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NEWS.md

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Changelog for rd3.yaml

Version 2.0-beta-0.9.0

  • Primary RD3 tables were moved up an level and reference tables were moved to a nested folder. Referenced tables IDs are now formatted like so: rd3_lookups_<table>

  • Pluralized all primary tables: subjects, samples, and files. The table subjectinfo and labinfo remains the same.

  • All ref entities were changed to rd3_lookups-*

  • Added ontology tags where possible; preparation for Beacon integration

  • renamed patch to partOfRelease

  • removed patch_comment as this should go in the releases lookup

  • added compound attribute for row-level metadata to all tables, i.e., recordMetadata that has the columns comments, dateRecordCreated, recordCreatedBy, dateRecordUpdated, wasUpdatedBy

  • ERNs are now stored in the organisations reference table. Please use rd3_lookups_organisations

  • subjects table updates: removed id; subjectID is now the primary key

  • subjects table updates: renamed phenopacketID to mostRecentPhenopacketFile

  • subjectinfo updates: removed id; subjectID is now the primary key

  • subjectinfo updates: renamed dateofBirth to dateOfBirth

  • subjectinfo updates: renamed ageOfDeath to ageAtDeath

  • subjectinfo updates: renamed ageOfDiagnosis to ageAtDiagnosis

  • subjectinfo updates: renamed Country_of_origin to countryOfBirth

  • samples updates: removed id; sampleID is now the primary key

  • samples updates: renamed anatomicalLocation to anatomicallocation

  • labinfo updates: removed id; experimentID is now the primary key

  • labinfo updates: changed data type of sequencingCenter from string to xref

  • files updates: renamed typeFile to fileFormat

  • files updates: added subjectID: reference rd3_subjects

  • files updates: added sampleID: references rd3_samples

  • files updates: added experimentID: references rd3_labinfo

  • files updates: renamed filepath_sandbox to fenderFilePath

  • files updates: added gearshiftFilePath

  • files updates: renamed extraInfo to comments and moved to recordMetadata

  • lookups: renamed organisation to organisations; ERNs are now stored in organisations

  • lookups: expanded tissueTypes table to link values to ontologies

  • lookups: split variant entities into a new nested package rd3_variants

  • lookups: split RD3 specific lookups into rd3_info