OWL modeling of EQ phenotypes

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 (Dependent 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

"Local" 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 of a class ("not" in Manchester syntax) rather than negation of a statement:

shape that inheres_in some opercle and not round

Presence/absence phenotype

The presence or absence of a structure should be expressed a negation of the has_part property. For example, "frontal bone, absent":

not (has_part some frontal)

For "present":

has_part some frontal

If the absence is within a particular structure:

has_part some (dorsal_fin that not (has_part some actinotrichium))

Count phenotype

Counts can be expressed as a generalization of presence/absence. Both exact counts and maximum or minimums can be expressed. So, for the character "Number of scales on dorsal fin", state 0: 45, state 1: >45,

state 0:

has_part some (dorsal_fin that has_part exactly 45 scale)

state 1:

has_part some (dorsal_fin that has_part min 46 scale)

Measurements

A direct measurement of the magnitude of some quality of a structure.

length that inheres_in some femur and has_measurement some (has_quantity value 10.3f and has_unit value cm)

The properties has_measurement, has_quantity, and has_unit need to be standardized - there may be some in OBO_REL that can be used. This version assumes that cm is available as an individual in some units terminology.