Feature/extend_map_phenotype

[VarenyaJ]

Completed PRs/Issue

PR Title: PR #3 – Feature/extend_map_phenotype (Branch: feature/extend_map_phenotype → develop)
PR Type: Enhancement
Status: Completed

Background

Baseline phenotype mapping only extracted raw HPO IDs. This PR extended parsing to capture and validate both term labels and ontology consistency using hpotk.

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Scope

Outline

Enhance phenotype mapping to support label + ID parsing and ontology validation.

Included/Required

• Extended regex to parse both HPO term labels and numeric IDs.
• Integrated hpotk ontology lookups.
• Added warnings for obsolete IDs, label mismatches, missing ontology terms.
• Added GENO ontology zygosity codes to Genotype.

Optional

• Graceful handling of protobuf fields with try/except.
• Backwards compatibility for sheets without labels.

Not included

• No changes to preprocessing/audit pipeline.
• No CLI options added.

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Technical Plan / Implementation Details

• Updated mapper._map_phenotype to use hpotk.TermId validation.
• Batch validation via ObsoleteTermIdsValidator, PhenotypicAbnormalityValidator, and AnnotationPropagationValidator.
• Introduced Genotype.zygosity_code property → GA4GH GENO CURIE mapping.
• Extended loader to normalize "HPO Term" columns.

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Validation & Testing

• Tested against Python_headers_phenocopy_transformation.xlsx and Sydney_Python_transformation.xlsx.
• Verified ontology lookups and warning generation.
• All existing test suites passed without regressions.

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Milestones

• Extend HPO parsing with labels.
• Integrate ontology validation.
• Add GENO zygosity code mapping.
• Confirm tests pass with new sample files.

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Outcome

• Phenotype mapping is more robust and ontology-aware.
• CLI now warns about obsolete IDs, label mismatches, and unparsable cells.