def _process_article_row(self, row):
model = Model(self.g)
# don't bother in test mode
if self.testMode:
return
iarticle_id = self._make_internal_id('article', row['article_id'])
self.id_hash['article'][row['article_id']] = iarticle_id
rtype = None
if row['journal'] != '':
rtype = Reference.ref_types['journal_article']
reference = Reference(self.g, iarticle_id, rtype)
if row['title'] is not None:
reference.setTitle(row['title'].strip())
if row['year'] is not None:
reference.setYear(row['year'])
reference.addRefToGraph()
if row['pubmed_id'] is not None:
pmid = 'PMID:'+str(row['pubmed_id'])
self.id_hash['article'][row['article_id']] = pmid
model.addSameIndividual(iarticle_id, pmid)
model.addComment(pmid, iarticle_id.replace("_:", ''))
return
def _process_article_row(self, row):
# don't bother in test mode
if self.testMode:
return
iarticle_id = self._make_internal_id('article', row['article_id'])
self.id_hash['article'][row['article_id']] = iarticle_id
rtype = None
if row['journal'] != '':
rtype = Reference.ref_types['journal_article']
r = Reference(iarticle_id, rtype)
if row['title'] is not None:
r.setTitle(row['title'].strip())
if row['year'] is not None:
r.setYear(row['year'])
r.addRefToGraph(self.g)
if row['pubmed_id'] is not None:
pmid = 'PMID:'+str(row['pubmed_id'])
self.id_hash['article'][row['article_id']] = pmid
self.gu.addSameIndividual(self.g, iarticle_id, pmid)
self.gu.addComment(self.g, pmid, iarticle_id)
return
def _get_pubs(self, entry, g):
"""
Extract mentioned publications from the reference list
:param entry:
:return:
"""
ref_to_pmid = {}
entry_num = entry['mimNumber']
model = Model(g)
if 'referenceList' in entry:
reflist = entry['referenceList']
for r in reflist:
if 'pubmedID' in r['reference']:
pub_id = 'PMID:' + str(r['reference']['pubmedID'])
ref = \
Reference(
g, pub_id,
Reference.ref_types['journal_article'])
else:
# make blank node for internal reference
pub_id = \
'_:OMIM' + str(entry_num) + 'ref' + \
str(r['reference']['referenceNumber'])
ref = Reference(g, pub_id)
title = author_list = source = citation = None
if 'title' in r['reference']:
title = r['reference']['title']
ref.setTitle(title)
if 'authors' in r['reference']:
author_list = r['reference']['authors']
ref.setAuthorList(author_list)
citation = re.split(r'\.\,', author_list)[0] + ' et al'
if 'source' in r['reference']:
source = r['reference']['source']
citation = '; '.join(
list(filter(None.__ne__, [citation, title, source])))
ref.setShortCitation(citation)
ref.addRefToGraph()
ref_to_pmid[r['reference']['referenceNumber']] = pub_id
# add is_about for the pub
omim_id = 'OMIM:'+str(entry_num)
g.addTriple(omim_id, model.object_properties['mentions'],
pub_id)
return ref_to_pmid
def _get_pubs(self, entry, graph):
"""
Extract mentioned publications from the reference list
:param entry:
:return:
"""
ref_to_pmid = {}
entry_num = entry['mimNumber']
if 'referenceList' in entry:
reflist = entry['referenceList']
for rlst in reflist:
if 'pubmedID' in rlst['reference']:
pub_id = 'PMID:' + str(rlst['reference']['pubmedID'])
ref = Reference(graph, pub_id,
self.globaltt['journal article'])
else:
# make blank node for internal reference
pub_id = '_:OMIM' + str(entry_num) + 'ref' + str(
rlst['reference']['referenceNumber'])
ref = Reference(graph, pub_id)
title = author_list = source = citation = None
if 'title' in rlst['reference']:
title = rlst['reference']['title']
ref.setTitle(title)
if 'authors' in rlst['reference']:
author_list = rlst['reference']['authors']
ref.setAuthorList(author_list)
citation = re.split(r'\.\,', author_list)[0] + ' et al'
if 'source' in rlst['reference']:
source = rlst['reference']['source']
citation = '; '.join([
tok for tok in [citation, title, source]
if tok is not None
])
ref.setShortCitation(citation)
ref.addRefToGraph()
ref_to_pmid[rlst['reference']['referenceNumber']] = pub_id
# add is_about for the pub
omim_id = 'OMIM:' + str(entry_num)
graph.addTriple(omim_id, self.globaltt['mentions'], pub_id)
return ref_to_pmid
def _get_pubs(self, entry, g):
"""
Extract mentioned publications from the reference list
:param entry:
:return:
"""
ref_to_pmid = {}
du = DipperUtil()
entry_num = entry['mimNumber']
gu = GraphUtils(curie_map.get())
if 'referenceList' in entry:
reflist = entry['referenceList']
for r in reflist:
if 'pubmedID' in r['reference']:
pub_id = 'PMID:' + str(r['reference']['pubmedID'])
ref = Reference(pub_id, Reference.ref_types['journal_article'])
else:
# make blank node for internal reference
pub_id = '_OMIM' + str(entry_num) + 'ref' + str(r['reference']['referenceNumber'])
if self.nobnodes:
pub_id = ':' + pub_id
ref = Reference(pub_id)
title = author_list = source = citation = None
if 'title' in r['reference']:
title = r['reference']['title']
ref.setTitle(title)
if 'authors' in r['reference']:
