Minutes_MiniStd_2019 10 - airr-community/airr-standards GitHub Wiki
- Species information for cell and locus annotations (#137)
- Rename MiAIRR field "Organism" to "Species" (#266)
- Human Population Genetics XT (#264)
- Date: Fri, 2019-11-08 14:30 UTC
- Present: Ahmad, Brian, Christian, Florian, Francisco, John, Sri
- Inclusion of species information for cell and locus annotations
(#137) was approved.
- Introduction of the fields
cell_speciesandlocus_species, will be added to the schema via #260. - Principle of "layering" (i.e. specialized keys deeper down in in the schema hierachy can override more general definitions of the same feature that took place further up) will be added to the docs.
- Introduction of the fields
- Rename "Organism" to "Species":
- The designation for this field is formally incorrect as an organism is an individual of a species, not the species itself. However, it is the latter one that we are aiming to annotate in this field. This could lead to confusion when using the term as a suffix (e.g., #137). The current term is derived from the INSDC Feature Table, which uses rather creative semantics to make it fit.
- There is a consensus that the MiAIRR name should be changed. As
this breaks compatibility it will be slated for inclusion in
AIRRv2. Whether the key
organismwill be changed at the same time, is up for discussion with with DataRep (#266).
- Human Population Genetics XT: We will get feedback from GLDB WG in their November call. The proposal will be put to a vote in MiniStd Call 2019-11, please comment on Github (#264, #265).
- Documentation of effective changes to the standard/schema: While nearly all changes made to the standard over the last two years are documented in some Github ticket, there is no comprehensive log that would summarize all changes. DataRep will discuss how they think this can be done with creating too much overhead.
- Deprecation vs. renaming of fields: While we have a procedure to document deprecation of fields (#248), it is unclear how to document renaming, especially how to keep the information what the new field name is.
- Relation between MiAIRR Set 6 and DataRep
Rearrangement:- This has been an area of overlapping responsibility for some time. Although it has not been an issue until now that two WG basically define similar items, it is probably time to get this sorted out.
- As DataRep is the larger stakeholder, the proposal is that they set the standard definition for rearrangement data (e.g, as published in [Vander Heiden, 2018]). The MiAIRR "Set 6" would then be described as the subset of rearrangement fields from the DataRep standard that are recommended as the minimal information that one should store in INSDC repositories. For these fields, MiniStd will provide a mechanism for mapping the data to the INSDC Feature Table.
- Essentially, DataRep becomes the owner/definer of rearrangement data fields. MiniStd would no longer define these fields, but it would identify a subset of the rearrangement fields defined in the DataRep standard that it considers minimal via the inclusion of these fields into MiAIRR Set 6. In addition, implementations of MiAIRR would provide a mechanism/procedure for mapping those minimal rearrangement fields to the INSDC repositories.
- DataRep will discuss this on Monday.
- John: Are there current statistics on how many AIRR data sets are available via SRA/Genbank/TLS? No, Christian will collect these numbers for the next call.
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