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Example of confusion created by the host/symbiont triad #17045
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Very good point, I agree
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The problem is that not all symbiotic interactions involve a host and hostee. There are many where the relationship is equal - like a lichen. That’s why we made all of the “other organism” terms and had that structure. |
parasitism, mutualism, commensalism if I remember correctly from undergraduate biology. |
But do they really grow inside the symbiont, rather than in the vicinity of?
…On Fri, Mar 15, 2019 at 10:51 AM Michelle ***@***.***> wrote:
The problem is that not all symbiotic interactions involve a host and
hostee. There are many where the relationship is equal - like a lichen.
That’s why we made all of the “other organism” terms and had that structure.
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First, I don't think we should really try to capture the parasitism, mutualism, commensalism aspect, because it can change for a particular species in a generation. But I'm trying to figure what these mean as processes. Looking at the annotations for "growth of symbiont in host" For example this paper These are not GO processes, they are pathogen host interaction phenotypes (if we knock out this gene is the symbiont still viable/can it infect the host). They are essentially assays to see if the gene affects viability or pathogenicity. They are not informative about the biological process. The term refer to the process 'growth' (i.e increase in size) but I would bet that these have only been used for viability/proliferation of a "population". I really think we need to remove these terms to be biologically sound. |
Luckily they are hardly used. ... |
To explain this better. We no longer have "organismal proliferation" in GO. We only have proliferation terms to apply to specific expansion of specific cell types in developemnt. Proliferation is really "growth+division" (i.e viability) of a population. It encompasses all essential processes and it isn't just about an increase in size. here we are talking about "proliferation + life cycle stage" (so an additional differentia, on top of "proliferation of a population", which is already disallowed). We need to be careful that we aren't using GO terms to capture viability+ lifecycle stage, because this is impossible to model logically at the process level (every essential process would contribute). |
Above, Chris asked:
My comment was referring not just to the 'growth in' terms but also to the others Pascale suggested obsoleting. Pascale suggested in her first post:
What I was saying was that we need more than just these - we need ones to capture the interactions where there is no host/hostee relationship. That's were the "other organism" terms came in. But what I hear Val arguing is that even the above growth terms that Pascale noted are not allowed since they involve proliferation and not a cell getting larger. I didn't realize that cell proliferation was no longer allowed to be used outside a multicellular organism. (I've missed so much!) :) I'm wondering if we need a "host colonization" process term - would something like that be allowed? Michelle |
Yes, difficult to keep up with all the changes! and the changes to the changes, sometimes back to the original! To me "host colonization" sounds much more like the process that we need to capture. I'm looking under |
"host colonization" or similar might work as a grouping term for cases where pathogen host terms are strangely grouped in a biologically unintuitive way. I opened a ticket for this here. |
PROPOSAL
Perhaps we need both 'cell proliferation in host cell' and 'host cell colonization'.
Change labels:
Obsolete ?
Equivalent Development terms:
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I don't think we should have these term in GO: cell proliferation in host (part of colonization): Any symbiont process that contributes to the ability of the symbiont to population expansion inside a host. they would generate exactly the same issues as the cell proliferation term: It will be used to annotate viability/inviability phenotypes (i.e this pathogen can grow and divide in the host). This is a phenotype, and if we include it , it will be a "stub". For example, any essential gene, or any gene required for host colonization would be annotated to "growth of symbiont in host" In these instances, it is better to make no annotation if you cannot say something more specific about the process. If people want to annotate population viability/inviability they should use a phenotype ontology instead. |
changed labels and adjusted definitions for #17045
Everything proposed here was done. |
Hello,
Trying to illustrate why I think we should not systematically make the host/symbiont triad:
PARENT CLASS: GO:0044112 growth in other organism involved in symbiotic interaction
-> no annotations
But, do we expect the host to grow in the symbiont ? The only possibility here is 'growth of symbiont in host'
I would prefer to obsolete that class, as well as 3 of its children:
GO:0044110 growth involved in symbiotic interaction
-> 5 annotations by MTBBASE; should have been 'growth of symbiont in host cell'
GO:0044153 growth on or near surface of other organism involved in symbiotic interaction
and its child GO:0044151 growth of organism on or near symbiont surface
-> no annotations
These terms seem sufficient to represent what needs to be captured:
@jimhu-tamu @mgiglio99 @cmungall @pmasson55 @nsuvarnaiari @jrr-cpt @ValWood
Do you agree to obsolete the 3 terms ?
Thanks, Pascale
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