Difference between revisions of "Transitive homology"

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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.
 
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.
  
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== TAO classes with homology statements ==
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from latest KB:
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{|class="wikitable" style="text-align:center" border="1"
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|-
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! ID
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! name
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! Def
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|-
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| TAO:0000429
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| scaphium
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| 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.
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|-
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| TAO:0000525
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| intercalarium
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| 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.
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|-
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| TAO:0000637
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| claustrum cartilage
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| Postcranial axial cartilage and Weberian ossicle that is located dorsal to the scaphium. The claustrum cartilage is bilaterally paired.
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|-
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| TAO:0000698
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| tripus
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| 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.
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|-
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| TAO:0001171
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| os suspensorium
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| Endochondral bone and Weberian ossicle that is an element of the fourth vertebra that curves ventrally around the anterior head of the swim bladder.
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|-
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| TAO:0001253
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| neural arch 2
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| Neural arch that is the second after the neurocranium.
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|-
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| TAO:0001335
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| supradorsal
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| 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).
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|-
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| TAO:0001396
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| parapophysis + rib of vertebra 4
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| The parapophysis + rib, fused to the centrum, extends laterally then angles anteroventrally. A thin plate, the os suspensorium fuses to its median surface.
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|-
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| TAO:0001592
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| claustrum bone
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| Endochondral bone, membrane bone, and Weberian ossicle that is located dorsal to the scaphium. The claustrum bone is bilaterally paired.
 +
|-
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| TAO:0001877
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| neural arch 1
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| Neural arch that is the anteriormost neural arch.
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|-
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| TAO:0001878
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| rib of vertebra 2
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| Rib that articulates with the parapophysis of the second centrum.
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|-
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| TAO:0001884
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| accessory neural arch
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| 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.
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|-
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| TAO:0001885
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| neural spine 1
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| Neural spine that is associated with the first vertebra.
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|-
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| TAO:0001888
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| supraneural 1 bone
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| Supraneural bone located dorsal to vertebra 1.
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|-
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| TAO:0001889
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| supraneural 1 cartilage
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| Postcranial axial cartilage located dorsal to vertebra 1.
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|}
 
== High Level Overview ==
 
== High Level Overview ==
  

Latest revision as of 02:29, 18 March 2010

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:

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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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