Paper Interpretation
digoal/blog
从论文 PDF 文件或论文 PDF URL 生成通俗易懂、图文并茂、带批判性评估的中文 Markdown 解读，并保存到当前项目的 markdown 目录。Use when the user asks to interpret,精读,解读,summarize,explain,analyze, or write an article from an academic paper PDF…
A skill your agent uses when you need full-text PDFs for a list of DOIs, such as a meta-analysis screening set.
Install Fulltext Retrieval
$ npx skills add Aperivue/medsci-skills --skill fulltext-retrieval -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install Aperivue/medsci-skills fulltext-retrieval --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/fulltext-retrieval .claude/skills/fulltext-retrieval && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "fulltext-retrieval" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/fulltext-retrieval into .claude/skills/fulltext-retrieval/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fulltext-retrieval", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/Aperivue/medsci-skills/tree/main/skills/fulltext-retrievalType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add Aperivue/medsci-skills --skill fulltext-retrieval -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install Aperivue/medsci-skills fulltext-retrieval --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/fulltext-retrieval .agents/skills/fulltext-retrieval && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "fulltext-retrieval" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/fulltext-retrieval into .agents/skills/fulltext-retrieval/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fulltext-retrieval", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add Aperivue/medsci-skills --skill fulltext-retrieval -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install Aperivue/medsci-skills fulltext-retrieval --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/fulltext-retrieval .cursor/skills/fulltext-retrieval && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "fulltext-retrieval" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/fulltext-retrieval into .cursor/skills/fulltext-retrieval/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fulltext-retrieval", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/Aperivue/medsci-skills.git --path skills/fulltext-retrieval--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add Aperivue/medsci-skills --skill fulltext-retrieval -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install Aperivue/medsci-skills fulltext-retrieval --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/fulltext-retrieval .gemini/skills/fulltext-retrieval && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "fulltext-retrieval" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/fulltext-retrieval into .gemini/skills/fulltext-retrieval/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fulltext-retrieval", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install Aperivue/medsci-skills fulltext-retrievalInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add Aperivue/medsci-skills --skill fulltext-retrieval -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/fulltext-retrieval .github/skills/fulltext-retrieval && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "fulltext-retrieval" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/fulltext-retrieval into .github/skills/fulltext-retrieval/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fulltext-retrieval", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add Aperivue/medsci-skills --skill fulltext-retrieval -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install Aperivue/medsci-skills fulltext-retrieval --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/fulltext-retrieval .opencode/skills/fulltext-retrieval && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "fulltext-retrieval" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/fulltext-retrieval into .opencode/skills/fulltext-retrieval/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fulltext-retrieval", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
fulltext-retrieval- GitHub stars
- 331
- Token cost
- ~1.9k tokens
- SKILL.md length
- 730 words
- Files
- 13 (incl. references)
- Skills in repo
- 54
- Repo updated
- First seen
- Licence
- MIT
At a glance
A skill your agent uses when you need full-text PDFs for a list of DOIs, such as a meta-analysis screening set.
- You need full-text PDFs for a list of DOIs
- SKILL.md covers Pipeline, Run, Output and Retrieval report (--report), plus 2 more sections
- Runs Python, Shell and JavaScript scripts from its folder; calls python and pip
- Such as a meta-analysis screening set
What it does
Fulltext Retrieval is an agent skill from Aperivue/medsci-skills. Use when you need full-text PDFs for a list of DOIs, such as a meta-analysis screening set. Batch-downloads open-access copies via Unpaywall, PMC, OpenAlex and Crossref, lists paywalled papers for manual access, and can convert PDFs to Markdown.
Its SKILL.md is about 1.9k tokens, which your agent loads only when the skill is triggered. The skill folder holds 16 other files, including reference files (for example `fetch_oa.py`, `fetch_oa_report_challenge/expected/projection.json` and `fetch_oa_report_challenge/extracted_text.json`).
It sits in Documents & Office, covering Academic paper search, PDF and Markdown. It works with arXiv. The repository describes itself as: Agent Skills for medical research — literature search, reporting-guideline & citation checks, statistics, publication figures, submission. Works with Claude Code, Codex, Cursor &… The licence is MIT.
