def _process_collection(self, collection_id, label, page):
"""
This function will process the data supplied internally
about the repository from Coriell.
Triples:
Repository a ERO:collection
rdf:label Literal(label)
foaf:page Literal(page)
:param collection_id:
:param label:
:param page:
:return:
"""
# ############# BUILD THE CELL LINE REPOSITORY #############
for graph in [self.graph, self.testgraph]:
# TODO: How to devise a label for each repository?
model = Model(graph)
reference = Reference(graph)
repo_id = 'CoriellCollection:' + collection_id
repo_label = label
repo_page = page
model.addIndividualToGraph(
repo_id, repo_label, self.globaltt['collection'])
reference.addPage(repo_id, repo_page)
return
def _process_collection(self, collection_id, label, page):
"""
This function will process the data supplied internally
about the repository from Coriell.
Triples:
Repository a ERO:collection
rdf:label Literal(label)
foaf:page Literal(page)
:param collection_id:
:param label:
:param page:
:return:
"""
# ############# BUILD THE CELL LINE REPOSITORY #############
for graph in [self.graph, self.testgraph]:
# TODO: How to devise a label for each repository?
model = Model(graph)
reference = Reference(graph)
repo_id = 'CoriellCollection:' + collection_id
repo_label = label
repo_page = page
model.addIndividualToGraph(repo_id, repo_label,
self.globaltt['collection'])
reference.addPage(repo_id, repo_page)
return
def _process_nlx_157874_1_view(self, raw, limit=None):
"""
This table contains the Elements of Morphology data .
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.
Turtle:
<eom id> a owl:Class
rdf:label Literal(eom label)
oboInOwl:has_related_synonym 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)
TEC_note: URL are not literals.
:param raw:
:param limit:
:return:
"""
src_key = 'tables'
model = Model(self.graph)
col = self.resources[src_key]['columns']
with open(raw, 'r') as rawread:
reader = csv.reader(rawread, delimiter='\t', quotechar='\"')
row = next(reader)
if not self.check_fileheader(col, row):
pass
for row in reader:
# head -1 dvp.pr_nlx_157874_1|tr '\t' '\n'|
# sed "s|\(.*\)|# \1 = row[col.index('\1')]|g"
morphology_term_id = row[col.index(
'morphology_term_id')].strip()
# morphology_term_num = row[col.index('morphology_term_num')]
morphology_term_label = row[col.index(
'morphology_term_label')].strip()
morphology_term_url = row[col.index(
'morphology_term_url')].strip()
# terminology_category_label = row[
# col.index('terminology_category_label')]
# terminology_category_url = row[col.index('terminology_category_url')]
# subcategory = row[col.index('subcategory')]
objective_definition = row[col.index(
'objective_definition')].strip()
subjective_definition = row[col.index(
'subjective_definition')].strip()
comments = row[col.index('comments')].strip()
synonyms = row[col.index('synonyms')].strip()
replaces = row[col.index('replaces')].strip()
small_figure_url = row[col.index('small_figure_url')].strip()
large_figure_url = row[col.index('large_figure_url')].strip()
# e_uid = row[col.index('e_uid')]
# v_uid = row[col.index('v_uid')]
# v_uuid = row[col.index('v_uuid')]
# v_lastmodified = row[col.index('v_lastmodified')]
# v_status = row[col.index('v_status')]
# v_lastmodified_epoch = row[col.index('v_lastmodified_epoch')]
# Add morphology term to graph as a class
# with label, type, and description.
model.addClassToGraph(morphology_term_id,
morphology_term_label)
# Assemble the description text
if subjective_definition != '' and not (re.match(
r'.+\.$', subjective_definition)):
# add a trailing period.
subjective_definition = subjective_definition + '.'
if objective_definition != '' and not (re.match(
r'.+\.$', objective_definition)):
# add a trailing period.
objective_definition = objective_definition + '.'
