pgxdb_biosamples_extract_biocharacteristics_mappings.pl Perl Code Documentation

The “pgxdb_biosamples_extract_biocharacteristics_mappings.pl” script is a helper for getting an overview map of all combinations of icdom :: icdot :: NCIT diagnostic codes. It parses over all biosamples in progenetix and arraymap, and maps out all code combinations through the use of a key concatenated from the icdom::icdot::NCIT codes of each sample.

Cave: A possible incomplete mapping could result from multiple codes of the same prefix type being assigned to the same sample - this is neither probable nor highly relevant but should be checked through some other annotation QC script.

2021-01-18