PubMed Search Skill

Direct PubMed/PMC API access via web_fetch. No dependencies required.

API Endpoints

Function	Endpoint
Search	eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi
Summary	eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi
Fetch	eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi
Similar	eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi
Citations	icite.od.nih.gov/api/pubs
PMC Full Text	www.ncbi.nlm.nih.gov/pmc/utils/oa/oa.fcgi

1. Search (with Sort)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=QUERY&retmax=20&retmode=json&sort=SORT

Sort options:

• sort=relevance — Best Match (ML-based, default)
• sort=pub_date — Most Recent

Example:

?db=pubmed&term=gastric+cancer[mh]+AND+artificial+intelligence[mh]&retmax=10&retmode=json&sort=pub_date

Returns: idlist (PMIDs), count, querytranslation

2. Get Summaries (titles, authors, PMCID)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=PMID1,PMID2&retmode=json

Returns: title, authors, journal, pubdate, pmcid (if available)

3. Fetch Abstracts

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=PMID1,PMID2&rettype=abstract&retmode=xml

Returns: Full abstract XML with all metadata

4. Count Only (fast)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=QUERY&retmax=0&retmode=json

Use retmax=0 for fast count without retrieving IDs.

5. Find Similar Articles

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=pubmed&id=PMID&cmd=neighbor_score&retmode=json

Returns related articles ranked by similarity score.

6. Citation Counts (iCite)

https://icite.od.nih.gov/api/pubs?pmids=PMID1,PMID2,PMID3

Returns: citation_count, relative_citation_ratio, nih_percentile, etc.

7. PMC Full Text / PDF URLs

https://www.ncbi.nlm.nih.gov/pmc/utils/oa/oa.fcgi?id=PMCID

Returns OA article links including PDF URLs.

8. RIS Export

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=PMID1,PMID2&rettype=medline&retmode=text

Returns MEDLINE format (convertible to RIS).

Query Syntax

See references/query-syntax.md for MeSH terms and search fields.

Workflow Example

# 1. Search with relevance sort
search = web_fetch("...esearch.fcgi?term=gastric+cancer+AI&sort=relevance&retmax=20")
pmids = search["idlist"]

# 2. Get summaries
summaries = web_fetch(f"...esummary.fcgi?id={','.join(pmids)}")

# 3. Fetch abstracts for top hits
abstracts = web_fetch(f"...efetch.fcgi?id={pmids[0]},{pmids[1]}&rettype=abstract")

# 4. Get citation counts
citations = web_fetch(f"https://icite.od.nih.gov/api/pubs?pmids={','.join(pmids)}")

Rate Limits

• Without API key: 3 req/s
• With API key: 10 req/s (add &api_key=KEY)
• Respect 1 second between calls

Get API key: https://www.ncbi.nlm.nih.gov/account/settings/