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Search PubMed for articles by query; return top N PMIDs with titles, year, journal, and link.
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Baseado na classificação ocupacional SOC
Manage the BioAPEX current-feature workflow from scoping through review and completion
Turn an analysis request into a Slurm-ready execution plan with commands, resource assumptions, and job structure.
Scale a buffer recipe to a target volume and compute component masses/volumes.
Save a fetched summary or document to the knowledge base for later retrieval (e.g. after PubMed/UniProt lookup).
Interpret scRNA clusters using marker genes and suggest cell type or state.
Critically evaluate a perturbation hypothesis — challenge assumptions, propose negative controls, and flag confounders.
| name | pubmed_search |
| description | Search PubMed for articles by query; return top N PMIDs with titles, year, journal, and link. |
| 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 |
User asks for literature search, papers on a topic, or "find papers about X".
Build URL: NCBI E-utilities esearch:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term={query}&retmax={max_results}&retmode=jsonFetch: Use fetch_url with the constructed URL.
Parse: From JSON response, extract idlist (PMIDs) and optionally run efetch for titles/summaries, or use esummary:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id={comma-separated PMIDs}&retmode=jsonPresent: For each article, show PMID, title, year, journal, and link https://pubmed.ncbi.nlm.nih.gov/{PMID}/.