Literature Review
K-Dense-AI/scientific-agent-skills
Runs systematic, scoping or narrative literature reviews across PubMed, arXiv, bioRxiv and Semantic Scholar, with citation checks and Markdown or PDF output.
Conduct literature searches for meta-analysis using Python with uv, query PubMed and other databases, deduplicate results, and store round-based bibliographies with notes.
Install Ma Search Bibliography
$ npx skills add htlin222/meta-pipe --skill ma-search-bibliography -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install htlin222/meta-pipe ma-search-bibliography --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/htlin222/meta-pipe.git skills-src && mkdir -p .claude/skills && cp -r skills-src/ma-search-bibliography .claude/skills/ma-search-bibliography && 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 "ma-search-bibliography" agent skill from https://github.com/htlin222/meta-pipe/tree/main/ma-search-bibliography into .claude/skills/ma-search-bibliography/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ma-search-bibliography", 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/htlin222/meta-pipe/tree/main/ma-search-bibliographyType 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 htlin222/meta-pipe --skill ma-search-bibliography -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install htlin222/meta-pipe ma-search-bibliography --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/htlin222/meta-pipe.git skills-src && mkdir -p .agents/skills && cp -r skills-src/ma-search-bibliography .agents/skills/ma-search-bibliography && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "ma-search-bibliography" agent skill from https://github.com/htlin222/meta-pipe/tree/main/ma-search-bibliography into .agents/skills/ma-search-bibliography/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ma-search-bibliography", 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 htlin222/meta-pipe --skill ma-search-bibliography -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install htlin222/meta-pipe ma-search-bibliography --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/htlin222/meta-pipe.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/ma-search-bibliography .cursor/skills/ma-search-bibliography && 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 "ma-search-bibliography" agent skill from https://github.com/htlin222/meta-pipe/tree/main/ma-search-bibliography into .cursor/skills/ma-search-bibliography/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ma-search-bibliography", 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/htlin222/meta-pipe.git --path ma-search-bibliography--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 htlin222/meta-pipe --skill ma-search-bibliography -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install htlin222/meta-pipe ma-search-bibliography --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/htlin222/meta-pipe.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/ma-search-bibliography .gemini/skills/ma-search-bibliography && 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 "ma-search-bibliography" agent skill from https://github.com/htlin222/meta-pipe/tree/main/ma-search-bibliography into .gemini/skills/ma-search-bibliography/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ma-search-bibliography", 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 htlin222/meta-pipe ma-search-bibliographyInstalls 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 htlin222/meta-pipe --skill ma-search-bibliography -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/htlin222/meta-pipe.git skills-src && mkdir -p .github/skills && cp -r skills-src/ma-search-bibliography .github/skills/ma-search-bibliography && 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 "ma-search-bibliography" agent skill from https://github.com/htlin222/meta-pipe/tree/main/ma-search-bibliography into .github/skills/ma-search-bibliography/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ma-search-bibliography", 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 htlin222/meta-pipe --skill ma-search-bibliography -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install htlin222/meta-pipe ma-search-bibliography --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/htlin222/meta-pipe.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/ma-search-bibliography .opencode/skills/ma-search-bibliography && 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 "ma-search-bibliography" agent skill from https://github.com/htlin222/meta-pipe/tree/main/ma-search-bibliography into .opencode/skills/ma-search-bibliography/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ma-search-bibliography", 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
ma-search-bibliography- GitHub stars
- 139
- Token cost
- ~2.1k tokens
- SKILL.md length
- 813 words
- Files
- 29 (incl. scripts, references)
- Skills in repo
- 15
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Conduct literature searches for meta-analysis using Python with uv, query PubMed and other databases, deduplicate results, and store round-based bibliographies with notes.
- Works in 9 steps: Translate PICO terms into… → Initialize Python tooling with uv in… → Run search scripts with uv run from… → …
- Updating the evidence corpus
- SKILL.md covers Overview, Inputs, Outputs and Workflow, plus 7 more sections
- Runs Python and R scripts from its folder; calls uv
What it does
Ma Search Bibliography is an agent skill from htlin222/meta-pipe. Conduct literature searches for meta-analysis using Python with uv, query PubMed and other databases, deduplicate results, and store round-based bibliographies with notes. Use when building or updating the evidence corpus.
