New: 98,000+ skills indexed from GitHub repos with 100+ stars · every skill safety-checkedBrowse top skillsTop skills
Esc to closeBrowse all skills
Submit a skillBrowse skills
Submit a skillBrowse skills

Agent skill

Bibliography

by aipoch in aipoch/medical-research-skills

Classifies and organizes literature by theme, method, and conclusion; use when you need to batch-read a folder of PDF/MD/DOCX/TXT files and output a structured CSV for literature reviews and…

MITAuto-check passedDocuments & Office

Install Bibliography

skills CLI
$ npx skills add aipoch/medical-research-skills --skill bibliography -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install aipoch/medical-research-skills bibliography --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/scientific-skills/Other/bibliography .claude/skills/bibliography && rm -rf skills-src

Use ~/.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/

Facts

Skill name
bibliography
GitHub stars
2k
Token cost
~1.6k tokens
SKILL.md length
695 words
Files
4 (incl. references, assets)
Skills in repo
567
Repo updated
First seen
Licence
MIT

At a glance

Classifies and organizes literature by theme, method, and conclusion; use when you need to batch-read a folder of PDF/MD/DOCX/TXT files and output a structured CSV for literature reviews and…

  • Works in 4 steps: Input Reading and Normalization → Generate the Summary Markdown First… → Field Extraction Rules (Theme / Method /… → …
  • You need to batch-read a folder of PDF/MD/DOCX/TXT files and output a structured CSV for literature reviews and annotation management
  • SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 1 more section
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Bibliography is an agent skill from aipoch/medical-research-skills. Classifies and organizes literature by theme, method, and conclusion; use when you need to batch-read a folder of PDF/MD/DOCX/TXT files and output a structured CSV for literature reviews and annotation management.

Its SKILL.md is about 1.6k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files, including reference files and assets (for example `bibliography_audit_result_v1.json` and `references/guide.md`).

It sits in Documents & Office, covering Citation management, Word documents and CSV and tabular files. It works with Microsoft Word. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

  • You need to batch-read a folder of PDF/MD/DOCX/TXT files and output a structured CSV for literature reviews and annotation management
  • Tasks that involve Citation management
  • Tasks that involve Word documents

Example prompts

  • “Use the bibliography skill to classify and organizes literature by theme, method, and conclusion; use when you need to batch-read a folder of…”
  • “/bibliography”

Workflow steps

4 steps, taken from the step headings in SKILL.md.

  1. Input Reading and Normalization
  2. Generate the Summary Markdown First (Single Source of Truth)
  3. Field Extraction Rules (Theme / Method / Conclusion)
  4. CSV Output Constraints

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. 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

    No scripts in the folder and no shell commands in SKILL.md (its code samples are markdown).

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    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

Bibliography loads about 1.6k tokens when it runs, and up to ~2.5k if it reads all its reference files. Until then it costs about 57 tokens; SKILL.md has 695 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~57
When it runs · the whole SKILL.md, loaded when a task matches
~1.6k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~2.5k

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 aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 695 words, ~1,575 tokens.

Download SKILL.mdSave it as .claude/skills/bibliography/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.
name
bibliography
description
Classifies and organizes literature by theme, method, and conclusion; use when you need to batch-read a folder of PDF/MD/DOCX/TXT files and output a structured CSV for literature reviews and annotation management.
license
MIT
author
AIPOCH

Source: https://github.com/aipoch/medical-research-skills

Bibliography

When to Use

  • You are conducting a literature review and need consistent summaries plus structured metadata (theme/method/conclusion) across many papers.
  • You have a mixed-format reading folder (.pdf, .md, .docx, .txt) and want a single CSV for downstream analysis (e.g., Excel, R, Python).
  • You need to organize annotations by keywords (theme), experimental methods (method), and key conclusions (conclusion).
  • You want a two-step pipeline: first generate a human-readable summary Markdown, then generate a machine-friendly CSV from that Markdown.
  • You need robust handling of PDFs by converting them to Markdown first (via pdf-extract) and then using only Markdown content for extraction.

