collected notes for next update

[reece]

schema changes

• drop sqlalchemy
• protein assoc in tx record
• overhaul genes: use tax_id as primary id
• exon set fingerprint table w/enum
• schema migration (yoyo, likely)
• separate alignment regions from features (i.e., CDS, exons)
• 1° class alignment objects w/ids
• store full tx-level cigar, including introns
• consider using fully-justified alignments w/cigars
• features and feature projections

data changes

• support refseq, lrg, ensembl
• gene
• enable custom transcripts

processing

• load from gff3
• automated loading process → much faster updates

architecture changes

• backends: RDS + sqlite backends
• REST interface
• continue docker deployment
• UTA Python client (rather than direct sql)

[akeeeshi]

Hi @reece

Is there an expected release date for this upcoming update?

[reece]

@akeeeshi : A UTA data update depends on resolving a technical issue in some cython code. I think it's likely that we'll have a UTA data update within the next month.

The UTA structural overhaul depends on finding financial support for it. I am in discussions for that, but nothing certain yet.

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This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.

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This issue was closed because it has been stalled for 7 days with no activity.

[reece]

This issue was closed by stalebot. It has been reopened to give more time for community review. See biocommons coding guidelines for stale issue and pull request policies. This resurrection is expected to be a one-time event.

[github-actions[bot]]

This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 7 days.

[github-actions[bot]]

This issue was closed because it has been stalled for 7 days with no activity.