SCRUM-4441 Rewrite LinkML model for VEPGENE and VEPTRANSCRIPT loader data types

[markquintontulloch]

Moves away from the "association of an association" model to just having a single class for VEP consequences that is attached to a CuratedVariantGenomicLocationAssociation (multivalued).

The gene-level consequence is simply the most severe transcript-level consequence for a variant amongst all the transcripts associated with a gene, so this can simply be indicated by a boolean rather than having separate gene- and transcript-level consequence classes.

Position slots prefixed with 'calculated_' to clearly indicate that these coordinates are determined by the VEP based on input files as opposed to source/curated values.

[chris-grove]

@markquintontulloch Looks good and I generally approve; one question, do we have the deleted enumerations noted elsewhere? I don't want to lose this information if this is the only place it has been noted.

enums:

  vep_consequence_levels:
    permissible_values:
      high:
      moderate:
      low:
      modifier:

  sift_prediction_levels:
    permissible_values:
      deleterious:
      tolerated:

  polyphen_prediction_levels:
    permissible_values:
      possibly_damaging:
      probably_damaging:
      benign:

[markquintontulloch]

@chris-grove permissible values listed in attributes

[chris-grove]

@markquintontulloch OK, got it, thanks