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Convert-Pheno-0.34
⭐ Starred 11

Changes for version 0.34 - 2026-08-03

  • Expanded CDISC support with version-aware ODM 1.3 and 2.0 Snapshot input plus Dataset-XML v1.0 with Define-XML v2 metadata
  • Added experimental cBioPortal clinical study package input with entity-aware BFF, PXF and OMOP-CDM output
  • Added mCODE 4.0 profile detection and primary cancer stage mapping to FHIR R4 input
  • Added user-controlled terminology enrichment for CDISC Dataset-JSON and Dataset-XML, including exact NCI identifier resolution from Define-XML
  • Replaced --search-audit-tsv with --term-audit, supporting TSV, compressed TSV and color-coded XLSX reports
  • Improved mixed and fuzzy terminology search with all-word and typo-tolerant retrieval
  • Added domain-aware Athena-OHDSI standard concept resolution for OMOP output and versioned SQLite database bundles

Documentation

README.md
TODO.md

Modules

Convert::Pheno
Convert clinical and phenotypic data between supported models

Provides

Convert::Pheno::Audit::Terminology
in lib/Convert/Pheno/Audit/Terminology.pm
Convert::Pheno::BFF::Biosample
in lib/Convert/Pheno/BFF/Biosample.pm
Convert::Pheno::BFF::DerivedEntities
in lib/Convert/Pheno/BFF/DerivedEntities.pm
Convert::Pheno::BFF::ToOMOP
in lib/Convert/Pheno/BFF/ToOMOP.pm
Convert::Pheno::BFF::ToPXF
in lib/Convert/Pheno/BFF/ToPXF.pm
Convert::Pheno::CBioPortal::ToBFF
in lib/Convert/Pheno/CBioPortal/ToBFF.pm
Convert::Pheno::CDISC::DefineXML
in lib/Convert/Pheno/CDISC/DefineXML.pm
Convert::Pheno::CDISC::ODM
in lib/Convert/Pheno/CDISC/ODM.pm
Convert::Pheno::CDISC::ODM::Detector
in lib/Convert/Pheno/CDISC/ODM/Detector.pm
Convert::Pheno::CDISC::ODM::Metadata
in lib/Convert/Pheno/CDISC/ODM/Metadata.pm
Convert::Pheno::CDISC::ODM::Metadata::Provider
in lib/Convert/Pheno/CDISC/ODM/Metadata.pm
Convert::Pheno::CDISC::ODM::Record
in lib/Convert/Pheno/CDISC/ODM/Record.pm
Convert::Pheno::CDISC::ODM::Util
in lib/Convert/Pheno/CDISC/ODM/Util.pm
Convert::Pheno::CDISC::ODM::V1
in lib/Convert/Pheno/CDISC/ODM/V1.pm
Convert::Pheno::CDISC::ODM::V2
in lib/Convert/Pheno/CDISC/ODM/V2.pm
Convert::Pheno::CDISC::SDTM::Normalizer
in lib/Convert/Pheno/CDISC/SDTM/Normalizer.pm
Convert::Pheno::CDISC::SDTM::Terminology
in lib/Convert/Pheno/CDISC/SDTM/Terminology.pm
Convert::Pheno::CDISC::SDTM::ToBFF
in lib/Convert/Pheno/CDISC/SDTM/ToBFF.pm
Convert::Pheno::CLI::Args
in lib/Convert/Pheno/CLI/Args.pm
Convert::Pheno::CSV
in lib/Convert/Pheno/CSV.pm
Convert::Pheno::Context
in lib/Convert/Pheno/Context.pm
Convert::Pheno::ConversionRequest
in lib/Convert/Pheno/ConversionRequest.pm
Convert::Pheno::DB::Bundle
in lib/Convert/Pheno/DB/Bundle.pm
Convert::Pheno::DB::SQLite
in lib/Convert/Pheno/DB/SQLite.pm
Convert::Pheno::DB::Similarity
in lib/Convert/Pheno/DB/Similarity.pm
Convert::Pheno::Emit::OMOP
in lib/Convert/Pheno/Emit/OMOP.pm
Convert::Pheno::ExecutionContext
in lib/Convert/Pheno/ExecutionContext.pm
