NTR: various transmembrane transport

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standard parents and defs

val

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/7196

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and purine nucleoside transmembrane transport

Original comment by: ValWood

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• summary: NTR: triose-phosphate transmembrane transport --> NTR: triose-phosphate transmembrane transport etc

Original comment by: ValWood

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• summary: NTR: triose-phosphate transmembrane transport etc --> NTR: triose-phosphate transmembrane transport
• assigned_to: nobody --> rfoulger

Original comment by: rebeccafoulger

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also hexose transmembrane transport (high affinity nd low affinity hexose transport should be under this new term)

copper ion transmembrane transport copper ion import, copper ion ecport, high affinity copper ion transport and plasma membrane copper ion transport should be under this)

acetate transmembrane transprot

also gluconate transemmbrane transport and positive regulation of gluconate transmembrane transport

Original comment by: ValWood

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• summary: NTR: triose-phosphate transmembrane transport --> NTR: various transmembrane transport
• assigned_to: rfoulger --> nobody

Original comment by: ValWood

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• assigned_to: nobody --> rfoulger

Original comment by: rebeccafoulger

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For hexose terms, we have both GO:0008646 and GO:0008647 directly under TM transport:

carbohydrate transmembrane transport ; GO:0034219. --%high-affinity hexose transport ; GO:0008646 --%low-affinity hexose transport ; GO:0008647

Looks to me like they'd be better off under just hexose transport ; GO:0008645 if not all hexose transport is across a membrane.

Will work out the parentage of your other terms to fit with CHEMI. cheers, Becky

Original comment by: rebeccafoulger

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Hi Becky in that case can we have

carbohydrate transmembrane transport --hexose transmembrane transport ----high affinity terms.

I don't know if any hexose transport which isn't transmembrane, but I guess there could be?

My motivation is to have all gene products involved in transmembrane transport annotated to transmembrane trasnsport as a high level term, if this parentage doesn't happen some things will map only to transport (which includes priotein targetting, nucleocytoplasmic transport, vesicle-mediated, microtubule mediated etc)

Cheers

Val

Original comment by: ValWood

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Hi Val,

I've just spoken to Jen and she reminded me that process terms have to be multistep events. Are all the TM transport terms >1 step??

We have 200 x transport terms that have a x transmembrane transport function term as a child, but no x transmembrane transport process term as a child. Presumably for the multi-step reason.

Becky

Original comment by: rebeccafoulger

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Well, all transmembrane transport is mutistep if you consider its regulation.....

Aside from that, is it still a hard and fast rule that processes need to be multistep considering the ongoing discussion about merging the process and function ontologies? (I don't know the answer to this but Midori might)

From a users perspective its not good for all of the tranmembrane transport processes not to have acommon parent of "transmembrane transport". You could turn the question around and not allow any x transport term in process if it turned out to be performed by a single molecule and these would not get annotated to a process, only a function (i.e it doens't apply only to transmembrane transport, but to transport in general)

I don't think the multistep is the reason for the current situation, it's just becasue we didn't know whether they were transported by any other mechanism when we revised the transport section of the ontology. In my annotation I have to get around this by creating an IEA mapping to "transmembrane transport" for any transmembrane transporter which does not have this parent, but this isn't ideal.

Original comment by: ValWood

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also NTR phosphate transmembrane transport

Original comment by: ValWood

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Added the following terms:

purine nucleoside transmembrane transport ; GO:0035427 hexose transmembrane transport ; GO:0035428 gluconate transmembrane transport ; GO:0035429 regulation of gluconate transmembrane transport ; GO:0035430 negative regulation of gluconate transmembrane transport ; GO:0035431 positive regulation of gluconate transmembrane transport ; GO:0035432 acetate transmembrane transport ; GO:0035433 (also in your other SF entry) copper ion transmembrane transport ; GO:0035434 phosphate transmembrane transport ; GO:0035435

The triose-phosphate term got a bit complicated when Jane and I looked into it to standardise with GO:CHE, so I'll come back to that one.

Becky

Original comment by: rebeccafoulger

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Added: triose phosphate transmembrane transport ; GO:0035436

Think that's all from this request. I've sent round the list to the transport mailing group to see if any x transport terms can be moved directly under TM transport.

cheers, Becky

Original comment by: rebeccafoulger

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• status: open --> closed-accepted

Original comment by: rebeccafoulger

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• milestone: --> PomBase

Original comment by: mah11