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Annotation

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.

Tags

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

TODO

• [ ] 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

Notes

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)