OWL modeling of EQ phenotypes

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Revision as of 15:13, 20 October 2010 by Jpb15 (talk | contribs)

This page documents OWL class expressions for particular categories of phenotypes modeled as EQs. This is to provide explicit examples of EQs representing common character types and also to help clarify a classification of phenotypes. This classification will be helpful when communicating about these phenotypes and also for directing design of curatorial user interfaces facilitating input of various types of EQs. The examples all use the OWL Manchester syntax.

Basic phenotype

A quality of a singe physical entity. Example: “sigmoid-shaped supraorbital bone”:

sigmoid that inheres_in some supraorbital_bone

Relational phenotype

Relational qualities are those that exist between multiple entities. For example, “parietal fused with supraoccipital” is represented as:

fused_with that inheres_in some parietal and towards some supraoccipital

Comparative phenotype

In the systematics literature, the size of a structure is often compared to the size of different structure, or it is compared to the same structure in another taxon.

Compared to another structure

For example, an author may compare the length of one bone relative to another (e.g., state 0: "frontal length greater than parietal length" vs. state 1: frontal length shorter than parietal length"). State 0 is represented as:

length that inheres_in some frontal and increased_in_magnitude_relative_to some (length that inheres_in some parietal)

Compared to same structure in another taxon

Comparison of the length of one bone across species (e.g., “state 0: frontal large” vs. “state 1: frontal small”, with taxonomic distribution recorded in the character by taxon matrix).

Reference to a particular taxon

When referencing a particular (possibly outgroup) taxon:

length that inheres_in some frontal and increased_in_magnitude_relative_to some (length that inheres_in some frontal and in_taxon some Ictaluridae)

Local relative phenotypes without explicit taxonomic references

"Anonymous" relative length classes must be defined for the character and then used across all phenotype annotations for that character:

Class: character_1_state_0

  • EquivalentTo: length and inheres_in some frontal and increased_in_magnitude_relative_to some character_1_state_1

Class: character_1_state_1

  • EquivalentTo: length and inheres_in some frontal and decreased_in_magnitude_relative_to some character_1_state_0

Complementary phenotype

Many characters are of this form - character: "shape of opercle"; state 0: "round", state 1: "not round". The author is not specifying what the shape of the opercle in state 1 is except that it is not round. This is more usefully expressed as complementation rather than negation:

shape that inheres_in some opercle and complement_of round

Presence/absence phenotype

Count phenotype

Measurements