Taxonomy

omnipath-utils resolves organism identifiers across naming systems used by different databases.

ensure_* functions

Each function accepts any supported organism representation and returns the requested name form:

from omnipath_utils.taxonomy import (
    ensure_ncbi_tax_id,
    ensure_common_name,
    ensure_latin_name,
    ensure_ensembl_name,
    ensure_kegg_code,
    ensure_mirbase_name,
    ensure_oma_code,
)

Input forms

All ensure_* functions accept any of these as input:

Form	Example
NCBI Taxonomy ID (int)	9606
NCBI Taxonomy ID (str)	'9606'
Common name	'human'
Latin name	'Homo sapiens'
Short latin	'hsapiens'
Ensembl name	'hsapiens'
KEGG code	'hsa'
miRBase code	'hsa'
OMA code	'HUMAN'
UniProt code	'HUMAN'

Examples

ensure_ncbi_tax_id('human')     # 9606
ensure_ncbi_tax_id('hsapiens')  # 9606
ensure_ncbi_tax_id('hsa')       # 9606
ensure_ncbi_tax_id(9606)         # 9606

ensure_common_name(10090)        # 'mouse'
ensure_latin_name(9606)          # 'Homo sapiens'
ensure_ensembl_name(9606)        # 'hsapiens'
ensure_kegg_code(9606)           # 'hsa'

Returns None if the organism is not recognized.

List all organisms

from omnipath_utils.taxonomy import all_organisms

orgs = all_organisms()
# dict: {9606: {'common_name': 'human', ...}, 10090: {...}, ...}

Supported organisms

omnipath-utils ships with 22 organisms pre-configured in organisms.yaml, including all major model organisms:

NCBI Tax ID	Common name	KEGG	Ensembl
9606	human	hsa	hsapiens
10090	mouse	mmu	mmusculus
10116	rat	rno	rnorvegicus
9913	cow	bta	btaurus
9031	chicken	gga	ggallus
7955	zebrafish	dre	drerio
7227	fruitfly	dme	dmelanogaster
6239	nematode	cel	celegans
4932	yeast	sce	scerevisiae
3702	thale cress	ath	athaliana

And more. Use all_organisms() for the complete list.