Validate ccf.owl partonomy against Uberon using renci uberongraph endpoint. (secondary checks for overlaps and subClassOf)

uber_check.py

import rdflib
from SPARQLWrapper import SPARQLWrapper, JSON
import time

g = rdflib.Graph()
g.parse('http://purl.org/ccf/latest/ccf.owl')

ccf_po_query = """
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX ccf: <https://purl.org/ccf/latest/ccf.owl#> 
SELECT DISTINCT ?o ?s ?olabel ?slabel
   WHERE { ?s ccf:ccf_part_of ?o . 
           ?o rdfs:label ?olabel .
           ?s rdfs:label ?slabel .
       FILTER(STRSTARTS(STR(?o), "http://purl.obolibrary.org/obo/UBERON_")) 
       FILTER(STRSTARTS(STR(?s), "http://purl.obolibrary.org/obo/UBERON_")) 
    }"""

ccf_po = g.query(ccf_po_query)

sparql = SPARQLWrapper('https://stars-app.renci.org/uberongraph/sparql')
sparql.setReturnFormat(JSON)

ask_uberon_po = """
PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> 
ASK
FROM <http://reasoner.renci.org/ontology>
FROM <http://reasoner.renci.org/redundant>
{ <%s> part_of: <%s> }"""

ask_uberon_overlaps = """
PREFIX overlaps: <http://purl.obolibrary.org/obo/RO_0002131> 
ASK
FROM <http://reasoner.renci.org/ontology>
FROM <http://reasoner.renci.org/redundant>
 { <%s> overlaps: <%s> }"""

ask_uberon_subclassof = """
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
ASK FROM <http://reasoner.renci.org/ontology/closure>
    { <%s> rdfs:subClassOf <%s> }"""

def ask_uberon(r, q):
    q = ask_uberon_po % (r['s'], r['o'])
    sparql.setQuery(q)
    results = sparql.query().convert()
    return results['boolean']


passing = len(ccf_po)
for r in ccf_po:
    fillers = (r['slabel'], r['s'], r['olabel'], r['o'])
    if not ask_uberon(r, ask_uberon_po):
        passing -= 1
        if ask_uberon(r, ask_uberon_subclassof):
            print(ask_uberon_subclassof)
            print('Uberon supports (%s)[%s] subClassOf (%s)[%s], not part_of' % fillers)
        elif ask_uberon(r, ask_uberon_overlaps):
            print('Uberon supports (%s)[%s] overlaps (%s)[%s], but not part_of' % fillers)
        else:
            print('Uberon does not (currently) support (%s)[%s] part_of (%s)[%s].' % fillers)
    time.sleep(0.02) # Seems the server doesn't like  to be hit too often

print("%d ccf_part_of relationship validated by Uberon" % passing)

Current output:

Uberon does not (currently) support ureter part_of kidney.
Uberon does not (currently) support rectum part_of pelvic cavity.
Uberon does not (currently) support ileocecal valve part_of caecum.
Uberon does not (currently) support heart right ventricle part_of right cardiac chamber.
Uberon does not (currently) support heart part_of chest cavity.
Uberon does not (currently) support white pulp of spleen part_of spleen pulp.
Uberon does not (currently) support spleen primary B follicle part_of spleen lymphoid follicle.
Uberon does not (currently) support colon part_of abdominal cavity.
Uberon does not (currently) support renal tubule part_of nephron.
Uberon does not (currently) support small intestine part_of abdominal cavity.
Uberon does not (currently) support red pulp of spleen part_of spleen pulp.
Uberon does not (currently) support minor calyx part_of kidney calyx.
Uberon does not (currently) support heart left ventricle part_of left cardiac chamber.
Uberon does not (currently) support right cardiac chamber part_of cardiac chamber.
Uberon does not (currently) support right kidney part_of kidney.
Uberon does not (currently) support kidney part_of abdominal cavity.
Uberon does not (currently) support left kidney part_of kidney.
Uberon does not (currently) support spleen part_of abdominal cavity.
Uberon does not (currently) support major calyx part_of kidney calyx.
Uberon does not (currently) support left cardiac chamber part_of cardiac chamber.
Uberon does not (currently) support outer cortex of kidney part_of cortex of kidney.
Uberon does not (currently) support right cardiac atrium part_of right cardiac chamber.
Uberon does not (currently) support collecting duct of renal tubule part_of renal tubule.
Uberon does not (currently) support spleen secondary B follicle part_of spleen lymphoid follicle.
Uberon does not (currently) support left cardiac atrium part_of left cardiac chamber.

54 ccf_part_of relationship validated by Uberon