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PubMed

Lets an agent search and read biomedical literature through the NCBI E-utilities that power PubMed: find article IDs (PMIDs), pull document summaries and abstracts, follow links to related or full-text records, and inspect database metadata.

The API key is optional. PubMed works without one at a lower request rate; adding an NCBI key raises the rate limit (from 3 to 10 requests per second).

What it can do​

MethodWhat it does
pubmed_searchSearch for matching record IDs (esearch). Entrez query syntax, with optional date filters and sorting.
pubmed_summaryGet document summaries for IDs (esummary): titles, authors, journal, dates.
pubmed_fetchFetch full records / abstracts for IDs (efetch). Text or XML - efetch has no JSON output.
pubmed_linkFind related or linked records (elink), e.g. related articles or PMC full text.
pubmed_infoDescribe an Entrez database, or list all databases (einfo).
pubmed_requestGeneric passthrough to any E-utility for full coverage.

How to get your key (optional)​

You can skip this entirely - PubMed works keyless.

  1. Sign in or create an account at NCBI.
  2. Open Account Settings (ncbi.nlm.nih.gov/account/settings).
  3. Find API Key Management and create a key.
  4. Paste it into FlyMyAI - or leave the field blank to use PubMed at the lower keyless rate.

Fields to fill​

FlyMyAI fieldWhere it comes from
PUBMED_API_KEYOptional - NCBI -> Account Settings -> API Key Management. Leave blank to run keyless.

Troubleshooting​

  • 429 Too Many Requests - you hit the rate limit. Add an NCBI API key to raise it, or slow down the calls.
  • Empty results from pubmed_search - check the Entrez query syntax (e.g. crispr AND 2023[pdat]). Field tags like [au], [ti], [pdat] are case-sensitive in some contexts.
  • pubmed_fetch returns text/XML, not JSON - efetch has no JSON mode; the content arrives under a raw field. Use pubmed_summary for structured JSON metadata.
  • No related articles from pubmed_link - set linkname to pubmed_pubmed for related articles, or db=pmc to find free full-text links.
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