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Agent skill

Literature

by TianGzlab in TianGzlab/OmicsClaw

Load when extracting GEO accessions, dataset metadata, and downloadable references from a scientific paper (PDF / URL / DOI / PubMed ID / raw text) for downstream omics analysis.

Apache-2.0Auto-check passedResearch & Science

Install Literature

skills CLI
$ npx skills add TianGzlab/OmicsClaw --skill literature -a claude-code

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

GitHub CLI
$ gh skill install TianGzlab/OmicsClaw literature --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/TianGzlab/OmicsClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/literature .claude/skills/literature && 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
literature
GitHub stars
161
Token cost
~1.2k tokens
SKILL.md length
479 words
Files
19 (incl. references)
Skills in repo
88
Repo updated
First seen
Licence
Apache-2.0

At a glance

Load when extracting GEO accessions, dataset metadata, and downloadable references from a scientific paper (PDF / URL / DOI / PubMed ID / raw text) for downstream omics analysis.

  • Tasks that involve Academic paper search
  • SKILL.md covers When to use, Use from a step, API and Methods and parameters, plus 5 more sections
  • Runs Python scripts from its folder; calls python
  • Tasks that involve Scientific writing

What it does

Literature is an agent skill from TianGzlab/OmicsClaw. Load when extracting GEO accessions, dataset metadata, and downloadable references from a scientific paper (PDF / URL / DOI / PubMed ID / raw text) for downstream omics analysis. Skip when the dataset is already in hand; the paper names no dataset to fetch.

Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 22 other files, including reference files (for example `INDEX.md`, `_api.py` and `_lib/__init__.py`).

It sits in Research & Science, covering Academic paper search, Scientific writing and PDF. It works with PubMed. The repository describes itself as: Conversational & memory-enabled AI research partner for multi-omics analysis. CLI + Desktop App (installers in Releases). From biological idea to full research paper. The licence is Apache-2.0.

When your agent uses it

  • Tasks that involve Academic paper search
  • Tasks that involve Scientific writing
  • Tasks that involve PDF

Example prompts

  • “/literature”

Requirements

  • Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit 90a3bec. 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, from the files we listed), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    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

Literature loads about 1.2k tokens when it runs, and up to ~1.6k if it reads all its reference files. Until then it costs about 67 tokens; SKILL.md has 479 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~67
When it runs · the whole SKILL.md, loaded when a task matches
~1.2k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~1.6k

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 TianGzlab/OmicsClaw at commit 90a3bec, republished under its Apache-2.0 licence (© TianGzlab). 479 words, ~1,170 tokens.

Download SKILL.mdSave it as .claude/skills/literature/SKILL.md (or your agent's skills folder). This skill also uses 18 other files; get the full folder from GitHub.
name
literature
description
Load when extracting GEO accessions, dataset metadata, and downloadable references from a scientific paper (PDF / URL / DOI / PubMed ID / raw text) for downstream omics analysis. Skip when the dataset is already in hand; the paper names no dataset to fetch.
trigger
parse paper, literature, GEO accession, download dataset, PDF extract, PubMed, DOI
tags
literature, pdf, doi, pubmed, geo, metadata

literature

When to use

Extract GEO accessions and heuristic study metadata from paper text. Read local papers explicitly with read_document or fetch remote papers with fetch_text. Skip when the dataset is already in hand.

Use from a step

python
import pandas as pd
from skills._sdk.notebook import load_skill, read_input, write_output
library = load_skill('literature')
text = read_input('paper.txt', reader=library.read_document)
result = library.extract(text)
write_output(result, 'tables/result.csv')

examples/example_step.py runs offline and supports fresh-kernel replay. Pure computations return objects; CLI and steps own writes.

API

<!-- api:begin generated from _api.py; regenerate with run.py api <skill dir> --write -->
extract(data)

Extract GEO accessions and heuristic study metadata from text.

:param data: Local paper text; URLs and paths are treated as text, never fetched. :returns: A DataFrame of kind/accession pairs, with metadata in attrs['run_info']. :raises ValueError: data is empty or not a string.

methodology(data)

Extract stated numeric method parameters with exact source spans.

:param data: Paper text containing supported parameter names and numeric values. :returns: A DataFrame with param, operator, value, quote, start and end columns. :raises TypeError: data is not text.

read_document(data)

Read a local PDF or UTF-8 text file; use as reader= in read_input.

:param data: Local Path or path string; no network requests are made. :returns: Extracted text with empty PDF pages omitted. :raises ImportError: Install pypdf with install_skill_deps for PDFs. :raises OSError: The file cannot be read.

fetch_text(data, *, input_type='url')

Fetch article text explicitly from a URL, DOI or PubMed reference.

:param data: Reference sent to the remote service; results may change between requests. :param input_type: Default url; doi and pubmed resolve their respective endpoints. :returns: HTML/XML with tags removed and whitespace collapsed, as in the CLI. :raises ImportError: Install requests with install_skill_deps if unavailable. :raises ValueError: The reference type or URL scheme is unsupported. :raises Exception: HTTP and network errors propagate instead of becoming article text.

