PyOBO
=====
|build| |pypi_version| |python_versions| |pypi_license| |zenodo| |black| |bioregistry|
Tools for biological identifiers, names, synonyms, xrefs, hierarchies, relations, and properties through the
perspective of OBO.
Example Usage
-------------
Note! PyOBO is no-nonsense. This means that there's no repetitive
prefixes in identifiers. It also means all identifiers are strings,
no exceptions.
Note! The first time you run these, they have to download and cache
all resources. We're not in the business of redistributing data,
so all scripts should be completely reproducible. There's some
AWS tools for hosting/downloading pre-compiled versions in
``pyobo.aws`` if you don't have time for that.
Note! PyOBO can perform grounding in a limited number of cases, but
it is *not* a general solution for named entity recognition (NER) or grounding.
It's suggested to check `Gilda <https://github.com/indralab/gilda>`_
for a no-nonsense solution.
Mapping Identifiers and CURIEs
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Get mapping of ChEBI identifiers to names:
.. code-block:: python
import pyobo
chebi_id_to_name = pyobo.get_id_name_mapping('chebi')
name = chebi_id_to_name['132964']
assert name == 'fluazifop-P-butyl'
Or, you don't have time for two lines:
.. code-block:: python
import pyobo
name = pyobo.get_name('chebi', '132964')
assert name == 'fluazifop-P-butyl'
Get reverse mapping of ChEBI names to identifiers:
.. code-block:: python
import pyobo
chebi_name_to_id = pyobo.get_name_id_mapping('chebi')
identifier = chebi_name_to_id['fluazifop-P-butyl']
assert identifier == '132964'
Maybe you live in CURIE world and just want to normalize something like
`CHEBI:132964`:
.. code-block:: python
import pyobo
name = pyobo.get_name_by_curie('CHEBI:132964')
assert name == 'fluazifop-P-butyl'
Sometimes you accidentally got an old CURIE. It can be mapped to the more recent
one using alternative identifiers listed in the underlying OBO with:
.. code-block:: python
import pyobo
# Look up DNA-binding transcription factor activity (go:0003700)
# based on an old id
primary_curie = pyobo.get_primary_curie('go:0001071')
assert primary_curie == 'go:0003700'
# If it's already the primary, it just gets returned
assert 'go:0003700' == pyobo.get_priority_curie('go:0003700')
Mapping Species
~~~~~~~~~~~~~~~
Some resources have species information for their term. Get a mapping of WikiPathway identifiers
to species (as NCBI taxonomy identifiers):
.. code-block:: python
import pyobo
wikipathways_id_to_species = pyobo.get_id_species_mapping('wikipathways')
# Apoptosis (Homo sapiens)
taxonomy_id = wikipathways_id_to_species['WP254']
assert taxonomy_id == '9606'
Or, you don't have time for two lines:
.. code-block:: python
import pyobo
# Apoptosis (Homo sapiens)
taxonomy_id = pyobo.get_species('wikipathways', 'WP254')
assert taxonomy_id == '9606'
Grounding
~~~~~~~~~
Maybe you've got names/synonyms you want to try and map back to ChEBI synonyms.
Given the brand name `Fusilade II` of `CHEBI:132964`, it should be able to look
it up and its preferred label.
.. code-block:: python
import pyobo
prefix, identifier, name = pyobo.ground('chebi', 'Fusilade II')
assert prefix == 'chebi'
assert identifier == '132964'
assert name == 'fluazifop-P-butyl'
