Ncbi Sequence Fetch
google-deepmind/science-skills
Retrieve protein and nucleotide sequences from NCBI databases using E-utilities.
Retrieve extensive literature (PubMed) and patent associated with a specific chemical compound via PubChem.
Install General Chemical Literature
$ npx skills add learningmatter-mit/AtomisticSkills --skill general-chemical-literature -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills general-chemical-literature --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/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/general-chemical-literature .claude/skills/general-chemical-literature && 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 "general-chemical-literature" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/general-chemical-literature into .claude/skills/general-chemical-literature/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "general-chemical-literature", 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/learningmatter-mit/AtomisticSkills/tree/main/skills/general-chemical-literatureType 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 learningmatter-mit/AtomisticSkills --skill general-chemical-literature -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills general-chemical-literature --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/general-chemical-literature .agents/skills/general-chemical-literature && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "general-chemical-literature" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/general-chemical-literature into .agents/skills/general-chemical-literature/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "general-chemical-literature", 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 learningmatter-mit/AtomisticSkills --skill general-chemical-literature -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills general-chemical-literature --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/general-chemical-literature .cursor/skills/general-chemical-literature && 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 "general-chemical-literature" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/general-chemical-literature into .cursor/skills/general-chemical-literature/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "general-chemical-literature", 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/learningmatter-mit/AtomisticSkills.git --path skills/general-chemical-literature--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 learningmatter-mit/AtomisticSkills --skill general-chemical-literature -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills general-chemical-literature --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/general-chemical-literature .gemini/skills/general-chemical-literature && 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 "general-chemical-literature" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/general-chemical-literature into .gemini/skills/general-chemical-literature/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "general-chemical-literature", 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 learningmatter-mit/AtomisticSkills general-chemical-literatureInstalls 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 learningmatter-mit/AtomisticSkills --skill general-chemical-literature -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/general-chemical-literature .github/skills/general-chemical-literature && 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 "general-chemical-literature" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/general-chemical-literature into .github/skills/general-chemical-literature/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "general-chemical-literature", 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 learningmatter-mit/AtomisticSkills --skill general-chemical-literature -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills general-chemical-literature --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/general-chemical-literature .opencode/skills/general-chemical-literature && 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 "general-chemical-literature" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/general-chemical-literature into .opencode/skills/general-chemical-literature/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "general-chemical-literature", 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
general-chemical-literature- GitHub stars
- 176
- Token cost
- ~515 tokens
- SKILL.md length
- 181 words
- Files
- 4 (incl. scripts)
- Skills in repo
- 129
- Repo updated
- First seen
- Licence
- MIT
At a glance
Retrieve extensive literature (PubMed) and patent associated with a specific chemical compound via PubChem.
- Tasks that involve Intellectual property
- SKILL.md covers Goal, Instructions, Examples and Constraints
- Runs Python scripts from its folder
- Tasks that involve Academic paper search
What it does
General Chemical Literature is an agent skill from learningmatter-mit/AtomisticSkills. Retrieve extensive literature (PubMed) and patent associated with a specific chemical compound via PubChem.
Its SKILL.md is about 520 tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including scripts (for example `examples/aspirin/README.md`, `examples/aspirin/xrefs_aspirin.json` and `scripts/get_xrefs.py`).
It sits in Legal & Compliance, covering Intellectual property and Academic paper search. It works with PubMed. The repository describes itself as: Integrating AtomisticSkills into Agentic IDEs (Cursor, Claude Code, Codex, Google Antigravity, Hermes Agent, etc). The licence is MIT.
When your agent uses it
- Tasks that involve Intellectual property
- Tasks that involve Academic paper search
Example prompts
- “/general-chemical-literature”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit 6257444. 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 1 file in scripts/ (Python), which the agent can run.
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):
github.com
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
General Chemical Literature loads about 515 tokens when it runs. Until then it costs about 34 tokens; SKILL.md has 181 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); the scripts in this folder are not scanned.
SKILL.md
The full file from learningmatter-mit/AtomisticSkills at commit 6257444, republished under its MIT licence (© learningmatter-mit). 181 words, ~515 tokens.
Download SKILL.mdSave it as
.claude/skills/general-chemical-literature/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.- name
- general-chemical-literature
- description
- Retrieve extensive literature (PubMed) and patent associated with a specific chemical compound via PubChem.
- metadata.category
- general, chemistry, drug-discovery, materials
- metadata.venv
- cpu
Chemical Literature and Patent Mapping
Goal
To programmatically check if a specific chemical compound exists in recent literature or patent databases. This skill uses PubChem's PUG-REST XRefs endpoint to extract an exhaustive list of associated PubMed IDs and Patent numbers.
This is incredibly useful as an autonomous "novelty check" for generated molecules.
Instructions
1. Extract Literature and Patents by CID
Provide the CID of the target molecule. By default, the script will output the absolute total number of hits but limits the JSON save array to 1000 to prevent memory flooding for ubiquitous molecules (like Aspirin, which has over 100,000 patents). Adjust --limit as needed.