Key Features

  • Batch scans an input directory for .pdf, .md, .docx, and .txt literature files.
  • Converts PDFs to Markdown via pdf-extract, then ignores non-Markdown artifacts (e.g., image folders).
  • Extracts and normalizes, per document:
    • Title
    • Summary (prefer original abstract)
    • Keywords (theme)
    • Experimental Methods (method names only)
    • Key Conclusions (single sentence)
    • Commentary (one-sentence, tactful evaluation)
  • Produces exactly two outputs:
    1. A consolidated Summary Markdown saved under outputs/
    2. A single CSV generated from that Summary Markdown
  • Enforces UTF-8 output to prevent garbled characters; fills missing fields with "Not recognized" instead of leaving blanks.
  • Uses the CSV field order and headers defined in assets/bibliography_template.csv.

Dependencies

  • pdf-extract (version: not specified; required when PDFs are present)
  • Input formats supported (no external version constraints specified):
    • PDF
    • Markdown (.md)
    • DOCX (.docx)
    • Plain text (.txt)

Example Usage

Goal

Read all literature files in a folder, generate a consolidated summary Markdown, then generate a CSV following assets/bibliography_template.csv.

Inputs
  • Input directory (example): ./inputs/literature/
  • Output directory: ./outputs/
  • Output CSV path (example): ./outputs/bibliography.csv
Expected Outputs (exactly two files)
  • ./outputs/bibliography_summary.md
  • ./outputs/bibliography.csv
Example Summary Markdown Structure (generated first)
md
# Bibliography Summary

## Document 1
- Title: <Title>
- Summary: <Prefer the original Abstract; if missing, use the closest equivalent section>
- Keywords: keyword1 | keyword2 | keyword3
- Experimental Methods: <method1; method2; ... (names only)>
- Key Conclusions: <one sentence covering all main points>
- Commentary: <one tactful sentence>

## Document 2
...
Example CSV (generated from the Summary Markdown)

The CSV must follow the header order defined in:

  • assets/bibliography_template.csv

Rules:

  • One row per document.
  • No empty cells; use Not recognized when extraction fails.
  • Save as UTF-8.

Implementation Details

1) Input Reading and Normalization
  • Traverse the input directory and process files with extensions:
    • .pdf, .md, .docx, .txt

PDF handling

  • If PDFs exist, convert them to Markdown using pdf-extract.
  • Use only the generated .md content; ignore image directories or other byproducts.
  • Locate pdf-extract as follows:
    1. First, look for a sibling skill directory containing SKILL.md at the same level as this skill’s parent directory.
    2. If not found, ask the user to confirm the actual pdf-extract path.

DOCX handling

  • Extract body text while preserving title/paragraph order as much as possible.

MD/TXT handling

  • Read text directly.
  • If garbled characters appear or key fields cannot be recognized, attempt to detect and read using the original encoding (commonly GB18030 / GBK) before extraction.
Show full SKILL.md (265 more words)Show less
2) Generate the Summary Markdown First (Single Source of Truth)

Before producing the CSV, generate a consolidated Summary Markdown containing, for each document:

  • Title
  • Summary
    • Prefer the original Abstract.
    • If no “Abstract” exists, use the closest equivalent section (e.g., “Summary”, “Highlights”, or an “Objective–Method–Result–Conclusion” style segment).
  • Keywords
  • Experimental Methods
  • Key Conclusions
  • Commentary
    • Exactly one sentence.
    • Avoid harsh criticism; if the work has low value, use tactful phrasing.

This Summary Markdown must be saved with UTF-8 encoding and stored under outputs/. The CSV must be generated only from this Markdown (not directly from raw files).