# When failure happens...
prefix, identifier, name = pyobo.ground('chebi', 'Definitely not a real name')
assert prefix is None
assert identifier is None
assert name is None
If you're not really sure which namespace a name might belong to, you
can try a few in a row (prioritize by ones that cover the appropriate
entity type to avoid false positives in case of conflicts):
.. code-block:: python
import pyobo
# looking for phenotypes/pathways
prefix, identifier, name = pyobo.ground(['efo', 'go'], 'ERAD')
assert prefix == 'go'
assert identifier == '0030433'
assert name == 'ubiquitin-dependent ERAD pathway'
Cross-referencing
~~~~~~~~~~~~~~~~~
Get xrefs from ChEBI to PubChem:
.. code-block:: python
import pyobo
chebi_id_to_pubchem_compound_id = pyobo.get_filtered_xrefs('chebi', 'pubchem.compound')
pubchem_compound_id = chebi_id_to_pubchem_compound_id['132964']
assert pubchem_compound_id == '3033674'
If you don't have time for two lines:
.. code-block:: python
import pyobo
pubchem_compound_id = pyobo.get_xref('chebi', '132964', 'pubchem.compound')
assert pubchem_compound_id == '3033674'
Get xrefs from Entrez to HGNC, but they're only available through HGNC
so you need to flip them:
.. code-block:: python
import pyobo
hgnc_id_to_ncbigene_id = pyobo.get_filtered_xrefs('hgnc', 'ncbigene')
ncbigene_id_to_hgnc_id = {
ncbigene_id: hgnc_id
for hgnc_id, ncbigene_id in hgnc_id_to_ncbigene_id.items()
}
mapt_hgnc = ncbigene_id_to_hgnc_id['4137']
assert mapt_hgnc == '6893'
Since this is a common pattern, there's a keyword argument `flip`
that does this for you:
.. code-block:: python
import pyobo
ncbigene_id_to_hgnc_id = pyobo.get_filtered_xrefs('hgnc', 'ncbigene', flip=True)
mapt_hgnc_id = ncbigene_id_to_hgnc_id['4137']
assert mapt_hgnc_id == '6893'
If you don't have time for two lines (I admit this one is a bit confusing) and
need to flip it:
.. code-block:: python
import pyobo
hgnc_id = pyobo.get_xref('hgnc', '4137', 'ncbigene', flip=True)
assert hgnc_id == '6893'
Remap a CURIE based on pre-defined priority list and `Inspector Javert's Xref
Database <https://cthoyt.com/2020/04/19/inspector-javerts-xref-database.html>`_:
.. code-block:: python
import pyobo
# Map to the best source possible
mapt_ncbigene = pyobo.get_priority_curie('hgnc:6893')
assert mapt_ncbigene == 'ncbigene:4137'
# Sometimes you know you're the best. Own it.
assert 'ncbigene:4137' == pyobo.get_priority_curie('ncbigene:4137')
Find all CURIEs mapped to a given one using Inspector Javert's Xref Database:
.. code-block:: python
import pyobo
# Get a set of all CURIEs mapped to MAPT
mapt_curies = pyobo.get_equivalent('hgnc:6893')
assert 'ncbigene:4137' in mapt_curies
assert 'ensembl:ENSG00000186868' in mapt_curies
If you don't want to wait to build the database locally for the ``pyobo.get_priority_curie`` and
``pyobo.get_equivalent``, you can use the following code to download a release from
`Zenodo <https://zenodo.org/record/3757266>`_:
.. code-block:: python
import pyobo.resource_utils
pyobo.resource_utils.ensure_inspector_javert()
Properties
~~~~~~~~~~
Get properties, like SMILES. The semantics of these are defined on an OBO-OBO basis.
.. code-block:: python
import pyobo
# I don't make the rules. I wouldn't have chosen this as the key for this property. It could be any string
chebi_smiles_property = 'http://purl.obolibrary.org/obo/chebi/smiles'
chebi_id_to_smiles = pyobo.get_filtered_properties_mapping('chebi', chebi_smiles_property)
smiles = chebi_id_to_smiles['132964']
assert smiles == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'
If you don't have time for two lines:
.. code-block:: python
import pyobo
smiles = pyobo.get_property('chebi', '132964', 'http://purl.obolibrary.org/obo/chebi/smiles')
assert smiles == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'
Hierarchy
~~~~~~~~~
Check if an entity is in the hierarchy:
.. code-block:: python
import networkx as nx
import pyobo
# check that go:0008219 ! cell death is an ancestor of go:0006915 ! apoptotic process
assert 'go:0008219' in pyobo.get_ancestors('go', '0006915')
# check that go:0070246 ! natural killer cell apoptotic process is a
# descendant of go:0006915 ! apoptotic process
apopototic_process_descendants = pyobo.get_descendants('go', '0006915')
assert 'go:0070246' in apopototic_process_descendants
