Handling and writing OBO
Project description
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.
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'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 NoneGet 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'Get properties, like SMILES. The semantics of these are defined on an OBO-OBO basis.
import pyobo
# I dont 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'Installation 
PyOBO can be installed from PyPI with:
$ pip install pyoboIt can be installed in development mode from GitHub with:
$ git clone https://github.com/pyobo/pyobo.git
$ cd pyobo
$ pip install -e .Release history Release notifications | RSS feed
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