3) Field Extraction Rules (Theme / Method / Conclusion)
  • Keywords (theme)
    • Prefer the original keywords from the document.
    • Separate multiple keywords with |.
    • If no keywords are found, generate 3–5 keyword phrases based on the abstract and append:
      • (generated based on abstract)
  • Experimental Methods (method)
    • Output method names only (no long descriptions).
  • Key Conclusions (conclusion)
    • One sentence that covers all main points.
4) CSV Output Constraints
  • Output exactly one CSV file at the end.
  • CSV field order and headers must match assets/bibliography_template.csv.
  • Encoding must be UTF-8 to avoid garbled characters.
  • If any field cannot be extracted, write Not recognized (never leave empty).
  • Only two files may be generated in total:
    1. Summary Markdown
    2. CSV
  • No temporary/intermediate/auxiliary files may be left behind (including extracted text dumps, caches, logs, images, backups). If conversion/extraction requires intermediate artifacts, keep them in memory or ensure all non-target files are deleted before final output.
  • Do not use PowerShell to directly write/manipulate CSV/Markdown to avoid encoding/newline issues; always generate and save using UTF-8.
Reference
  • Detailed rules and field descriptions: references/guide.md

© aipoch, 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 3 other files (references, assets) in scientific-skills/Other/bibliography of aipoch/medical-research-skills.

  • SKILL.md
  • assets/bibliography_template.csv
  • bibliography_audit_result_v1.json
  • references/guide.md

Open the folder on GitHubat commit 686e09d

Compare with similar skills

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.

Bibliography compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bibliography this skillaipoch/medical-research-skills2k—~1.6kAutomated safety check: PassMIT
Document Converterwentorai/Research-Claw858—~1.3kAutomated safety check: PassCustom licence
File ReadingWide-Moat/open-computer-use1261 repos~3.1kAutomated safety check: PassProprietary
Extracting Lab Tablesmaziyarpanahi/openmed5.5k—~2.1kAutomated safety check: PassApache-2.0
Light File ReadingLight0305/Light-skills641—~4.1kAutomated safety check: PassMIT
Heavy File Ingestion Claude CodeNateBJones-Projects/OB14.7k—~614Automated safety check: PassCustom licence

Similar skills

  • Document Converter

    wentorai/Research-Claw

    Convert Office documents (PPTX, DOCX, XLSX, PDF, HTML, CSV, JSON, XML, images) to Markdown using Microsoft MarkItDown.

    858 GitHub stars~1.3k tokensUpdated 1 mo ago
    Documents & OfficeAuto-check passed

  • File Reading

    Wide-Moat/open-computer-use

    A skill your agent uses when a file has been uploaded but its content is NOT in your context — only its path at /mnt/user-data/uploads/ is listed in an uploadedfiles block.

    126 GitHub starsUsed in 1 repo~3.1k tokens
    Documents & OfficeAuto-check passed

  • Extracting Lab Tables

    maziyarpanahi/openmed

    Detects and extracts tabular laboratory panels from PDFs, scans, and images into structured rows ready for OpenMed and FHIR.

    5.5k GitHub stars~2.1k tokensUpdated today
    Documents & OfficeAuto-check passed

  • Light File Reading

    Light0305/Light-skills

    Light 多格式文件深度理解常驻技能：强大地读 Word / PDF / PPTX / Excel / CSV / 图片 / 视频 / 代码 / 压缩包，不只提取文字，而是理解结构 / 图表 / 数据 / 格式要求 / 隐含意图，产结构化"理解笔记"五面 （结构逻辑·关键内容·格式约束·视觉风格·可复用）并映射到下游技能动作（这个文件→接下来能做什么）。

    641 GitHub stars~4.1k tokensUpdated 3 mo ago
    Documents & OfficeAuto-check passed

  • Heavy File Ingestion Claude Code

    NateBJones-Projects/OB1

    Use in Claude Code when a user asks to read, analyze, summarize, or extract from a heavyweight file such as PDF, DOCX, PPTX, XLSX, CSV, or TSV.

