Convert-Pheno-0.35

Changes for version 0.35 - 2026-09-19

Added a native desktop application and expanded the Mojolicious API for JSON and file-based conversions
Added experimental i2b2, PCORnet CDM and Sentinel CDM table-package input with BFF, PXF and OMOP-CDM output
Added directory and ZIP table-package input for OMOP-CDM, including streaming support
Added optional Mapping V2 dataset and cohort metadata for built-in multi-entity BFF conversions
Added opt-in 'datasetId' propagation from mapping metadata to BFF individuals and biosamples for backend compatibility
Marked the JSON-only Python HTTP API for future deprecation in favor of Mojolicious

Documentation

README.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::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::Parser

in lib/Convert/Pheno/CDISC/ODM/Parser.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::ClinicalCDM::Claims

in lib/Convert/Pheno/ClinicalCDM/Claims.pm

Convert::Pheno::ClinicalCDM::I2B2

in lib/Convert/Pheno/ClinicalCDM/I2B2.pm

Convert::Pheno::ClinicalCDM::ToBFF

in lib/Convert/Pheno/ClinicalCDM/ToBFF.pm

Convert::Pheno::ClinicalCDM::Util

in lib/Convert/Pheno/ClinicalCDM/Util.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::Execution::Files

in lib/Convert/Pheno/Execution/Files.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::HTTP::Jobs

in lib/Convert/Pheno/HTTP/Jobs.pm

Convert::Pheno::HTTP::Projects

in lib/Convert/Pheno/HTTP/Projects.pm

Convert::Pheno::HTTP::Service

in lib/Convert/Pheno/HTTP/Service.pm

Convert::Pheno::HTTP::Service::Error

in lib/Convert/Pheno/HTTP/Service.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::Metadata

in lib/Convert/Pheno/Mapping/Metadata.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::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::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::ClinicalCDM

in lib/Convert/Pheno/Source/ClinicalCDM.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::TablePackage

in lib/Convert/Pheno/Source/TablePackage.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

To install Convert::Pheno, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Convert::Pheno

CPAN shell

perl -MCPAN -e shell
install Convert::Pheno

For more information on module installation, please visit the detailed CPAN module installation guide.

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Changes for version 0.35 - 2026-09-19

Documentation

Modules

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