PubMed REST API Search
davila7/claude-code-templates
Searches PubMed directly through its E-utilities REST API, with guidance on Boolean and MeSH query syntax, batch retrieval and citation data.
Search biomedical literature and retrieve records via PubMed E-utilities
Install Pubmed API
$ npx skills add wentorai/research-plugins --skill pubmed-api -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install wentorai/research-plugins pubmed-api --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/wentorai/research-plugins.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/literature/search/pubmed-api .claude/skills/pubmed-api && 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 "pubmed-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/pubmed-api into .claude/skills/pubmed-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubmed-api", 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/wentorai/research-plugins/tree/main/skills/literature/search/pubmed-apiType 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 wentorai/research-plugins --skill pubmed-api -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install wentorai/research-plugins pubmed-api --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/literature/search/pubmed-api .agents/skills/pubmed-api && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "pubmed-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/pubmed-api into .agents/skills/pubmed-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubmed-api", 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 wentorai/research-plugins --skill pubmed-api -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install wentorai/research-plugins pubmed-api --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/literature/search/pubmed-api .cursor/skills/pubmed-api && 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 "pubmed-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/pubmed-api into .cursor/skills/pubmed-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubmed-api", 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/wentorai/research-plugins.git --path skills/literature/search/pubmed-api--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 wentorai/research-plugins --skill pubmed-api -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install wentorai/research-plugins pubmed-api --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/literature/search/pubmed-api .gemini/skills/pubmed-api && 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 "pubmed-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/pubmed-api into .gemini/skills/pubmed-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubmed-api", 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 wentorai/research-plugins pubmed-apiInstalls 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 wentorai/research-plugins --skill pubmed-api -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/literature/search/pubmed-api .github/skills/pubmed-api && 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 "pubmed-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/pubmed-api into .github/skills/pubmed-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubmed-api", 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 wentorai/research-plugins --skill pubmed-api -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install wentorai/research-plugins pubmed-api --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/literature/search/pubmed-api .opencode/skills/pubmed-api && 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 "pubmed-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/pubmed-api into .opencode/skills/pubmed-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubmed-api", 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
pubmed-api- GitHub stars
- 298
- Used in
- 1 other repo
- Token cost
- ~1.6k tokens
- SKILL.md length
- 576 words
- Files
- 1
- Skills in repo
- 405
- Repo updated
- First seen
- Licence
- MIT
At a glance
Search biomedical literature and retrieve records via PubMed E-utilities
- Tasks that involve Academic paper search
- SKILL.md covers Overview, Authentication, Core Endpoints and Rate Limits, plus 2 more sections
- Calls curl; reaches eutils.ncbi.nlm.nih.gov
What it does
Pubmed API is an agent skill from wentorai/research-plugins. Search biomedical literature and retrieve records via PubMed E-utilities
Its SKILL.md is about 1.6k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Academic paper search. It works with PubMed and NCBI. The repository describes itself as: 350+ academic research skills, MCP configs, and plugins for Research-Claw and AI agents. The licence is MIT.
When your agent uses it
- Tasks that involve Academic paper search
Example prompts
- “/pubmed-api”
Requirements
- A credential in YOUR_API_KEY
What it can do on your machine
Read from SKILL.md and the folder at commit bf44b3c. 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
Shell commands in SKILL.md call:
curl
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
eutils.ncbi.nlm.nih.gov
Also links to:
ncbi.nlm.nih.govpubmed.ncbi.nlm.nih.gov
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
Pubmed API loads about 1.6k tokens when it runs. Until then it costs about 21 tokens; SKILL.md has 576 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 wentorai/research-plugins at commit bf44b3c, republished under its MIT licence (© wentorai). 576 words, ~1,636 tokens.
Download SKILL.mdSave it as
.claude/skills/pubmed-api/SKILL.md (or your agent's skills folder).- name
- pubmed-api
- description
- Search biomedical literature and retrieve records via PubMed E-utilities
PubMed E-utilities API Guide
Overview
PubMed is the premier biomedical literature database maintained by the National Center for Biotechnology Information (NCBI) at the US National Library of Medicine. It indexes over 36 million citations and abstracts from MEDLINE, life science journals, and online books. The Entrez Programming Utilities (E-utilities) provide programmatic access to the entire PubMed database and other NCBI databases.