Get the subhierarchy below a given node:
.. code-block:: python
# get the descendant graph of go:0006915 ! apoptotic process
apopototic_process_subhierarchy = pyobo.get_subhierarchy('go', '0006915')
# check that go:0070246 ! natural killer cell apoptotic process is a
# descendant of go:0006915 ! apoptotic process through the subhierarchy
assert 'go:0070246' in apopototic_process_subhierarchy
Get a hierarchy with properties pre-loaded in the node data dictionaries:
.. code-block:: python
import pyobo
prop = 'http://purl.obolibrary.org/obo/chebi/smiles'
chebi_hierarchy = pyobo.get_hierarchy('chebi', properties=[prop])
assert 'chebi:132964' in chebi_hierarchy
assert prop in chebi_hierarchy.nodes['chebi:132964']
assert chebi_hierarchy.nodes['chebi:132964'][prop] == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'
Relations
~~~~~~~~~
Get all orthologies (``ro:HOM0000017``) between HGNC and MGI (note: this is one way)
.. code-block:: python
>>> import pyobo
>>> human_mapt_hgnc_id = '6893'
>>> mouse_mapt_mgi_id = '97180'
>>> hgnc_mgi_orthology_mapping = pyobo.get_relation_mapping('hgnc', 'ro:HOM0000017', 'mgi')
>>> assert mouse_mapt_mgi_id == hgnc_mgi_orthology_mapping[human_mapt_hgnc_id]
If you want to do it in one line, use:
.. code-block:: python
>>> import pyobo
>>> human_mapt_hgnc_id = '6893'
>>> mouse_mapt_mgi_id = '97180'
>>> assert mouse_mapt_mgi_id == pyobo.get_relation('hgnc', 'ro:HOM0000017', 'mgi', human_mapt_hgnc_id)
Writings Tests that Use PyOBO
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
If you're writing your own code that relies on PyOBO, and unit
testing it (as you should) in a continuous integration setting,
you've probably realized that loading all of the resources on each
build is not so fast. In those scenarios, you can use some of the
pre-build patches like in the following:
.. code-block:: python
import unittest
import pyobo
from pyobo.mocks import get_mock_id_name_mapping
mock_id_name_mapping = get_mock_id_name_mapping({
'chebi': {
'132964': 'fluazifop-P-butyl',
},
})
class MyTestCase(unittest.TestCase):
def my_test(self):
with mock_id_name_mapping:
# use functions directly, or use your functions that wrap them
pyobo.get_name('chebi', '1234')
Installation
------------
PyOBO can be installed from `PyPI <https://pypi.org/project/pyobo/>`_ with:
.. code-block:: sh
$ pip install pyobo
It can be installed in development mode from `GitHub <https://github.com/pyobo/pyobo>`_
with:
.. code-block:: sh
$ git clone https://github.com/pyobo/pyobo.git
$ cd pyobo
$ pip install -e .
Curation of the Bioregistry
---------------------------
In order to normalize references and identify resources, PyOBO uses the
`Bioregistry <https://github.com/bioregistry/bioregistry>`_. It used to be a part of PyOBO, but has since
been externalized for more general reuse.
At `src/pyobo/registries/metaregistry.json <https://github.com/pyobo/pyobo/blob/master/src/pyobo/registries/metaregistry.json>`_
is the curated "metaregistry". This is a source of information that contains
all sorts of fixes for missing/wrong information in MIRIAM, OLS, and OBO Foundry; entries that don't appear in
any of them; additional synonym information for each namespace/prefix; rules for normalizing xrefs and CURIEs, etc.
Other entries in the metaregistry:
- The ``"remappings"->"full"`` entry is a dictionary from strings that might follow ``xref:``
in a given OBO file that need to be completely replaced, due to incorrect formatting
- The ``"remappings"->"prefix"`` entry contains a dictionary of prefixes for xrefs that need
to be remapped. Several rules, for example, remove superfluous spaces that occur inside
CURIEs or and others address instances of the GOGO issue.
- The ``"blacklists"`` entry contains rules for throwing out malformed xrefs based on
full string, just prefix, or just suffix.
Troubleshooting
---------------
The OBO Foundry seems to be pretty unstable with respect to the URLs to OBO resources. If you get an error like:
.. code-block::
pyobo.getters.MissingOboBuild: OBO Foundry is missing a build for: mondo
Then you should check the corresponding page on the OBO Foundry (in this case, http://www.obofoundry.org/ontology/mondo.html)
and make update to the ``url`` entry for that namespace in the Bioregistry.