When your agent uses it
- You need full-text PDFs for a list of DOIs
- Such as a meta-analysis screening set
Example prompts
- “/fulltext-retrieval”
Requirements
- Python 3
- Node.js
- A Bash shell
What it can do on your machine
Read from SKILL.md and the folder at commit 3b14ae2. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships script files (Python, Shell and JavaScript), which the agent can run.
Shell commands in SKILL.md call:
pythonpip
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
pypi.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Fulltext Retrieval loads about 1.9k tokens when it runs, and up to ~2.7k if it reads all its reference files. Until then it costs about 66 tokens; SKILL.md has 730 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from Aperivue/medsci-skills at commit 3b14ae2, republished under its MIT licence (© Aperivue). 730 words, ~1,938 tokens.
Download SKILL.mdSave it as
.claude/skills/fulltext-retrieval/SKILL.md (or your agent's skills folder). This skill also uses 12 other files; get the full folder from GitHub.- name
- fulltext-retrieval
- description
- Use when you need full-text PDFs for a list of DOIs, such as a meta-analysis screening set. Batch-downloads open-access copies via Unpaywall, PMC, OpenAlex and Crossref, lists paywalled papers for manual access, and can convert PDFs to Markdown.
- metadata.triggers
- PDF download, fulltext retrieval, open access PDF, batch download papers, meta-analysis PDF, PDF to markdown, convert PDF
Fulltext Retrieval Skill
Batch download open-access full-text PDFs from a DOI list using legitimate OA APIs only.
Paywalled articles fail by design and are listed in manual_needed.txt for institutional access
or ILL; never work around a paywall or publisher access control.
Pipeline
DOI → arXiv (10.48550/arXiv.* DOIs) → Unpaywall → PMC (Europe PMC / OA FTP / web) → OpenAlex → Crossref → landing pageEach DOI goes through these sources in order until a valid PDF (≥10 KB, %PDF- header) is found.
arXiv DOIs (10.48550/arXiv.2401.01234, version suffixes, old-style hep-th/9901001, or a bare
arXiv: id) resolve directly to the arXiv PDF first.
Run
Requires Python 3.10+ (stdlib only) and a contact email, which Unpaywall's Terms of Service require. The script paces its requests (0.3–0.5 s delays) for the APIs' rate limits.
python "${CLAUDE_SKILL_DIR}/fetch_oa.py" dois.txt --output pdfs/ --email your@email.com
# Verbose mode for debugging (per-DOI source trace)
python "${CLAUDE_SKILL_DIR}/fetch_oa.py" dois.txt -o pdfs/ -e your@email.com --verboseInput formats:
- Plain text — one DOI per line.
- TSV / CSV with header, or a Markdown pipe table — must contain a
DOIcolumn; optionalPMID,Title, andFirstAuthor(surname or full name) columns.
A PMID makes the PMC lookup more reliable (PMID → PMCID conversion). Supply Title where
available: a DOI-only worklist can download a PDF but cannot establish title agreement.
FirstAuthor is optional additional evidence.
Output
- PDFs saved as
{DOI_safe}.pdf(slashes replaced with underscores). pdfs/retrieval_report.json— structured per-DOI report (below); override with--report PATH.<output>/manual_needed.txt— DOIs that could not be retrieved via OA; when a PMCID was resolved, the line also carries it and the PubMed Central article URL to open in a browser.- Summary with arXiv/OA/PMC/fail/skip counts.
Retrieval report (--report)
Every run writes the report (default <output>/retrieval_report.json), schema 2:
{
"schema_version": 2,
"generated_by": "fetch_oa.py",
"counts": {"total": 4, "retrieved": 3, "not_retrieved": 1, "title_mismatch": 1,
"source_identity": {"consistent": 1, "conflict": 1, "unresolved": 1, "unavailable": 1}},
"items": [
{"doi": "10.1000/synthetic.example", "pmid": "", "title": "Example title",
"first_author": "", "status": "oa", "source": "unpaywall",
"file": "10.1000_synthetic.example.pdf", "size_bytes": 482113, "page_count": 9,
"file_sha256": "<SHA-256 of the downloaded file>", "title_match": "match",
"source_identity": {"status": "consistent", "reason": "title_and_identifier_agree",
"text_scope": "first_page_front_matter", "title_match": "match",
"doi_match": "match", "observed_identifiers": ["10.1000/synthetic.example"],
"first_author_match": "unavailable"}}
]
}status (arxiv | oa | pmc | skip | fail), source, and counts.retrieved describe the
resolver result, including existing files (skip). They do not count identity-verified
papers. No PDF is automatically deleted or rejected. page_count comes from Poppler's
pdfinfo (null without it) and is recorded, not judged — a 3-page "article" or a 4-page "book"
is worth opening.