Show full SKILL.md (215 more words)Show less
run_info(data, *, keep=True)

Read heuristic metadata and the accession lists extracted from text.

:param data: Accession table returned by extract. :param keep: Default True; use False to remove metadata from the table. :returns: An independent metadata dictionary. :raises KeyError: The table has no extraction diagnostics.

accession_figure(data)

Plot accession counts by GEO accession kind.

:param data: Accession table returned by extract. :returns: A matplotlib Figure, including zero counts for missing kinds. :raises KeyError: kind is absent.

<!-- api:end -->

Methods and parameters

extract performs local regex/keyword extraction only. methodology returns exact quotes and character spans for stated numeric parameters. read_document reads UTF-8 text or PDF, and fetch_text explicitly requests URL/DOI/PubMed text. Neither function downloads datasets; the CLI retains its optional GEO download workflow.

Gotchas

  • extract returns uppercase, deduplicated and sorted GEO identifiers. methodology never fills absent parameter defaults. read_document raises when pypdf is missing or input cannot be read. fetch_text propagates failures rather than treating an error message as paper text. Metadata labels remain heuristics, not validated study annotations.

Inputs and outputs

extracted_metadata.json, source.txt, report.md and result.json at the output root. The CLI creates data/ and optionally downloads into per-GSE directories; --data-dir chooses another destination. The original source.txt write remains best-effort. The function library writes no files.

CLI

bash
python skills/literature/literature_parse.py --demo --output /tmp/literature

See also

Dependencies

pandas, matplotlib, pypdf, requests

© TianGzlab, Apache-2.0. 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 18 other files (references) in skills/literature of TianGzlab/OmicsClaw.

  • SKILL.md
  • INDEX.md
  • _api.py
  • _lib/__init__.py
  • _lib/extractor.py
  • _lib/input_kind.py
  • core/__init__.py
  • core/downloader.py
  • core/extractor.py
  • core/parser.py
  • examples/example_step.py
  • literature_parse.py
  • references/methodology.md
  • references/output_contract.md
  • references/parameters.md
  • requirements.txt
  • tests
  • … and 2 more

Open the folder on GitHubat commit 90a3bec

Compare with similar skills

Literature 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.

Literature compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Literature this skillTianGzlab/OmicsClaw161—~1.2kAutomated safety check: PassApache-2.0
Citation ManagementK-Dense-AI/claude-scientific-writer2.4k2 repos~3.9kAutomated safety check: NotesMIT
Journal Selector for Manuscriptshuangwb8/ChineseResearchLaTeX2.9k—~1.7kAutomated safety check: PassMIT
Reference CheckerLiuxiangjian-ai/reference-checker-skill140—~5.4kAutomated safety check: PassMIT
Literature DownloaderLucaswangzcx/literature-downloader-skill239—~1.4kAutomated safety check: PassMIT
Citation Managementforyourhealth111-pixel/Vibe-Skills3.6k—~7.6kAutomated safety check: NotesMIT

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Works with

Categories

Questions about Literature

What does Literature do?

Load when extracting GEO accessions, dataset metadata, and downloadable references from a scientific paper (PDF / URL / DOI / PubMed ID / raw text) for downstream omics analysis. Literature is an agent skill from TianGzlab/OmicsClaw. Load when extracting GEO accessions, dataset metadata, and downloadable references from a scientific paper (PDF / URL / DOI / PubMed ID / raw text) for downstream omics analysis.

When should I use Literature?

Literature fits situations like: tasks that involve Academic paper search; tasks that involve Scientific writing; tasks that involve PDF.

How do I install Literature in Claude Code?

Run `npx skills add TianGzlab/OmicsClaw --skill literature -a claude-code`. Or copy the skill folder (skills/literature in TianGzlab/OmicsClaw) into .claude/skills/literature in your project. Claude Code loads it when a task matches its description.

How do I install Literature in Codex?

Run `npx skills add TianGzlab/OmicsClaw --skill literature -a codex`. Or copy the skill folder (skills/literature in TianGzlab/OmicsClaw) into .agents/skills/literature in your project. Codex loads it when a task matches its description.

Can I use Literature 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 TianGzlab/OmicsClaw --skill literature -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/literature, .gemini/skills/literature, .github/skills/literature and .opencode/skills/literature in your project.

What does Literature need to run?

Going by SKILL.md and its folder, Literature needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Literature 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 Literature 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 Literature use?

Literature is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Literature use?

About 1.2k tokens (SKILL.md is roughly 4.7k 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 391 tokens, read only when the agent opens those files.

What are the alternatives to Literature?

Skills that share tags, products or a category with Literature: Citation Management (K-Dense-AI/claude-scientific-writer, 2.4k stars), Journal Selector for Manuscripts (huangwb8/ChineseResearchLaTeX, 2.9k stars), Reference Checker (Liuxiangjian-ai/reference-checker-skill, 140 stars) and Literature Downloader (Lucaswangzcx/literature-downloader-skill, 239 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Literature?

TianGzlab (a GitHub organization) maintains it in TianGzlab/OmicsClaw, which has 161 GitHub stars. The repository holds 88 skills in this directory. The repository was last updated on October 7, 2026.

Source: TianGzlab/OmicsClaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.