def convert(value):
if value == 'Projection neuron':
e = ilxtr.ProjectionPhenotype
else:
e = value
id = OntId(e.strip()) if ':' in e else e.strip()
if id.prefix == 'ILX':
t = id.asInstrumented()
id = t.asPreferred()
return id
def things(self):
def process(k, v):
if ',' in v:
return [rdflib.Literal(_.strip()) for _ in v.split(',')]
elif k == 'synonyms':
return [rdflib.Literal(v)]
else:
return rdflib.Literal(v)
lexical = 'synonyms', 'molecule', 'comments', 'hiddenlabel'
for row in self.byCol.rows:
if not any(row):
continue
idents = {k:OntTerm(v) for k, v in row._asdict().items() if v and k not in lexical}
lex = {k:process(k, v) for k, v in row._asdict().items() if v and k in lexical}
members = set(idents.values())
mol = lex['molecule']
hl = lex['hiddenlabel'] if 'hiddenlabel' in lex else mol
label = f'{mol} (indicator)'
id = OntId('TEMPIND:' + mol)
thing = {'id': id,
'label': rdflib.Literal(label),
'hiddenLabel': hl,
'synonyms': lex['synonyms'],
'members': members,}
yield thing
def convert(value):
if value == 'Projection neuron':
e = ilxtr.ProjectionPhenotype
else:
e = value
return OntId(e.strip()) if ':' in e else e.strip()
def triples_data(self):
s = ilxtr.PhenotypeIndicator
yield s, a, owl.Class
yield s, rdfs.label, rdflib.Literal('phenotype indicator')
for thing in self.things:
yield from self.indicator(thing)
# FIXME rework the sheet and move this stuff to it
# or start editing the indicators file directly
# making use of OntGraph diff utilities
sst = OntId('TEMPIND:Sst').u
yield sst, a, owl.Class
yield sst, rdfs.subClassOf, ilxtr.PhenotypeIndicator
yield sst, rdfs.label, rdflib.Literal('somatostatin (indicator)')
yield sst, skos.hiddenLabel, rdflib.Literal('Sst')
yield sst, NIFRID.synonym, rdflib.Literal('Sst')
yield sst, NIFRID.synonym, rdflib.Literal('SOM')
yield sst, NIFRID.synonym, rdflib.Literal('somatostatin')
sst_members = (OntId('ilxtr:SST-flp'),
OntId('PTHR:10558'),
OntId('NIFEXT:5116'),
OntId('NCBIGene:20604'),
OntId('PR:000015665'),
OntId('JAX:013044'),
OntId('JAX:028579'),)
for i in sst_members:
yield i.u, rdfs.subClassOf, sst
# pv fix
pheno = rdflib.Namespace(ilxtr[''] + 'Phenotype/')
pv = OntId('TEMPIND:Pvalb').u
yield pv, rdfs.label, rdflib.Literal('parvalbumin (indicator)')
yield pv, skos.hiddenLabel, rdflib.Literal('PV')
yield pv, NIFRID.synonym, rdflib.Literal('PV')
yield pv, NIFRID.synonym, rdflib.Literal('Pvalb')
yield pv, NIFRID.synonym, rdflib.Literal('parvalbumin')
#yield pv, ilxtr.indicatesDisplayOfPhenotype, pheno.parvalbumin # as restriction ...
yield from ((pv, rdf.type, owl.Class),
(pv, rdfs.subClassOf, ilxtr.PhenotypeIndicator),)
pv_members = (OntId('JAX:008069'),
OntId('JAX:021189'),
OntId('JAX:021190'),
OntId('JAX:022730'),
OntId('JAX:017320'),
ilxtr.Pvalb,
OntId('PTHR:11653'),
ilxtr['PV-cre'],
OntId('PR:000013502'),
OntId('NCBIGene:19293'),
OntId('NIFEXT:6'),)
for i in pv_members:
s = i.u if isinstance(i, OntId) else i
yield s, rdfs.subClassOf, pv