医学公开数据库查询与登记｜个人思维图谱小站

医学公开数据库查询与登记

使用有明确接口的公开数据库查询方法保存请求、筛选、分页与来源，可用于医学文献、临床试验及药物资料检索。

正文

references/ncbi-gene.md

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 PubMed, OMIM, sequences)

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

Target databases include pubmed, omim, nuccore, and protein; discover supported links with EInfo. BioSystems is retired; use current KEGG/Reactome resources for pathways.

Example — gene to PubMed:

/elink.fcgi?dbfrom=gene&db=pubmed&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