QC for duplicate labels/exact synonyms in EFO#2628
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aleixpuigb merged 3 commits intomasterfrom Feb 19, 2026
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Add a new QC step to detect duplicate lexical strings across rdfs:label and oboInOwl:hasExactSynonym. Introduces a SPARQL extraction (label-synonym-dup-extract.sparql), a Python detector script (detect_label_synonym_duplicates.py) that normalizes values and writes a TSV report, and hooks the check into the Makefile (label_synonym_dup_check) so it's run as part of qc. Adds LABEL_DUP_EXPERIMENTAL Makefile flag to run in non-failing experimental mode and generates intermediate label-synonym-data.tsv via ROBOT.
Remove the LABEL_DUP_EXPERIMENTAL variable and the LABEL_DUP_ARGS conditional block, and hardcode the output path for the detect_label_synonym_duplicates.py invocation. The label_synonym_dup_check target now calls the script with an explicit -o reports/label-synonym-duplicates.tsv, simplifying the Makefile and removing the experimental flag handling.
zoependlington
approved these changes
Feb 19, 2026
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This pull request introduces a new quality control (QC) check to detect duplicate lexical strings across
rdfs:labelandoboInOwl:hasExactSynonymproperties in ontology terms. The check is integrated into the build process and produces a report highlighting potential collisions, helping to improve ontology consistency and avoid ambiguous naming.SPARQL extraction for label/synonym data:
label-synonym-dup-extract.sparqlto extract allrdfs:labelandoboInOwl:hasExactSynonymvalues from ontology classes, filtering out deprecated and blank nodes.New duplicate detection QC integration:
label_synonym_dup_checktarget to theqcrule in theMakefile, ensuring the duplicate check runs as part of QC and GitHub Actions workflows.detect_label_synonym_duplicates.pythat processes a ROBOT-generated TSV file, normalizes label/synonym values, identifies duplicate clusters across distinct terms, and writes a wide-format TSV report.