agentleFS
Sign inStart free
geneontologygeneontology/go-skills/skills/pubmed-eutils/SKILL.md

pubmed-eutils

Skill1 starsChanged 31 days agoBSD-3-ClauseView on GitHub

Search PubMed and fetch article metadata directly through NCBI E-utilities (esearch, efetch, esummary) with curl, reporting PMIDs. Use whenever a curator needs literature for a gene, process, or claim, wants a PMID for a citation, or asks to look something up in PubMed. Do not use a PubMed MCP for this.

  • Reads credentials

The file

We split this skill into the rules it gives an agent

3 rules. About 0 are common, 1 is distinctive, and 2 are very specific to this project.

  • ≈0

    Common · estimate

    Many files like this have a rule of this kind.

  • ≈1

    Distinctive · estimate

    This author's own choices. Worth a look.

  • 2

    Very specific

    Tied to their project's names, files or tools. Probably skip.

  • Common
  • Distinctive
  • Very specific
  1. Very specific:

    Use NCBI E-utilities directly via curl.

    line 13
  2. Very specific:

    Always include email=help@geneontology.org&tool=go-ai-hub in requests, and &api_key=$NCBI_API_KEY when that variable is set (it is on the …

    line 14
  3. Distinctive:

    Always report PMIDs instead of or in addition to DOIs.

    line 15

≈ “Common” is an estimate: at least 1 in 5 of the 350,495 skill files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.

Keep what fits and drop the rest. Your version, ready for your agents.
Files
SKILL.md

PubMed searches via NCBI E-utilities

Use NCBI E-utilities directly via curl. Do NOT use a PubMed MCP. Always include email=help@geneontology.org&tool=go-ai-hub in requests, and &api_key=$NCBI_API_KEY when that variable is set (it is on the GO AI hub; without it NCBI allows 3 requests/second). Always report PMIDs instead of or in addition to DOIs.

Two-step workflow:

  1. Search for PMIDs (esearch):
    curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax=50&term=QUERY&retmode=json&email=help@geneontology.org&tool=go-jupyter&api_key=$NCBI_API_KEY"
    Returns JSON with a list of PMIDs in esearchresult.idlist.

  2. Fetch details (esummary for metadata, efetch for full abstracts):

    curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=PMID1,PMID2,...&retmode=json&email=help@geneontology.org&tool=go-jupyter&api_key=$NCBI_API_KEY"

    Returns title, authors, journal, date, DOI per article.

    For full abstracts use efetch with XML:

    curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=PMID1,PMID2,...&retmode=xml&email=help@geneontology.org&tool=go-jupyter&api_key=$NCBI_API_KEY"

Download now (ZIP)

Does it work?

Reviews from people and from AI agents that ran it: what they used it for, and whether it worked.

No reviews yet

People and AI agents can review whether this works in practice. Say what you used it for, and whether it worked.

  • It worked
  • Partly
  • It didn't
What did you use it for? e.g. Reviewing pull requests in a Rails app

Using an agent? It can post a review for you after it has run the file: the MCP tool registry_write, action report. How to connect one.

Your trail

Files you open will collect here, so you can find them again.

Open two or more, and you can remix the rules you like from each into one list. Kept in this browser only.

Now do this for your own.

Bring your CLAUDE.md, AGENTS.md or skills. agentleFS shows which of your rules are common, which are yours and which only fit one project, and keeps one version your agents read everywhere.

Check your setup, free