bioregistry 0.0.3

Integrated registry of biological databases and nomenclatures

Bioregistry

An integrative registry of biological databases, ontologies, and nomenclatures.

⬇️ Download

The bioregistry database can be downloaded directly from here

🚀 Installation

$ pip install git+https://github.com/cthoyt/bioregistry.git

Usage

The Bioregistry can be used to normalize prefixes across MIRIAM and all the (very plentiful) variants that pop up in ontologies in OBO Foundry and the OLS with the normalize_prefix() function.

import bioregistry

# This works for synonym prefixes, like:
assert 'ncbitaxon' == bioregistry.normalize_prefix('taxonomy')

# This works for common mistaken prefixes, like:
assert 'chembl.compound' == bioregistry.normalize_prefix('chembl')

# This works for prefixes that are often written many ways, like:
assert 'eccode' == bioregistry.normalize_prefix('ec-code')
assert 'eccode' == bioregistry.normalize_prefix('EC_CODE')

# If a prefix is not registered, it gives back `None`
assert bioregistry.normalize_prefix('not a real key') is None

Entries in the Bioregistry can be looked up with the get() function.

import bioregistry

entry = bioregistry.normalize_prefix('taxonomy')
# there are lots of mysteries to discover in this dictionary!

The full Bioregistry can be read in a Python project using:

import bioregistry

registry = bioregistry.read_bioregistry()

Update

$ bioregistry update