These synonyms can now be used in searches of the Phenoscape Knowledgebase. For example, you can see the French synonyms for ‘paired fin’. One can imagine ultimately being able to select a preferred language or term label when browsing the ontology in the Knowledgebase.

These were the first set of foreign terms to be added to the teleost ontology, and we had to tweak the Phenoscape Knowledgebase interface to display the diacritical marks correctly. We are ready to accept more! Please send me anything you’d like added or changed to the TAO term tracker.

[1] Chanet, B., & Desoutter-Meniger, M. (2008). French-English glossary of terms found in Chabanaud’s published works on Pleuronectiformes. Cybium, Electronic Publication no 1:1-23. PDF download

We used the Synchronization Tool (an Obo-Edit plugin) to compare XAO to several external ontologies. The tool made it efficient to find and add missing cross-references and terms, and to resolve conflicting data (e.g., differing definitions). By the end of the week, we updated XAO with all relevant terms from the Amphibian Anatomy Ontology (AAO), Vertebrate Anatomy Ontology (VAO), Uber Ontology (UBERON), and Common Anatomy Reference Ontology (CARO).

Erik, VG, and Christina worked hard the rest of the week to make XAO is_a complete and to update definitions, relationships, and synonyms for existing terms. With XAO’s new release, the ontology is now 25% larger than before. The newest version of XAO will be available for downloaded soon from the OBO Foundry.

Open access links to online versions of the paper are given below:

Wasila M. Dahdul; John G. Lundberg; Peter E. Midford; James P. Balhoff; Hilmar Lapp; Todd J. Vision; Melissa A. Haendel; Monte Westerfield; Paula M. Mabee.  2010.  The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age.  Systematic Biology.  View full text or download PDF.

The ‘5 K Karacters Goal’ was much more ambitious that we realized, resulting in the addition of 205 terms to the Teleost Anatomy Ontology, and more to other ontologies (Phenotype and Trait Ontology, Spatial Ontology, Teleost Taxonomy Ontology). At the end of the curation drive, 4,174 out of 5,445 characters were curated. This resulted in 243,577 phenotypes (unique taxon-phenotype assertions) — now up to 333,987 phenotypes (see tally at kb.phenoscape.org).

Peter Midford and I recently attend the two-day Relations Ontology workshop in Denver, Colorado. The goal of the meeting was to further develop the Relations Ontology (RO) by moving relations from RO proposed (ontology for relations yet to be officially added to RO) to RO, and adding any new relations proposed by attendees. Impressively, almost all of the items on the original agenda were covered, and an ‘action list’ was produced to focus efforts subsequent to the meeting.

Phenoscape had several relations on the agenda, and Peter and I have summarized the discussion, definitions, and examples used.

On Monday afternoon, Wasila and Peter presented proposals for the following relations for the section organized by Suzi Lewis and Melissa Haendel on spatial relations:

1. Overlaps

Peter presented examples and definition for overlaps. Overlaps is particularly useful for Phenoscape so that we can represent a joint without having to create new terms for the parts of bones that participate in the joint. We can simply say, for example, that bone X overlaps joint XY. After brief discussion, it was decided that this relation will be added to RO with the proposed definition.

Examples:

bone overlaps joint

axon overlaps axon tract

definition:

X overlaps Y =def. for every t and every x, if x instance_of X at t, then there is some instance y of Y at t such that (x overlaps y at t)

where

x overlaps y at t =def there is some z such that z is part_of x at t and z part_of y at t

Note that it can be the case that X overlaps Y as thus defined, even though Y does not overlaps

2. Attached_to and connected_to:

Wasila presented examples of these two relations and definitions given by the FMA (although the FMA definitions are reversed from how we use them in our use cases). There was discussion of whether or not it is useful to distinguish between fiat and bona fide boundaries, whether a single “connected” relation could suffice for all use cases, and whether a force-connected definition would be better to use. However, the overriding point was that biologists clearly make the distinction between attached and connected, and it was decided that attached_to and connected_to would be added to RO pending development of their formal definitions.

