PubMed (pubmed.ncbi.nlm.nih.gov). Use this skill for ANY PubMed request — searching and reading data. Whenever a task involves PubMed, use this skill instead of calling the API directly.
1 次安装
编程
Search Pubmed
试用Search biomedical literature on PubMed via NCBI E-Utilities. Use this skill whenever the user needs to search for scientific papers, biomedical articles, lif...
它能做什么
Search biomedical literature on PubMed via NCBI E-Utilities. Use this skill whenever the user needs to search for scientific papers, biomedical articles, life science research, or any PubMed-indexed content. Triggers: 'search literature', 'find papers', 'PubMed', 'NCBI', 'PMID', 'biomedical', 'scientific articles', 'life science', 'organism research', 'gene/disease/drug papers'. Also use for any mention of searching literature about bacteria, plants, animals, diseases, genes, proteins, drugs, or clinical/biological topics — even if the user doesn't explicitly say 'PubMed'.
技能文档
PubMed Literature Search
Search PubMed (and other NCBI databases) via the E-Utilities API, using a bundled
Python script that wraps Biopython's Bio.Entrez.
Quick start
python scripts/search_pubmed.py "" [--max N] [--db DB] [--pmid ID] [--full]
The script lives at scripts/search_pubmed.py relative to this skill directory.
Run it from the workspace root, using the skill's install path to locate the script.
If the skill is installed at .claude/skills/search-pubmed/, invoke it as:
python .claude/skills/search-pubmed/scripts/search_pubmed.py "cancer AND immunotherapy"
Common patterns
Keyword search (default)
python .claude/skills/search-pubmed/scripts/search_pubmed.py "Sinorhizobium fredii biofilm"
Control result count
python .claude/skills/search-pubmed/scripts/search_pubmed.py "CRISPR" --max 20
Boolean logic (AND / OR / NOT)
python .claude/skills/search-pubmed/scripts/search_pubmed.py "hopanoid AND rhizobium"
python .claude/skills/search-pubmed/scripts/search_pubmed.py "mouse OR rat"
Field-qualified search
python .claude/skills/search-pubmed/scripts/search_pubmed.py "hopanoid[Title/Abstract]"
python .claude/skills/search-pubmed/scripts/search_pubmed.py "Smith J[Author] AND 2024[Date - Publication]"
PMID lookup
# Fast — title / author / journal / DOI only (1 request)
python .claude/skills/search-pubmed/scripts/search_pubmed.py --pmid 41185614
# With abstract (2 requests)
python .claude/skills/search-pubmed/scripts/search_pubmed.py --pmid 41185614 --full
# Multiple PMIDs
python .claude/skills/search-pubmed/scripts/search_pubmed.py --pmid 41185614,42332334 --full
Other NCBI databases
python .claude/skills/search-pubmed/scripts/search_pubmed.py "TP53" --db nucleotide
python .claude/skills/search-pubmed/scripts/search_pubmed.py "cancer" --db pmc
Parameters
| Parameter | Description | Default |
|---|---|---|
query | Search keywords (Entrez syntax supported) | Required (or use --pmid) |
--max N | Maximum results to return | 10 |
--db NAME | Target NCBI database | pubmed |
--email ADDR | NCBI contact email (optional, avoids warning) | — |
--api-key KEY | NCBI API Key (optional, raises rate limit) | — |
--pmid ID | Lookup by PMID directly, skip search | — |
--full | Include abstract text (with --pmid) | off |
Output format
Each result includes:
- PMID — PubMed ID (clickable link:
https://pubmed.ncbi.nlm.nih.gov/PMID) - Title — article title
- Author — first author | last author
- Source — journal abbreviation
- Date — publication date
- DOI — digital object identifier (when available)
Rate limits
| Condition | Limit |
|---|---|
| No API key | 3 requests/sec |
With API key (--api-key) | 10 requests/sec |
A typical search uses 2 requests (search + summaries). PMID lookup uses 1 (or 2 with --full).
Staying within the rate limit is generally not a concern for interactive use.
Search tips
- Start broad, then narrow. Use
ANDto add terms, not to restrict fields. - Try synonyms and alternative classifications. Example: Sinorhizobium fredii
is also classified as Ensifer fredii — search both with
"Sinorhizobium fredii" OR "Ensifer fredii". - Zero results is information. A null result may indicate a genuine research gap — tell the user this explicitly.
- Use
[Title/Abstract]qualifier for precision when a broad search returns too many off-topic hits. - When cross-searching two topics (e.g., organism X + pathway Y), if the AND query returns 0, run them separately to show the user the landscape — how many papers exist on each side of the gap.
- A PubMed gap doesn't mean a total gap. When you identify a research gap in PubMed, suggest the user cross-check gene/protein databases (NCBI Gene, UniProt, KEGG) for genomic evidence — genes may be annotated but unstudied in the literature.
Dependencies
- Python 3.6+
biopythonpackage:pip install biopython
Bundled resources
scripts/search_pubmed.py— the search executablereferences/entrez-help.md— NCBI Entrez query syntax reference
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