Annotation, assembly and liftover are recurring themes because they are tied to (updating) reference genomes. Here we track a next generation annotation system which will support versions of annotation with a matching reference genome. In the future we'll build this out with pangenome support.

• assigned: pjotrp,zsloan,arthurc,robw
• priority: medium
• type: enhancement
• status: open, in progress
• keywords: mapping, architecture

• [ ] Point out where annotation is used in code (@zsloan)
• [ ] Come up with a storage model to replace the existing Mariadb tables (pjotrp, aruni)
• [ ] Implement storage backend
• [ ] Create examples to replace existing code
• [ ] Replace all code to allow for selecting versions

• GeneList table

is only used here, with all position fields being the ones that would ideally account for assembly (txStart, txEnd, cdsStart, cdsEnd, exonStarts, exonEnds - no idea why this last one has an "s" after Start/End)

• https://github.com/genenetwork/genenetwork2/blob/df36cc808e21202075d32559c9f295087bd8aee2/wqflask/base/trait.py#L528-L597

where max LRS locus position is fetched for traits

• - Search queries

notably the Position Search (the most "ambitious" version of this would allow for querying based off of different assemblies, but I can't think of a good way to do this with SQL)