.. |build| image:: https://github.com/pyobo/pyobo/workflows/Tests/badge.svg
:target: https://github.com/pyobo/pyobo/actions?query=workflow%3ATests
:alt: Build Status
.. |coverage| image:: https://codecov.io/gh/pyobo/pyobo/coverage.svg?branch=master
:target: https://codecov.io/gh/pyobo/pyobo?branch=master
:alt: Coverage Status
.. |docs| image:: http://readthedocs.org/projects/pyobo/badge/?version=latest
:target: http://pyobo.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. |python_versions| image:: https://img.shields.io/pypi/pyversions/pyobo.svg
:alt: Stable Supported Python Versions
.. |pypi_version| image:: https://img.shields.io/pypi/v/pyobo.svg
:alt: Current version on PyPI
.. |pypi_license| image:: https://img.shields.io/pypi/l/pyobo.svg
:alt: MIT License
.. |zenodo| image:: https://zenodo.org/badge/203449095.svg
:target: https://zenodo.org/badge/latestdoi/203449095
:alt: Zenodo
.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
:target: https://github.com/psf/black
:alt: Black Code Style
.. |bioregistry| image:: https://img.shields.io/static/v1?label=Powered%20by&message=Bioregistry&color=BA274A&style=flat&logo=image/png;base64,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
:target: https://github.com/biopragmatics/bioregistry
:alt: Powered by the Bioregistry
Raw data
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"name": "pyobo",
"maintainer": "Charles Tapley Hoyt",
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"requires_python": ">=3.8",
"maintainer_email": "cthoyt@gmail.com",
"keywords": "Open Biomedical Ontologies, OBO",
"author": "Charles Tapley Hoyt",
"author_email": "cthoyt@gmail.com",
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"description": "PyOBO\n=====\n|build| |pypi_version| |python_versions| |pypi_license| |zenodo| |black| |bioregistry|\n\nTools for biological identifiers, names, synonyms, xrefs, hierarchies, relations, and properties through the\nperspective of OBO.\n\nExample Usage\n-------------\nNote! PyOBO is no-nonsense. This means that there's no repetitive\nprefixes in identifiers. It also means all identifiers are strings,\nno exceptions.\n\nNote! The first time you run these, they have to download and cache\nall resources. We're not in the business of redistributing data,\nso all scripts should be completely reproducible. There's some\nAWS tools for hosting/downloading pre-compiled versions in\n``pyobo.aws`` if you don't have time for that.\n\nNote! PyOBO can perform grounding in a limited number of cases, but\nit is *not* a general solution for named entity recognition (NER) or grounding.\nIt's suggested to check `Gilda <https://github.com/indralab/gilda>`_\nfor a no-nonsense solution.\n\nMapping Identifiers and CURIEs\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nGet mapping of ChEBI identifiers to names:\n\n.. code-block:: python\n\n import pyobo\n\n chebi_id_to_name = pyobo.get_id_name_mapping('chebi')\n\n name = chebi_id_to_name['132964']\n assert name == 'fluazifop-P-butyl'\n\nOr, you don't have time for two lines:\n\n.. code-block:: python\n\n import pyobo\n\n name = pyobo.get_name('chebi', '132964')\n assert name == 'fluazifop-P-butyl'\n\nGet reverse mapping of ChEBI names to identifiers:\n\n.. code-block:: python\n\n import pyobo\n\n chebi_name_to_id = pyobo.get_name_id_mapping('chebi')\n\n identifier = chebi_name_to_id['fluazifop-P-butyl']\n assert identifier == '132964'\n\nMaybe you live in CURIE world and just want to normalize something like\n`CHEBI:132964`:\n\n.. code-block:: python\n\n import pyobo\n\n name = pyobo.get_name_by_curie('CHEBI:132964')\n assert name == 'fluazifop-P-butyl'\n\nSometimes you accidentally got an old CURIE. It can be mapped to the more recent\none using alternative identifiers listed in the underlying OBO with:\n\n.. code-block:: python\n\n import pyobo\n\n # Look