Extending taxonomy info (adding new levels) in BIOM format

Ideas and Suggestions
1

I have a question related to the taxonomy format supported by QIIME and BIOM, namely there are seven different taxonomic ranks and prefixes in use - kgd (k__), phy (p__), cls (c__), ord (o__), fam (f__), gen (g__), and spe (s__).

Is it possible to somehow incorporate other taxonomic levels (OTU classifications) here, e.g. BOLD BINs (International Barcode of Life project (iBOL) Barcode Index Numbers (BINs)) or UNITE SHs (UNITE - Unified system for the DNA based fungal species linked to the classification), so that these could be used as complementary information in the subsequent QIIME community analysis.

If it's not possible to indicate their presence in the taxonomy attribute, how would you suggest including this information in the BIOM file.

2

HI @Kessy_A, welcome to :qiime2:!

You can add any number or type of taxonomic ranks with or without rank prefixes. The only "requirement" is to have the ID and taxonomy separated by a tab, and then the taxonomic ranks should be separated by a semi-colon. If you'd like to add extra ranks and their own unique rank prefixes you can follow the approach we take with RESCRIPt.

That is, behind the scenes, we've opted to use these prefix-rank associations.

1 Like