Its SKILL.md is about 2.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 30 other files, including scripts and reference files (for example `references/api-setup.md`, `references/database-auth.md` and `references/prisma-flowchart-guide.md`).
It sits in Research & Science, covering Citation management, Academic paper search and Literature review. It works with Python, PubMed and Prisma. The repository describes itself as: Claude Code-powered end-to-end meta-analysis automation: AI-assisted literature review, screening, extraction, analysis, and manuscript generation for systematic reviews and….
When your agent uses it
- Updating the evidence corpus
- Tasks that involve Citation management
- Tasks that involve Academic paper search
Example prompts
- “/ma-search-bibliography”
Requirements
- Python 3
Workflow steps
9 steps, taken from the first numbered list in SKILL.md.
- Translate PICO terms into database-specific queries and save them in queries.txt.
- Initialize Python tooling with uv in tooling/python/ using uv init and uv add dependencies.
- Run search scripts with uv run from tooling/python/ (avoid direct python3 calls).
- Use uv tool for any one-off CLI utilities (do not install them globally).
- Always search PubMed + Scopus as the mandatory minimum (PRISMA requires ≥2 databases). Optionally extend to Embase and Cochrane if defined…
- Export results to .bib and record the run date, database, and query hash in log.md.
- Deduplicate by DOI, PMID, and title, then save dedupe.bib.
- If running updates, increment the round folder name and record deltas.
- Generate PRISMA flowchart after search completion using generate_prisma_flowchart.R (see below).
What it can do on your machine
Read from SKILL.md and the folder at commit 5c5c3f0. 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 11 files in scripts/ (Python and R, from the files we listed), which the agent can run.
Shell commands in SKILL.md call:
uv
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use uv, which can reach the network depending on how they are called.
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
Ma Search Bibliography loads about 2.1k tokens when it runs, and up to ~9.5k if it reads all its reference files. Until then it costs about 61 tokens; SKILL.md has 813 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: notes
The automated check noted patterns worth knowing about, such as sudo or a known installer.
- NoteMentions a .env fileSKILL.md:52
- Read API keys from `.env` in the project root. - NoteMentions a .env fileSKILL.md:112
- `scripts/env_utils.py` loads `.env` credentials.
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); the scripts in this folder are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 813 words (~2,069 tokens).
“Run reproducible database searches, capture the search strategy, and produce versioned .bib files.”
- name
- ma-search-bibliography
Files
SKILL.md and 28 other files (scripts, references) in ma-search-bibliography of htlin222/meta-pipe.
- SKILL.md
- references/api-setup.md
- references/database-auth.md
- references/emtree-synonyms-template.csv
- references/prisma-flowchart-guide.md
- references/prisma-flowchart-quickstart.md
- references/pubmed-eutils.md
- references/zotero-setup.md
- scripts/bib_subset_by_ids.py
- scripts/build_queries.py
- scripts/cochrane_fetch.py
- scripts/ctgov_fetch.py
- scripts/db_counts.py
- scripts/dedupe_bib.py
- scripts/embase_fetch.py
- scripts/enrich_abstracts.py
- scripts/env_utils.py
- scripts/expand_terms.py
- scripts/generate_prisma_flowchart.R
- … and 10 more
Open the folder on GitHubat commit 5c5c3f0
Compare with similar skills
Ma Search Bibliography 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 |
|---|---|---|---|---|---|---|
| Ma Search Bibliography this skillhtlin222/meta-pipe | 139 | — | ~2.1k | Automated safety check: Notes | Custom licence | |
| Literature ReviewK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Notes | MIT | |
| Literature Review Toolsbrycewang-stanford/Auto-Empirical-Research-Skills | 4.6k | — | ~2.5k | Automated safety check: Notes | Custom licence | |
| Literature Reviewneflibata-feng/MyArxiv-Agent | 126 | 20 repos | ~5.9k | Automated safety check: Notes | MIT | |
| Citation ManagementK-Dense-AI/claude-scientific-writer | 2.4k | 2 repos | ~3.9k | Automated safety check: Notes | MIT | |
| Preprint Search on bioRxivLigphiDonk/Oh-my--paper | 739 | 12 repos | ~3.7k | Automated safety check: Pass | MIT |
Similar skills
Literature Review Tools
brycewang-stanford/Auto-Empirical-Research-Skills
Recommend AND run open-source AI tools, agents, Claude Code / Codex skills, and MCP servers for any stage of a literature review — searching, reading, extracting, synthesizing, screening…
Literature Review
neflibata-feng/MyArxiv-Agent
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.).
