Pyobo
📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures
Install / Use
/learn @biopragmatics/PyoboREADME
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.
Mapping Identifiers and CURIEs
Get mapping of ChEBI identifiers to names:
import pyobo
chebi_id_to_name = pyobo.get_id_name_mapping("chebi")
assert "fluazifop-P-butyl" == chebi_id_to_name["132964"]
# or more directly
assert "fluazifop-P-butyl" == pyobo.get_name("chebi", "132964")
Get reverse mapping of ChEBI names to identifiers:
import pyobo
chebi_name_to_id = pyobo.get_name_id_mapping("chebi")
assert "132964" == chebi_name_to_id["fluazifop-P-butyl"]
Maybe you live in CURIE world and just want to normalize something like
CHEBI:132964:
import pyobo
assert "fluazifop-P-butyl" == pyobo.get_name_by_curie("CHEBI:132964")
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
from pyobo import Reference
# 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 Reference.from_curie("go:0003700") == pyobo.get_primary_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)
assert "9606" == wikipathways_id_to_species["WP254"]
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
reference = pyobo.ground("chebi", "Fusilade II")
assert reference.prefix == "chebi"
assert reference.identifier == "132964"
assert reference.name == "fluazifop-P-butyl"
# When failure happens...
reference = pyobo.ground("chebi", "Definitely not a real name")
assert reference 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
reference = pyobo.ground(["efo", "go"], "ERAD")
assert reference.prefix == "go"
assert reference.identifier == "0030433"
assert reference.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"
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 pyobo
from pyobo import Reference
# check that go:0008219 ! cell death is an ancestor of go:0006915 ! apoptotic process
assert Reference.from_curie("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 Reference.from_curie("go:0070246") in apopototic_process_descendants
Get the sub-hierarchy below a given node:
import pyobo
from pyobo import Reference
# 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 Reference.from_curie("go:0070246") in apopototic_process_subhierarchy
Get a hierarchy with properties preloaded in the node data dictionaries:
import pyobo
from pyobo import Reference
prop = "http://purl.obolibrary.org/obo/chebi/smiles"
chebi_hierarchy = pyobo.get_hierarchy("chebi", properties=[prop])
assert Reference.from_curie("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 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
