Ontology meeting 2012-09-26: Difference between revisions
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--[isa]nuclear import ; GO:0051170 | --[isa]nuclear import ; GO:0051170 | ||
Comment for GO:0006913: Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed. | Comment for GO:0006913: Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed. | ||
===Annotation relationships=== | |||
Following on from the annotation call on Tues, at which there was a lot of confusion. I explained what we meant by 'actively_involved_in' v/s 'involved_in', and that you can be actively involved in something directly or indirectly, as described in Chris's handy figure: | |||
[[Image: Capable of.jpg|200px]] | |||
as well as the difference between being actively and passively involved in a process. I don't really think I got the message across, so we need to figure out a better way of explaining this - perhaps with a simplfied version of the above? But the consensus seemed to be that no-one had been annotating the passive participants of a process, so I think we can probably use 'actively_involved_in' for all process annotations. | |||
Revision as of 05:26, 26 September 2012
60-minute meeting
MINUTES: Becky
ATTENDEES:
Transmembrane Transport
BACKGROUND
The builds keep failing because several 'x transport' terms have an 'x transport' XP and an 'x transport' definition, but have a 'y transmembrane transport' parent or ancestor.
E.g.
purine-containing compound transmembrane transport ; GO:0072530 --[isa]purine nucleobase transport ; GO:0006863 --[isa]purine nucleoside transport ; GO:0015860 --[isa]purine nucleotide transport ; GO:0015865
[Term] id: GO:0015865 ! purine nucleotide transport intersection_of: GO:0006810 ! transport intersection_of: transports_or_maintains_localization_of CHEBI:26395 ! purine nucleotide
OPTIONS
- Rename all 'x transport' terms that have a TM transport parent to 'x transmembrane transport'. Also need to update definitions and XPs.
- Move all 'x transport' terms OUT from under a 'TM transport' parent. Keep their definitions and XPs as 'x transport'.
Need to decide what we mean by 'transmembrane transport' and whether we can assume that most/all transporters are acting across a membrane.
EXPORT & IMPORT
There's been email discussion (see email thread: process start and end location relations) about adding generic export and import terms. What would be the differentia for these?
- Problem 1: For generic 'protein export', the export can be from an organelle OR a cell, so we'd need an 'or' grouping, which we can't do in obo.
- Problem 2: Not all export/import is across a membrane (e.g. nuclear import/export)
nucleocytoplasmic transport ; GO:0006913 --[isa]nuclear export ; GO:0051168 --[isa]nuclear import ; GO:0051170 Comment for GO:0006913: Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed.
Annotation relationships
Following on from the annotation call on Tues, at which there was a lot of confusion. I explained what we meant by 'actively_involved_in' v/s 'involved_in', and that you can be actively involved in something directly or indirectly, as described in Chris's handy figure:
as well as the difference between being actively and passively involved in a process. I don't really think I got the message across, so we need to figure out a better way of explaining this - perhaps with a simplfied version of the above? But the consensus seemed to be that no-one had been annotating the passive participants of a process, so I think we can probably use 'actively_involved_in' for all process annotations.