Transitive homology

This page explores the transitive closure of the homologous_to relation. Currently in OBD this is a binary class-level relation that holds between two taxon-specific anatomical entities.

I propose the following expansion to OWL-DL instance-level quantified axioms:

 homologous_to(A,B) ==>
 Class: A
 SubClassOf: descendedFrom some (hasDescendant some B)
 Class: B
 SubClassOf: descendedFrom some (hasDescendant some A)

If we make the simplifying assumption that directlyDescendsFrom is functional then it follows that class-level homology is transitive. What are the consequences of making this strong assumption? We can explore this with existing phenoscape data.

TAO classes with homology statements

from latest KB:

• TAO:0000429-scaphium Neural arch and Weberian ossicle that is reduced in size relative to other neural arches. Scaphium has a process which articulates with the first centrum.
• TAO:0000525-intercalarium Neural arch and Weberian ossicle that has been modified in shape relative to other neural arches. Intercalarium includes three parts: an anterolateral process (the manubrium) which is embedded in the interossicular ligament and the ascending and articulating processes.
• TAO:0000637-claustrum cartilage Postcranial axial cartilage and Weberian ossicle that is located dorsal to the scaphium. The claustrum cartilage is bilaterally paired.
• TAO:0000698-tripus Endochondral bone, membrane bone, and Weberian ossicle that is an element of third vertebra. Anteriorly it attaches to the interosseus ligament and posteriorly it extends as a transformator process embedded in the tunica externa of the swimbladder.
• TAO:0001171-os suspensorium Endochondral bone and Weberian ossicle that is an element of the fourth vertebra that curves ventrally around the anterior head of the swim bladder.
• TAO:0001592-claustrum bone Endochondral bone, membrane bone, and Weberian ossicle that is located dorsal to the scaphium. The claustrum bone is bilaterally paired.

High Level Overview

This is a high level part_of view of all homology relationships, projected onto TAO:

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• homology statements are generalized to the TAO, taxa not shown
• clusters of homology relationships are shown in 4 distinct boxes
• vertebra clustered into a box
• only relations shown are homology and part_of

Here we can see there are 4 distinct clusters, according to the vertebra number affected

Otophysi intercalarium

this is annotated to be homologous to the neural arch 2 and vertebra 2 in Teleosti. From this, what can be said of the relationship between these two entities?

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Note that for compactness reasons this diagram doesn't show the part_of relations.

• intercalarium part_of v2

presumably there should be some kind of relationship between "rib of v2" and "v2"

Otophysi tripus

this is annotated to be homologous to (i) the fusion of parapophysis + rib of v3 and (ii) the fusion of parapophysis + rib of v3 + rib of v4 in Teleosti. What can be said from this of the relation between (i) and (ii)

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