update equivalence axiom for GO:0015165 - pyrimidine nucleotide-sugar transmembrane transporter activity

[krchristie]

This term seems like it needs an update to its equivalence axion 'transmembrane transporter activity' and ('transports or maintains localization of' some 'pyrimidine nucleotide-sugar')

to be consistent with its name and definition to indicate: and ('results in transport across' some membrane)

[pgaudet]

Hi @cmungall

I would like to know what is the difference bewteen

'transmembrane transporter activity' and ('transports or maintains localization of' some 'pyrimidine nucleotide-sugar')

and 'transporter activity' and ('transports or maintains localization of' some 'pyrimidine nucleotide-sugar') and ('results in transport across' some membrane)

I don't think that there is difference in the logic; but should we favor one over the other ?

[RLovering]

Hi I think you have got the wrong definition for transporter activity, this is: Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. But not sure how this fits with the discussion above sorry Ruth

[pgaudet]

Hi @RLovering I am not sure how this fits either. But the definition for transmembrane transporters is now 'Enables the transfer of a pyrimidine nucleotide-sugar from one side of a membrane to the other. '; does that not seem OK to you ?

Thanks, Pascale

[pgaudet]

see #14436

[RLovering]

yes, that definition looks like it follows other similar definitions Thanks Ruth

[ValWood]

1. Is this about "transporter activity/transmembrane transporter activity

OR

2. pyrimidine nucleotide-sugar transporter activity/pyrimidine nucleotide-sugar transmembrane transporter activity

I would be concerned if 1, but if 2 I can ignore ;)

[pgaudet]

I (try to) will create a design pattern based on 'transporter activity' and ('transports or maintains localization of' x') and ('results in transport across' some membrane)

[pgaudet]

I have created the design pattern (https://github.com/geneontology/go-ontology/blob/master/src/design_patterns/mf_transmembrane_transporter_activity.yaml) using 'transmembrane transporter activity' and ('transports or maintains localization of' some 'pyrimidine nucleotide-sugar')

... otherwise it's not possible to create logical definitions for other types of transmembrane transporters such as antiporters, synporters and channels.

I am going to standardize the logical axioms as much as I can.

Pascale

[pgaudet]

https://github.com/geneontology/go-ontology/issues/14580

[pgaudet]

I think I fixed all TM transporters, using the pattern

'transmembrane transporter activity' and ('transports or maintains localization of' some 'xxx')

Thanks, Pascale

[pgaudet]

See also https://github.com/geneontology/go-ontology/tree/master/src/design_patterns