Extensions/x-attribute

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Synopsis

Logical definitions for "Regulation of Biological Attribute/Quality Terms"

URLs

Description

Terms under the GO regulation of biological quality node have simple logical definitions:

[Term]
id: GO:0030832  ! regulation of actin filament length
intersection_of: GO:0065007  ! biological regulation
intersection_of: regulates BATTO:0000011  ! actin filament length


The complexity is pushed to a separate ontology of attributes - currently in the GO extensions repo, but may be moved to a separate ontology maintained by multiple groups

[Term]
id: BATTO:0000011
name: actin filament length
is_a: BATTO:0000057 {is_inferred="true"} ! cellular component size
intersection_of: BATTO:0000001  ! biological attribute
intersection_of: affects_quality PATO:0000122  ! length
intersection_of: attribute_of GO:0005884  ! actin filament


Attribute Ontology

The attribute ontology is defined according to the general pattern

 'biological attribute' AND
    'affects quality' some PATO:nnnn AND
    'attribute_of' some <ENTITY> AND
    'occurs_in' some <OBJECT>

Note that the attributes are not themselves qualities. We use the occurs_in relation, which renders them occurrents, which is useful for describing a quality that changes over time. This also brings uniformity to the GO regulation pattern - the GO term "regulation of biological quality" is really regulating the progression of that quality through time.

Numbers

Counts are represented like this:

[Term]
id: BATTO:0000112
name: myofibril number
is_a: BATTO:0000001 ! biological attribute
intersection_of: BATTO:0000001  ! biological attribute
intersection_of: affects_quality PATO:0000070  ! count
intersection_of: attribute_of GO:0030016  ! myofibril

This is a departure from the previous pattern whereby we avoided terms like "count" which are not true qualities in the BFO sense since they do not inhere_in anything - we avoid the use of the inheres_in relation, although this may be implicit in the connection between the affected quality and the target of the attribute_of relation.

Locations

The location of the attribute is represented as follows:

[Term]
id: BATTO:0000041
name: calcium ion concentration in cytosol
is_a: BATTO:0000040 ! calcium ion concentration
intersection_of: BATTO:0000001  ! biological attribute
intersection_of: affects_quality PATO:0000033 ! concentration of
intersection_of: attribute_of CHEBI:39124 ! calcium ion
intersection_of: occurs_in GO:0005829 ! cytosol