ID translation, taxonomy, orthology and reference lists for molecular biology
Project description
omnipath-utils
ID translation, taxonomy, and reference lists for molecular biology.
Quick Start
from omnipath_utils.mapping import map_name, map_names
from omnipath_utils.taxonomy import ensure_ncbi_tax_id
from omnipath_utils.reflists import is_swissprot
# Translate gene symbol to UniProt
map_name('TP53', 'genesymbol', 'uniprot')
# {'P04637', ...}
# Translate multiple
map_names(['TP53', 'EGFR'], 'genesymbol', 'uniprot')
# {'P04637', 'P00533', ...}
# Resolve organism
ensure_ncbi_tax_id('human') # 9606
ensure_ncbi_tax_id('hsapiens') # 9606
# Check if reviewed
is_swissprot('P04637') # True
Installation
pip install omnipath-utils
With database and web service:
pip install "omnipath-utils[server]"
Web Service
omnipath-utils build --organisms 9606
omnipath-utils serve --port 8082
curl "http://localhost:8082/mapping/translate?identifiers=TP53,EGFR&id_type=genesymbol&target_id_type=uniprot"
Documentation
https://saezlab.github.io/omnipath-utils
License
GPL-3.0-or-later
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