E-utilities consist of a suite of server-side programs that accept URL-based requests and return structured data. These tools are essential for biomedical researchers, systematic reviewers, and developers building health informatics applications. The API supports complex search queries using MeSH (Medical Subject Headings) terms, boolean operators, and field-specific searches.
The API is free and does not require authentication for basic usage. Registering for an NCBI API key raises the rate limit from 3 to 10 requests per second, which is recommended for any automated workflow.
Authentication
No authentication required for basic usage (3 requests/second). For higher rate limits (10 requests/second), register for a free API key at https://www.ncbi.nlm.nih.gov/account/ and include it in requests:
&api_key=YOUR_API_KEYIncluding tool and email parameters in requests helps NCBI contact you if there are issues with your application.
Core Endpoints
ESearch: Search and Retrieve PMIDs
- URL:
GET https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi - Parameters:
Param Type Required Description db string Yes Database name (e.g., pubmed, pmc) term string Yes Search query (supports boolean operators and field tags) retmax integer No Maximum number of IDs returned (default: 20, max: 10000) retstart integer No Index of first ID to retrieve (for pagination) retmode string No Response format: xml (default) or json sort string No Sort order: relevance, pub_date, author, journal datetype string No Date type for range filter: pdat, mdat, edat mindate string No Start date (YYYY/MM/DD) maxdate string No End date (YYYY/MM/DD) usehistory string No Set to "y" to store results on server for subsequent retrieval - Example:
bash curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CRISPR+AND+cancer[Title]&retmax=10&retmode=json&sort=pub_date" - Response: JSON/XML with
esearchresultcontainingcount(total hits),idlist(array of PMIDs), and optionallywebenvandquerykeyfor history server.
Show full SKILL.md (258 more words)Show less
EFetch: Retrieve Full Records
- URL:
GET https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi - Parameters:
Param Type Required Description db string Yes Database name id string Yes Comma-separated list of PMIDs (or use WebEnv/query_key) rettype string No Return type: abstract, medline, full, xml retmode string No Format: xml, text WebEnv string No Web environment from ESearch with usehistory=y query_key string No Query key from ESearch - Example:
bash curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=33116299,34735795&rettype=abstract&retmode=xml" - Response: XML with complete PubMed records including
MedlineCitationwithArticle(title, abstract, authors, journal),MeSHHeadingList, andPubmedData(DOI, publication status).
ESummary: Retrieve Document Summaries
- URL:
GET https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi - Parameters:
Param Type Required Description db string Yes Database name id string Yes Comma-separated PMIDs retmode string No Response format: xml or json version string No Set to "2.0" for enhanced XML format - Example:
bash curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=33116299&retmode=json&version=2.0" - Response: JSON with document summary including
uid,title,authors,source(journal),pubdate,doi, andpmcid.
Rate Limits
Without API key: 3 requests per second. With API key: 10 requests per second. Exceeding limits results in temporary IP blocking. For large-scale data mining, use the NCBI FTP site for bulk downloads. Always include a delay of at least 334ms (or 100ms with API key) between requests. Weekend and evening hours (US Eastern time) are less congested.
Common Patterns
Systematic Literature Search
Perform a structured search using MeSH terms and field qualifiers:
# Search for clinical trials on diabetes treatment from the last 2 years
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=diabetes[MeSH]+AND+treatment[Title]+AND+clinical+trial[Publication+Type]&mindate=2024/01/01&maxdate=2026/03/09&datetype=pdat&retmax=100&retmode=json"Pipeline: Search then Fetch
Use the history server to efficiently search and then retrieve records:
# Step 1: Search and store results
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=machine+learning+AND+radiology&retmax=0&usehistory=y&retmode=json"
# Step 2: Fetch records using WebEnv and query_key from step 1
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&WebEnv=WEBENV_VALUE&query_key=1&retmax=50&rettype=abstract&retmode=xml"Retrieve Structured Metadata for Citation Management
Get JSON summaries for a batch of known PMIDs:
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=33116299,34735795,35363452&retmode=json&version=2.0"References
- Official documentation: https://www.ncbi.nlm.nih.gov/books/NBK25501/
- E-utilities quick start: https://www.ncbi.nlm.nih.gov/books/NBK25500/
- PubMed search help: https://pubmed.ncbi.nlm.nih.gov/help/
© wentorai, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in skills/literature/search/pubmed-api of wentorai/research-plugins.
