| name | pubmed_fetch_abstract |
| description | Fetch and summarize a PubMed article by PMID (abstract, key methods, key findings). |
| category | bio/literature |
| version | 1 |
| requires_tools | ["fetch_url"] |
| requires_network | true |
| user_invocable | true |
| species | any |
| modality | literature |
| stage | utilities |
| stability | experimental |
| safety_level | low |
PubMed Fetch Abstract
When to use
User provides a PMID or asks for the abstract/summary of a specific paper.
Inputs
- pmid: PubMed ID (e.g. 12345678)
Steps
-
Fetch: Use fetch_url with:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id={pmid}&retmode=xml or rettype=abstract
-
Parse: Extract title, authors, journal, year, abstract text from XML/response.
-
Summarize: Provide:
- Full citation (title, authors, journal, year)
- Abstract (full or first ~500 chars if very long)
- Optional: 1–2 sentences on key methods and key findings.
-
Link: Include https://pubmed.ncbi.nlm.nih.gov/{pmid}/.
Output format
- Citation block
- Abstract
- Key methods / findings (brief)
- URL
Failure modes
- Invalid or missing PMID: report "Article not found."
- Parse error: return raw abstract if available.