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Convert-Pheno-0.30
⭐ Starred 11

Changes for version 0.30 - 2026-04-14

  • Refactored BFF internals to support entity-aware and multi-entity conversion
  • Added BFF entity output mode via --entities/--out-dir/--out-entity while keeping legacy -obff behavior for individuals
  • PXF input can now emit first-class biosamples, and datasets/cohorts can be synthesized from the normalized individuals collection
  • Refactored the mapping file to an entity-aware layout with beacon.individuals plus optional beacon.{datasets,cohorts,biosamples}
  • Refreshed mapping tables and improved mapping-file documentation
  • Improved PXF <-> BFF round-trip mapping and preserved/restored Phenopackets vitalStatus
  • Added configurable fallback for PXF subject.vitalStatus via --default-vital-status
  • Added --search-audit-tsv and improved SQLite exact-search reporting
  • Reworked CLI internals, expanded test coverage and removed the legacy RDF module

Modules

Convert::Pheno
A module to interconvert common data models for phenotypic data

Provides

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::CDISC
in lib/Convert/Pheno/CDISC.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::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::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::BFF::Individuals::Tabular
in lib/Convert/Pheno/Mapping/BFF/Individuals/Tabular.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::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::REDCap
in lib/Convert/Pheno/REDCap.pm
Convert::Pheno::Runner
in lib/Convert/Pheno/Runner.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::Utils::Default
in lib/Convert/Pheno/Utils/Default.pm
Convert::Pheno::Utils::Schema
in lib/Convert/Pheno/Utils/Schema.pm

Other files