Open the folder on GitHubat commit bf44b3c
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in wentorai/research-plugins, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Pubmed API 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 |
|---|---|---|---|---|---|---|
| Pubmed API this skillwentorai/research-plugins | 298 | 1 repos | ~1.6k | Automated safety check: Pass | MIT | |
| PubMed REST API Searchdavila7/claude-code-templates | 32k | 14 repos | ~3.9k | Automated safety check: Pass | MIT | |
| Pubmed Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~2.1k | Automated safety check: Notes | Apache-2.0 | |
| Ncbi Sequence Fetchgoogle-deepmind/science-skills | 3.2k | 1 repos | ~2.3k | Automated safety check: Notes | Apache-2.0 | |
| Journal Skillsaipoch/medical-research-skills | 2k | — | ~1.7k | Automated safety check: Pass | MIT | |
| Pubmed Databasejaechang-hits/SciAgent-Skills | 371 | 1 repos | ~4.4k | Automated safety check: Pass | CC-BY-4.0 |
Similar skills
Pubmed Database
google-deepmind/science-skills
Search PubMed for scientific literature, including published clinical trials.
Ncbi Sequence Fetch
google-deepmind/science-skills
Retrieve protein and nucleotide sequences from NCBI databases using E-utilities.
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…
Pubmed Database
jaechang-hits/SciAgent-Skills
Programmatic PubMed access via NCBI E-utilities REST API. An agent skill from jaechang-hits/SciAgent-Skills.
Scientific DB Pubmed Database
affaan-m/ECC
Direct PubMed and NCBI E-utilities search workflows for biomedical literature, MeSH queries, PMID lookup, citation retrieval, and API-backed literature monitoring.
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Related
Categories
Questions about Pubmed API
What does Pubmed API do?
Search biomedical literature and retrieve records via PubMed E-utilities. Pubmed API is an agent skill from wentorai/research-plugins.
When should I use Pubmed API?
Pubmed API fits situations like: tasks that involve Academic paper search.
How do I install Pubmed API in Claude Code?
Run `npx skills add wentorai/research-plugins --skill pubmed-api -a claude-code`. Or copy the skill folder (skills/literature/search/pubmed-api in wentorai/research-plugins) into .claude/skills/pubmed-api in your project. Claude Code loads it when a task matches its description.
How do I install Pubmed API in Codex?
Run `npx skills add wentorai/research-plugins --skill pubmed-api -a codex`. Or copy the skill folder (skills/literature/search/pubmed-api in wentorai/research-plugins) into .agents/skills/pubmed-api in your project. Codex loads it when a task matches its description.
Can I use Pubmed API 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 wentorai/research-plugins --skill pubmed-api -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/pubmed-api, .gemini/skills/pubmed-api, .github/skills/pubmed-api and .opencode/skills/pubmed-api in your project.
What does Pubmed API need to run?
Going by SKILL.md and its folder, Pubmed API needs the command-line tools its instructions call (curl). Our summary lists: A credential in YOUR_API_KEY.
Does Pubmed API access the network?
SKILL.md names 3 domains. In commands or code: eutils.ncbi.nlm.nih.gov; the agent is likely to contact it when it follows the instructions. As links in the text: ncbi.nlm.nih.gov and pubmed.ncbi.nlm.nih.gov. This is read from the text; nothing was executed.
Is Pubmed API 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 Pubmed API use?
Pubmed API 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 Pubmed API use?
About 1.6k tokens (SKILL.md is roughly 6.5k 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 Pubmed API?
Skills that share tags, products or a category with Pubmed API: PubMed REST API Search (davila7/claude-code-templates, 32k stars), Pubmed Database (google-deepmind/science-skills, 3.2k stars), Ncbi Sequence Fetch (google-deepmind/science-skills, 3.2k stars) and Journal Skills (aipoch/medical-research-skills, 2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Pubmed API?
wentorai (a GitHub user) maintains it in wentorai/research-plugins, which has 298 GitHub stars. The repository holds 405 skills in this directory. The repository was last updated on June 19, 2026.
Source: wentorai/research-plugins on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.