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Okay - following another long discussion with David, we may have a possible solution.
Briefly, the main problem with any sort of generic movement term is that a lot of things move and it's hard restricting the term so it doesn't cover everything. So we decided we could restrict it to just the movement of cellular components (which includes whole cells). There is actually a term that's...
2009-11-17 17:04:40 UTC in Gene Ontology
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I like this idea - I think the process would be the combination of at least two nuclease functions (one at each end of the excised section)...
2009-11-17 16:20:45 UTC in Gene Ontology
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Added:
methane-oxidizing organelle ; GO:0044227
synonyms: methane-oxidizing compartment, methanotroph intracytoplasmic membrane-bound compartment.
2009-11-17 14:23:56 UTC in Gene Ontology
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Okay - the consensus here and on the mailing lists seems to be that we classify these bacterial structures as organelles, so I've copied everything I could find that could be a prokaryotic organelle under the appropriate 'organelle' parent. I've also added something to the def of 'organelle' to make it clear that it includes prokaryotic structures.
2009-11-17 14:02:26 UTC in Gene Ontology
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other organism ; GO:0044215
other organism cell ; GO:0044216
other organism part ; GO:0044217
other organism cell membrane ; GO:0044218.
2009-11-17 13:01:21 UTC in Gene Ontology
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Oh yeah - there probably should be really - immune system proteins that act at the symbiont surface etc. I've just added a term 'other organism' to cc as parent to host, so it would go as another child under this. We'll be switching these terms for annotation relations at some stage in the future though, so won't add it unless someone asks for it before then...
2009-11-17 11:14:37 UTC in Gene Ontology
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apical pole of neuron ; GO:0044225
basal pole of neuron ; GO:0044226.
2009-11-13 16:41:24 UTC in Gene Ontology
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Well, we know the mechanism for cillia and flagella, but what about movement where we don't know the underlying mechanism? I'm sure I can come up with a bacterial example for you ;-)
(I don't think the microtubule-based movement term is wrong, btw, I just think it needs another, generic movement parent)
2009-11-13 16:39:52 UTC in Gene Ontology
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David and I have discussed this - he had added 'cilium movement involved in ciliary motility ; GO:0060294' with the beat freq children but it is still part_of 'ciliary cell motility' (i.e. the cell itself moving) so that doesn't work for Ruth's nasal cilia which stay still.
So we still need a generic parent to 'cilium movement involved in ciliary motility ; GO:0060294' which itself I think...
2009-11-13 15:39:03 UTC in Gene Ontology
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I also think that cell junction shouldn't be part of the plasma membrane. David and I had a conversation about this yesterday and we came to the conclusion that this parentage causes a problem in particular for cell-substrate junctions where you might want to annotate the substrate proteins (e.g. extracellular matrix proteins) which definitely are not part of the plasma membrane.
Also...
2009-11-13 15:19:06 UTC in Gene Ontology
