On this page... (hide)

  1. 1. Overview
  2. 2. Classification of phenes
  3. 3. Example ontology
  4. 4. Software implementation
  5. 5. OWLDEF patterns

1.  Overview

The basic pattern for defining a phene (phenotypic property) is

X equivalentTo: phene-of some Y

where Y specified the property of the entity with the phenotypic characteristic X.

2.  Classification of phenes

We further distinguish phenes of continuants (in BFO), endurants (in DOLCE) or presentials (in GFO) based on the relation that is needed to express Y. We distinguish:

  • qualitative phenes: phene-of some (has-quality some Y) and phene-of some (not has-quality some Y)
  • structural phenes: phene-of some (has-part some Y) and phene-of some (not has-part some Y)
  • dispositional phenes: phene-of some (has-disposition some Y and phene-of some (not has-disposition some Y)
    • using the has-disposition-realized-by pattern: phene-of som (has-disposition some (realized-by only Y) and phene-of some (not has-disposition some (realized-by only Y))
  • participatory phenes: phene-of some (participates-in some Y) and phene-of some (not participates-in some Y)

Top-level classification of phenes

3.  Example ontology

The example ontology is based on a fragment of the FMA and the Gene Ontology. In addition, the assertion that canonical pancreatic beta cells (from FMA) have a canonical function which is realized by Insulin secretion (from GO) is added, and the assertion that the canonical function realized by Insulin secretion is a function of beta cells is also added.

We have also converted two versions of the FMA according to our method, and explicitly distinguish between canonical and non-canonical entities. There is a version in OWL 2.0 (http://bioonto.de/fma1.owl) and another version in OWL 2.0 EL (http://bioonto.de/elvira-fma.owl) (converted to EL using the EL Vira software).

4.  Software implementation

To convert phenotype ontologies in the OBO Flatfile Format to OWL based on the patterns we provide, please use the OWLDEF software available here.

5.  OWLDEF patterns

We describe how to make canonical ontologies such as the FMA compatible with our method by redefining relations in these ontologies to explicitly refer to canonical entities. Based on our top-level ontology of phenes, we also provide OWLDEF patterns for their application in the OBO Flatfile Format:

Relation OWLDEF Example
CC-pheneOf-has-part ?X subClassOf Phene and pheneOf some (has-part some ?Y) having an appendix as part
CC-pheneOf-lacks-part ?X subClassOf Phene and pheneOf some not (has-part some

?Y)

not having an appendix as part
CC-pheneOf-part-of ?X subClassOf Phene and pheneOf some (part-of some ?Y) being part of an appendix
CC-pheneOf-not-part-of ?X subClassOf Phene and pheneOf some not (part-of some ?Y) not being part of an appendix
CC-pheneOf-has-quality ?X subClassOf Phene and pheneOf some (has-quality some ?Y) having a color
CC-pheneOf-lacks-quality ?X subClassOf Phene and pheneOf some not (has-quality some

?Y)

not having a size
CC-pheneOf-has-quality-value-of ?X subClassOf Phene and pheneOf some (has-quality some (?Y

and has-value some ?Z))

having color #4F1A33 (in RGB color space)
CC-pheneOf-lacks-quality-value-of ?X subClassOf Phene and pheneOf some (has-quality some (?Y

and not (has-value some ?Z)))

not having a mass of 0.12g
CC-pheneOf-has-quality-value-in ?X subClassOf Phene and pheneOf some (has-quality some (?Y

and has-value-in some ?Z))

being between 1.2 and 1.7 meters in height
CC-pheneOf-lacks-quality-value-in ?X subClassOf Phene and pheneOf some (has-quality some (?Y

and not (has-value-in some ?Z)))

not having between 13 and 18 gm/dL hemoglobin concentration
CC-pheneOf-has-disposition ?X subClassOf Phene and pheneOf some (has-disposition some

?Y)

being able to hear
CC-pheneOf-lacks-disposition ?X subClassOf Phene and pheneOf some not (has-disposition

some ?Y)

not being able to hear
CC-pheneOf-has-disposition-realized-

by

?X subClassOf Phene and pheneOf some (has-disposition some

(realized-by only ?Y))

being able to hear
CC-pheneOf-lacks-disposition-realized-

by

?X subClassOf Phene and pheneOf some not (has-disposition

some (realized-by only ?Y))

not being able to hear
CC-pheneOf-plays-p-role ?X subClassOf Phene and pheneOf some (plays-p-role some

?Y)

playing the role of catalyst within some process