Ontology meeting 2016-01-21
Attendees:
Minutes:
Fun with regulates axioms
https://github.com/geneontology/go-ontology/issues/12235
DNA methylation and gene expression
Stemming from latest assert report
ADD GO:1901535 'regulation of DNA demethylation' GO:0010468 'regulation of gene expression'
because 'DNA demethylation' (and 'DNA methylation') is_a 'regulation of gene expression, epigenetic'. Should it be part_of instead?
Latest assertions
The list in yesterday's assert report (email "[go-ontology] build-go-assert-inferences - Build # 173 - Fixed!") is really long, 402 added axioms presumably as a result of the synapse branch merge. Has anyone had a chance to review them all?
Logical definitions for 'response to chemical' terms
Logical defs for 'response to chemical' terms point to 'response to stimulus', while 'cellular response to chemical' points to 'cellular response to chemical stimulus':
id: GO:1903842
name: response to arsenite ion
intersection_of: GO:0050896 ! response to stimulus
intersection_of: has_input CHEBI:22633 ! arsenite ion
relationship: has_input CHEBI:22633 {is_inferred="true"} ! arsenite ion
but
id: GO:1903843
name: cellular response to arsenite ion
intersection_of: GO:0070887 ! cellular response to chemical stimulus
intersection_of: has_input CHEBI:22633 ! arsenite ion
relationship: has_input CHEBI:22633 {is_inferred="true"} ! arsenite ion
Was this intentional - shouldn't the former point more specifically to 'response to chemical'? (which is_a 'response to stimulus') Of course, the 'response to chemical' parentage is inferred anyway.