Difference between revisions of "VTO Taxonomy Resources"

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=Resources for Constructing a Vertebrate Taxonomy Ontology =
 
=Resources for Constructing a Vertebrate Taxonomy Ontology =
  
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There are two types of resources useful for building taxonomic ontologies: taxonomic resources which provide hierarchy and nomenclature resources which provide information about names.  Both types of resources are used in taxonomic ontologies and listed here.
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Note: The material on this section has been moved and incorporated into the main [[Ontologies]] page.
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== Fish ==
 
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The TTO is derived from the catalog of fishes, which provides some taxonomy information and a great deal of nomenclature in the form of synonyms.  It is updated several times a year and TTO should be rebuilt by requesting the appropriate files from Stan Blum.
 
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The TTO also incorporates some common names from Fishbase and cross references (xrefs) from the Global Names Index.
 
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Information for extinct taxa has been added as needed by curation, and the taxonomy is, as a rule, from the curated publication.
 
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== Amphibians ==
 
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The ATO is derived from the AmphibiaWeb list, which provides both taxonomy and some synonyms from ITIS and ???.
 
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== Birds ==
 
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IOU checklist provides a current taxonomy and some common names, but no taxonomic synonyms.
 
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== Mammals ==
 
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Wilson and Reader (1993) is the standard, but the available electronic version of their taxonomy is IP encumbered. NCBI and/or ITIS may be the best starting point.
 
  
 
= Tools =
 
= Tools =
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The tool source is available at [https://github.com/NESCent/Taxonomy-Ontology-Tool GitHub].
 
The tool source is available at [https://github.com/NESCent/Taxonomy-Ontology-Tool GitHub].
  
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== Generated Taxonomic Ontology ==
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== TTOUpdate ==
  
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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 version generated for the NESCent-sponsored Visual Systems Working Group is at [https://github.org/NESCent/Taxonomy-Ontology-Tool Github].
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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.
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== TTOUpdate ==
 
  
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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).  Do 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.
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[[Category:Taxonomy]]
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[[Category:Ontology]]

Latest revision as of 20:58, 1 November 2011

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.

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.

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