The Teleost Anatomy Ontology

The Teleost Anatomy Ontology (TAO) is a multi-species anatomy ontology for teleost fishes.  In this first post about the TAO, I’ll introduce the structure of the ontology and its development, and discuss some of the challenges we’ve come across in building a multi-species ontology. You can browse the TAO by using the NCBO BioPortal.

Development of the TAO

The TAO was originally cloned on the Zebrafish Anatomy Ontology (ZFA), and the upper level classes in both ontologies (e.g., anatomical structure, portion of organism substance) are based on the Common Anatomy Reference Ontology (CARO).  Current development of the TAO is concentrated on the skeletal system, which is often the focus of morphology-based evolutionary studies in ichthyology, owing to the fact that it varies significantly across teleosts and is well-preserved in fossil specimens.  Terms (classes) in the TAO have relationships to other terms, for example:

extrascapular is_a dermal bone

extrascapular part_of pectoral girdle

Growth of the TAO is enabled by term requests from data curators and the ichthyological community, and the TAO is updated frequently to include new terms, refined definitions, synonym additions, and structural changes. We currently maintain manual synchronization of the TAO and ZFA, but a synchronization tool is in development and will help us automate this process. Synchronization between the multi-species TAO and a single-species ZFA presents the challenge of maintaining equivalent structural hierarchies between the two ontologies.  This is because the addition of new terms to the TAO can sometimes require the creation of parent terms necessary for the TAO but redundant for the ZFA (see TAO and ZFA synchronization). 

Synonyms

Accommodating different names (synonyms) used to refer to the same bone is another challenge in building a multi-species anatomy ontology.  Ontologies accommodate synonyms by designating a primary term name along with assigned synonyms; for example, extrascapular is a primary term in the TAO, with supratemporal recorded as its synonym. Of course, different communities of taxonomic experts may have preferences for one term over another, and we plan to allow users of our future database to choose their ‘preferred term’ when using our tools. 

Representing synonyms is usually a straightforward exercise, but we’ve recently come across a situation in which a bone name will need to be designated as both a primary term name and a synonym of another primary term. The infraorbital series is a set of bones that typically lie below and posterior to the eye in fishes.  The general condition for teleosts is that the last bone of the series is the dermosphenotic, which is often times referred to in the ichthyological literature by its position in the series.  For example, the dermosphenotic is called infraorbital 5 in cyprinid fishes (including Danio rerio), whereas it is called infraorbital 6 in characiform fishes. In order to represent the usage of these terms in the TAO, dermosphenotic will be a primary term with several synonyms including ‘infraorbital 5’ and ‘infraorbital 6’, names that are also primary term names. I’m currently working up definitions for these terms, and you’ll see the proposed definitions shortly on the TAO term tracker.

New anatomical relations

The addition of new terms is not the only way that the TAO is developing.  Peter Midford and I attended the Relations Ontology meeting earlier this week to discuss our need for several new anatomical relations, including attached_to, connected_to, and homologous_to. In an upcoming post, we’ll summarize the results of the meeting and provide examples of our use of the new relations.   The new relations will be added to the next version of the Relations Ontology, and therefore available for use in the TAO.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

Follow

Get every new post delivered to your Inbox.

Join 577 other followers

%d bloggers like this: