def build_transgenic_lines(self):
triples = []
for ind, tl in self.cre.iterrows():
_id = tl['stock_number'] if tl['stock_number'] else tl['id']
prefix = tl['transgenic_line_source_name']
line_type = tl['transgenic_line_type_name']
if prefix not in ['JAX', 'MMRRC', 'AIBS']:
print('WARNING:', 'unknown prefix')
continue
elif prefix == 'AIBS':
prefix = 'AllenTL'
_class = self.ns[prefix][str(_id)]
triples.append((_class, rdf.type, owl.Class))
triples.append((_class, rdfs.label, rdflib.Literal(tl['name'])))
triples.append((_class, definition, rdflib.Literal(tl['description'])))
triples.append((_class, rdfs.subClassOf, ilxtr.transgenicLine))
triples.append((_class, ilxtr.hasTransgenicType, ilxtr[line_type + 'Line']))
# TODO aspects.ttl?
transgenic_lines = simpleOnt(filename='tasic-transgenic-lines',
path='ttl/generated/',
prefixes=self.prefixes,
triples=triples,
comment='Tasic transgenic lines for cell types',
branch=self.branch)
transgenic_lines._graph.write()
return transgenic_lines
def build_transgenic_lines(self):
"""
init class | "transgenic_line_source_name":"stock_number" a Class
add superClass | rdfs:subClassOf ilxtr:transgenicLine
add *order* | ilxtr:useObjectProperty ilxtr:<order>
add name | rdfs:label "name"
add def | definition: "description"
add transtype | rdfs:hasTransgenicType "transgenic_line_type_name"
"""
triples = []
for cell_specimen in self.neuron_data:
for tl in cell_specimen['donor']['transgenic_lines']:
_id = tl['stock_number'] if tl['stock_number'] else tl['id']
prefix = tl['transgenic_line_source_name']
line_type = tl['transgenic_line_type_name']
if line_type == 'driver' and 'CreERT2' in tl['name']:
line_type = 'inducibleDriver'
if prefix not in ['JAX', 'MMRRC', 'AIBS']:
print(tc.red('WARNING:'), 'unknown prefix', prefix,
json.dumps(tl, indent=4))
continue
elif prefix == 'AIBS':
prefix = 'AllenTL'
_class = self.ns[prefix][str(_id)]
triples.append((_class, rdf.type, owl.Class))
triples.append(
(_class, rdfs.label, rdflib.Literal(tl['name'])))
triples.append(
(_class, definition, rdflib.Literal(tl['description'])))
triples.append((_class, rdfs.subClassOf, ilxtr.transgenicLine))
triples.append((_class, ilxtr.hasTransgenicType,
ilxtr[line_type + 'Line']))
# TODO aspects.ttl?
transgenic_lines = simpleOnt(
filename='allen-transgenic-lines',
local_base=graphBase.local_base,
path='ttl/generated/',
prefixes=self.prefixes,
triples=triples,
comment='Allen transgenic lines for cell types',
branch=self.branch,
calling__file__=__file__,
)
transgenic_lines._graph.write()
rdflib.Literal(1, datatype=rdflib.XSD.nonNegativeInteger)),
blankC(owl.onClass, ilxtr.aspect)),
restG(blankC(owl.onProperty, ilxtr.hasPrimaryAspect_dAdT),
blankC(owl.maxQualifiedCardinality,
rdflib.Literal(1, datatype=rdflib.XSD.nonNegativeInteger)),
blankC(owl.onClass, ilxtr.changeType))))))
)
embed()
"""
methods_core = simpleOnt(
filename=filename,
prefixes=prefixes,
imports=imports,
triples=triples,
comment=comment,
branch=branch,
_repo=_repo,
calling__file__=__file__,
)
methods_core._graph.add_namespace('asp', str(asp))
methods_core._graph.add_namespace(
'ilxtr', str(ilxtr)) # FIXME why is this now showing up...
#methods_core._graph.add_namespace('tech', str(tech))
methods_core._graph.add_namespace('HBP_MEM', OntCuries['HBP_MEM'])
def main():
# TODO aspects.ttl?
collector.write()
'ctb-488+smRabies-HA'
'ctb-555'
'CHEBI:52673'
'ctb-555+smRabies'
'ctb-647'
'CHEBI:137394'
'ctb-647+smRabies-OLLAS'
'phal-647'
'CHEBI:137394'
# amusment regarding dashes... PHA-L -> PHAL
'https://www.ncbi.nlm.nih.gov/pubmed/2391562')
methods_helper = simpleOnt(filename=filename,
prefixes=prefixes,
imports=imports,
triples=triples,
comment=comment,
branch=branch,
_repo=_repo)
def main():
methods_helper._graph.add_namespace('asp', str(asp))
methods_helper._graph.add_namespace(
'ilxtr', str(ilxtr)) # FIXME why is this now showing up...
methods_helper._graph.add_namespace('prot', str(prot))
methods_helper._graph.add_namespace('tech', str(tech))
methods_helper._graph.add_namespace('HBP_MEM', OntCuries['HBP_MEM'])
methods_helper._graph.write(
) # note to self, simpleOnt calls write as well