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/get_xrefs.py \
--cid 2244 \
--limit 50 \
--outdir research/aspirin_literature \
--output xrefs_aspirin.jsonExamples
We can pull cross-references for Aspirin (CID: 2244), saving the top 50 identifiers.
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/get_xrefs.py \
--cid 2244 \
--limit 50 \
--outdir ${CLAUDE_SKILL_DIR}/examples/aspirin \
--output xrefs_aspirin.jsonConstraints
- Novelty Assessment Limitation: If 0 PMIDs or Patents are returned, it strongly implies the molecule is highly novel (or purely computational), but it does not guarantee absolute non-existence.
- Link Generation: The script automatically prints actionable links (
pubmed.ncbi.nlm.nih.gov/andpatents.google.com/patent/) for the top 5 results for immediate verification. - Network Limits: Handled internally via standard exponential backoff.
Author: Bowen Deng Contact: GitHub @learningmatter-mit
© learningmatter-mit, 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 (scripts) in skills/general-chemical-literature of learningmatter-mit/AtomisticSkills.
- SKILL.md
- examples/aspirin/README.md
- examples/aspirin/xrefs_aspirin.json
- scripts/get_xrefs.py
Open the folder on GitHubat commit 6257444
Compare with similar skills
General Chemical 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| General Chemical Literature this skilllearningmatter-mit/AtomisticSkills | 176 | — | ~515 | Automated safety check: Pass | MIT | |
| Ncbi Sequence Fetchgoogle-deepmind/science-skills | 3.2k | 1 repos | ~2.3k | Automated safety check: Notes | Apache-2.0 | |
| Paper to Chinese Patent DrafterYuan1z0825/nature-skills | 47k | 1 repos | ~1.1k | Automated safety check: Pass | Apache-2.0 | |
| 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 | |
| Citation Managementneflibata-feng/MyArxiv-Agent | 126 | 19 repos | ~8.1k | Automated safety check: Notes | MIT |
Similar skills
Paper to Chinese Patent Drafter
Yuan1z0825/nature-skills
Drafts Chinese invention patent applications and technical disclosures from research papers or inventor materials, tying each claim feature to source evidence.
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.
Citation Management
neflibata-feng/MyArxiv-Agent
Comprehensive citation management for academic research. An agent skill from neflibata-feng/MyArxiv-Agent.
Paper Search
openags/paper-search-mcp
Search, download, and read academic papers from 20+ sources (arXiv, PubMed, Semantic Scholar, CrossRef, etc).
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Related
Works with
Categories
Questions about General Chemical Literature
What does General Chemical Literature do?
Retrieve extensive literature (PubMed) and patent associated with a specific chemical compound via PubChem. General Chemical Literature is an agent skill from learningmatter-mit/AtomisticSkills. Retrieve extensive literature (PubMed) and patent associated with a specific chemical compound via PubChem.
When should I use General Chemical Literature?
General Chemical Literature fits situations like: tasks that involve Intellectual property; tasks that involve Academic paper search.
How do I install General Chemical Literature in Claude Code?
Run `npx skills add learningmatter-mit/AtomisticSkills --skill general-chemical-literature -a claude-code`. Or copy the skill folder (skills/general-chemical-literature in learningmatter-mit/AtomisticSkills) into .claude/skills/general-chemical-literature in your project. Claude Code loads it when a task matches its description.
How do I install General Chemical Literature in Codex?
Run `npx skills add learningmatter-mit/AtomisticSkills --skill general-chemical-literature -a codex`. Or copy the skill folder (skills/general-chemical-literature in learningmatter-mit/AtomisticSkills) into .agents/skills/general-chemical-literature in your project. Codex loads it when a task matches its description.
Can I use General Chemical 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 learningmatter-mit/AtomisticSkills --skill general-chemical-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/general-chemical-literature, .gemini/skills/general-chemical-literature, .github/skills/general-chemical-literature and .opencode/skills/general-chemical-literature in your project.
What does General Chemical Literature need to run?
Going by SKILL.md and its folder, General Chemical Literature needs Python for the scripts in its folder. Our summary lists: Python 3.
Does General Chemical Literature access the network?
SKILL.md names 1 domain. As links in the text: github.com. This is read from the text; nothing was executed.
Is General Chemical 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does General Chemical Literature use?
General Chemical Literature 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 General Chemical Literature use?
About 515 tokens (SKILL.md is roughly 2.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to General Chemical Literature?
Skills that share tags, products or a category with General Chemical Literature: Ncbi Sequence Fetch (google-deepmind/science-skills, 3.2k stars), Paper to Chinese Patent Drafter (Yuan1z0825/nature-skills, 47k 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 General Chemical Literature?
learningmatter-mit (a GitHub organization) maintains it in learningmatter-mit/AtomisticSkills, which has 176 GitHub stars. The repository holds 129 skills in this directory. The repository was last updated on October 7, 2026.
Source: learningmatter-mit/AtomisticSkills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.