def _add_therapy_drug_association(self, drug_id, disease_id, therapy_status_id):
"""
Create an association linking a drug and disease with
RO:0002606 (substance_that_treats) and any supporting information
such as FDA approval and source (not implemented)
:param drug_id: Id as curie of the drug
:param disease_id: Id as curie of the disease
:param therapy_status: (Optional) String label of therapy approval status
:return: None
"""
gu = GraphUtils(curie_map.get())
# Placeholder relationship, note this does not exist in RO
relationship_id = "RO:has_approval_status"
gu.addTriple(self.graph, drug_id, gu.object_properties['substance_that_treats'], disease_id)
# Make association
drug_disease_annot = self.make_cgd_id("assoc{0}{1}".format(drug_id, disease_id))
therapy_disease_assoc = Assoc(self.name)
therapy_disease_assoc.set_subject(drug_id)
therapy_disease_assoc.set_relationship(gu.object_properties['substance_that_treats'])
therapy_disease_assoc.set_object(disease_id)
therapy_disease_assoc.set_association_id(drug_disease_annot)
therapy_disease_assoc.add_association_to_graph(self.graph)
gu.addTriple(self.graph, drug_disease_annot, relationship_id, therapy_status_id)
def _add_component_pathway_association(self, gene_curie, pathway_curie,
pathway_label, eco_curie):
pathway = Pathway(self.graph)
pathway.addPathway(pathway_curie, pathway_label)
pathway.addComponentToPathway(gene_curie, pathway_curie)
association = Assoc(self.graph, self.name)
association.sub = gene_curie
association.rel = self.globaltt['involved in']
association.obj = pathway_curie
association.set_association_id()
association.add_evidence(eco_curie)
association.add_association_to_graph()
def _add_component_pathway_association(
self, eco_map, component, component_prefix, pathway_id,
pathway_prefix, pathway_label, go_ecode):
pathway = Pathway(self.graph)
pathway_curie = "{}:{}".format(pathway_prefix, pathway_id)
gene_curie = "{}:{}".format(component_prefix, component.strip())
eco_curie = eco_map[go_ecode]
pathway.addPathway(pathway_curie, pathway_label)
pathway.addComponentToPathway(gene_curie, pathway_curie)
association = Assoc(self.graph, self.name)
association.sub = gene_curie
association.rel = pathway.object_properties['involved_in']
association.obj = pathway_curie
association.set_association_id()
association.add_evidence(eco_curie)
association.add_association_to_graph()
return
def _add_component_pathway_association(
self, eco_map, component, component_prefix, pathway_id,
pathway_prefix, pathway_label, go_ecode):
pathway = Pathway(self.graph)
pathway_curie = "{}:{}".format(pathway_prefix, pathway_id)
gene_curie = "{}:{}".format(component_prefix, component.strip())
eco_curie = eco_map[go_ecode]
pathway.addPathway(pathway_curie, pathway_label)
pathway.addComponentToPathway(gene_curie, pathway_curie)
association = Assoc(self.graph, self.name)
association.sub = gene_curie
association.rel = self.globaltt['involved in']
association.obj = pathway_curie
association.set_association_id()
association.add_evidence(eco_curie)
association.add_association_to_graph()
return
def make_association(self, record):
"""
contstruct the association
:param record:
:return: modeled association of genotype to mammalian phenotype
"""
# prep record
# remove description and mapp Experiment Type to apo term
experiment_type = record['Experiment Type'].split('(')[0]
experiment_type = experiment_type.split(',')
record['experiment_type'] = list()
for exp_type in experiment_type:
exp_type = exp_type.lstrip().rstrip()
record['experiment_type'].append(
{
'id': self.apo_term_id[exp_type],
'term': exp_type,
})
sgd_phenotype = record['Phenotype']
pheno_obj = {
'entity': {
'term': None,
'apo_id': None
},
'quality': {
'term': None,
'apo_id': None
},
'has_quality': False # False = phenotype was descriptive and don't bother looking for a quality
}
phenotype = record['Phenotype']
if ':' in phenotype:
pheno_obj['has_quality'] = True
ent_qual = sgd_phenotype.split(': ')
entity = ent_qual[0]
quality = ent_qual[1]
pheno_obj['entity']['term'] = entity
pheno_obj['entity']['apo_id'] = self.apo_term_id[entity]
pheno_obj['quality']['term'] = quality
pheno_obj['quality']['apo_id'] = self.apo_term_id[quality]
else:
pheno_obj['entity']['term'] = phenotype
pheno_obj['entity']['apo_id'] = self.apo_term_id[phenotype]
record['pheno_obj'] = pheno_obj
# begin modeling
model = Model(self.graph)
# define the triple
gene = 'SGD:{}'.format(record['SGDID'])
relation = Model.object_properties['has_phenotype'] # has phenotype
if record['pheno_obj']['has_quality']:
pheno_label = '{0}:{1}'.format(
record['pheno_obj']['entity']['term'],
record['pheno_obj']['quality']['term'])
pheno_id = 'MONARCH:{0}{1}'.format(
record['pheno_obj']['entity']['apo_id'].replace(':', '_'),
record['pheno_obj']['quality']['apo_id'].replace(':', '_')
)
g2p_assoc = Assoc(self.graph, self.name, sub=gene, obj=pheno_id, pred=relation)
else:
pheno_label = record['pheno_obj']['entity']['term']
pheno_id = record['pheno_obj']['entity']['apo_id']
g2p_assoc = Assoc(self.graph, self.name, sub=gene, obj=pheno_id, pred=relation)
assoc_id = g2p_assoc.make_association_id(definedby='yeastgenome.org', subject=gene, predicate=relation,
object=pheno_id)
g2p_assoc.set_association_id(assoc_id=assoc_id)
# add to graph to mint assoc id
g2p_assoc.add_association_to_graph()
model.addLabel(subject_id=gene, label=record['Gene Name'])
# add the association triple
model.addTriple(subject_id=gene, predicate_id=relation, obj=pheno_id)
# make pheno subclass of UPHENO:0001001
model.addTriple(subject_id=pheno_id, predicate_id=Model.object_properties['subclass_of'], obj='UPHENO:0001001')
# label nodes
# pheno label
model.addLabel(subject_id=pheno_id, label=pheno_label)
g2p_assoc.description = self._make_description(record)
# add the references
references = record['Reference']
references = references.replace(' ', '')
references = references.split('|')
# created RGDRef prefix in curie map to route to proper reference URL in RGD
if len(references) > 0:
# make first ref in list the source
g2p_assoc.add_source(identifier=references[0])
ref_model = Reference(
self.graph, references[0],
Reference.ref_types['publication']
)
ref_model.addRefToGraph()
if len(references) > 1:
# create equivalent source for any other refs in list
for ref in references[1:]:
model.addSameIndividual(sub=references[0], obj=ref)
# add experiment type as evidence
for exp_type in record['experiment_type']:
g2p_assoc.add_evidence(exp_type['id'])
model.addLabel(subject_id=exp_type['id'], label=exp_type['term'])
try:
g2p_assoc.add_association_to_graph()
except Exception as e:
print(e)
return
def make_association(self, record):
"""
contstruct the association
:param record:
:return: modeled association of genotype to mammalian??? phenotype
"""
# prep record
# remove description and mapp Experiment Type to apo term
experiment_type = record['Experiment Type'].split('(')[0]
experiment_type = experiment_type.split(',')
record['experiment_type'] = list()
for exp_type in experiment_type:
