Table 2

Translation between variables in EQ templates and logic based OBO or OWL class intersections

EQ syntax

OBO syntax

OWL Manchester syntax


E = <E>

Intersection_of: <Q>

<Q> that inheres_in some <E>

Q = <Q>

Intersection_of: inheres_in <E>

E = <E>

Intersection_of: <Q>

<Q> that inheres_in some <E>

Q = <Q>

Intersection_of: inheres_in <E>

and towards some <E2>

E2 = <E2>

Intersection_of: towards <E2>

E = <E>

Intersection_of: <Q>

<Q> that inheres_in some <E>

Q = <Q>

Intersection_of: inheres_in <E>

and has_qualifier some <E2>

M = <M>

Intersection_of: has_qualifier <M>


Phenotypes can be written using EQ syntax or as logical expressions in general purpose ontology languages such as OBO or OWL. Template variables are indicated by the angle brackets. For example, if <E> = 'femur' and <Q> = 'decreased diameter', then the OWL expression would be decreased_diameter that inheres_in some femur. Note that the qualifier relation is not yet in the Relations Ontology and is not formally defined, and is used as a placeholder for now.

Mungall et al. Genome Biology 2010 11:R2   doi:10.1186/gb-2010-11-1-r2

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