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ncbi-gene.md

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1# NCBI Gene (E-utilities)

NCBI Gene (E-utilities)

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3## Base URL

4```

5https://eutils.ncbi.nlm.nih.gov/entrez/eutils/

6```

Base URL

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

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8## Auth

9API key optional but recommended. Without key: 3 req/sec. With key: 10 req/sec.

10Free key from: https://www.ncbi.nlm.nih.gov/account/settings/

11Pass as: `&api_key=YOUR_KEY`

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

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13## Key Endpoints

Key Endpoints

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15### eSearch — Search for gene IDs

16```

17GET /esearch.fcgi?db=gene&term={query}&retmode=json&retmax={n}

18```

20Parameters:

21- `db=gene` (required)

22- `term` — search query (e.g. `BRCA1[gene]+AND+human[orgn]`)

23- `retmode=json`

24- `retmax` — max results (default 20)

25- `retstart` — pagination offset

27Example:

28```

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

30```

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

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32### eSummary — Get gene metadata

33```

34GET /esummary.fcgi?db=gene&id={gene_ids}&retmode=json

35```

37Key response fields: `name`, `description`, `chromosome`, `maplocation`, `otheraliases`, `nomenclaturesymbol`, `organism`

39Example:

40```

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

42```

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

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

45```

46GET /efetch.fcgi?db=gene&id={gene_ids}&rettype=gene_table&retmode=text

47```

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

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

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49### eLink — Cross-database links (gene to PubMed, OMIM, sequences)

50```

51GET /elink.fcgi?dbfrom=gene&db={target_db}&id={gene_id}&retmode=json

52```

54Target databases include `pubmed`, `omim`, `nuccore`, and `protein`; discover supported links with EInfo. BioSystems is retired; use current KEGG/Reactome resources for pathways.

56Example — gene to PubMed:

57```

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

59```

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

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61## Rate Limits

62- Without API key: 3 requests/second

63- With API key: 10 requests/second

64- For bulk: use `usehistory=y` with eSearch, then retrieve via `query_key` and `WebEnv`

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

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