def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(graph_type, are_bnodes_skolemized, 'ctd')
self.dataset = Dataset(
'ctd', 'CTD', 'http://ctdbase.org', None,
'http://ctdbase.org/about/legal.jsp')
if 'test_ids' not in config.get_config() \
or 'gene' not in config.get_config()['test_ids']:
logger.warning("not configured with gene test ids.")
self.test_geneids = []
else:
self.test_geneids = config.get_config()['test_ids']['gene']
if 'test_ids' not in config.get_config() \
or 'disease' not in config.get_config()['test_ids']:
logger.warning("not configured with disease test ids.")
self.test_diseaseids = []
else:
self.test_diseaseids = config.get_config()['test_ids']['disease']
self.g = self.graph
self.geno = Genotype(self.graph)
self.pathway = Pathway(self.graph)
return
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(
graph_type,
are_bnodes_skolemized,
'ctd',
ingest_title='Comparative Toxicogenomics Database',
ingest_url='http://ctdbase.org',
license_url=None,
data_rights='http://ctdbase.org/about/legal.jsp'
# file_handle=None
)
if 'gene' not in self.all_test_ids:
LOG.warning("not configured with gene test ids.")
self.test_geneids = []
else:
self.test_geneids = self.all_test_ids['gene']
if 'disease' not in self.all_test_ids:
LOG.warning("not configured with disease test ids.")
self.test_diseaseids = []
else:
self.test_diseaseids = self.all_test_ids['disease']
self.geno = Genotype(self.graph)
self.pathway = Pathway(self.graph)
return
def _process_pathway_ko(self, limit):
"""
This adds the kegg orthologous group (gene) to the canonical pathway.
:param limit:
:return:
"""
LOG.info("Processing KEGG pathways to kegg ortholog classes")
if self.test_mode:
graph = self.testgraph
else:
graph = self.graph
line_counter = 0
raw = '/'.join((self.rawdir, self.files['pathway_ko']['file']))
with open(raw, 'r', encoding="iso-8859-1") as csvfile:
filereader = csv.reader(csvfile, delimiter='\t', quotechar='\"')
for row in filereader:
line_counter += 1
(ko_id, pathway_id) = row
if self.test_mode and pathway_id not in self.test_ids['pathway']:
continue
pathway_id = 'KEGG-' + pathway_id
ko_id = 'KEGG-' + ko_id
p = Pathway(graph)
p.addGeneToPathway(ko_id, pathway_id)
if not self.test_mode and limit is not None and line_counter > limit:
break
return
def parse(self, limit=None):
"""
Override Source.parse()
Parses version and interaction information from CTD
Args:
:param limit (int, optional) limit the number of rows processed
Returns:
:return None
"""
if limit is not None:
LOG.info("Only parsing first %d rows", limit)
LOG.info("Parsing files...")
if self.test_only:
self.test_mode = True
self.geno = Genotype(self.graph)
self.pathway = Pathway(self.graph)
src_key = 'chemical_disease_associations'
self._parse_ctd_file(limit, src_key)
# self._parse_ctd_file(limit, 'gene_pathway')
# self._parse_ctd_file(limit, 'gene_disease')
src_key = 'publications'
file_path = '/'.join((self.rawdir, self.api_fetch[src_key]['file']))
if os.path.exists(file_path) is True:
self._parse_curated_chem_disease(file_path, limit)
else:
LOG.error('Batch Query file "%s" does not exist', file_path)
LOG.info("Done parsing files.")
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 _process_pathways(self, limit=None):
"""
This method adds the KEGG pathway IDs.
These are the canonical pathways as defined in KEGG.
We also encode the graphical depiction
which maps 1:1 with the identifier.
Triples created:
<pathway_id> is a GO:signal_transduction
<pathway_id> rdfs:label <pathway_name>
<gene_id> RO:involved_in <pathway_id>
:param limit:
:return:
"""
logger.info("Processing pathways")
if self.testMode:
g = self.testgraph
else:
g = self.graph
model = Model(g)
line_counter = 0
path = Pathway(g)
raw = '/'.join((self.rawdir, self.files['pathway']['file']))
with open(raw, 'r', encoding="iso-8859-1") as csvfile:
filereader = csv.reader(csvfile, delimiter='\t', quotechar='\"')
for row in filereader:
line_counter += 1
(pathway_id, pathway_name) = row
if self.testMode and \
pathway_id not in self.test_ids['pathway']:
continue
pathway_id = 'KEGG-'+pathway_id.strip()
path.addPathway(pathway_id, pathway_name)
# we know that the pathway images from kegg map 1:1 here.
# so add those
image_filename = re.sub(r'KEGG-path:', '', pathway_id) + '.png'
image_url = \
'http://www.genome.jp/kegg/pathway/map/'+image_filename
model.addDepiction(pathway_id, image_url)
if not self.testMode and \
limit is not None and line_counter > limit:
break
logger.info("Done with pathways")
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 parse(self, limit=None):
"""
Override Source.parse()
Parses version and interaction information from CTD
Args:
:param limit (int, optional) limit the number of rows processed
Returns:
:return None
"""
if limit is not None:
logger.info("Only parsing first %d rows", limit)
logger.info("Parsing files...")
# pub_map = dict()
# file_path = '/'.join((self.rawdir,
# self.static_files['publications']['file']))
# if os.path.exists(file_path) is True:
# pub_map = self._parse_publication_file(
# self.static_files['publications']['file']
# )
if self.testOnly:
self.testMode = True
if self.testMode:
self.g = self.testgraph
else:
self.g = self.graph
self.geno = Genotype(self.g)
self.pathway = Pathway(self.g)
self._parse_ctd_file(
limit, self.files['chemical_disease_interactions']['file'])
self._parse_ctd_file(limit, self.files['gene_pathway']['file'])
self._parse_ctd_file(limit, self.files['gene_disease']['file'])
self._parse_curated_chem_disease(limit)
logger.info("Done parsing files.")
return
def parse(self, limit=None):
"""
Override Source.parse()
Parses version and interaction information from CTD
Args:
:param limit (int, optional) limit the number of rows processed
Returns:
:return None
"""
if limit is not None:
LOG.info("Only parsing first %d rows", limit)
LOG.info("Parsing files...")
if self.test_only:
self.test_mode = True
self.geno = Genotype(self.graph)
self.pathway = Pathway(self.graph)
src_key = 'chemical_disease_associations'
self._parse_ctd_file(limit, src_key)
