Q2 Semantic types

Oleg · February 2, 2022, 11:40pm

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!

cdiener · February 3, 2022, 12:43am

The developer documentation has some pointers...

Nicholas_Bokulich · February 3, 2022, 11:45am

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]:

github.com

biocore/gemelli/blob/master/gemelli/q2/plugin_setup.py#L66-L82


plugin.methods.register_function(
    function=rclr_transformation,
    inputs={'table': FeatureTable[Frequency]},
    parameters=None,
    outputs=[('rclr_table', FeatureTable[Composition])],
    input_descriptions={'table': DESC_BIN},
    parameter_descriptions=None,
    output_descriptions={'rclr_table': 'A rclr transformed table. '
                                       'Note: zero/missing values have NaNs'},
    name='Robust centered log-ratio (rclr) transformation.'
         'Note: This is run automatically '
         ' within CTF/RPCA/Auto-RPCA so there no '
         'need to run rclr before those functions.',
    description=("A robust centered log-ratio transformation of only "
                 "the observed values (non-zero) of the input table."),
    citations=[citations['Martino2019']]
)

A (partial) list of semantic type definitions exists here, but clearly could use a bit better description for the FeatureTable[Composition] type:
https://docs.qiime2.org/2021.11/semantic-types/#common-semantic-types