up DNA-binding transcription factor activity (go:0003700)\n # based on an old id\n primary_curie = pyobo.get_primary_curie('go:0001071')\n assert primary_curie == 'go:0003700'\n\n # If it's already the primary, it just gets returned\n assert 'go:0003700' == pyobo.get_priority_curie('go:0003700')\n\nMapping Species\n~~~~~~~~~~~~~~~\nSome resources have species information for their term. Get a mapping of WikiPathway identifiers\nto species (as NCBI taxonomy identifiers):\n\n.. code-block:: python\n\n import pyobo\n\n wikipathways_id_to_species = pyobo.get_id_species_mapping('wikipathways')\n\n # Apoptosis (Homo sapiens)\n taxonomy_id = wikipathways_id_to_species['WP254']\n assert taxonomy_id == '9606'\n\nOr, you don't have time for two lines:\n\n.. code-block:: python\n\n import pyobo\n\n # Apoptosis (Homo sapiens)\n taxonomy_id = pyobo.get_species('wikipathways', 'WP254')\n assert taxonomy_id == '9606'\n\nGrounding\n~~~~~~~~~\nMaybe you've got names/synonyms you want to try and map back to ChEBI synonyms.\nGiven the brand name `Fusilade II` of `CHEBI:132964`, it should be able to look\nit up and its preferred label.\n\n.. code-block:: python\n\n import pyobo\n\n prefix, identifier, name = pyobo.ground('chebi', 'Fusilade II')\n assert prefix == 'chebi'\n assert identifier == '132964'\n assert name == 'fluazifop-P-butyl'\n\n # When failure happens...\n prefix, identifier, name = pyobo.ground('chebi', 'Definitely not a real name')\n assert prefix is None\n assert identifier is None\n assert name is None\n\nIf you're not really sure which namespace a name might belong to, you\ncan try a few in a row (prioritize by ones that cover the appropriate\nentity type to avoid false positives in case of conflicts):\n\n.. code-block:: python\n\n import pyobo\n\n # looking for phenotypes/pathways\n prefix, identifier, name = pyobo.ground(['efo', 'go'], 'ERAD')\n assert prefix == 'go'\n assert identifier == '0030433'\n assert name == 'ubiquitin-dependent ERAD pathway'\n\nCross-referencing\n~~~~~~~~~~~~~~~~~\nGet xrefs from ChEBI to PubChem:\n\n.. code-block:: python\n\n import pyobo\n\n chebi_id_to_pubchem_compound_id = pyobo.get_filtered_xrefs('chebi', 'pubchem.compound')\n\n pubchem_compound_id = chebi_id_to_pubchem_compound_id['132964']\n assert pubchem_compound_id == '3033674'\n\nIf you don't have time for two lines:\n\n.. code-block:: python\n\n import pyobo\n\n pubchem_compound_id = pyobo.get_xref('chebi', '132964', 'pubchem.compound')\n assert pubchem_compound_id == '3033674'\n\nGet xrefs from Entrez to HGNC, but they're only available through HGNC\nso you need to flip them:\n\n.. code-block:: python\n\n import pyobo\n\n hgnc_id_to_ncbigene_id = pyobo.get_filtered_xrefs('hgnc', 'ncbigene')\n ncbigene_id_to_hgnc_id = {\n ncbigene_id: hgnc_id\n for hgnc_id, ncbigene_id in hgnc_id_to_ncbigene_id.items()\n }\n mapt_hgnc = ncbigene_id_to_hgnc_id['4137']\n assert mapt_hgnc == '6893'\n\nSince this is a common pattern, there's a keyword argument `flip`\nthat does this for you:\n\n.. code-block:: python\n\n import pyobo\n\n ncbigene_id_to_hgnc_id = pyobo.get_filtered_xrefs('hgnc', 'ncbigene', flip=True)\n mapt_hgnc_id = ncbigene_id_to_hgnc_id['4137']\n assert mapt_hgnc_id == '6893'\n\nIf you don't have time for two lines (I admit this one is a bit confusing) and\nneed to flip it:\n\n.. code-block:: python\n\n import pyobo\n\n hgnc_id = pyobo.get_xref('hgnc', '4137', 'ncbigene', flip=True)\n assert hgnc_id == '6893'\n\nRemap a CURIE based on pre-defined priority list and `Inspector Javert's Xref\nDatabase <https://cthoyt.com/2020/04/19/inspector-javerts-xref-database.html>`_:\n\n.. code-block:: python\n\n import pyobo\n\n # Map to the best source possible\n mapt_ncbigene = pyobo.get_priority_curie('hgnc:6893')\n assert mapt_ncbigene == 'ncbigene:4137'\n\n # Sometimes you know you're the best. Own it.