What’s new in TTO

In past months, the TTO (Teleost Taxonomy Ontology) has undergone some changes that will, we hope, make it more useful by connecting it with other taxonomic resources. Here, I will discuss three changes that have been added since last January, but check as more (and important) connections will be coming soon.

When the TTO was first built, we followed the pattern of the NCBI taxonomic ontology that was generated from the NCBI taxonomy database. One design feature of this ontology was the inclusion of terms for taxonomic ranks (e.g., family, genus, etc.) as a separate ‘tree’ of terms with the same ontology. The ontology file contained two root nodes, one for taxon terms, the other for taxonomic rank terms. We had long felt that ranks should exist in a separate ontology (more correctly a vocabulary) that could be shared across ontologies for different taxonomic groups. After several rounds of discussion on the obo-discuss list, we were invited in January to add the taxonomic rank vocabulary to the OBO library of ontologies of interest.

This acceptance allowed us both to register the rank vocabulary and to finally strip out the tree of rank terms from TTO and replace the internal rank tags with ‘has_rank’ links to terms in the (external) rank vocabulary. However, the new rank vocabulary is more than just the set of ranks that we used in tagging taxa in TTO.  The rank vocabulary  incorporates rank terms from two additional sources: first the rank terms that appear in the NCBI taxonomy itself, and also terms from a rank vocabulary developed for TDWG.  We hope that other taxonomic ontologies will be able to make use of this vocabulary.

More recently, we have gone back to the NCBI taxonomy and added cross references between our terms and lexically identical names in NCBI.  As TTO’s names are mostly drawn from the Catalog of Fishes, the exact relation between TTO terms and NCBI names is not, in some cases clear, which lead to the decision to leave the relationship at the level of a cross reference.

In the same release (156), common names, contributed by FishBase were added as synonyms.  As of now, approximately 16,000 taxa have common names with cross references back to their source in FishBase.  We hope to be able to add more common names and eventually include appropriate language tags to these names.

I’ve already started work on our next integration target, but I’ll save that for a later post.

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