author_list = r['reference']['authors']
ref.setAuthorList(author_list)
citation = re.split('\.\,', author_list)[0] + ' et al'
if 'source' in r['reference']:
source = r['reference']['source']
citation = '; '.join(du.flatten([citation, title, source]))
ref.setShortCitation(citation)
ref.addRefToGraph(g)
ref_to_pmid[r['reference']['referenceNumber']] = pub_id
# add is_about for the pub
omim_id = 'OMIM:'+str(entry_num)
gu.addTriple(g, omim_id, gu.object_properties['mentions'], pub_id)
return ref_to_pmid
def _process_allele_phenotype(self, limit):
"""
Make allele to phenotype associations using derived_pheno_class
and derived_pheno_manifest cvterm in the flybase db, an example entry is:
FBal0257663 @FBcv0000351:lethal@ | @FBcv0000308:female limited@,
with @FBal0130657:Scer\GAL4<up>dome-PG14</up>@
The first term is the phenotype, and all follow up terms are qualifiers,
self.globaltt['has_qualifier'])
Our previous approach was to use the genotype id associated with
FBal0257663/FBal0130657 , however, this required us to create blank
nodes and was considered unnecessarily granular
Note that sometimes identifiers do not exist for a term, eg
@:heat sensitive | tetracycline conditional@
derived_pheno_class - FBcv terms, these are phenotypes
derived_pheno_manifest - Anatomy terms FBbt, we currently
make phenotype IRI equivalents that end up in UPheno, but
this is being developed and updated, see
https://github.com/monarch-initiative/dipper/issues/770
Adds triples to self.graph
:param limit: number of rows to process
:return: None
"""
model = Model(self.graph)
src_key = 'allele_phenotype'
raw = '/'.join((self.rawdir, self.queries[src_key]['file']))
LOG.info("processing allele phenotype associations")
col = self.queries[src_key]['columns']
transgenic_alleles = self._get_foreign_transgenic_alleles()
# flybase terms - terms we prefix with FlyBase:
fly_prefixes = ['FBal', 'FBti', 'FBab', 'FBba', 'FBtp']
# a alphanumeric id followed by a colon then
# any character but a colon bordered by @s
term_regex = re.compile(r'@([\w]*):([^:@]*)@')
id_regex = re.compile(r'([a-zA-Z]+)(\d+)')
with open(raw, 'r') as tsvfile:
reader = csv.reader(tsvfile, delimiter='\t')
row = next(reader) # headers
self.check_fileheader(col, row)
for row in reader:
allele_id = row[col.index('allele_id')]
pheno_desc = row[col.index('pheno_desc')]
pheno_type = row[col.index('pheno_type')]
pub_id = row[col.index('pub_id')]
pub_title = row[col.index('pub_title')]
pmid_id = row[col.index('pmid_id')]
# Don't get phenotypes for transgenic alleles
if allele_id in transgenic_alleles:
continue
allele_curie = 'FlyBase:' + allele_id
terms = re.findall(term_regex, pheno_desc)
if not terms:
LOG.warning('Could not @terms@ in description: %s',
pheno_desc)
continue
term_ids, term_labels = zip(*terms)
id_match = re.match(id_regex, term_ids[0])
if id_match is not None:
prefix, reference = id_match.group(1, 2)
else:
raise ValueError("Could not parse id {}".format(
term_ids[0]))
# derived_pheno_class should all start with a FBcv term
if pheno_type == 'derived_pheno_class' and prefix != 'FBcv':
LOG.warning(
'derived_pheno_class does not '
'start with FBcv: %s', pheno_desc)
continue
# Create phenotype curie
if pheno_type == 'derived_pheno_class':
phenotype_curie = prefix + ':' + reference
elif pheno_type == 'derived_pheno_manifest':
# These are not proper FBcv phenotype terms
# but rather anatomical entities, go terms, sometimes free text
# skip parsing for now
continue
else:
raise ValueError(
"Unexpected phenotype type: {}".format(pheno_type))
if pmid_id:
ref_curie = 'PMID:' + pmid_id
else:
ref_curie = 'FlyBase:' + pub_id
reference = Reference(self.graph, ref_curie)
reference.setTitle(pub_title)
reference.addRefToGraph()
assoc = G2PAssoc(self.graph, self.name, allele_curie,
phenotype_curie,
self.globaltt['has phenotype'])
assoc.add_source(ref_curie)
# Associations need to be disambiguated via their qualifiers
# see http://flybase.org/reports/FBal0207398 as an example
assoc.set_association_id(
assoc.make_association_id(self.name, allele_curie,
self.globaltt['has phenotype'],
phenotype_curie, term_ids[1:]))
assoc.add_association_to_graph()
assoc_id = assoc.get_association_id()
# add the rest as qualifiers
for term in term_ids[1:]:
if term:
# FBal, GO, FBti, FBab ...
id_match = re.match(id_regex, term)
if id_match is not None:
prefix, reference = id_match.group(1, 2)
if prefix in fly_prefixes:
term_curie = 'FlyBase:' + term
else:
term_curie = prefix + ':' + reference
else:
raise ValueError(
"Could not parse id {}".format(term))
else:
# There is not an id for a term,
# eg @:heat sensitive | tetracycline conditional@
continue
self.graph.addTriple(assoc_id,
self.globaltt['has_qualifier'],
term_curie)
if limit is not None and reader.line_num > limit:
break