Question design patterns for regulation

geneontology / go-ontology

Source ontology files for the Gene Ontology

http://geneontology.org/page/download-ontology

Creative Commons Attribution 4.0 International

220 stars 40 forks source link

Question design patterns for regulation #16504

Open pgaudet opened 5 years ago

pgaudet commented 5 years ago

Hello,

For biological regulation terms, we have 3 possible genera:

some terms start with: 'biological process' and 'regulates' some 'x'
other have 'biological regulation' and 'regulates' some 'x'
and others have 'regulation of biological process' 'regulates' some 'x' (for eg GO:1900400)

Is this OK ? Do we want to make all these uniform ? (the ontology documentation gives instructions to do the second option here).

Thanks, Pascale

ukemi commented 5 years ago

I thought @cmungall had said we would use whatever is in the design pattern template.

pgaudet commented 5 years ago

Right - so it's 'biological regulation' and 'regulates' some %s" (https://github.com/geneontology/go-ontology/blob/master/src/design_patterns/regulation.yaml).

Can all terms with a different logical definition be changed ? (we may have another ticket for that somewhere).

Thanks, Pascale

ukemi commented 5 years ago

I thought there was already a ticket out there to have that done by script.

ValWood commented 3 years ago

Is this current?

cmungall commented 3 years ago

$ obo-grep.pl  -r 'intersection_of: GO:0008150' go-edit.obo | obo-grep.pl -r 'intersection_of: regulates ' - | grep -c '^id:'
3294
$ obo-grep.pl  -r 'intersection_of: GO:0065007' go-edit.obo | obo-grep.pl -r 'intersection_of: regulates ' - | grep -c '^id:'
228

still 228 with BR as genus

happy to close this issue as this should all fall out of DP work