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Convert-Pheno-0.28
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Changes for version 0.28 - 2025-04-18

  • Internal parameter 'ncpuhost' renamed to 'threadshost'
  • BFF.pm renamed to Bff2Pxf.pm
  • Organized some modules into DB and Utils
  • <--slq2csv> CSVs now mantain the order of header fields from <.sql> (i.e., easier csv import)
  • OMOP information moved from OMOP.pm to OMOP::Definitions.pm
  • String similarity functions moved to Similarity.pm
  • Added --search <fuzzy> mode (default: 0.9 token-based + 0.1 Levenshtein distance)
  • Added --levenshtein-weight parameter
  • In 'omop2bff' conversion:
    • Added property "_visit" to 'interventionsOrProcedures' term
    • Added 'P' string to age (to conform with ISO8601) generated via condition_start_date + birth_datetime
    • Added DateTime::Format::ISO8601 module to simplify ome time-related calculations
  • Added "basic" 'bff2omop' conversion. To be further tested and improved in next releases
  • Added 'visitId' property to 'mapping.json' schema that lands in "_visit.id" on array-based terms

Documentation

convert-pheno
A script to interconvert common data models for phenotypic data

Modules

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

Provides

Convert::Pheno::Bff2Omop
in lib/Convert/Pheno/Bff2Omop.pm
Convert::Pheno::Bff2Pxf
in lib/Convert/Pheno/Bff2Pxf.pm
Convert::Pheno::CDISC
in lib/Convert/Pheno/CDISC.pm
Convert::Pheno::CSV
in lib/Convert/Pheno/CSV.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::IO::CSVHandler
in lib/Convert/Pheno/IO/CSVHandler.pm
Convert::Pheno::IO::FileIO
in lib/Convert/Pheno/IO/FileIO.pm
Convert::Pheno::OMOP
in lib/Convert/Pheno/OMOP.pm
Convert::Pheno::OMOP::Definitions
in lib/Convert/Pheno/OMOP/Definitions.pm
Convert::Pheno::PXF
in lib/Convert/Pheno/PXF.pm
Convert::Pheno::RDF
in lib/Convert/Pheno/RDF.pm
Convert::Pheno::REDCap
in lib/Convert/Pheno/REDCap.pm
Convert::Pheno::Utils::Default
in lib/Convert/Pheno/Utils/Default.pm
Convert::Pheno::Utils::Mapping
in lib/Convert/Pheno/Utils/Mapping.pm
Convert::Pheno::Utils::Schema
in lib/Convert/Pheno/Utils/Schema.pm

Other files