Things to do for the MiAIRR v2 release

[bussec]

This is a shopping list for AIRR v2.0 from the MiAIRR prespective. We will convert this to Milestones once v1.3 is out and it is confirmed that we will stick with the Milestone feature for the time being.

• Renaming MiAIRR organism field to species (Rename organism to species? #266)
  • Confirmed by MiniStd in Dec 19
  • Confirmed by DataRep in Mar 20 (i.e. will rename the corresponding key)
• Document changes regarding authority over rearrangement object / MiAIRR Set 6
• Single-cell extension (Cell object specifications - ScXT #320, MiAIRR single-cell extension (scXT) #211, Single-cell reactivity data annotation/linkage #207, Single-cell expression data annotation/linkage #206, Introduce Receptor schema #404, File formats for a MIAIRR singe cell exporter #409, Receptor, Cell and Rearrangement schema representations #410)
• Formalize a machine-readable way to remove and rename fields (Field deprecation protocol? #248)
• Human Population Genetics XT (Human population genetics Extension #318, Add country information to subject and sample #265, Human Population Genetics Extension #264)
• Changes to Non-nullable status (Change and document MiAIRR requirement levels #319, Revisit MiAIRR non-nullable fields #310)
• Gene naming discussion (Additional gene annotation fields #295, Should we add fields for gene family and gene on rearrangements? #258)
• Find maintainer for updated XLS/XML sheets for NCBI submission (no issue yet)
• Fix MiAIRR Set 4 documentation (Fix NCBI implementation doc to represent changes to Set 4 #330)
• Annotation of chimeric subjects (How to indicate xenografted or transgenic animals #137, Representation of bone-marrow chimerism #334)
• Annotation of transgenes (How to indicate xenografted or transgenic animals #137)
• Document discussions around age field as a general example how to handle ranges and different units (separate magnitude and unit for age? #192)
• Deprecate ethnicity and race field (no issue yet)
• Deprecate MiAIRR field names and replace them with title property (Deprecate MiAIRR field name #380)

[bcorrie]

@bussec I wonder if we should include the Clone definition/extension in v2.0?
Open issues and pull requests:
#323, #317, #271
and closed pull requests:
#294, #256

[bussec]

I am not opposed to this in general, but I expect that especially #317 will be an can of worms, given our current discussions on #320. But we need to resolve this stuff at some point at its better rather sooner than later as a lot of things are blocked by this.

[bussec]

I am also not 100% sure whether clones actually affect MiAIRR... but they should be in the 2.0 release for sure.