Transitive homology

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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:

ID name Def
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:0001253 neural arch 2 Neural arch that is the second after the neurocranium.
TAO:0001335 supradorsal Supradorsals are small paired nodules of cartilage positioned at the distal ends of neural arches and the proximal end of neural spines (Arratia et al., 2001).
TAO:0001396 parapophysis + rib of vertebra 4 The parapophysis + rib, fused to the centrum, extends laterally then angles anteroventrally. A thin plate, the os suspensorium fuses to its median surface.
TAO:0001592 claustrum bone Endochondral bone, membrane bone, and Weberian ossicle that is located dorsal to the scaphium. The claustrum bone is bilaterally paired.
TAO:0001877 neural arch 1 Neural arch that is the anteriormost neural arch.
TAO:0001878 rib of vertebra 2 Rib that articulates with the parapophysis of the second centrum.
TAO:0001884 accessory neural arch Neural arch that is located posterior to the neurocranium and anterior to neural arch 1. The accessory neural arch is not associated with a vertebral centrum.
TAO:0001885 neural spine 1 Neural spine that is associated with the first vertebra.
TAO:0001888 supraneural 1 bone Supraneural bone located dorsal to vertebra 1.
TAO:0001889 supraneural 1 cartilage Postcranial axial cartilage located dorsal to vertebra 1.

High Level Overview

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

TAO-all-p.png

  • 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?

TAO-0000525-TTO-352.png

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)

TAO-0000698-TTO-352.png