exp_type = exp_type.lstrip().rstrip()
record['experiment_type'].append({
'id': self.apo_term_id[exp_type],
'term': exp_type,
})
sgd_phenotype = record['Phenotype']
pheno_obj = {
'entity': {
'term': None,
'apo_id': None
},
'quality': {
'term': None,
'apo_id': None
},
'has_quality':
False # descriptive and don't bother looking for a quality
}
phenotype = record['Phenotype']
if ':' in phenotype:
pheno_obj['has_quality'] = True
ent_qual = sgd_phenotype.split(': ')
entity = ent_qual[0]
quality = ent_qual[1]
pheno_obj['entity']['term'] = entity
pheno_obj['entity']['apo_id'] = self.apo_term_id[entity]
pheno_obj['quality']['term'] = quality
pheno_obj['quality']['apo_id'] = self.apo_term_id[quality]
else:
pheno_obj['entity']['term'] = phenotype
pheno_obj['entity']['apo_id'] = self.apo_term_id[phenotype]
record['pheno_obj'] = pheno_obj
# begin modeling
model = Model(self.graph)
# define the triple
gene = 'SGD:{}'.format(record['SGDID'])
relation = self.globaltt['has phenotype']
if record['pheno_obj']['has_quality']:
pheno_label = '{0}:{1}'.format(
record['pheno_obj']['entity']['term'],
record['pheno_obj']['quality']['term'])
pheno_id = 'MONARCH:{0}{1}'.format(
record['pheno_obj']['entity']['apo_id'].replace(':', '_'),
record['pheno_obj']['quality']['apo_id'].replace(':', '_'))
g2p_assoc = Assoc(self.graph,
self.name,
sub=gene,
obj=pheno_id,
pred=relation)
else:
pheno_label = record['pheno_obj']['entity']['term']
pheno_id = record['pheno_obj']['entity']['apo_id']
g2p_assoc = Assoc(self.graph,
self.name,
sub=gene,
obj=pheno_id,
pred=relation)
assoc_id = g2p_assoc.make_association_id('yeastgenome.org', gene,
relation, pheno_id)
g2p_assoc.set_association_id(assoc_id=assoc_id)
# add to graph to mint assoc id
g2p_assoc.add_association_to_graph()
model.addLabel(subject_id=gene, label=record['Gene Name'])
# add the association triple
model.addTriple(subject_id=gene, predicate_id=relation, obj=pheno_id)
model.addTriple(subject_id=pheno_id,
predicate_id=self.globaltt['subclass_of'],
obj=self.globaltt['Phenotype'])
# label nodes
# pheno label
model.addLabel(subject_id=pheno_id, label=pheno_label)
g2p_assoc.description = self._make_description(record)
# add the references
references = record['Reference']
references = references.replace(' ', '')
references = references.split('|')
# created Ref prefix in curie map to route to proper reference URL in SGD
if len(references) > 0:
# make first ref in list the source
g2p_assoc.add_source(identifier=references[0])
ref_model = Reference(self.graph, references[0],
self.globaltt['publication'])
ref_model.addRefToGraph()
if len(references) > 1:
# create equivalent source for any other refs in list
for ref in references[1:]:
model.addSameIndividual(sub=references[0], obj=ref)
# add experiment type as evidence
for exp_type in record['experiment_type']:
g2p_assoc.add_evidence(exp_type['id'])
model.addLabel(subject_id=exp_type['id'], label=exp_type['term'])
try:
g2p_assoc.add_association_to_graph()
except Exception as e:
print(e)
return
def make_association(self, record):
"""
contstruct the association
:param record:
:return: modeled association of genotype to mammalian phenotype
"""
# prep record
# remove description and mapp Experiment Type to apo term
experiment_type = record['Experiment Type'].split('(')[0]
experiment_type = experiment_type.split(',')
record['experiment_type'] = list()
for exp_type in experiment_type:
exp_type = exp_type.lstrip().rstrip()
record['experiment_type'].append({
'id': self.apo_term_id[exp_type],
'term': exp_type,
})
