pyobo 0.6.0

Mapping Identifiers and CURIEs

Get mapping of ChEBI identifiers to names:

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:

import pyobo

name = pyobo.get_name('chebi', '132964')
assert name == 'fluazifop-P-butyl'

Get reverse mapping of ChEBI names to identifiers:

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:

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:

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):

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:

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.

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):

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:

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:

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:

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:

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:

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:

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:

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:

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.

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:

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:

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:

# 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:

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)

>>> 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:

>>> 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:

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')