1 / 12

The Teleost Taxonomy Ontology: An Overview

The Teleost Taxonomy Ontology: An Overview. Peter Midford. Overview. Why a taxonomy ontology? What’s in the TTO? What’s?. Why a taxonomy ontology?. Ontologies support reasoning We needed a name resource responsive to our curation effort

lydia-serrano
Download Presentation

The Teleost Taxonomy Ontology: An Overview

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. The Teleost Taxonomy Ontology: An Overview • Peter Midford

  2. Overview • Why a taxonomy ontology? • What’s in the TTO? • What’s?

  3. Why a taxonomy ontology? • Ontologies support reasoning • We needed a name resource responsive to our curation effort • Curation of manuscript names, fossil taxa and others

  4. How is TTO structured? • Taxa are Ontology Classes • Ontology structure is simpler than TAO, but ontology is larger • Taxonomic ranks are annotations, not used for reasoning • Terms have synonyms • Types: taxonomic, common name, misspelling • Scopes: exact, broader, narrower, unknown • Terms may reference other resources

  5. Taxonomic Rank Ontology has_rank Teleostei Class is_a Ostariophysi is_a has_rank Siluriformes Order is_a has_rank Ictaluridae Family is_a has_rank "Elliops" Genus Ictalurus is_a "Channel Catfish" has_rank Ictalurus punctatus Species "Silurus punctatus"

  6. Alternative Models • Taxa as individuals • species as individuals • clades as individuals • Ranks as meta-classes • Taxa as qualities

  7. The Taxonomic Rank Vocabulary • 59 Terms for taxonomic ranks • Includes botanical synonyms (e.g., division) • Terms from • ranks used in the NCBI taxonomy • TDWG rank vocabulary • https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary

  8. Current Statistics Terms: 38,895 Orders: 60 Families: 551 Genera: 5107 Species: 30,865 Fossil Taxa: 154 Synonyms: 43215

  9. Catalog of Fishes TTOUpdate Where does TTO fit? Phenoscape KB TTO Phenex TAO Curation Effort

  10. Extracting from Catalog of Fishes • CoF files provided by William Eschmeyer and Stan Blum • Extract all cataloged names, attach synonyms to their valid names • Extract additional names from free-text comments and attach as synonyms • Write as OBO format ontology file

  11. Ongoing efforts • Linking to other resources • GNI (export TCS from TTOUpdate) • Cross reference to NCBI taxon ids • More common names (from Fishbase) • Ongoing improvements to name extraction in TTOUpdate

  12. Acknowledgements • William Eschmeyer for making CoF available (and Stan Blum for the export) • Phenoscape collaborators and curators • NESCent

More Related