Difference between revisions of "Transitive homology"

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   SubClassOf: descendedFrom some (hasDescendant some A)
 
   SubClassOf: descendedFrom some (hasDescendant some A)
  
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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.
 +
 
 +
== TAO classes with homology statements ==
 +
 
 +
from latest KB:
 +
 
 +
{|class="wikitable" style="text-align:center" border="1"
 +
|-
 +
! ID
 +
! name
 +
! Def
 +
|-
 +
| 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
 +
| 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
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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
 +
| 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
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| Rib that articulates with the parapophysis of the second centrum.
 +
|-
 +
| 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.
 +
|-
 +
| TAO:0001889
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| 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:
 +
 
 +
[[Image: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 ==
 
== Otophysi intercalarium ==
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[[Image:TAO-0000525-TTO-352.png]]
 
[[Image: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 ==
 
== Otophysi tripus ==

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:

Error creating thumbnail: Unable to save thumbnail to destination
  • 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?

Error creating thumbnail: Unable to save thumbnail to destination

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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