source_identity.status | Meaning / action |
|---|---|
consistent | Complete normalized title and a compatible DOI/arXiv identifier occur in the bounded first-page front matter, with no supplement / preface / table-of-contents heading and no retraction / erratum / correction / corrigendum / expression-of-concern heading there; an optional supplied author must also match. Evidence agrees, but this is not independent source verification or claim validation. |
conflict | Both the title and observed identifier differ. Inspect the PDF and requested record. |
unresolved | Evidence is incomplete or ambiguous: title-only, DOI-only, missing author, multiple identifiers, a matching title with another DOI/version, or a supplement / preface / table-of-contents file that names the work without being it (supplement_or_front_matter). A retraction notice, erratum, correction, corrigendum or expression of concern whose heading line sits in that area is likewise unresolved (correction_or_retraction_notice). Inspect before using as evidence. |
unavailable | No usable extracted text, Poppler unavailable, no output PDF, or the PDF changed during assessment. No current identity assessment was possible. |
Evidence is limited to the first page before a recognized abstract/body/reference heading (at
most 40 lines / 4,000 characters), so a title cited in the body or references does not count. A
title_match of match needs the complete normalized title on up to six consecutive lines;
partial overlap is unavailable and low overlap an advisory mismatch. Cover sheets, unusual
reading order, short or changed titles and DOI footers outside that area can stay unresolved.
PDF metadata and the filename alone are not identity evidence. Explicit arXiv versions must
agree; a preprint/published-version DOI difference needs review, not automatic rejection.
Show full SKILL.md (197 more words)Show less
Downstream reports must preserve source_identity and file_sha256, keep unresolved items
visible, and check the hash still identifies the file being used. Older reports without identity
evidence remain unassessed; do not infer identity from retrieved or title_match=match.
Full-text conversion does not resolve an identity warning.
Attach PDFs into Zotero ("Find Available PDF")
For paywalled-but-licensed papers the OA resolvers miss, references/find_available_pdf.js is a
user-run snippet for Zotero's Tools → Developer → Run JavaScript (no-code equivalent:
right-click → "Find Available PDF"). It triggers Zotero's own addAvailablePDF /
addAvailablePDFs, so it reuses the user's OpenURL resolver / institutional proxy config;
no credentials, proxy hosts, or institutional identifiers are hard-coded or leave the Zotero
client. It is user-initiated and depends on the live Zotero session, so record its results
manually — they are not reproducible CI evidence. /lit-sync Phase 2.7 orchestrates both routes
and reconciles them in a report.
PDF → Markdown Conversion (Optional)
Convert downloaded PDFs to Markdown when the same papers will be read repeatedly (data extraction from k≥5 studies, a meta-analysis pipeline); for one-pass screening, read the PDF directly.
# Install (one-time)
pip install pymupdf4llm
# Convert all PDFs in a directory (.md files land alongside the .pdf files)
python "${CLAUDE_SKILL_DIR}/pdf_to_md.py" pdfs/ -v
# Custom output directory
python "${CLAUDE_SKILL_DIR}/pdf_to_md.py" pdfs/ -o markdown/
# First 10 pages only (useful for long supplements)
python "${CLAUDE_SKILL_DIR}/pdf_to_md.py" pdfs/ --pages 0-9
# Overwrite existing conversions
python "${CLAUDE_SKILL_DIR}/pdf_to_md.py" pdfs/ --forceImages are skipped, so figures survive only as caption text. Scanned-only PDFs (no text layer)
convert poorly. pdf_to_md.py needs pymupdf4llm
(AGPL-3.0), an optional dependency; fetch_oa.py stays stdlib-only.
© Aperivue, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 12 other files (references) in skills/fulltext-retrieval of Aperivue/medsci-skills.
