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
line_counter = 0
path = Pathway(g, self.nobnodes)
gu = GraphUtils(curie_map.get())
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
gu.addDepiction(g, 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 _process_nlx_157874_1_view(self, raw, limit=None):
"""
This table contains the Elements of Morphology data that has been
screen-scraped into DISCO.
Note that foaf:depiction is inverse of foaf:depicts relationship.
Since it is bad form to have two definitions,
we concatenate the two into one string.
Triples:
<eom id> a owl:Class
rdf:label Literal(eom label)
OIO:hasRelatedSynonym Literal(synonym list)
IAO:definition Literal(objective_def. subjective def)
foaf:depiction Literal(small_image_url),
Literal(large_image_url)
foaf:page Literal(page_url)
rdfs:comment Literal(long commented text)
:param raw:
:param limit:
:return:
"""
gu = GraphUtils(curie_map.get())
line_counter = 0
with open(raw, 'r') as f1:
f1.readline() # read the header row; skip
filereader = csv.reader(f1, delimiter='\t', quotechar='\"')
for line in filereader:
line_counter += 1
(morphology_term_id, morphology_term_num,
morphology_term_label, morphology_term_url,
terminology_category_label, terminology_category_url,
subcategory, objective_definition, subjective_definition,
comments, synonyms, replaces, small_figure_url,
large_figure_url, e_uid, v_uid, v_uuid,
v_last_modified) = line
# note:
# e_uid v_uuid v_last_modified terminology_category_url
# subcategory v_uid morphology_term_num
# terminology_category_label hp_label notes
# are currently unused.
# Add morphology term to graph as a class
# with label, type, and description.
gu.addClassToGraph(self.graph, morphology_term_id,
morphology_term_label)
# Assemble the description text
if subjective_definition != '' and not (
re.match(r'.+\.$', subjective_definition)):
# add a trailing period.
subjective_definition = subjective_definition.strip() + '.'
if objective_definition != '' and not (
re.match(r'.+\.$', objective_definition)):
# add a trailing period.
objective_definition = objective_definition.strip() + '.'
definition = \
' '.join(
(objective_definition, subjective_definition)).strip()
gu.addDefinition(self.graph, morphology_term_id, definition)
# <term id> FOAF:depicted_by literal url
# <url> type foaf:depiction
# do we want both images?
# morphology_term_id has depiction small_figure_url
if small_figure_url != '':
gu.addDepiction(self.graph, morphology_term_id,
small_figure_url)
# morphology_term_id has depiction large_figure_url
if large_figure_url != '':
gu.addDepiction(self.graph, morphology_term_id,
large_figure_url)
# morphology_term_id has comment comments
if comments != '':
gu.addComment(self.graph, morphology_term_id,
comments.strip())
if synonyms != '':
for s in synonyms.split(';'):
gu.addSynonym(
self.graph, morphology_term_id, s.strip(),
gu.properties['hasExactSynonym'])
# morphology_term_id hasRelatedSynonym replaces (; delimited)
if replaces != '' and replaces != synonyms:
for s in replaces.split(';'):
gu.addSynonym(
self.graph, morphology_term_id, s.strip(),
gu.properties['hasRelatedSynonym'])
# morphology_term_id has page morphology_term_url
gu.addPage(self.graph, morphology_term_id, morphology_term_url)
if limit is not None and line_counter > limit:
break
return