\n assert 'ncbigene:4137' == pyobo.get_priority_curie('ncbigene:4137')\n\nFind all CURIEs mapped to a given one using Inspector Javert's Xref Database:\n\n.. code-block:: python\n\n import pyobo\n\n # Get a set of all CURIEs mapped to MAPT\n mapt_curies = pyobo.get_equivalent('hgnc:6893')\n assert 'ncbigene:4137' in mapt_curies\n assert 'ensembl:ENSG00000186868' in mapt_curies\n\nIf you don't want to wait to build the database locally for the ``pyobo.get_priority_curie`` and\n``pyobo.get_equivalent``, you can use the following code to download a release from\n`Zenodo <https://zenodo.org/record/3757266>`_:\n\n.. code-block:: python\n\n import pyobo.resource_utils\n\n pyobo.resource_utils.ensure_inspector_javert()\n\nProperties\n~~~~~~~~~~\nGet properties, like SMILES. The semantics of these are defined on an OBO-OBO basis.\n\n.. code-block:: python\n\n import pyobo\n\n # I don't make the rules. I wouldn't have chosen this as the key for this property. It could be any string\n chebi_smiles_property = 'http://purl.obolibrary.org/obo/chebi/smiles'\n chebi_id_to_smiles = pyobo.get_filtered_properties_mapping('chebi', chebi_smiles_property)\n\n smiles = chebi_id_to_smiles['132964']\n assert smiles == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'\n\nIf you don't have time for two lines:\n\n.. code-block:: python\n\n import pyobo\n\n smiles = pyobo.get_property('chebi', '132964', 'http://purl.obolibrary.org/obo/chebi/smiles')\n assert smiles == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'\n\nHierarchy\n~~~~~~~~~\nCheck if an entity is in the hierarchy:\n\n.. code-block:: python\n\n import networkx as nx\n import pyobo\n\n # check that go:0008219 ! cell death is an ancestor of go:0006915 ! apoptotic process\n assert 'go:0008219' in pyobo.get_ancestors('go', '0006915')\n\n # check that go:0070246 ! natural killer cell apoptotic process is a\n # descendant of go:0006915 ! apoptotic process\n apopototic_process_descendants = pyobo.get_descendants('go', '0006915')\n assert 'go:0070246' in apopototic_process_descendants\n\nGet the subhierarchy below a given node:\n\n.. code-block:: python\n\n # get the descendant graph of go:0006915 ! apoptotic process\n apopototic_process_subhierarchy = pyobo.get_subhierarchy('go', '0006915')\n\n # check that go:0070246 ! natural killer cell apoptotic process is a\n # descendant of go:0006915 ! apoptotic process through the subhierarchy\n assert 'go:0070246' in apopototic_process_subhierarchy\n\nGet a hierarchy with properties pre-loaded in the node data dictionaries:\n\n.. code-block:: python\n\n import pyobo\n\n prop = 'http://purl.obolibrary.org/obo/chebi/smiles'\n chebi_hierarchy = pyobo.get_hierarchy('chebi', properties=[prop])\n\n assert 'chebi:132964' in chebi_hierarchy\n assert prop in chebi_hierarchy.nodes['chebi:132964']\n assert chebi_hierarchy.nodes['chebi:132964'][prop] == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'\n\nRelations\n~~~~~~~~~\nGet all orthologies (``ro:HOM0000017``) between HGNC and MGI (note: this is one way)\n\n.. code-block:: python\n\n >>> import pyobo\n >>> human_mapt_hgnc_id = '6893'\n >>> mouse_mapt_mgi_id = '97180'\n >>> hgnc_mgi_orthology_mapping = pyobo.get_relation_mapping('hgnc', 'ro:HOM0000017', 'mgi')\n >>> assert mouse_mapt_mgi_id == hgnc_mgi_orthology_mapping[human_mapt_hgnc_id]\n\nIf you want to do it in one line, use:\n\n.. code-block:: python\n\n >>> import pyobo\n >>> human_mapt_hgnc_id = '6893'\n >>> mouse_mapt_mgi_id = '97180'\n >>> assert mouse_mapt_mgi_id == pyobo.get_relation('hgnc', 'ro:HOM0000017', 'mgi', human_mapt_hgnc_id)\n\nWritings Tests that Use PyOBO\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nIf you're writing your own code that relies on PyOBO, and unit\ntesting it (as you should) in a continuous integration setting,\nyou've probably realized that