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The bioregistry database can be downloaded as:
The manually curated portions of these data are available under the CC0 1.0 Universal License.
There is preliminary work in generating a knowledge graph around the information in the Bioregistry, including the relations between resources, providers, and registries. It can be viewed on the Network Data Exchange (NDEx).
See the Swagger API documentation.
The Python source code can be found at
bioregistry/bioregistry.
It can be installed with pip install bioregistry
or in development mode by following
these instructions.
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.get('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()
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