    4.7k GitHub stars~614 tokensUpdated yesterday
    Documents & OfficeAuto-check passed

  • Heavy File Ingestion Claude Desktop

    NateBJones-Projects/OB1

    Use in Claude Desktop when a user asks to read, analyze, summarize, or extract from a heavyweight file such as PDF, DOCX, PPTX, XLSX, CSV, or TSV.

    4.7k GitHub stars~547 tokensUpdated yesterday
    Documents & OfficeAuto-check passed

More from aipoch/medical-research-skills

All 567 skills in this repo

  • Academic Poster Generator

    aipoch/medical-research-skills

    Complete workflow for generating academic research posters from PDF literature; use when you need to extract paper content from PDFs and produce a LaTeX-based poster…

    2k GitHub stars~2.2k tokensUpdated 21 days ago
    Auto-check passed

  • Diagnostic Study Quality Assessment Quadas

    aipoch/medical-research-skills

    Analyzes clinical diagnostic accuracy studies for bias using the QUADAS-2 tool.

    2k GitHub stars~1.4k tokensUpdated 21 days ago
    Auto-check passed

  • Exploratory Data Analysis

    aipoch/medical-research-skills

    Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats.

    2k GitHub stars~3.7k tokensUpdated 21 days ago
    Auto-check passed

  • Iso Certification

    aipoch/medical-research-skills

    A toolkit for preparing ISO 13485:2016 certification documentation for medical device QMS.

    2k GitHub stars~1.8k tokensUpdated 21 days ago
    Auto-check passed

  • Journal Skills

    aipoch/medical-research-skills

    Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for journal…

    2k GitHub stars~1.7k tokensUpdated 21 days ago
    Auto-check passed

  • Latex Posters

    aipoch/medical-research-skills

    Creates academic-poster writing packages for LaTeX using beamerposter, tikzposter, or baposter.

    2k GitHub stars~1.3k tokensUpdated 21 days ago
    Auto-check passed

Works with

Categories

Questions about Bibliography

What does Bibliography do?

Classifies and organizes literature by theme, method, and conclusion; use when you need to batch-read a folder of PDF/MD/DOCX/TXT files and output a structured CSV for literature reviews and…. Bibliography is an agent skill from aipoch/medical-research-skills. Classifies and organizes literature by theme, method, and conclusion; use when you need to batch-read a folder of PDF/MD/DOCX/TXT files and output a structured CSV for literature reviews and annotation management.

When should I use Bibliography?

Bibliography fits situations like: you need to batch-read a folder of PDF/MD/DOCX/TXT files and output a structured CSV for literature reviews and annotation management; tasks that involve Citation management; tasks that involve Word documents.

How do I install Bibliography in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill bibliography -a claude-code`. Or copy the skill folder (scientific-skills/Other/bibliography in aipoch/medical-research-skills) into .claude/skills/bibliography in your project. Claude Code loads it when a task matches its description.

How do I install Bibliography in Codex?

Run `npx skills add aipoch/medical-research-skills --skill bibliography -a codex`. Or copy the skill folder (scientific-skills/Other/bibliography in aipoch/medical-research-skills) into .agents/skills/bibliography in your project. Codex loads it when a task matches its description.

Can I use 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 aipoch/medical-research-skills --skill 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/bibliography, .gemini/skills/bibliography, .github/skills/bibliography and .opencode/skills/bibliography in your project.

What does Bibliography need to run?

SKILL.md names no scripts, command-line tools or credentials: Bibliography is instructions for the agent only.

Does Bibliography access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Bibliography 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 Bibliography use?

Bibliography is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Bibliography use?

About 1.6k tokens (SKILL.md is roughly 6.3k 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 894 tokens, read only when the agent opens those files.

What are the alternatives to Bibliography?

Skills that share tags, products or a category with Bibliography: Document Converter (wentorai/Research-Claw, 858 stars), File Reading (Wide-Moat/open-computer-use, 126 stars), Extracting Lab Tables (maziyarpanahi/openmed, 5.5k stars) and Light File Reading (Light0305/Light-skills, 641 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bibliography?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.