Extensions/x-attribute: Difference between revisions
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When new terms are added to VT or TO they may end up duplicating what is in BATTO. In these cases, the BATTO term will be obsoleted and replaced_by the relevant term. | When new terms are added to VT or TO they may end up duplicating what is in BATTO. In these cases, the BATTO term will be obsoleted and replaced_by the relevant term. | ||
We periodically bring in the latest VT and TO ontologies plus associated logical definitions - http://code.google.com/p/phenotype-ontologies/ | We periodically bring in the latest VT and TO ontologies (plus associated logical definitions - http://code.google.com/p/phenotype-ontologies/ ). See the Makefile for details. | ||
[[Category:Regulation]] | [[Category:Regulation]] | ||
[[Category:Cross Products]] | [[Category:Cross Products]] |
Revision as of 14:42, 6 June 2013
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
* Jenkins job on BBOP: build-bio-attributes
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
Curation of attribute ontology
Should largely be automated, but the ontology can be edited in oboedit (will switch to OWL later).
- Classification should be automatic. Avoid asserting is_a
- Do not edit any term in VT or TO namespace. These are merged automatically. Contact VT or TO editors
When new terms are added to VT or TO they may end up duplicating what is in BATTO. In these cases, the BATTO term will be obsoleted and replaced_by the relevant term.
We periodically bring in the latest VT and TO ontologies (plus associated logical definitions - http://code.google.com/p/phenotype-ontologies/ ). See the Makefile for details.