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NCBI Gene (E-utilities)

Base URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/

Auth

API key optional but recommended. Without key: 3 req/sec. With key: 10 req/sec. Free key from: https://www.ncbi.nlm.nih.gov/account/settings/ Pass as: &api_key=YOUR_KEY

Key Endpoints

eSearch — Search for gene IDs

GET /esearch.fcgi?db=gene&term={query}&retmode=json&retmax={n}

Parameters: - db=gene (required) - term — search query (e.g. BRCA1[gene]+AND+human[orgn]) - retmode=json - retmax — max results (default 20) - retstart — pagination offset

Example:

/esearch.fcgi?db=gene&term=BRCA1[gene]+AND+human[orgn]&retmode=json&retmax=5

eSummary — Get gene metadata

GET /esummary.fcgi?db=gene&id={gene_ids}&retmode=json

Key response fields: name, description, chromosome, maplocation, otheraliases, nomenclaturesymbol, organism

Example:

/esummary.fcgi?db=gene&id=672&retmode=json

eFetch — Full gene records (XML/text only, no JSON)

GET /efetch.fcgi?db=gene&id={gene_ids}&rettype=gene_table&retmode=text

GET /elink.fcgi?dbfrom=gene&db={target_db}&id={gene_id}&retmode=json

Target databases: biosystems (pathways), pubmed, omim, nuccore, protein

Example — gene to pathways:

/elink.fcgi?dbfrom=gene&db=biosystems&id=672&retmode=json

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