医学公开数据库查询与登记

references/ncbi-protein.md

Overview

Protein sequence records (RefSeq, GenBank, UniProt imports) accessible via NCBI E-utilities with db=protein.

Base URL

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

Authentication

• API key (recommended): Register at https://www.ncbi.nlm.nih.gov/account/ and append &api_key=YOUR_KEY.
• Without key: 3 requests/second. With key: 10 requests/second.
• Provide tool and email parameters for identification.

Key Endpoints

1. ESearch -- Search protein records

GET esearch.fcgi?db=protein&term=QUERY&retmax=N&retmode=json

Param	Description
term	Search query (Entrez syntax). Fields: [Protein Name], [Organism], [Accession], [Gene Name]
retmax	Max UIDs per response (default 20); use small batches and history for large sets.
idtype	Set acc to return accession.version IDs instead of default numeric UIDs.
retstart	Offset for pagination
usehistory	y to store results on server (use with large sets)

Example -- search human insulin:

GET esearch.fcgi?db=protein&term=insulin+AND+homo+sapiens[Organism]&retmax=5&retmode=json

Response (JSON):

{
  "esearchresult": {
    "count": "1523",
    "retmax": "5",
    "idlist": ["116734704", "1240286123", "110591076", ...],
    "querytranslation": "insulin AND \"Homo sapiens\"[Organism]"
  }
}

2. EFetch -- Retrieve protein records

GET efetch.fcgi?db=protein&id=IDS&rettype=TYPE&retmode=MODE

rettype	retmode	Output
fasta	text	FASTA sequence
gp	text	GenPept flat file
gp	xml	GenPept XML (INSDSeq)
acc	text	Accession list
seqid	text	SeqID list
ft	text	Feature table

Example -- fetch FASTA for NP_000198.1 (human insulin):

GET efetch.fcgi?db=protein&id=NP_000198.1&rettype=fasta&retmode=text

Response:

>NP_000198.1 insulin preproprotein [Homo sapiens]
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAED
LQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN

Example -- fetch GenPept XML for multiple IDs:

GET efetch.fcgi?db=protein&id=NP_000198.1,NP_001278826.1&rettype=gp&retmode=xml

3. ESummary -- Brief record summaries

GET esummary.fcgi?db=protein&id=IDS&retmode=json

Returns: accession, title, organism, length, taxonomy, create/update dates.

4. ELink -- Find related records

GET elink.fcgi?dbfrom=protein&db=gene&id=NP_000198.1&retmode=json

Links protein to gene, nucleotide, structure, taxonomy, etc.

Common Search Patterns

# By accession
term=NP_000198.1[Accession]

# By gene name + organism
term=BRCA1[Gene Name] AND human[Organism]

# RefSeq only
term=insulin AND srcdb_refseq[Properties]

# By sequence length range
term=100:500[Sequence Length] AND kinase[Protein Name]

ELink resolves protein accessions as well as numeric UIDs: the live NP_000198.1 probe resolved UID 4557671 and Gene 3630. Preserve both the accession version and the resolved UID in provenance.

Rate Limits

• Without API key: 3 requests/second
• With API key: 10 requests/second
• Large batch downloads: use usehistory=y with WebEnv/query_key, then fetch in chunks of 500