definition = ' '.join(
(objective_definition, subjective_definition))
model.addDefinition(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 != '':
model.addDepiction(morphology_term_id, small_figure_url)
# morphology_term_id has depiction large_figure_url
if large_figure_url != '':
model.addDepiction(morphology_term_id, large_figure_url)
# morphology_term_id has comment comments
if comments != '':
model.addComment(morphology_term_id, comments)
for syn in synonyms.split(';'):
model.addSynonym(morphology_term_id, syn.strip(),
self.globaltt['has_exact_synonym'])
# morphology_term_id has_related_synonym replaces (; delimited)
if replaces not in ['', synonyms]:
for syn in replaces.split(';'):
model.addSynonym(morphology_term_id, syn.strip(),
self.globaltt['has_related_synonym'])
# <morphology_term_id> <foaf:page> morphology_term_url
if morphology_term_id is not None:
reference = Reference(self.graph, morphology_term_id,
self.globaltt['web page'])
# TEC 201905:
# Not so sure we need explicit <eom_uri> <webpage> <eom_url>.
# since <eom_uri> IS the <eom_url>.
reference.addPage(morphology_term_id, morphology_term_url)
if limit is not None and reader.line_num > limit:
break
def _get_process_allelic_variants(self, entry, g):
model = Model(g)
reference = Reference(g)
geno = Genotype(g)
if entry is not None:
# to hold the entry-specific publication mentions
# for the allelic variants
publist = {}
entry_num = entry['mimNumber']
# process the ref list just to get the pmids
ref_to_pmid = self._get_pubs(entry, g)
if 'allelicVariantList' in entry:
allelicVariantList = entry['allelicVariantList']
for al in allelicVariantList:
al_num = al['allelicVariant']['number']
al_id = 'OMIM:'+str(entry_num)+'.'+str(al_num).zfill(4)
al_label = None
al_description = None
if al['allelicVariant']['status'] == 'live':
publist[al_id] = set()
if 'mutations' in al['allelicVariant']:
al_label = al['allelicVariant']['mutations']
if 'text' in al['allelicVariant']:
al_description = al['allelicVariant']['text']
m = re.findall(r'\{(\d+)\:', al_description)
publist[al_id] = set(m)
geno.addAllele(
al_id, al_label, geno.genoparts['variant_locus'],
al_description)
geno.addAlleleOfGene(
al_id, 'OMIM:'+str(entry_num),
geno.object_properties[
'is_sequence_variant_instance_of'])
for r in publist[al_id]:
pmid = ref_to_pmid[int(r)]
g.addTriple(
pmid, model.object_properties['is_about'],
al_id)
# look up the pubmed id in the list of references
if 'dbSnps' in al['allelicVariant']:
dbsnp_ids = \
re.split(r',', al['allelicVariant']['dbSnps'])
for dnum in dbsnp_ids:
did = 'dbSNP:'+dnum.strip()
model.addIndividualToGraph(did, None)
model.addSameIndividual(al_id, did)
if 'clinvarAccessions' in al['allelicVariant']:
# clinvarAccessions triple semicolon delimited
# each >1 like RCV000020059;;;
rcv_ids = \
re.split(
r';;;',
al['allelicVariant']['clinvarAccessions'])
rcv_ids = [
(re.match(r'(RCV\d+);*', r)).group(1)
for r in rcv_ids]
for rnum in rcv_ids:
rid = 'ClinVar:'+rnum
model.addXref(al_id, rid)
reference.addPage(
al_id, "http://omim.org/entry/" +
str(entry_num)+"#" + str(al_num).zfill(4))
elif re.search(
r'moved', al['allelicVariant']['status']):
# for both 'moved' and 'removed'
moved_ids = None
if 'movedTo' in al['allelicVariant']:
moved_id = 'OMIM:'+al['allelicVariant']['movedTo']
moved_ids = [moved_id]
model.addDeprecatedIndividual(al_id, moved_ids)
else:
logger.error('Uncaught alleleic variant status %s',
al['allelicVariant']['status'])
# end loop allelicVariantList
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:
"""
model = Model(self.graph)
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, v_status, v_lastmodified_epoch) = 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.
