PAMGO The Other Organism String
We decided to put "by other organism" into the terms referring to processes performed by an organism involving a host to clarify which organism was doing what, e.g. "modification by other organism of host morphology or physiology via secreted substance". You would use these terms to annotate the gene products of the smaller organism, i.e. the "other organism" referred to in the term. I think this gets confusing if you then look at the terms for interactions where there isn't a definable host or symbiont, as they also refer to "other organism", e.g. "modification of morphology or physiology of other organism during symbiotic interaction". In these cases, the "other organism" isn't the organism you're annotating! I think it might be better to use the string "by organism", rather than "by other organism", e.g.
- modification by organism of host morphology or physiology via secreted substance
- positive regulation by organism of host signal transduction pathway
- formation by organism of haustorium for nutrient acquisition from host
Does that seem reasonable?
COMMENT FROM Mchibuco 13:15, 8 August 2006 (PDT)
I think you raise a good point that it gets confusing when we indiscriminately use the phrase "by other organism," but I think before we just cut the word "other" we need to recall the Biological Process Ontology Guidelines, which state that:
"Symbiotic relationships may be between two organisms of similar sizes or of differing sizes, and most of the processes under symbiosis, encompassing mutualism through parasitism have child terms to specify the sizes of the organisms involved. These terms use the nomenclature host for the larger organism and symbiont for the smaller organism. For interactions where there is no clear host or symbiont, the wording other organism is used, and terms are appended with during symbiotic interaction to make it clear that they represent processes occurring during symbiosis."
In other words, I think we should use the more encompassing phrase "by other organism" or the shortened version "by organism" only in cases where we can not say "by host" or "by symbiont" explicitly.
In the first two examples, I would say:
- modification by symbiont of host morphology or physiology via secreted substance
- positive regulation by symbiont of host signal transduction pathway
This is because both definitions already use the word "host" so I think it is appropriate to say "symbiont," because by definition if it's a host, then it is a host to something, e.g. a symbiont. To say anything less is to obfuscate unnecessarily.
In the third example, we have more difficulty, because as I understand it, although a haustorium is a pathogen-derived structure, it is in effect an interface with a host cell membrane. Hence, I would ask this: is a haustorium a pathogenic structure or a joint host-pathogen structure? Although a host cell membrane will not form the invaginations it does in a haustorial context in the absence of a haustorium, I still see it as a joint interface caused by the pathogen, but that requires the host.
9/11/06 While Marcuus is correct here, of course, according to "the letter of the law" so to speak, I think that not attributing the haustorium to the symbiont (and instead attributing it to both symbiont and host)will probably cause unnecessary confusion. I think that most people who work with organisms that produce haustoria commonly talk about these organisms as "forming haustoria" etc. -- that is, as the work of the symbiont. While the haustorium may end up as a joint interface, it seems like it is really the symbiont that is carrying out the action to make it happen.
Jane and I wrote the documentation, so it would be easy enough to change it to something else if we decide on a new format. The only thing that I think might be problematic about saying 'modification by symbiont of host morphology or physiology' or similar is that it might not be clear from the term string who the term should be used by, whether it is a term to annotate symbiont gps or host gps to. I think if you say 'by organism', it's clear(er) that it is a term for the annotation of symbiont gps.
In the light of Marcus's comments about haustoria, should we have both host and symbiont terms for the formation of a haustorium?
I agree with Marcus's suggestion on using "by symbiont" and "by host" whenever possible. I think it is more clear than "by organism" since whoever's gene product one is annotating will be the one in the "by ____" phrase. Also the definitions will say this too. I think using "by organism" is much more vague since both the symbiont and host could be the "organism" referred to.
I wholeheartedly agree with Michelle about 'by organism'.
I also agree with Michelle. Organism is vague.
Can anyone remember why it was we decided not to go for specifying 'host' and 'symbiont' in the terms in the first place? I remember there was some specific reason that we didn't do it, but I can't for the life of me remember what it might have been...
I'm finally getting started on all the discussion on the wiki -- sorry it took so long. I don't think there ever was any specific reason NOT to specify. Remember that when we created the first 30 or so terms, we were doing only those terms useful for annotating genes in a microbe that was interacting with a host (in our case, a plant host). Therefore, in all of those early terms (back when it was blessedly simple), it was clear to say "adhesion to host by other organism" and all was clear. I very much agree with Michelle, Marcus and others that using "other organism" will be very vague and confusing, especially to people who aren't annotating genes to these terms every day. We should use "by host" and "by symbiont" whenever possible, and if that's not possible, then somehow we have to make it very clear who is doing what to whom.....
I agree that it is confusing, but I also think we did have a specific reason for it. I think the initial reason we wanted to use "other organism" to refer to the other organism was because we didn't want pathogen researchers to think that this term didn't apply to them. It may be cleared up by always putting the definition of symbiont and host in the definition field in each instance in which we use symbiont and host, but most people do not assume symbiosis includes pathogenicity and parasitism.
In places where the parent term has directionality (e.g. interaction with host), symbiont is probably the correct word. In places where no directionality is not explicit, symbiont and host is not appropriate.
Okay - I've changed all of the term names which contained 'host' and 'other organism' so that they now say 'host' and 'symbiont'.
- I think we also need to change to inverse strings to say 'host' too - e.g. we have:
modification of protein function in other organism during symbiotic interaction
---[i] modification by symbiont of host protein function
---[i] modification by organism of symbiont protein function
so presumably we'd change the bottom term to be 'modification by host of symbiont protein function'?
Yes, that is exactly right. All the reciprocal sibling terms should have the "host" and "symbont" inserted where missing. I think one of the issues that came up in the course of discussion on "the other Organism String" is the fact that users may not know which terms to annotate their gene products to.
modification of protein function in other organism during symbiotic interaction ---[i] modification by symbiont of host protein function (1) ---[i] modification by organism(host) of symbiont protein function (2)
It is obvious to me now but probably because I have worked through this a lot. so probably the suggestion is to have a statement in the comment section to indicate which terms should have host gene products annotated to (2) and which, symbiont gene products (1).
Jan 15, 2007 We think problem raised by Bryan can be solved by having more narrow synonyms of "by symbiont" So for eg. "acquisition of nutrients by symbiont..................." would have the following synonyms
"acquisition of nutrients by pathogen..................." "acquisition of nutrients by mutualist..................." "acquisition of nutrients by commensal..................."
These more narrow synonyms should be used for all terms where the symbiont is the acting organism
Should that be commensalist rather than commensal?
commensalist is fine