- SKILL.md
- fetch_oa.py
- fetch_oa_report_challenge/expected/projection.json
- fetch_oa_report_challenge/extracted_text.json
- fetch_oa_report_challenge/results.json
- fetch_oa_report_challenge/run_challenge.py
- fetch_oa_report_challenge/verify.sh
- fetch_oa_report_challenge/worklist.tsv
- pdf_to_md.py
- references/find_available_pdf.js
- skill.yml
- tests/test_pdf_to_md.py
- tests/test_source_identity.py
Open the folder on GitHubat commit 3b14ae2
Compare with similar skills
Fulltext Retrieval next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Fulltext Retrieval this skillAperivue/medsci-skills | 331 | — | ~1.9k | Automated safety check: Pass | MIT | |
| Paper Interpretationdigoal/blog | 8.6k | — | ~1.5k | Automated safety check: Pass | GPL-2.0 | |
| Paper LensYSQ-boop/paper-lens | 101 | — | ~1.3k | Automated safety check: Pass | Apache-2.0 | |
| Paper Interpreterchujianyun/skills | 740 | — | ~810 | Automated safety check: Pass | Custom licence | |
| Omh Paper Learningrlaope/oh-my-hermes | 3.2k | — | ~2.2k | Automated safety check: Pass | MIT | |
| Paper2htmlcnfjlhj/ai-collab-playbook | 453 | — | ~2.4k | Automated safety check: Pass | None |
Similar skills
Paper Lens
YSQ-boop/paper-lens
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Omh Paper Learning
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[omh] Paper or paper PDF to understand: explain a supplied paper or paper/PDF at a selected level while preserving full section coverage and source evidence boundaries.
Paper2html
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A skill your agent uses when turning an academic paper PDF/arXiv/OpenReview page/local LaTeX source into a single-file Chinese HTML deep-reading page, especially when the user wants a Cheat-Sheet…
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Related
Works with
Categories
Questions about Fulltext Retrieval
What does Fulltext Retrieval do?
A skill your agent uses when you need full-text PDFs for a list of DOIs, such as a meta-analysis screening set. Fulltext Retrieval is an agent skill from Aperivue/medsci-skills. Use when you need full-text PDFs for a list of DOIs, such as a meta-analysis screening set.
When should I use Fulltext Retrieval?
Fulltext Retrieval fits situations like: you need full-text PDFs for a list of DOIs; such as a meta-analysis screening set.
How do I install Fulltext Retrieval in Claude Code?
Run `npx skills add Aperivue/medsci-skills --skill fulltext-retrieval -a claude-code`. Or copy the skill folder (skills/fulltext-retrieval in Aperivue/medsci-skills) into .claude/skills/fulltext-retrieval in your project. Claude Code loads it when a task matches its description.
How do I install Fulltext Retrieval in Codex?
Run `npx skills add Aperivue/medsci-skills --skill fulltext-retrieval -a codex`. Or copy the skill folder (skills/fulltext-retrieval in Aperivue/medsci-skills) into .agents/skills/fulltext-retrieval in your project. Codex loads it when a task matches its description.
Can I use Fulltext Retrieval in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add Aperivue/medsci-skills --skill fulltext-retrieval -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/fulltext-retrieval, .gemini/skills/fulltext-retrieval, .github/skills/fulltext-retrieval and .opencode/skills/fulltext-retrieval in your project.
What does Fulltext Retrieval need to run?
Going by SKILL.md and its folder, Fulltext Retrieval needs Python, a shell and JavaScript for the scripts in its folder and the command-line tools its instructions call (python and pip). Our summary lists: Python 3; Node.js; A Bash shell.
Does Fulltext Retrieval access the network?
SKILL.md names 1 domain. As links in the text: pypi.org. This is read from the text; nothing was executed.
Is Fulltext Retrieval safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Fulltext Retrieval use?
Fulltext Retrieval is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Fulltext Retrieval use?
About 1.9k tokens (SKILL.md is roughly 7.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 765 tokens, read only when the agent opens those files.
What are the alternatives to Fulltext Retrieval?
Skills that share tags, products or a category with Fulltext Retrieval: Paper Interpretation (digoal/blog, 8.6k stars), Paper Lens (YSQ-boop/paper-lens, 101 stars), Paper Interpreter (chujianyun/skills, 740 stars) and Omh Paper Learning (rlaope/oh-my-hermes, 3.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Fulltext Retrieval?
Aperivue (a GitHub organization) maintains it in Aperivue/medsci-skills, which has 331 GitHub stars. The repository holds 54 skills in this directory. The repository was last updated on October 5, 2026.
Source: Aperivue/medsci-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.