Ontology managers¶

pronto¶

from pronto import Ontology

cl = Ontology("http://purl.obolibrary.org/obo/cl/cl-simple.obo")

len(cl.terms())

term = cl["CL:0002116"]

term

Term('CL:0002116', name='B220-low CD38-positive unswitched memory B cell')

term.definition

Definition('A B220-low CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-low, CD38-positive, IgD-positive, CD138-negative, and IgG-negative.', xrefs={Xref('GOC:rhs'), Xref('GOC:dsd'), Xref('PMID:20123131'), Xref('GOC:tfm')})

term.is_leaf()

True

term.obsolete

False

Owlready2¶

https://owlready2.readthedocs.io/en/v0.37/onto.html

from owlready2 import get_ontology

* Owlready2 * Warning: optimized Cython parser module 'owlready2_optimized' is not available, defaulting to slower Python implementation

The following cell keeps timing out.

cl = get_ontology("http://purl.obolibrary.org/obo/cl/cl-simple.owl").load()

cl_dict = {i.name: i.label[0] for i in cl.classes()}

cl.search(label="T cell")

cl_dict["CL_0000084"]

x = cl.ontology["CL_0000084"]

x = next(x)