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Rename "subtype" to "genotype" #41
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Following from #48 (comment), expanding the scope of this issue to establish standard metadata column names pertaining to Dengue serotype, genotype, and the various methods we employ to derive them for a specific strain (NCBI, Nextclade, augur clades (Nextstrain)). Below is a proposed standardization along with suggested modifications:
Feel free to suggest other naming conventions along with written justification. This also leaves room for the potential inclusion of |
Thanks for this very organized summary! Based on comments here, we may want to use |
Thanks for linking some more recent discussion on naming! I'm open to changing I ran a quick PubMed search and it looks like the dengue literature uses
|
It's probably a good idea to change from |
Thanks for clarifying as an optional path, I went ahead and updated the table above accordingly |
Context
In response to comment:
Description
Currently we have
ncbi_serotype
because we are relying on "NCBI" annotation as the source of serotype assignment. No change to the column name herenextclade_subtype
because we are using "nextclade" for genotype assignment. Rename this to "nextclade_genotype"Of course feel free to comment on this GitHub Issue with other suggestions.
Optionally, we could reorder the metadata columns such that
ncbi_serotype
andnextclade_genotype
are next to each other to make this distinction more obvious to people manually looking at the metadata file.The text was updated successfully, but these errors were encountered: