Copy the summary annotation record feature from LOVD+ and extend functionality

[ifokkema]

LOVD+ has a feature called Summary Annotation Record, where each unique variant can have one (and one only) record summarizing information from all observations of this variant. By default, this contains the variant's effect, but it's a custom object and can, therefore, be extended with custom columns.

This Summary Annotation Record should then be used to make the life of the curator a bit easier and should copy the curator's variant effect value to all new observations of the variant.

Tasks:

Building the feature:

• Decide on how to link - LOVD+'s method of linking is more stable for variants that don't change, but not currently compatible with LOVD3. LOVD's method of linking is flexible but is not stable in case a variant gets deleted and recreated, which may happen frequently. Also, when hg38 comes, you don't want to be unclear about which build has the ID (and what of variants that don't have a description under a certain build?).
• Copy the Summary Annotation Record feature from LOVD+.
  • Table setup
    • Enforce key on the DBID column? Depends on linking strategy as well.
  • Custom column setup
  • Viewing the record
  • Adding the record
  • Editing the record
• Setup up some basic custom columns
  • Variant effect - Store reported/concluded or only concluded?

Integration with LOVD3:

• Auto generate Summary Annotation Records upon curation of variant?
• Have the record itself mention conflicts in the concluded variant effect?
  • Have the record fix this with one click?
• Have new submissions copy the concluded effect from the SAR?
  • At what stage? Submission? Curation?
• Prevent updating a DBID when there's a SAR?