医学公开数据库查询与登记

references/ncbi-taxonomy.md

Overview

Taxonomic classification data (names, lineages, ranks) for all organisms in NCBI databases. Accessible via E-utilities with db=taxonomy.

Base URL

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

Authentication

• API key (recommended): Append &api_key=YOUR_KEY (register at ncbi.nlm.nih.gov/account).
• Without key: 3 req/sec. With key: 10 req/sec.
• Provide tool and email parameters.

Key Endpoints

1. ESearch -- Search taxonomy by name

GET esearch.fcgi?db=taxonomy&term=QUERY&retmode=json

Param	Description
term	Organism name, common name, or taxid. Fields: [Scientific Name], [Common Name], [All Names], [Rank]
retmax	Max IDs returned (default 20)

Example -- search by scientific name:

GET esearch.fcgi?db=taxonomy&term=Homo+sapiens[Scientific Name]&retmode=json

Response:

{
  "esearchresult": {
    "count": "1",
    "idlist": ["9606"]
  }
}

Example -- search by common name:

GET esearch.fcgi?db=taxonomy&term=dog[Common Name]&retmode=json

2. EFetch -- Retrieve full taxonomy records

GET efetch.fcgi?db=taxonomy&id=TAXIDS&retmode=xml

Note: Taxonomy EFetch only supports XML output.

Example -- fetch human taxonomy (taxid 9606):

GET efetch.fcgi?db=taxonomy&id=9606&retmode=xml

Response (abbreviated XML):

<TaxaSet>
  <Taxon>
    <TaxId>9606</TaxId>
    <ScientificName>Homo sapiens</ScientificName>
    <OtherNames>
      <CommonName>human</CommonName>
    </OtherNames>
    <Rank>species</Rank>
    <Division>Primates</Division>
    <GeneticCode><GCId>1</GCId><GCName>Standard</GCName></GeneticCode>
    <MitoGeneticCode><MGCId>2</MGCId><MGCName>Vertebrate Mitochondrial</MGCName></MitoGeneticCode>
    <Lineage>cellular organisms; Eukaryota; Opisthokonta; Metazoa; ... ; Hominidae; Homo</Lineage>
    <LineageEx>
      <Taxon><TaxId>131567</TaxId><ScientificName>cellular organisms</ScientificName><Rank>no rank</Rank></Taxon>
      <Taxon><TaxId>2759</TaxId><ScientificName>Eukaryota</ScientificName><Rank>superkingdom</Rank></Taxon>
      <!-- ... each ancestor node ... -->
    </LineageEx>
  </Taxon>
</TaxaSet>

3. ESummary -- Brief taxonomy summaries

GET esummary.fcgi?db=taxonomy&id=TAXIDS&retmode=json

Example -- multiple taxa:

GET esummary.fcgi?db=taxonomy&id=9606,10090,7227&retmode=json

Response includes: lowercase JSON keys scientificname, commonname, rank, division, taxid, genus, species (XML uses different capitalization).

4. ELink -- Cross-link taxonomy to other databases

GET elink.fcgi?dbfrom=taxonomy&db=protein&id=9606&term=insulin

Find all protein records for a given taxid, optionally filtered by keyword.

Common Search Patterns

# All species under a genus
term=Drosophila[Next Level] AND species[Rank]

# Search Taxonomy by taxid directly
term=9606[Taxonomy ID]

# By rank
term=Mammalia[Scientific Name] AND class[Rank]

# Taxonomy subtree search
term=9605[Subtree]

txid9606[Organism:exp] is a sequence-database search expression, not a Taxonomy field. Discover Taxonomy search fields with einfo.fcgi?db=taxonomy&retmode=json; resolve scientific names to taxids before subtree searches.

Useful Cross-references

Link	Description
taxonomy_protein	All proteins for a taxon
taxonomy_gene	All genes for a taxon
taxonomy_nuccore	All nucleotide records for a taxon
taxonomy_genome	Genome assemblies for a taxon

Rate Limits

• Without API key: 3 requests/second
• With API key: 10 requests/second
• EFetch supports multiple taxids in a single call (comma-separated)