Taxallnomy

Description:

    Taxallnomy is an extension of NCBI Taxonomy in which all taxa comprising it are organized in a balanced hierarchy, i.e all leaf (end) nodes are in the same hierarchical level.

    The creation of taxallnomy was motivated by the fact that the taxonomic tree provided by NCBI Taxonomy is unbalanced and several taxa on it miss for some ranks. Since NCBI Taxonomy is the main source of taxonomic information, the lackness of those ranks could turn in a complicated issue for those analyses that rely on the rank classification of the organisms, e.g. metagenomic profiles and phylogenetic tree annotations.

    So, we created an algorithm that takes the taxonomic tree from NCBI Taxonomy and fulfill all those missing ranks in a lineage by assigning ranks to an unranked node or by deleting unranked nodes throughout the tree. The result of this process is a balanced taxonomic tree in which each level corresponds to a taxonomic rank defined in the Linnean classification system and used by NCBI Taxonomy (e.g. Kingdom, Phylum, Class, etc.).

    In this web interface, you'll be able to explore the taxallnomy's hierarchical structure and query for taxonomic lineage with all ranks for those organisms comprising the NCBI Taxonomy. Please enjoy!

Database last update:

Enter here your input:

Try adding these Genus txids: 9030, 8500, 8507, 28376, 8468, 643744, 436494

Tree edition:
Font size: 12
Text angle: 40
Node Distance (x): 18
Node Distance (y): 10

Select taxonomic ranks:
Main ranks
Common ranks
All ranks
None

Tree structure:
Balanced tree
Original tree (NCBI Taxonomy)

Show/hide nodes by category:

Download result:
SVG
PNG (for smaller image)
Tabular
JSON
XML

Legend:

Taxon originally ranked on NCBI Taxonomy tree.

Taxon originally unranked on NCBI Taxonomy tree.

It was ranked by Taxallnomy algorithm (type 1).

Taxon created by Taxallnomy algorithm.

Its child taxon name was used to name it (type 2).

Taxon created by Taxallnomy algorithm.

Its parent taxon name was used to name it (type 3).

Unranked taxon (no rank) either in NCBI Taxonomy or taxallnomy tree.

Taxon in unclassified group.

Mouse commands:

Click on nodes: collapse;
Double-click on nodes: get children;
Shift+click on nodes: delete node;
drag & drop: drag tree.

Taxallnomy numbers:

Taxallnomy API for programmatic access to database:

    URL:

    Parameters:

    • txid: Taxonomy IDs separated by comma. E.g. 9606,9595,10090
    • rank (main|common|custom, default: common): taxonomic ranks to retrieve;
      • main: retrieves Superkingdom, Phylum, Class, Order, Family, Genus, Species.
      • common: retrieves the "main" taxonomic ranks plus Kingdom, Subphylum, Super- and Sub- of Class, Order and Family; Subgenus and Subspecies.
      • custom: retrieves the taxonomic ranks specified by the user (Requires srank).
    • srank: Specify the taxonomic ranks to be retrieved. Use this parameter along with custom option on rank parameter. Use comma between rank names. See here the valid rank names.
    • format (tab|json|xml, default: tab): output format.

    Some examples:

Download Taxallnomy database:

    If you intend to retrieve a lot of data, please consider downloading Taxallnomy database and loading it in a local MySQL database. Taxallnomy can be obtained at Taxallnomy SourceForge page.

    Script that generates the Taxallnomy database is available at GitHub page.

Citation:

    If you are using Taxallnomy, please consider citing our preprint. Details on the Taxallnomy algorithm can be also found in the manuscript.

    Sakamoto, T., Ortega, J.M. Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree. BMC Bioinformatics 22, 388 (2021). https://doi.org/10.1186/s12859-021-04304-3

Contact:

    If you have any suggestion to improve our work or any question, feel free to contact us by these email addresses:

  • tetsu@imd.ufrn.br (PhD Tetsu Sakamoto)
  • miguel@icb.ufmg.br (PhD J. Miguel Ortega)

Laboratório de Biodados

Universidade Federal de Minas Gerais
Belo Horizonte - Brazil