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 g in [self.graph, self.testgraph]:
# FIXME: How to devise a label for each repository?
gu = GraphUtils(curie_map.get())
repo_id = 'CoriellCollection:'+collection_id
repo_label = label
repo_page = page
gu.addIndividualToGraph(
g, repo_id, repo_label, self.terms['collection'])
gu.addPage(g, repo_id, repo_page)
return
def _get_process_allelic_variants(self, entry, g):
gu = GraphUtils(curie_map.get())
geno = Genotype(g)
du = DipperUtil()
if entry is not None:
publist = {} # to hold the entry-specific publication mentions for the allelic variants
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('\{(\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)]
gu.addTriple(g, pmid, gu.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(',', al['allelicVariant']['dbSnps'])
for dnum in dbsnp_ids:
did = 'dbSNP:'+dnum.strip()
gu.addIndividualToGraph(g, did, None)
gu.addEquivalentClass(g, al_id, did)
if 'clinvarAccessions' in al['allelicVariant']:
# clinvarAccessions triple semicolon delimited, each lik eRCV000020059;;1
rcv_ids = re.split(';;;', al['allelicVariant']['clinvarAccessions'])
rcv_ids = [(re.match('(RCV\d+)\;\;', r)).group(1) for r in rcv_ids]
for rnum in rcv_ids:
rid = 'ClinVar:'+rnum
gu.addXref(g, al_id, rid)
gu.addPage(g, al_id, "http://omim.org/entry/"+str(entry_num)+"#"+str(al_num).zfill(4))
elif re.search('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]
gu.addDeprecatedIndividual(g, 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:
"""
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
