transport and secretion

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The way Amelia explained the current arrangement (in SF 1021425) is that
secretion at the organ level, e.g. gastric acid secretion, doesn't fit the 'into,
out of, within or between cells' part of the transport def, nor the 'cellular
physiological process' parentage of transport. One could quibble about the
interpretation of 'between cells', but the parentage part of the argument is
fairly convincing, and makes me think we'll have to bring up the possibility of
adding a term for organismal level transport (renaming GO:0006810 to
'cellular transport' or some such). We've toyed with the idea a bit in the recent
past, but haven't actively pursued it to date.

m

link:
https://sourceforge.net/tracker/index.php?
func=detail&aid=1021425&group_id=36855&atid=440764

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Midori,

It strikes me you should also make a cellular secretion term as well as a
glandular secretion term.

-- Alex

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The small group that has started working on is_a complete biological process
has identified localization as an area that needs attention, so we'll sort this
out when David visits Hinxton next month. Amelia and I will remind them
about the need for cellular and organismal transport.

http://wiki.geneontology.org/index.php/Managers_13Sept06

m

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Midori,

Thanks for the update.

-- Alex

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When this is adressed would it be possible to have a grouping term for
'membrane transport' in the process or function ontology. It isn't possible to
currently retreive these terms in any way easily (because 'transport' and
transporter retreive things involved in nucleocytoplasmic transport and
secretion.

Biologists would expect to be able to retreive this set easily, and I have
recently reviewed a paper describing an ontology for precisely this
transporter subset. I have been trying to pull out this subset for analysis and
it leads to a very complicated set of queries to get the desired set. (This is in
addition to general revision of the transporter terms which Jen was looking
into).

thanks

Val

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Val - do you mean group all the terms having to do with transport across a membrane?
m

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Hi Midori,
yes (this excludes transport through the nuclear pore though). i.e includes carriers, ion channels and pumps etc. I.e the things covered by the transport classification system?

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added relationships
secretion by cell GO:0032940 is_a transport GO:0006810
protein secretion GO:0009306 is_a protein transport GO:0015031
neurotransmitter secretion GO:0007269 is_a neurotransmitter transport GO:0006836

proposed to the transport wg that transport becomes is_a cellular process

if anything else is left after that, please open a new item
m