drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/ncbi-gene.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
NCBI Gene (E-utilities)		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/ncbi-gene.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

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

eLink — Cross-database links (gene to pathways, PubMed, OMIM)

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

Rate Limits

• Without API key: 3 requests/second
• With API key: 10 requests/second
• For bulk: use usehistory=y with eSearch, then retrieve via query_key and WebEnv