Examples:

tooth attached_to bone

muscle attached_to bone

axon connected_to neuropil

3. Spatial Ontology

Wasila presented examples of how Phenoscape uses the Spatial Ontology, and much discussion centered on how to improve this relatively new and little used ontology. Some classes (e.g., anatomical region, anatomical surface) should be moved to CARO, and reference images would be helpful in providing examples for the different anatomical axes.

Homologous_to relation

We presented a proposal for homology relations on Tuesday morning. Melissa started with a couple of background slides and Peter continued with a presentation of the definition we developed as a group on Monday night. That definition was revised again on Tuesday afternoon and the Tuesday afternoon revision can be found below. It, along with earlier revisions is available on the wiki page (http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_homologous_to_relation).

Directly_descends_from – This is currently defined as follows

Example: Child’s arm directly_descends_from parent’s arm

definition:

x1 directly_descends_from x2 iff there are y1, y2 such that:

• y1 is an organism
• x1 is an anatomical structure
• x1 part_of y1
• y2 is an organism
• x2 is an anatomical structure
• x2 part_of y2
• y2 is a parent of y1
• the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of x2*.

* This clause still needs some work. Jim Balhoff added the following critique in discussion on the Phenoscape project list:

[Something that jumps out at me in the definition of directly_descends_from:

I would not say that genetic sequences "determine" any morphology. I would prefer something like "participates in the development of" the morphology of x1. Anyway, I don't see genetic sequences as an absolutely necessary component of homology (although they would very often be an important component).]

Descends_from – This is currently defined as follows:

Example: My arm descends_from ancestral primate forelimb.

definition:

descends_from is the instance level relation which is the transitive closure over directly_descends_from:

A in B descends_from C in D:

For all A(a) -> exists b, d, c: B(b) & C(c) & D(d)

• a part_of b
• a descends_from c
• c part_of d

(Note – B must be a subclade of the clade descending* from D)

Homologous_to – Defined for classes of anatomical structures and clades

Example: Human arm homologous to robin wing.

definition:

A1 in B1 homologous_to A2 in B2 iff exists A3, B3:

• A1 in B1 descends_from A3 in B3 &
• A2 in B2 descends_from A3 in B3

(Note B1 and B2 must both be subclades of the clade descending* from D)

(*In the genealogical sense)

After presenting the definition, Peter presented a number of examples of character optimization – these included a schematic overview and a tree of bilateralians with a reconstruction that indicated that a heart was not present in the most recent common ancestor of bilateralians. There were also other examples that indicated different common ancestors and presence/absence of homology for traditional and Ecdysozoa/Lophotrochozoa-based phylogenies. The presentation finished with a discussion of the homology evidence codes and their use in Phenote.

We are uncertain of the need to include time (e.g., replace the atemporal usage of exists with temporally scoped exists and existed). Fabian suggested that just to be on the safe side we can include time – it’s not useful but it could stop some people complaining and it won’t affect the logic at all.

This definition mentions clades, avoiding the issue of whether taxa are individuals, classes or both.

We will be revisiting these definitions in the future.

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.

The other good update from the Bioportal development is that terms can now be found by their synonyms as well. For example, try searching TAO for the ‘dermosphenotic’, which at present isn’t the name of a term in the ontology. Instead, you get the ‘infraorbital 5‘, for which dermosphenotic is a synonym.

Fish morphologists will note that this is actually problematic, since in reality the dermosphenotic is the synonym for the last infraorbital bone. In zebrafish, with which we seeded the TAO, this is indeed the 5th in the series of infraorbitals, but in other clades of teleosts it is the 6th or yet another one. But that’s another story, which we’ll highlight in a forthcoming post on building the TAO.

The ontologies were deposited into the OBO versioning system already in November, but a database loading problem prevented their functioning in the BioPortal browser earlier.