VTO Taxonomy Resources

Resources for Constructing a Vertebrate Taxonomy Ontology

Note: The material on this section has been moved and incorporated into the main Ontologies page.

Tools

VTO Construction Tool

This tool uses a script to construct a taxonomic ontology by specifying a starting taxonomy, then modifying it by removing branches and splicing corresponding pieces of alternate taxonomies (e.g., start with the NCBI taxonomy and replace the teleost part of the tree with the tree from the TTO). It also allows taxonomic synonyms to be extracted from taxonomies or name lists and attached to terms in the taxonomy. Currently, the tool generates a taxonomy in the OBO format, though support for an individual-based OWL format is in progress.

The tool source is available at GitHub.

Generated Taxonomic Ontology

This taxonomy covers vertebrates and was built by starting with the NCBI taxonomy for vertebrates and splicing in TTO (except hagfish), ATO, and the IOC taxonomy of living birds. Synonyms from ITIS and Catalog of Life were attached if the primary name matched a name in the existing taxonomy. Subspecies names were added to their parent species as synonyms (not subclasses). The taxonomy is currently in the OBO format used for TTO and ATO, which includes the use of the Taxonomic Rank Vocabulary to tag taxa with specified rank. The current version of the VTO is here. The file is large so be patient when browsing or downloading.

TTOUpdate

This tool is used to merge an existing TTO with a Catalog of Fishes update file, which will consist either of a single Microsoft Access database or three Excel (2003) files (one each for lineages, genera, and species). Does not use CSV or tab-delimited text files as the free-text comments, which include extractable synonyms, contain commas, tabs and line breaks, so rendering the common text formats unusable. TTO update includes libraries for reading the pre-2007 Excel formats which properly handle the various breaking characters.