Convert::Pheno::FHIR::Profile::MCode
in lib/Convert/Pheno/FHIR/Profile/MCode.pm
Convert::Pheno::FHIR::ToBFF
in lib/Convert/Pheno/FHIR/ToBFF.pm
Convert::Pheno::FHIR::Util
in lib/Convert/Pheno/FHIR/Util.pm
Convert::Pheno::IO::Atomic
in lib/Convert/Pheno/IO/Atomic.pm
Convert::Pheno::IO::CSVHandler
in lib/Convert/Pheno/IO/CSVHandler.pm
Convert::Pheno::IO::FileIO
in lib/Convert/Pheno/IO/FileIO.pm
Convert::Pheno::JSONLD
in lib/Convert/Pheno/JSONLD.pm
Convert::Pheno::Mapping::Compiler
in lib/Convert/Pheno/Mapping/Compiler.pm
Convert::Pheno::Mapping::Shared
in lib/Convert/Pheno/Mapping/Shared.pm
Convert::Pheno::Model::Bundle
in lib/Convert/Pheno/Model/Bundle.pm
Convert::Pheno::OMOP::Definitions
in lib/Convert/Pheno/OMOP/Definitions.pm
Convert::Pheno::OMOP::ParticipantStream
in lib/Convert/Pheno/OMOP/ParticipantStream.pm
Convert::Pheno::OMOP::Source
in lib/Convert/Pheno/OMOP/Source.pm
Convert::Pheno::OMOP::ToBFF
in lib/Convert/Pheno/OMOP/ToBFF.pm
Convert::Pheno::OMOP::ToBFF::Biosamples
in lib/Convert/Pheno/OMOP/ToBFF/Biosamples.pm
Convert::Pheno::OMOP::ToBFF::Individuals
in lib/Convert/Pheno/OMOP/ToBFF/Individuals.pm
Convert::Pheno::OMOP::Vocabulary
in lib/Convert/Pheno/OMOP/Vocabulary.pm
Convert::Pheno::OpenEHR::ToBFF
in lib/Convert/Pheno/OpenEHR/ToBFF.pm
Convert::Pheno::Operations
in lib/Convert/Pheno/Operations.pm
Convert::Pheno::PXF::ToBFF
in lib/Convert/Pheno/PXF/ToBFF.pm
Convert::Pheno::PXF::ToBFF::Biosamples
in lib/Convert/Pheno/PXF/ToBFF/Biosamples.pm
Convert::Pheno::PXF::ToBFF::Individuals
in lib/Convert/Pheno/PXF/ToBFF/Individuals.pm
Convert::Pheno::Pipeline
in lib/Convert/Pheno/Pipeline.pm
Convert::Pheno::REDCap
in lib/Convert/Pheno/REDCap.pm
Convert::Pheno::Runner
in lib/Convert/Pheno/Runner.pm
Convert::Pheno::Sink::FileSet
in lib/Convert/Pheno/Sink/FileSet.pm
Convert::Pheno::Source
in lib/Convert/Pheno/Source.pm
Convert::Pheno::Source::CBioPortal
in lib/Convert/Pheno/Source/CBioPortal.pm
Convert::Pheno::Source::CDISC::DatasetJSON
in lib/Convert/Pheno/Source/CDISC/DatasetJSON.pm
Convert::Pheno::Source::CDISC::DatasetXML
in lib/Convert/Pheno/Source/CDISC/DatasetXML.pm
Convert::Pheno::Source::CDISC::ODM
in lib/Convert/Pheno/Source/CDISC/ODM.pm
Convert::Pheno::Source::FHIR
in lib/Convert/Pheno/Source/FHIR.pm
Convert::Pheno::Source::OMOP
in lib/Convert/Pheno/Source/OMOP.pm
Convert::Pheno::Source::OpenEHR
in lib/Convert/Pheno/Source/OpenEHR.pm
Convert::Pheno::Source::Result
in lib/Convert/Pheno/Source/Result.pm
Convert::Pheno::Source::Structured
in lib/Convert/Pheno/Source/Structured.pm
Convert::Pheno::Source::Tabular
in lib/Convert/Pheno/Source/Tabular.pm
Convert::Pheno::Tabular::REDCap::Dictionary
in lib/Convert/Pheno/Tabular/REDCap/Dictionary.pm
Convert::Pheno::Tabular::Record
in lib/Convert/Pheno/Tabular/Record.pm
Convert::Pheno::Tabular::ToBFF
in lib/Convert/Pheno/Tabular/ToBFF.pm
Convert::Pheno::Utils::Default
in lib/Convert/Pheno/Utils/Default.pm
Convert::Pheno::Utils::Schema
in lib/Convert/Pheno/Utils/Schema.pm

Other files