data (rd3): integration of RD3 into the FairDataHub model

[davidruvolo51]

What are the main changes you did:

The purpose of this PR is to migrate RD3 to the FDH model. Rather than reimplementing RD3 in EMX2, it was decided to map RD3 to FDH. In order to migrate the RD3 to EMX2, the follow attributes were added to the FDH model. (These used Beacon v2 spec, existing FAIR data models, and existing ontologies.)

• Pedigree: for creating groups of related individuals
  • Pedigree Members: individuals mapped to a family with relationships, affected status, and disease
  • Pedigree Member Roles: ontology table for defining relationships (i.e., proband, bio mother, bio father)
  • Pedigree: added ref to pedigree in individuals table
• Clinical Table:
  • Added link in the individuals table
  • Added column to link the latest phenopacket file (Latest phenopacket file)
  • Changed FirstContact to Date of first contact
  • all attributes have human readable names
  • Updated profile tags for RD3
• Individuals
  • integrated Pedigree
  • Added ref back to IndividualsConsent table
  • Moved RD3 columns (MatchMakerPermission, NoIncidentalFindings) to consent table
  • Added human readable labels for RD3 variables
  • Dropped variables found in other tables (clinical, pedigree, etc.)
• Data releases
  • Friendlier names
  • Changed Data source to Data provider
• Solved status: add module for solved status
• Files: allow multiple file paths
• Add record retracted status (boolean)
• Add secondary affiliations to link individuals/samples/runs/etc to an organisation
• Added columns (and minor revisions) to biosamples, runs, and files.
• Dropped old RD3 schema
• Where possible, used friendlier column names/labels
• Debug template build

how to test:

• Go to preview

todo:

• updated docs in case of new feature
• Drop RD3 from the model?
• Which profiles should I use?