write Edit Bash(python:*) WebFetch
compatibility	No API key required for the deposition workflow itself. Optional Python helpers run via `uv run python` (stdlib-only, requests optional). The journal-policy check uses the Sherpa Romeo v2 API, which requires a free registered api-key; the bioRxiv/medRxiv preprint-to-publication check uses the keyless api.biorxiv.org content API.
metadata	{"skill-author":"AlterLab","version":"1.0.0","last_updated":"2026-06-06","depends_on":"alterlab-arxiv, alterlab-biorxiv (metadata/search), alterlab-open-science (data-repository & DMP choice)"}

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.

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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, SSRN, or OSF Preprints. See references/server_selection.md.
2. Submission metadata — title, authors + ORCID, abstract, **arXiv primary
   • cross-list categories** or bioRxiv/medRxiv subject collection, funding, declarations. See references/submission_metadata.md.
3. 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). See references/licensing.md.
4. Versioning & DOI — arXiv versions (v1, v2, …) are ; a withdrawal is a version with a tombstone, never a deletion; bioRxiv/medRxiv assign a DOI on posting and accept revisions.