Abstract
BackgroundNCBI Taxonomy is the main taxonomic source for several bioinformatics tools and databases since all organisms with sequence accessions deposited on INSDC are organized in its hierarchical structure. Despite the extensive use and application of this data source, an alternative representation of data as a table would facilitate the use of information for processing bioinformatics data. To do so, since some taxonomic-ranks are missing in some lineages, an algorithm might propose provisional names for all taxonomic-ranks.ResultsTo address this issue, we developed an algorithm that takes the tree structure from NCBI Taxonomy and generates a hierarchically complete taxonomic table, maintaining its compatibility with the original tree. The procedures performed by the algorithm consist of attempting to assign a taxonomic-rank to an existing clade or “no rank” node when possible, using its name as part of the created taxonomic-rank name (e.g. Ord_Ornithischia) or interpolating parent nodes when needed (e.g. Cla_of_Ornithischia), both examples given for the dinosaur Brachylophosaurus lineage. The new hierarchical structure was named Taxallnomy because it contains names for all taxonomic-ranks, and it contains 41 hierarchical levels corresponding to the 41 taxonomic-ranks currently found in the NCBI Taxonomy database. From Taxallnomy, users can obtain the complete taxonomic lineage with 41 nodes of all taxa available in the NCBI Taxonomy database, without any hazard to the original tree information. In this work, we demonstrate its applicability by embedding taxonomic information of a specified rank into a phylogenetic tree and by producing metagenomics profiles.ConclusionTaxallnomy applies to any bioinformatics analyses that depend on the information from NCBI Taxonomy. Taxallnomy is updated periodically but with a distributed PERL script users can generate it locally using NCBI Taxonomy as input. All Taxallnomy resources are available at http://bioinfo.icb.ufmg.br/taxallnomy.
Highlights
NCBI Taxonomy is the main taxonomic source for several bioinformatics tools and databases since all organisms with sequence accessions deposited on International Nucleotide Sequence Database Collaboration (INSDC) are organized in its hierarchical structure
In this work, we developed an algorithm that carefully takes the taxonomic tree provided by NCBI Taxonomy and generates a hierarchical taxonomic tree in which all lineages have the same depth and all hierarchical levels corresponding to a taxonomic-rank, it can be handled as a table of 41 columns
Several bioinformatics analyses and tools rely on the taxonomic information provided by NCBI Taxonomy
Summary
NCBI Taxonomy is the main taxonomic source for several bioinformatics tools and databases since all organisms with sequence accessions deposited on INSDC are organized in its hierarchical structure. Any analyses that involve molecular sequences are dependent on the NCBI Taxonomy [8], a reference taxonomic database with a huge compilation of taxonomic names and lineages of organisms that have a register of their DNA or protein sequence in one of the databases comprising the International Nucleotide Sequence Database Collaboration (INSDC) [9]. Since INSDC comprises the three main molecular sequence repositories, GenBank, ENA, and DBJJ, the information provided by NCBI Taxonomy is broadly used in biological databases covering diverse subjects that rely on data from INSDC, such as UniProtKB [10], Ensembl [11], Pfam [12], SMART [13], Panther [14], OMA [15] and miRBase [16]. Other main primary biological databases, such as PDB [17], ArrayExpress [18], and KEGG [19] link their accessions to taxonomic data from the NCBI Taxonomy database, demonstrating the undeniable contribution of this database to several bioinformatics fields
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