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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Standardize textual definition transmembrane transport #14436

Closed pgaudet closed 6 years ago

pgaudet commented 6 years ago

Hello,

Looking at the noted from the transport group http://wiki.geneontology.org/index.php/Transmembrane_transporters We should update all definitions to 'The process in which [x] is transported from one side of a membrane to the other.'' Now it's a mix of that and what the groups had decided on for the top level class transport,

The definition of transport ; GO:0006810 is: The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells, or within a multicellular organism by means of some external agent such as a transporter or pore.

I suppose that this also needs to match the DOS design patterns. The incorrect definitions seem to all come from TG.

Thanks, Pascale

ukemi commented 6 years ago

Hi @pgaudet ,

These definitions are for different granularities of transport. The first one is for transmembrane transport, the second is for general transport. I would go with the experts definitions whenever possible. We need to have the more general transport terms to describe the complexities of transport in anatomical structures like kidneys and digestive systems.

pgaudet commented 6 years ago

Hi all,

I standardizing the definitions and equivalence axioms of transmembrane transport as indicated in https://github.com/geneontology/go-ontology/blob/master/src/design_patterns/transmembrane_transport.yaml

ie: Equivalence axiom: transport and ('transports or maintains localization of' some %s) and ('results in transport across' some membrane)

Textual definition: "The process in which a x is transported across a membrane."

If anyone has feedback on this please let me know soon. @ValWood maybe ?

ValWood commented 6 years ago

I think that's OK. I did wonder why it was "transports or maintains localization of" rather than just "transports" but it might not need to be so specific because if it "results in transport across a membrane" it must be transport rather than localization?

pgaudet commented 6 years ago

right... that's a whole different issue. I had asked for that relation but I cannot see it yet. At the same time we'd have transport and transports some x

which sounds OK. I thought 'has input' might also be appropriate. Anyway for now I just want to standardize.

Thanks, Pascale

ValWood commented 6 years ago

OK sounds good. Easy to restandardize if necessary if they are already standardized ;)

pgaudet commented 6 years ago

That's what I thought !