model.addClassToGraph(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()
model.addDefinition(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 != '':
model.addDepiction(morphology_term_id,
small_figure_url)
# morphology_term_id has depiction large_figure_url
if large_figure_url != '':
model.addDepiction(morphology_term_id,
large_figure_url)
# morphology_term_id has comment comments
if comments != '':
model.addComment(morphology_term_id,
comments.strip())
if synonyms != '':
for s in synonyms.split(';'):
model.addSynonym(
morphology_term_id, s.strip(),
model.annotation_properties['hasExactSynonym'])
# morphology_term_id hasRelatedSynonym replaces (; delimited)
if replaces != '' and replaces != synonyms:
for s in replaces.split(';'):
model.addSynonym(
morphology_term_id, s.strip(),
model.annotation_properties['hasRelatedSynonym'])
# morphology_term_id has page morphology_term_url
reference = Reference(self.graph)
reference.addPage(morphology_term_id, morphology_term_url)
if limit is not None and line_counter > limit:
break
return
def _get_process_allelic_variants(self, entry, graph):
model = Model(graph)
reference = Reference(graph)
geno = Genotype(graph)
if entry is not None:
# to hold the entry-specific publication mentions
# for the allelic variants
publist = {}
entry_num = entry['mimNumber']
# process the ref list just to get the pmids
ref_to_pmid = self._get_pubs(entry, graph)
if 'allelicVariantList' in entry:
for alv in entry['allelicVariantList']:
al_num = alv['allelicVariant']['number']
al_id = 'OMIM:' + str(entry_num) + '.' + str(al_num).zfill(
4)
al_label = None
al_description = None
if alv['allelicVariant']['status'] == 'live':
publist[al_id] = set()
if 'mutations' in alv['allelicVariant']:
al_label = alv['allelicVariant']['mutations']
if 'text' in alv['allelicVariant']:
al_description = alv['allelicVariant']['text']
mch = re.findall(r'\{(\d+)\:', al_description)
publist[al_id] = set(mch)
geno.addAllele(al_id, al_label,
self.globaltt['variant_locus'],
al_description)
geno.addAlleleOfGene(al_id, 'OMIM:' + str(entry_num),
self.globaltt['is_allele_of'])
for ref in publist[al_id]:
pmid = ref_to_pmid[int(ref)]
graph.addTriple(pmid, self.globaltt['is_about'],
al_id)
# look up the pubmed id in the list of references
if 'dbSnps' in alv['allelicVariant']:
dbsnp_ids = re.split(
r',', alv['allelicVariant']['dbSnps'])
for dnum in dbsnp_ids:
did = 'dbSNP:' + dnum.strip()
model.addIndividualToGraph(did, None)
model.addSameIndividual(al_id, did)
# Note that RCVs are variant to disease associations
# in ClinVar, rather than variant entries
# so we make these xrefs instead of equivalents
if 'clinvarAccessions' in alv['allelicVariant']:
# clinvarAccessions triple semicolon delimited
# each >1 like RCV000020059;;;
rcv_ids = \
alv['allelicVariant']['clinvarAccessions'].split(';;;')
rcv_ids = [rcv[:12]
for rcv in rcv_ids] # incase more cruft
for rnum in rcv_ids:
rid = 'ClinVar:' + rnum
model.addXref(al_id, rid)
reference.addPage(
al_id, "http://omim.org/entry/" + '#'.join(
(str(entry_num), str(al_num).zfill(4))))
elif re.search(r'moved', alv['allelicVariant']['status']):
# for both 'moved' and 'removed'
moved_ids = None
if 'movedTo' in alv['allelicVariant']:
moved_id = 'OMIM:' + alv['allelicVariant'][
'movedTo']
moved_ids = [moved_id]
model.addDeprecatedIndividual(al_id, moved_ids)
else:
LOG.error('Uncaught alleleic variant status %s',
alv['allelicVariant']['status'])
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:
"""
model = Model(self.graph)
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,
v_status, v_lastmodified_epoch) = 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.
model.addClassToGraph(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()
model.addDefinition(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 != '':
model.addDepiction(morphology_term_id, small_figure_url)
# morphology_term_id has depiction large_figure_url
if large_figure_url != '':
model.addDepiction(morphology_term_id, large_figure_url)
# morphology_term_id has comment comments
if comments != '':
model.addComment(morphology_term_id, comments.strip())
if synonyms != '':
for s in synonyms.split(';'):
model.addSynonym(
morphology_term_id, s.strip(),
model.annotation_properties['hasExactSynonym'])
# morphology_term_id hasRelatedSynonym replaces (; delimited)
if replaces != '' and replaces != synonyms:
for s in replaces.split(';'):
model.addSynonym(
morphology_term_id, s.strip(),
model.annotation_properties['hasRelatedSynonym'])
# morphology_term_id has page morphology_term_url
reference = Reference(self.graph)
reference.addPage(morphology_term_id, morphology_term_url)
if limit is not None and line_counter > limit:
break
return
