def create_class(s):
factory.getOWLClass(IRI.create(s))
def add_anno(resource, prop, cont):
anno = factory.getOWLAnnotation(factory.getOWLAnnotationProperty(prop.getIRI()),
factory.getOWLLiteral(cont))
axiom = factory.getOWLAnnotationAssertionAxiom(resource.getIRI(), anno)
manager.addAxiom(ontology, axiom)
genericProteinNames = dict()
proteinCounter = 0
for tfile in os.listdir('/home/mencella/ttlfiles'):
print tfile
rdfModel = ModelFactory.createDefaultModel()
rdfModel.read(FileReader(tfile), "http://foobar#", "TURTLE")
p = rdfModel.createProperty(up + "mnemonic")
label = rdfModel.listStatements(0, p, 0)[0].getObject().toString()
iri = rdfModel.listStatements(0, RDF.type, rdfModel.createResource(up + "Protein"))[0].getSubject().toString()
cl = create_class(iri)
add_anno(cl, OWLRDFVocabulary.RDFS_LABEL, label)
cls = create_class(iri + "_all")
add_anno(cls, OWLRDFVocabulary.RDFS_LABEL, "All %s in the universe" % label)
manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(cl, factory.getOWLObjectSomeValuesFrom(create_relation("member-of"), cls)))
genericNames = []
first = True
for stmt1 in rdfModel.listStatements(0, RDF.type, rdfModel.createResource(up+"Structured_Name")):
def readFiles(i, q):
while True:
tfile = q.get()
size = q._qsize()
if size % 1000 == 0:
print "%d entries left in queue. " % size, time.strftime("%c")
rdfModel = ModelFactory.createDefaultModel()
try:
rdfModel.read(FileReader(input_directory + tfile), "http://foobar#", "TURTLE")
except:
print "Error with file: ", tfile
q.task_done()
#traceback.print_exc()
continue
iri_iter = rdfModel.listStatements(None, RDF.type, rdfModel.createResource(up + "Protein"))
while iri_iter.hasNext(): # iterate over all Protein iri's in file
iris = iri_iter.nextStatement().getSubject()
iri = iris.toString()
label = rdfModel.listStatements(iris, rdfModel.createProperty(up + "mnemonic"), None).nextStatement().getObject().toString()
# subclass
cl = create_class(iri)
add_anno(cl, OWLRDFVocabulary.RDFS_LABEL, label)
cls = create_class(iri + "_all")
add_anno(cls, OWLRDFVocabulary.RDFS_LABEL, "All %s in the universe" % label)
manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(cl, factory.getOWLObjectSomeValuesFrom(create_relation("member-of"), cls)))
# generic names
genericNames = []
first = True
for stmt0 in rdfModel.listStatements(iris, rdfModel.createProperty(up + "submittedName"), None):
name = stmt0.getObject()
for stmt1 in rdfModel.listStatements(name, RDF.type, rdfModel.createResource(up + "Structured_Name")):
for stmt2 in rdfModel.listStatements(stmt1.getSubject(), rdfModel.createProperty(up + "fullName"), None):
if first:
first = False
firstName = stmt2.getObject().toString()
genericNames.append(stmt2.getObject().toString())
if firstName not in genericProteinNames.keys():
ncl = create_class(onturi+"GENERICPROTEIN_%s" % proteinCounter)
ncla = create_class(onturi+"GENERICPROTEIN_%s_all" % proteinCounter)
proteinCounter += 1
for name in genericNames:
universe = "All %s in the universe" % name
add_anno(ncl, OWLRDFVocabulary.RDFS_LABEL, name) # add label
add_anno(ncla, OWLRDFVocabulary.RDFS_LABEL, universe) # add label
genericProteinNames[name] = ncl
genericProteinNames[universe] = ncla
ncl = genericProteinNames[firstName]
ncla = genericProteinNames["All %s in the universe" % firstName]
manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(cl, ncl))
manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(cls, ncla))
# isoforms
isoforms = collections.OrderedDict()
for stmt in rdfModel.listStatements(iris, rdfModel.createProperty(up + "sequence"), None):
isoforms[stmt.getObject().toString()] = 1
for iso in isoforms.keys():
icl = create_class(iso)
add_anno(icl, OWLRDFVocabulary.RDFS_LABEL, "Isoform of %s" % label) # add label
manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(icl, factory.getOWLObjectSomeValuesFrom(create_relation("isoform-of"), cl)))
manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(icl, cl))
# gofunctions
gofunctions = collections.OrderedDict()
for stmt in rdfModel.listStatements(rdfModel.createResource(iri), rdfModel.createProperty(up+"classifiedWith"), None):
if(stmt.getObject().toString().startswith("http://purl.obolibrary.org/obo/")):
gofunctions[stmt.getObject().toString()] = 1
for fun in gofunctions.keys():
# Decide whether this is a function/process or location
if create_class(fun) in loc_nodeset: # location
relation = "located-in"
else: # function/process
relation = "participates-in"
manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(cls, factory.getOWLObjectSomeValuesFrom(create_relation("has-member"),
factory.getOWLObjectSomeValuesFrom(create_relation(relation), create_class(fun)))))
organism = rdfModel.listStatements(rdfModel.createResource(iri), rdfModel.createProperty(up+"organism"), None).nextStatement().getObject().toString()
prefix = "http://purl.obolibrary.org/obo/NCBITaxon_"
slash = organism.rfind('/')
organism = prefix + organism[slash+1:]
manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(cl, factory.getOWLObjectSomeValuesFrom(create_relation("created-in-organism"), create_class(organism))))
#signals to queue job is done
q.task_done()
