def _get_mp_classes(self, mp_uri):
#self._logger.debug("_get_mp_classes")
#load the onotology
self.mp_ontology = OntologyClassReader()
opentargets_ontologyutils.mp.load_mammalian_phenotype_ontology(self.mp_ontology, mp_uri)
#TODO this is a moderately hideous bit of pointless munging, but I don't have time fix it now!
for mp_id,label in list(self.mp_ontology.current_classes.items()):
mp_class = {}
mp_class["label"] = label
if mp_id not in self.mp_ontology.classes_paths:
self._logger.warning("cannot find paths for "+mp_id)
continue
mp_class["path"] = self.mp_ontology.classes_paths[mp_id]['all']
mp_class["path_codes"] = self.mp_ontology.classes_paths[mp_id]['ids']
mp_id_key = mp_id.split("/")[-1].replace(":", "_")
self.mps[mp_id_key] = mp_class
self.mp_labels[mp_class["label"]] = mp_id
self.mp_to_label[mp_id] = mp_class["label"]
paths = []
for path in mp_class["path"]:
item = path[0]
paths.append(item)
self.top_levels[mp_id] = paths
def _process_ontology_data(self):
self.disease_ontology = OntologyClassReader()
opentargets_ontologyutils.efo.load_open_targets_disease_ontology(
self.disease_ontology, self.efo_uri)
'''
Get all phenotypes
'''
#becuse of opentargets_ontologyutils for legacy iterates over key,uri pairs
disease_phenotype_uris_counter = enumerate(self.disease_phenotype_uris)
utils = DiseaseUtils()
disease_phenotypes = utils.get_disease_phenotypes(
self.disease_ontology, self.hpo_uri, self.mp_uri,
disease_phenotype_uris_counter)
for uri, label in self.disease_ontology.current_classes.items():
properties = self.disease_ontology.parse_properties(URIRef(uri))
#create a text block definition/description by joining others together
definition = ''
if 'http://purl.obolibrary.org/obo/IAO_0000115' in properties:
definition = ". ".join(
properties['http://purl.obolibrary.org/obo/IAO_0000115'])
synonyms = []
if 'http://www.ebi.ac.uk/efo/alternative_term' in properties:
synonyms = properties[
'http://www.ebi.ac.uk/efo/alternative_term']
phenotypes = []
if uri in disease_phenotypes:
phenotypes = disease_phenotypes[uri]['phenotypes']
therapeutic_labels = [
item[0]
for item in self.disease_ontology.classes_paths[uri]['labels']
]
therapeutic_labels = self._remove_duplicates(therapeutic_labels)
efo = EFO(
code=uri,
label=label,
synonyms=synonyms,
phenotypes=phenotypes,
path=self.disease_ontology.classes_paths[uri]['all'],
path_codes=self.disease_ontology.classes_paths[uri]['ids'],
path_labels=self.disease_ontology.classes_paths[uri]['labels'],
therapeutic_labels=therapeutic_labels,
definition=definition)
id = self.disease_ontology.classes_paths[uri]['ids'][0][-1]
if uri in self.disease_ontology.children:
efo.children = self.disease_ontology.children[uri]
self.efos[id] = efo
def __init__(self, es_hosts, es_index, es_mappings, es_settings, eco_uri,
so_uri, workers_write, queue_write):
self.es_hosts = es_hosts
self.es_index = es_index
self.es_mappings = es_mappings
self.es_settings = es_settings
self.eco_uri = eco_uri
self.so_uri = so_uri
self.workers_write = workers_write
self.queue_write = queue_write
self.ecos = OrderedDict()
self.evidence_ontology = OntologyClassReader()
def _process_ontology_data(self):
self.disease_ontology = OntologyClassReader()
opentargets_ontologyutils.efo.load_open_targets_disease_ontology(self.disease_ontology, self.efo_uri)
'''
Get all phenotypes
'''
#becuse of opentargets_ontologyutils for legacy iterates over key,uri pairs
disease_phenotype_uris_counter = enumerate(self.disease_phenotype_uris)
utils = DiseaseUtils()
disease_phenotypes = utils.get_disease_phenotypes(self.disease_ontology, self.hpo_uri, self.mp_uri, disease_phenotype_uris_counter)
#for uri,label in self.disease_ontology.current_classes.items():
for uri in self.disease_ontology.classes_paths:
#get the short code form of the uri
classes_path = self.disease_ontology.classes_paths[uri]
id = classes_path['ids'][0][-1]
label = classes_path['labels'][0][-1]
if uri != classes_path["all"][0][-1]["uri"]:
raise RuntimeError('mismatch between uri and classes_path["all"][0][-1]["uri"] %s %s' % (uri, classes_path["all"][0][-1]["uri"]))
properties = self.disease_ontology.parse_properties(URIRef(uri))
#create a text block definition/description by joining others together
definition = ''
if 'http://purl.obolibrary.org/obo/IAO_0000115' in properties:
definition = ". ".join(properties['http://purl.obolibrary.org/obo/IAO_0000115'])
#build a set of all the relevant synonyms
synonyms = set()
#exact synonyms
if 'http://www.geneontology.org/formats/oboInOwl#hasExactSynonym' in properties:
synonyms.update(properties['http://www.geneontology.org/formats/oboInOwl#hasExactSynonym'])
#related synonyms (partially overlapping)
if 'http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym' in properties:
synonyms.update(properties['http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym'])
#generic synoynms
if 'http://www.geneontology.org/formats/oboInOwl#hasSynonym' in properties:
synonyms.update(properties['http://www.geneontology.org/formats/oboInOwl#hasSynonym'])
#narrow synonyms
if 'http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym' in properties:
synonyms.update(properties['http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym'])
#could have http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym, but that is better captured by parent term
phenotypes = []
if uri in disease_phenotypes:
phenotypes = disease_phenotypes[uri]['phenotypes']
if uri not in self.disease_ontology.classes_paths:
self.logger.warning("Unable to find %s", uri)
continue
therapeutic_labels = self.disease_ontology.therapeutic_labels[uri]
therapeutic_uris = self.disease_ontology.therapeutic_uris[uri]
therapeutic_codes = [self.disease_ontology.classes_paths[ta_uri]['ids'][0][-1] for ta_uri in therapeutic_uris]
efo = EFO(code=uri,
label=label,
synonyms=synonyms,
phenotypes=phenotypes,
path=classes_path['all'],
path_codes=classes_path['ids'],
path_labels=classes_path['labels'],
therapeutic_labels=therapeutic_labels,
therapeutic_codes=therapeutic_codes,
definition=definition
)
if uri in self.disease_ontology.children:
efo.children = self.disease_ontology.children[uri]
#logger.debug(str(classes_path['ids']))
self.logger.debug("done %s %s %s", id, uri, label)
if id in self.efos:
self.logger.warning("duplicate %s", id)
continue
self.efos[id] = efo
def __init__(self, loader, eco_uri, so_uri):
self.loader = loader
self.ecos = OrderedDict()
self.evidence_ontology = OntologyClassReader()
self.eco_uri = eco_uri
self.so_uri = so_uri