loading all of the resources on each\nbuild is not so fast. In those scenarios, you can use some of the\npre-build patches like in the following:\n\n.. code-block:: python\n\n import unittest\n import pyobo\n from pyobo.mocks import get_mock_id_name_mapping\n\n mock_id_name_mapping = get_mock_id_name_mapping({\n 'chebi': {\n '132964': 'fluazifop-P-butyl',\n },\n })\n\n class MyTestCase(unittest.TestCase):\n def my_test(self):\n with mock_id_name_mapping:\n # use functions directly, or use your functions that wrap them\n pyobo.get_name('chebi', '1234')\n\n\nInstallation\n------------\nPyOBO can be installed from `PyPI <https://pypi.org/project/pyobo/>`_ with:\n\n.. code-block:: sh\n\n $ pip install pyobo\n\nIt can be installed in development mode from `GitHub <https://github.com/pyobo/pyobo>`_\nwith:\n\n.. code-block:: sh\n\n $ git clone https://github.com/pyobo/pyobo.git\n $ cd pyobo\n $ pip install -e .\n\nCuration of the Bioregistry\n---------------------------\nIn order to normalize references and identify resources, PyOBO uses the\n`Bioregistry <https://github.com/bioregistry/bioregistry>`_. It used to be a part of PyOBO, but has since\nbeen externalized for more general reuse.\n\nAt `src/pyobo/registries/metaregistry.json <https://github.com/pyobo/pyobo/blob/master/src/pyobo/registries/metaregistry.json>`_\nis the curated \"metaregistry\". This is a source of information that contains\nall sorts of fixes for missing/wrong information in MIRIAM, OLS, and OBO Foundry; entries that don't appear in\nany of them; additional synonym information for each namespace/prefix; rules for normalizing xrefs and CURIEs, etc.\n\nOther entries in the metaregistry:\n\n- The ``\"remappings\"->\"full\"`` entry is a dictionary from strings that might follow ``xref:``\n in a given OBO file that need to be completely replaced, due to incorrect formatting\n- The ``\"remappings\"->\"prefix\"`` entry contains a dictionary of prefixes for xrefs that need\n to be remapped. Several rules, for example, remove superfluous spaces that occur inside\n CURIEs or and others address instances of the GOGO issue.\n- The ``\"blacklists\"`` entry contains rules for throwing out malformed xrefs based on\n full string, just prefix, or just suffix.\n\nTroubleshooting\n---------------\nThe OBO Foundry seems to be pretty unstable with respect to the URLs to OBO resources. If you get an error like:\n\n.. code-block::\n\n pyobo.getters.MissingOboBuild: OBO Foundry is missing a build for: mondo\n\nThen you should check the corresponding page on the OBO Foundry (in this case, http://www.obofoundry.org/ontology/mondo.html)\nand make update to the ``url`` entry for that namespace in the Bioregistry.\n\n.. |build| image:: https://github.com/pyobo/pyobo/workflows/Tests/badge.svg\n :target: https://github.com/pyobo/pyobo/actions?query=workflow%3ATests\n :alt: Build Status\n\n.. |coverage| image:: https://codecov.io/gh/pyobo/pyobo/coverage.svg?branch=master\n :target: https://codecov.io/gh/pyobo/pyobo?branch=master\n :alt: Coverage Status\n\n.. |docs| image:: http://readthedocs.org/projects/pyobo/badge/?version=latest\n :target: http://pyobo.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n.. |python_versions| image:: https://img.shields.io/pypi/pyversions/pyobo.svg\n :alt: Stable Supported Python Versions\n\n.. |pypi_version| image:: https://img.shields.io/pypi/v/pyobo.svg\n :alt: Current version on PyPI\n\n.. |pypi_license| image:: https://img.shields.io/pypi/l/pyobo.svg\n :alt: MIT License\n\n.. |zenodo| image:: https://zenodo.org/badge/203449095.svg\n :target: https://zenodo.org/badge/latestdoi/203449095\n :alt: Zenodo\n\n.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg\n :target: https://github.com/psf/black\n :alt: Black Code Style\n\n.. |bioregistry| image:: 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