SKILL.md
PubMed Literature Search Skill
This skill searches PubMed using the NCBI E-utilities API to find relevant scientific literature.
How to Use
When the user asks to search for literature, use the WebFetch tool to query PubMed's E-utilities API.
Step 1: Search for Articles
Use ESearch to find PMIDs matching a query:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=<QUERY>&retmode=json&retmax=<COUNT>Parameters:
term: URL-encoded search query (use+for spaces, standard PubMed syntax)retmax: Maximum results to return (default 20, max 10000)retstart: Offset for paginationsort: Sort order (relevance,pubdate,firstauthor)
Example query for vitiligo transcriptomics:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=vitiligo+transcriptome&retmode=json&retmax=20Step 2: Get Article Details
Use ESummary to retrieve article metadata from PMIDs:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=<PMID_LIST>&retmode=jsonParameters:
id: Comma-separated list of PMIDs from Step 1
Step 3: Get Abstracts (Optional)
Use EFetch to retrieve full abstracts:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=<PMID_LIST>&rettype=abstract&retmode=textSearch Syntax
PubMed supports advanced search operators:
| Operator | Example | Description |
|---|---|---|
AND |
vitiligo AND transcriptome |
Both terms required |
OR |
vitiligo OR depigmentation |
Either term |
NOT |
vitiligo NOT mouse |
Exclude term |
[tiab] |
vitiligo[tiab] |
Title/abstract only |
[au] |
smith[au] |
Author search |
[jour] |
nature[jour] |
Journal search |
[pdat] |
2020:2024[pdat] |
Publication date range |
[mesh] |
vitiligo[mesh] |
MeSH term |
"phrase" |
"gene expression" |
Exact phrase |
Example Workflow
When user asks: "Find recent papers on vitiligo RNA-seq"
- Search PubMed:
`` WebFetch: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=vitiligo+RNA-seq+2020:2024[pdat]&retmode=json&retmax=15&sort=pub_date ``
- Get summaries for found PMIDs:
`` WebFetch: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=12345,67890,11111&retmode=json ``
- Present results with:
- Title - Authors (first author et al.) - Journal, Year - PMID (link: https://pubmed.ncbi.nlm.nih.gov/PMID/)
Output Format
Present search results as a formatted table or list:
## Literature Search Results
**Query:** vitiligo transcriptome
| # | Title | Authors | Journal | Year | PMID |
|---|-------|---------|---------|------|------|
| 1 | Example title... | Smith J et al. | J Invest Dermatol | 2023 | [12345](https://pubmed.ncbi.nlm.nih.gov/12345/) |Tips
- Refine searches - Start broad, then add filters if too many results
- Use MeSH terms - More precise than keyword searching
- Date filters - Use
[pdat]for recent literature reviews - Combine queries - Build complex queries with AND/OR/NOT
- Check result count - ESearch returns total count in
esearchresult.count
Rate Limits
NCBI allows 3 requests/second without an API key. For higher throughput, users should register for an API key at: https://www.ncbi.nlm.nih.gov/account/settings/
Add API key to requests: &apikey=YOURKEY