Citation Management
K-Dense-AI/claude-scientific-writer
Finds papers in OpenAlex, PubMed and Google Scholar, turns DOIs, PMIDs and arXiv IDs into clean BibTeX, and validates citations for a manuscript or thesis.
Preprint Search on bioRxiv
LigphiDonk/Oh-my--paper
Searches bioRxiv life sciences preprints by keyword, author, date range or category with a Python script, returning JSON metadata and optional PDF downloads.
Paper Research on arXiv
XiaomiMiMo/MiMo-Code
Searches arXiv, fetches metadata, generates BibTeX, downloads PDFs and finds citations and related papers using a bundled Python script.
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Ma Screening Quality
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Related
Categories
Questions about Ma Search Bibliography
What does Ma Search Bibliography do?
Conduct literature searches for meta-analysis using Python with uv, query PubMed and other databases, deduplicate results, and store round-based bibliographies with notes. Ma Search Bibliography is an agent skill from htlin222/meta-pipe. Conduct literature searches for meta-analysis using Python with uv, query PubMed and other databases, deduplicate results, and store round-based bibliographies with notes.
When should I use Ma Search Bibliography?
Ma Search Bibliography fits situations like: updating the evidence corpus; tasks that involve Citation management; tasks that involve Academic paper search.
How do I install Ma Search Bibliography in Claude Code?
Run `npx skills add htlin222/meta-pipe --skill ma-search-bibliography -a claude-code`. Or copy the skill folder (ma-search-bibliography in htlin222/meta-pipe) into .claude/skills/ma-search-bibliography in your project. Claude Code loads it when a task matches its description.
How do I install Ma Search Bibliography in Codex?
Run `npx skills add htlin222/meta-pipe --skill ma-search-bibliography -a codex`. Or copy the skill folder (ma-search-bibliography in htlin222/meta-pipe) into .agents/skills/ma-search-bibliography in your project. Codex loads it when a task matches its description.
Can I use Ma Search Bibliography 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 htlin222/meta-pipe --skill ma-search-bibliography -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/ma-search-bibliography, .gemini/skills/ma-search-bibliography, .github/skills/ma-search-bibliography and .opencode/skills/ma-search-bibliography in your project.
What does Ma Search Bibliography need to run?
Going by SKILL.md and its folder, Ma Search Bibliography needs Python and R for the scripts in its folder and the command-line tools its instructions call (uv). Our summary lists: Python 3.
Does Ma Search Bibliography access the network?
SKILL.md contains no URLs. Its commands use uv, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Ma Search Bibliography safe to install?
Our automated static check of SKILL.md found notes only (mentions a .env file), nothing it rates as a warning. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Ma Search Bibliography use?
Ma Search Bibliography has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Ma Search Bibliography use?
About 2.1k tokens (SKILL.md is roughly 8.3k 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 7.4k tokens, read only when the agent opens those files.
What are the alternatives to Ma Search Bibliography?
Skills that share tags, products or a category with Ma Search Bibliography: Literature Review (K-Dense-AI/scientific-agent-skills, 48k stars), Literature Review Tools (brycewang-stanford/Auto-Empirical-Research-Skills, 4.6k stars), Literature Review (neflibata-feng/MyArxiv-Agent, 126 stars) and Citation Management (K-Dense-AI/claude-scientific-writer, 2.4k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Ma Search Bibliography?
htlin222 (a GitHub user) maintains it in htlin222/meta-pipe, which has 139 GitHub stars. The repository holds 15 skills in this directory. The repository was last updated on September 23, 2026.
Source: htlin222/meta-pipe on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.