| name | ncbi-taxonomy-veterinary |
| description | Query NCBI Taxonomy for veterinary species identification, taxonomic classification, and cross-referencing species names. Covers domestic, exotic, and wildlife species relevant to veterinary medicine. |
NCBI Taxonomy - Veterinary
Overview
NCBI (National Center for Biotechnology Information) Taxonomy is a comprehensive database of organism classification and names. For veterinary medicine, NCBI Taxonomy provides standardized species identifiers (TaxIDs), hierarchical taxonomic relationships, and links to genomic databases (GenBank, RefSeq, SRA). This skill covers species lookup, TaxID resolution, and programmatic access via Entrez API.
When to Use
- User looks up species classification, binomial name, or synonyms (e.g., "dog" → Canis lupus familiaris → TaxID 9615)
- User retrieves genomic data for a species (GenBank sequences, reference genomes)
- User performs phylogenetic analysis requiring standardized species nomenclature
- User links veterinary data to genomic research databases
- Keywords: NCBI, taxonomy, TaxID, binomial name, species classification, Entrez, GenBank, RefSeq, SRA
Key Veterinary Species TaxIDs
| Common Name | Binomial Name | TaxID | Notes |
|---|
| Dog | Canis lupus familiaris | 9615 | Primary veterinary species; ~30K+ genes sequenced |
| Cat | Felis catus | 9685 | Key veterinary species; complete reference genome |
| Horse | Equus caballus | 9796 | Equine medicine; draft/sport breeds |
| Cattle | Bos taurus | 9913 | Dairy/beef; major food animal |
| Sheep | Ovis aries | 9940 | Wool/meat; important research model |
| Swine | Sus scrofa domesticus | 9825 | Pork production; disease model |
| Chicken | Gallus gallus | 9031 | Poultry; avian medicine |
| Turkey | Meleagris gallopavo | 9103 | Poultry production |
| Rabbit | Oryctolagus cuniculus | 9986 | Research + pet; pharmaceuticals tested in rabbits |
| Guinea Pig | Cavia porcellus | 10141 | Research model; common exotic pet |
| Mouse | Mus musculus | 10090 | Reference mammalian genome; translational models |
| Rat | Rattus norvegicus | 10116 | Research toxicology model |
| Rhesus Macaque | Macaca mulatta | 9544 | Non-human primate; drug efficacy translational |
| Zebrafish | Danio rerio | 7955 | Aquaculture; vertebrate developmental model |
| Ferret | Mustela putorius furo | 9646 | Exotic pet; respiratory disease model |
| Hedgehog (African) | Atelerix albiventris | 9365 | Exotic pet medicine |
NCBI Taxonomy Structure
Hierarchical Classification:
Kingdom: Animalia
Phylum: Chordata
Class: Mammalia
Order: Carnivora
Family: Canidae
Genus: Canis
Species: C. lupus
Subspecies: C. l. familiaris (domestic dog)
TaxID: 9615
Taxonomic Ranks (from broadest to specific):
- Superkingdom (Eukaryota, Bacteria, Archaea)
- Kingdom (Animalia, Plantae, Fungi)
- Phylum (Chordata, Arthropoda, Mollusca)
- Class (Mammalia, Aves, Reptilia, Amphibia)
- Order (Carnivora, Primates, Rodentia)
- Family (Canidae, Felidae, Equidae)
- Genus (Canis, Felis, Equus)
- Species (lupus, catus, caballus)
- Subspecies (familiaris for domestic dog)
Querying NCBI Taxonomy
Web Interface:
https://www.ncbi.nlm.nih.gov/taxonomy
Search Examples:
- Enter "dog" → Returns Canis lupus familiaris (TaxID 9615) + alternate names
- Enter "9615" → Returns full taxonomy for domestic dog
- Enter "feline" → Returns Felis catus, Felis silvestris, etc. (all feline species)
- Enter "equine" → Returns horses, zebras, donkeys (family Equidae)
Web Results Include:
- Taxonomy browser (full hierarchy)
- Alternate names and synonyms
- Cross-references (GenBank accessions, RefSeq, SRA)
- Number of sequences available in GenBank
- Associated publications
Entrez API Programmatic Access
Entrez Query Syntax:
Query NCBI databases including Taxonomy via REST/XML API.
Base URL:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/
Example 1: Search for Species by Name
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?
db=taxonomy&term="Canis lupus familiaris"&rettype=json
Response:
{
"result": {
"uid": ["9615"],
"count": "1"
}
}
Example 2: Fetch Full Taxonomy Record for TaxID
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?
db=taxonomy&id=9615&rettype=xml
Response: (XML with full taxonomy, rank, lineage, alternate names)
Example 3: Search for All Dog Breeds (Canis lupus variants)
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?
