Is transports\_or\_maintains\_localization\_of needed for MF AE?

[dosumis]

(Ticket extracted from notes written by @RLovering & Rachael Huntley)
Looks like this is for processes only therefore annotations of transporters (MF) keep as has_direct_input ?

[dosumis]

Using the transports relation for MFs follows patterns used in ontology => correct folding.

e.g. of term in ontolgy:
acetate ester transmembrane transporter activity
EquivalentTo: 'transmembrane transporter activity'
and ('transports or maintains localization of' some 'acetate ester')

May be a case for pushing annotators to use TermGenie templates here?

[RLovering]

Hi David

thanks for breaking down all these queries. Great to have this use confirmed. Our problem is that the information associated with this relationship is incomplete:
GOC wiki page: transports_or_maintains_localization_of
GO Annotation Domain: None defined
GO Annotation Range: None defined
Usage: Use to relate a process of [edit: change 'of' to 'or] molecular function to a substance that is transported, localized or whose localization is maintained by that process or function.
Subsets:
GO:cellular_component
chemical
display_for_curators

I don't understand what the subsets are supposed to refer to, and I would question the inclusion of GO:cellular_component, as many of these should be 'moved' using the relationship 'results_in_movement_of' see very end of message.

When revising the documentation for transports_or_maintains_localization_of, would it be possible too provide a more specific GO CC term such as GO:0032991 macromolecular complex? This would also help with limiting the use of this relationship in the Protein2GO tool.

To be honest I am not sure why there needs to be these 2 relationships:
transports_or_maintains_localization_of
and results_in_movement_of
When the only difference is the size of the substance moved, I can see problems arising where decision needs to be made about whether the complex is an 'entity' or a 'substance'.
In addition, the maintains_localization_of is also a process relevant to organelles, but this is in theory not covered by the results_in_movement_of relationship. Should the results_in_movement_of relationship be extended to cover the maintenance aspect?

If keeping both relationships is a definite final decision I will create the wiki page with MF and BP examples of use and errors in use. I'll wait for your confirmation before proceeding with this though.

Best

Ruth

Compared with documentation for
GOC wiki page: results_in_movement_of
GO Annotation Domain: GO:0003674 (molecular_function) or GO:0008150 (biological_process)
GO Annotation Range: CL:0000000 (null) or GO:0005623 (cell) or WBbt:0004017 (null)
Usage: Relationship that links an entity with a process in which the entity moves from one location to another.
Subsets:
cell_or_anatomical
display_for_curators