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 pagination
sort: Sort order (relevance, pub_date, first_author)

Example query for vitiligo transcriptomics:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=vitiligo+transcriptome&retmode=json&retmax=20

Step 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=json

Parameters:

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=text

Search 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: &api_key=YOUR_KEY

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