MiGA is taxonomy-agnostic, which means that the same tools and
techniques can be applied to different reference taxonomies.
However, it is important to maintain a standardized scheme for
a given database if we want to leverage that database on
classification. For that reason, MiGA implements a top-level
taxonomic rank called
namespace, which tells us the taxonomic
scheme being followed. Some common schemes include:
-
SeqCode: Following the reference taxonomy reported by
The Code of
Nomenclature of Prokaryotes Described from Sequence Data
(SeqCode). This taxonomy should be fully compatible with
NCBI, but may not be compatible with some specific nodes
of GTDB.
-
NCBI: Following the taxonomy curated and maintained by
NCBI
Taxonomy. This taxonomy mostly follows the recommendation of
The International Code of Nomenclature of Prokaryotes
(ICNP), and should be fully compatible with SeqCode.
-
GTDB: Following the taxonomy curated and mainteined by
the Genome
Taxonomy Data Base. This taxonomy introduces a complete
taxonomic tree from species to phylum, but it includes some
temporary alpha-numeric identifiers that don't follow binomial
nomenclature as recognized by either ICNP or SeqCode. Therefore,
it can be incompatible with SeqCode and NCBI, but
it offers non-missingness as well as largely standardized ranks
on the basis of Relative Evolutionary Distances.
For additional information, please see the links above and the
associated publications.
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