Extensions/x-attribute
Synopsis
Logical definitions for "Regulation of Biological Attribute/Quality Terms"
URLs
- http://purl.obolibrary.org/obo/go/extensions/x-attribute.obo
- http://purl.obolibrary.org/obo/go/extensions/bio-attributes.obo
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