db=taxonomy&term="Canis lupus[orgn]"&retmax=100&rettype=json
Response: Returns TaxIDs for dog, wolf, dingo, and domestic dog variants
Python SDK (Biopython):
from Bio import Entrez
Entrez.email = "veterinarian@clinic.com"
handle = Entrez.esearch(db="taxonomy", term="Canis lupus familiaris")
record = Entrez.read(handle)
taxid = record["IdList"][0]
print(f"TaxID for dog: {taxid}")
handle = Entrez.efetch(db="taxonomy", id=taxid, rettype="xml")
taxonomy = Entrez.read(handle)
print(f"Lineage: {taxonomy[0]['Lineage']}")
print(f"Rank: {taxonomy[0]['Rank']}")
names = taxonomy[0]["OrgName"]["OrgMod"] if "OrgMod" in taxonomy[0]["OrgName"] else []
for name_info in names:
print(f"Synonym: {name_info['Subname']}")
Linking Taxonomy to Genomic Data
Genomic Database Cross-References:
GenBank: DNA sequences submitted by researchers
- Link: Search GenBank with species TaxID
- Example: Filter by "Canis lupus familiaris [organism]" to retrieve all dog sequences
- Use Case: Find canine tumor suppressor sequences, drug targets
RefSeq: Reference sequence database (non-redundant, curated genomes)
- Link: "Genome" tab in NCBI Taxonomy page
- Current Dog Genome: CanFam3.1 (dog TaxID 9615)
- Example: Download dog reference genome FASTA, align patient tumor WGS to reference
SRA (Sequence Read Archive): Raw sequencing data (fastq, bam files)
- Link: Search by species + disease context
- Example: "Canis lupus familiaris [organism] AND osteosarcoma [disease]"
- Use Case: Download canine osteosarcoma raw RNA-seq data for analysis
Entrez Gene: Gene nomenclature and annotations
- Link: Cross-indexed from taxonomy records
- Example: Query gene symbol "TP53" [organism: Canis lupus familiaris]
- Returns: Dog TP53 gene ID, genomic location (chromosome 5), homology to human/mouse
Workflow Example: Analyze Canine Cancer Gene Expression
1. Start: Patient dog with melanoma
2. Query NCBI Taxonomy: TaxID 9615 (Canis lupus familiaris)
3. Link to RefSeq: Download CanFam3.1 reference genome
4. Find target gene: Query Entrez Gene for "BRAF" [organism: dog]
5. Retrieve sequences: GenBank FASTA for canine BRAF orthologs
6. Download expression data: SRA search "dog melanoma" → retrieve RNA-seq fastq
7. Align & analyze: Map dog tumor RNAseq to reference, quantify BRAF expression
8. Compare to human: Map dog BRAF to human BRAF (NCBI HomoloGene)
9. Translational insight: High BRAF expression in dog → informs human melanoma mechanism
Species Synonyms & Nomenclature Issues
Common Challenges:
- "Dog" ≠ "Canis familiaris" (outdated subspecies classification)
- Modern classification: Canis lupus familiaris (dog is subspecies of gray wolf)
- NCBI Taxonomy lists all names: "domestic dog", "pet dog", "Canis familiaris" (synonym)
- Query flexibility: NCBI accepts any recognized name; returns standardized TaxID 9615
Example: Resolving Nomenclature
Query: "ferret" → NCBI returns multiple:
- Mustela putorius furo (domestic ferret) - TaxID 9646
- Mustela putorius (European polecat, wild ancestor)
- Mustela erminea (stoat, different species)
Veterinarian must verify: Are we discussing domesticated ferret (9646) or wild species?
Taxonomy Updates:
- NCBI Taxonomy is updated regularly as phylogenetic understanding evolves
- Old names may be deprecated; NCBI redirects to current classification
- Example: Some snake species reclassified; old names still searchable with notes
Programmatic Integration for Veterinary AI
Use Case 1: Standardize Patient Species in EHR
def standardize_species(species_name):
"""Convert user input to NCBI TaxID."""
handle = Entrez.esearch(db="taxonomy", term=species_name)
record = Entrez.read(handle)
if record["IdList"]:
return record["IdList"][0]
else:
return None
patient_species = standardize_species("cat")
Use Case 2: Retrieve Species-Specific Genes for Precision Medicine
def get_orthologous_gene(gene_symbol, target_species_taxid):
"""Find orthologous gene in target species."""
handle = Entrez.esearch(
db="gene",
term=f'{gene_symbol} [GENE] AND {target_species_taxid} [ORGN]'
)
result = Entrez.read(handle)
return result["IdList"]
dog_brca2 = get_orthologous_gene("BRCA2", 9615)
Use Case 3: Cross-Species Disease Modeling
canine_species = 9615
human_species = 9606
mouse_species = 10090
Rate Limits & Best Practices
Entrez API Limits:
Best Practices:
- Cache results locally; avoid redundant queries
- Use
retmax=10000 to batch searches (vs. multiple small queries)
- Implement backoff retry (if rate-limited, wait 1-2 seconds)
- Always provide
Entrez.email in scripts (NCBI monitors abuse)
- Batch Entrez calls: query multiple species in single request if possible
Limitations
- Incomplete Metadata: Some organisms lack complete genomic annotation (rare exotic species)
- Taxonomy Instability: Species nomenclature evolves; old publication names may not match current NCBI
- Limited Exotic Data: Well-characterized species (dog, cat, horse) have extensive data; rare species have sparse genomic resources
- Data Quality: Not all GenBank submissions are curated; sequence annotations may contain errors
- This is Reference Only: Taxonomy lookup does not provide clinical guidance; veterinary judgment required for translational decisions
Sources
Advanced Integration
VetClaw SDK provides convenience wrappers around Entrez API for species lookup and genomic data retrieval. See /sessions/charming-practical-mayer/mnt/OpenVet/vetclaw/vetclaw/sdk/ for Python/TypeScript NCBI Taxonomy client examples.