sgd_phenotype = record['Phenotype']
pheno_obj = {
'entity': {
'term': None,
'apo_id': None
},
'quality': {
'term': None,
'apo_id': None
},
'has_quality':
False # False = phenotype was descriptive and don't bother looking for a quality
}
phenotype = record['Phenotype']
if ':' in phenotype:
pheno_obj['has_quality'] = True
ent_qual = sgd_phenotype.split(': ')
entity = ent_qual[0]
quality = ent_qual[1]
pheno_obj['entity']['term'] = entity
pheno_obj['entity']['apo_id'] = self.apo_term_id[entity]
pheno_obj['quality']['term'] = quality
pheno_obj['quality']['apo_id'] = self.apo_term_id[quality]
else:
pheno_obj['entity']['term'] = phenotype
pheno_obj['entity']['apo_id'] = self.apo_term_id[phenotype]
record['pheno_obj'] = pheno_obj
# begin modeling
model = Model(self.graph)
# define the triple
gene = 'SGD:{}'.format(record['SGDID'])
relation = Model.object_properties['has_phenotype'] # has phenotype
if record['pheno_obj']['has_quality']:
pheno_label = '{0}:{1}'.format(
record['pheno_obj']['entity']['term'],
record['pheno_obj']['quality']['term'])
pheno_id = 'MONARCH:{0}{1}'.format(
record['pheno_obj']['entity']['apo_id'].replace(':', '_'),
record['pheno_obj']['quality']['apo_id'].replace(':', '_'))
g2p_assoc = Assoc(self.graph,
self.name,
sub=gene,
obj=pheno_id,
pred=relation)
else:
pheno_label = record['pheno_obj']['entity']['term']
pheno_id = record['pheno_obj']['entity']['apo_id']
g2p_assoc = Assoc(self.graph,
self.name,
sub=gene,
obj=pheno_id,
pred=relation)
assoc_id = g2p_assoc.make_association_id(
definedby='yeastgenome.org',
subject=gene,
predicate=relation,
object=pheno_id)
g2p_assoc.set_association_id(assoc_id=assoc_id)
# add to graph to mint assoc id
g2p_assoc.add_association_to_graph()
model.addLabel(subject_id=gene, label=record['Gene Name'])
# add the association triple
model.addTriple(subject_id=gene, predicate_id=relation, obj=pheno_id)
# make pheno subclass of UPHENO:0001001
model.addTriple(subject_id=pheno_id,
predicate_id=Model.object_properties['subclass_of'],
obj='UPHENO:0001001')
# label nodes
# pheno label
model.addLabel(subject_id=pheno_id, label=pheno_label)
# add the descripiton: all the unmodeled data in a '|' delimited list
description = [
'genomic_background: {}'.format(record['Strain Background']),
'allele: {}'.format(record['Allele']),
'chemical: {}'.format(record['Chemical']),
'condition: {}'.format(record['Condition']),
'details: {}'.format(record['Details']),
'feature_name: {}'.format(record['Feature Name']),
'gene_name: {}'.format(record['Gene Name']),
'mutant_type: {}'.format(record['Mutant Type']),
'reporter: {}'.format(record['Reporter']),
]
g2p_assoc.description = " | ".join(description)
# add the references
references = record['Reference']
references = references.replace(' ', '')
references = references.split('|')
# created RGDRef prefix in curie map to route to proper reference URL in RGD
if len(references) > 0:
# make first ref in list the source
g2p_assoc.add_source(identifier=references[0])
ref_model = Reference(self.graph, references[0],
Reference.ref_types['publication'])
ref_model.addRefToGraph()
if len(references) > 1:
# create equivalent source for any other refs in list
for ref in references[1:]:
model.addSameIndividual(sub=references[0], obj=ref)
# add experiment type as evidence
for exp_type in record['experiment_type']:
g2p_assoc.add_evidence(exp_type['id'])
model.addLabel(subject_id=exp_type['id'], label=exp_type['term'])
try:
g2p_assoc.add_association_to_graph()
except Exception as e:
print(e)
return
