VTO Taxonomy Resources

From phenoscape

Resources for Constructing a Vertebrate Taxonomy Ontology

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


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.


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.