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Fix chembl issue 584 #585

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Fix chembl issue 584 #585

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23821d4
We still add IDs to the labels file, but blank duplicate labels.
gaurav Sep 18, 2025
eed6d9e
Added check for malformed label file.
gaurav Sep 22, 2025
7e66c59
Added a maxsplit.
gaurav Sep 22, 2025
c158239
Support label files with unlabeled identifiers.
gaurav Sep 23, 2025
33a5913
Added support for blank labels and synonyms.
gaurav Sep 23, 2025
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2 changes: 1 addition & 1 deletion src/datahandlers/chembl.py
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ def pull_labels(self,ofname):

# Sometimes the CHEMBL label is identical to the chemblid. We don't want those (https://github.com/TranslatorSRI/Babel/issues/430).
if label == chemblid:
continue
label = ''

outf.write(f'{CHEMBLCOMPOUND}:{chemblid}\t{label}\n')

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20 changes: 16 additions & 4 deletions src/node.py
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Expand Up @@ -72,8 +72,13 @@ def load_synonyms(self,prefix):
with open(labelfname, 'r') as inf:
for line in inf:
x = line.strip().split('\t')
lbs[x[0]].add( ('http://www.geneontology.org/formats/oboInOwl#hasExactSynonym',x[1]) )
count_labels += 1
if len(x) == 1:
lbs[x[0]].add( ('http://www.geneontology.org/formats/oboInOwl#hasExactSynonym', '') )
elif len(x) == 2:
lbs[x[0]].add( ('http://www.geneontology.org/formats/oboInOwl#hasExactSynonym', x[1]) )
count_labels += 1
else:
logger.warning(f"Unexpected number of columns in {labelfname} ({len(x)}), skipping: {line.strip()}")
synfname = os.path.join(self.synonym_dir, prefix, 'synonyms')
if os.path.exists(synfname):
with open(synfname, 'r') as inf:
Expand Down Expand Up @@ -505,8 +510,15 @@ def load_extra_labels(self,prefix):
if os.path.exists(labelfname):
with open(labelfname,'r') as inf:
for line in inf:
x = line.strip().split('\t')
lbs[x[0]] = x[1]
x = line.strip().split('\t', maxsplit=1)
if len(x) == 1:
# We have an identifier, but we explicitly don't have a label.
lbs[x[0]] = ''
elif len(x) == 2:
# We have an identifier and a label.
lbs[x[0]] = x[1]
else:
logger.warning(f"bad line in {labelfname}: {line.strip()}")
self.extra_labels[prefix] = lbs

def apply_labels(self, input_identifiers, labels):
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