Q2 Semantic types

Hello everyone,

I was wondering if a detailed description of qiime2 feature-table semantic types exists? I found this repo which lacks any explanation

More specifically I would like to read about the difference between
FeatureTable[Composition] and FeatureTable[Frequency]

I assume that the first one represents the relative abundances when the second one represents actual counts. So, if we fit raw microbiome data it is FeatureTable[Composition] due to the compositional nature of microbiome data itself, and if we apply any sort of transformation, e.g., CLR then it becomes FeatureTable[Frequency]. That's how I understand it, but would like to verify:)

Thank you!

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The developer documentation has some pointers...

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Hi @Oleg ,

You have the right idea but the definitions are switched. FeatureTable[Frequency] consists of (usually raw) counts. FeatureTable[Composition] is rather vaguely named — but this was rather written to store compositionally aware (e.g., CLR transformed) counts.

See for example this function in the gemelli plugin, which accepts a FeatureTable[Frequency] table and outputs a CLR-transformed FeatureTable[Composition]:

A (partial) list of semantic type definitions exists here, but clearly could use a bit better description for the FeatureTable[Composition] type: