Difference between revisions of "Talk:PAMGO work in progress"

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==The 'other organism' string==
==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.
See [[PAMGO The Other Organism String]]


*modification by organism of host morphology or physiology via secreted substance
==Hypersensitive response==
*positive regulation by organism of host signal transduction pathway
See [[PAMGO Hypersensitive Response]]
*formation by organism of haustorium for nutrient acquisition from host


Does that seem reasonable?
== Modification of host protein function ==


===Marcus===
At the moment, modification of host protein function is a child of 'modification ... via secreted substance'. This seems OK to me, but are there any ways in which host protein function can be modified directly or via some other method?


COMMENT FROM [[User:Mchibuco|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:
===Candace_Michelle_Trudy@PAG===
In the literature, most of the macromolecules involved in the modification of host protein function are secreted so it is safe to conclude for now that host protein functions are modified mainly via secreted proteins and as such would be a child of  'modification ... via secreted substance" without creating a sibling term "modification ... via non-secreted substance".
"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:
However, we modified the definition....find below:
*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.
The process by which an organism effects a change in the function of a '''host protein via a direct''' '''interaction'''. The host is defined as the larger of the organisms involved in a symbiotic interaction.


Thoughts?
===Jane===


===Amelia===
<font color="red">Done.</font>


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.
== Modification/modulation of host defenses ==


In the light of Marcus's comments about haustoria, should we have both host and symbiont terms for the formation of a haustorium?
Host defenses consist of the induced defenses - the defense response mounted by the host - and the preexisting defenses, such as the cell wall and other defensive structures. We've got modification of host structure and modulation of host defense response, but nothing to encapsulate both - logically it seems like a term we should have since elsewhere we have structures like this:


===Michelle===
*evasion or tolerance of host defenses
**evasion or tolerance of host defense response


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.
Currently, we've got the term 'response to host defenses ; GO:0044413' (was 'avoidance of host defenses' but we renamed it), which is defined thus:


====Midori====
Any process, either constitutive or induced, by which an organism evades, suppresses or tolerates the effects of its host organism's defense(s). Host defenses may be induced by the presence of the organism or may be preformed (e.g. physical barriers). The host is defined as the larger of the organisms involved in a symbiotic interaction.
I wholeheartedly agree with Michelle about 'by organism'.


===David===
I am no longer sure that this term is correctly named, as there are situations where the symbiont induces host defenses, but the def of 'response to host defenses' only covers the "negative" aspects of the response. Perhaps 'response to host defenses' should be used as a term to encapsulate modification/modulation of host defenses?
I also agree with Michelle. Organism is vague.


===Amelia===
As yet I don't have any suggestion for a new name for 'response to host defenses', unfortunately!
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...


==Hypersensitive response==
See this SF item for response from TAIR:


https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1524725&group_id=36855


===Marcus===


I think Donghui Li’s thoughts (from the link above) on PCD and HR make it clear that [in plants] PCD comprises both developmentally-related forms of cell death and cell death in response to a pathogen. In this light, even if mechanisms underlying HR are not distinct from those of PCD (and the distinction is therefore artificial), I see HR as a useful narrower child term to capture the context of PCD as response to a pathogen. Therefore, I agree with Donghui that the terms should not be merged, and I offer further justification for not merging the terms.


What would happen if host cells were induced to die in response to a non-pathogenic symbiont, e.g. a case of non-HR PCD in response to an organism? It would be interesting to capture this information as distinct from HR type PCD. I found an interesting paper abstract (PMID: 16946237) that documents symbiont-induced apoptosis during light organ formation in the squid ''Euprymna'' ''scolopes'' by the marine luminous bacterium ''Vibrio'' ''fischeri''. I think it would be interesting to capture this case of non-HR PCD induced by another organism as distinct from HR PCD.


Currently there is no term for apoptosis induced by another organism (that I could find), with the exception of virus-infected cell apoptosis (GO:0006926). Although “induction of apoptosis by extracellular signals” (GO:0008624) is a possibility, all its children appear to be endogenous factors such as hormones, and I want to capture that another organism is causing the phenomenon. Perhaps killing of host cells (GO:0001907) would be the best term to use since it is under the IBO node (GO:0051704), but its definition is “any process mediated by an organism that results in the death of cells in the host organism…” In the case of the ''Euprymna''-''Vibrio'' interaction, although host PCD is triggered by a symbiont-induced signal, the killing is done via pathways endogenous to the host. That term is inappropriate for the same reason that it would be to characterize HR.


I believe we should create a new term “symbiont-induced programmed cell death” as a child of programmed cell death. We could move hypersensitive response from its current position as a child of programmed cell death to a child of the new term. We could create a new sibling for HR called “programmed cell death induced by non-pathogen symbiont.” This would allow us clearly to draw the distinction between PCD as a response to a pathogen and PCD as part of a beneficial symbiotic interaction. If HR had been merged upward into PCD, this distinction between symbiont-induced PCD and pathogen-specific PCD would not be possible. Furthermore, if a case arises where it is unclear whether PCD in a host that is induced by a symbiont is “harmful” or “beneficial” (as I imagine would happen sometimes), that case could be annotated to the new parent term “symbiont-induced programmed cell death.”


*programmed cell death (PCD) GO:0012501, Definition: Cell death resulting from activation of endogenous cellular processes.
===Trudy_Candace_Michelle@PAG===
**symbiont-induced programmed cell death GO:XXXXXXX, Definition: Cell death in a host resulting from activation of endogenous cellular processes after direct or indirect interaction with a symbiont. Comment: An example of direct interaction is penetration by hyphae, and examples of indirect interaction include encounter with secreted enzyme and interaction with MAMP such as cell wall fragment.
***hypersensitive response (HR) GO:0009626, Definition: The rapid death of plant cells in response to invasion by a pathogen.
***programmed cell death induced by non-pathogen symbiont GO:XXXXXXX, Definition: Cell death in a host resulting from activation of endogenous cellular processes after direct or indirect interaction with a non-pathogenic symbiont. Comment: This includes interactions typically viewed as beneficial from the perspective of the host, such as luminous bacteria in the light organs of marine squid.


== Modification of host protein function ==
We think it is okay to replace "avoidance of host defences" with response to
"response to [org] defenses". We have other suggestions to merge what were previously child terms of "avoidance of host defences" to the new parent term "response to [org] defenses" (See details below)


At the moment, modification of host protein function is a child of 'modification ... via secreted substance'. This seems OK to me, but are there any ways in which host protein function can be modified directly or via some other method?


== Modification/modulation of host defenses ==


Host defenses consist of the induced defenses - the defense response mounted by the host - and the preexisting defenses, such as the cell wall and other defensive structures. We've got modification of host structure and modulation of host defense response, but nothing to encapsulate both - logically it seems like a term we should have since elsewhere we have structures like this:
*evasion or tolerance of host defenses
**evasion or tolerance of host defense response
Currently, we've got the term 'response to host defenses ; GO:0044413' (was 'avoidance of host defenses' but we renamed it), which is defined thus:


Any process, either constitutive or induced, by which an organism evades, suppresses or tolerates the effects of its host organism's defense(s). Host defenses may be induced by the presence of the organism or may be preformed (e.g. physical barriers). The host is defined as the larger of the organisms involved in a symbiotic interaction.
response to [org] defenses
  evasion or tolerance of [org] defenses (merge to the parent term “response to [org] defenses”


I am no longer sure that this term is correctly named, as there are situations where the symbiont induces host defenses, but the def of 'response to host defenses' only covers the "negative" aspects of the response. Perhaps 'response to host defenses' should be used as a term to encapsulate modification/modulation of host defenses?
(MAKE AS MORE NARROW SYNONYMS OF THIS TERM: “evasion of [org] defenses,” “suppression of [org] defenses,” “tolerance of [org] defenses.
  response to [org] oxidative burst  (child of “response to [org] defenses”)
  response to [org] phytoalexins (child of “response to [org] defenses”)
  response to [org] nitric oxide (child of “response to [org] defenses”)
  evasion by virus of host defenses (obsolete this term)
  evasion of host defense response (GO:0030682) (merge to parent “response to [org] defenses”)
  evasion of host immune response (GO:0020012) (child of “response to [org] de fenses”)
  suppression of [org] defenses (merge to parent term “response to [org] defenses”
child terms include suppression of host processes (merged into terms up above)


As yet I don't have any suggestion for a new name for 'response to host defenses', unfortunately!
We do not need to add terms about “passive” and “active” evasion, etc.; on the other hand, having the words “constitutive” and “induced” in the definition is fine and desirable.


== Symbiont defenses ==
== Symbiont defenses ==
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The first one is OK, but I'm not sure about the second and third. Are there/might there be symbioses out there where the smaller partner is a multicellular organism with inflammatory responses and innate immunity which the host species regulates in some way? Most of the symbioses between larger organisms seem to be more behavioural...
The first one is OK, but I'm not sure about the second and third. Are there/might there be symbioses out there where the smaller partner is a multicellular organism with inflammatory responses and innate immunity which the host species regulates in some way? Most of the symbioses between larger organisms seem to be more behavioural...
===Candace_Michelle_Trudy
We would rather not have those children terms added under  “modulation by organism of symbiont defense response”. Just keep the parent term


== Innate immunity ==
== Innate immunity ==


At the moment our terms refer to 'innate immunity', whereas in the main GO, they talk about 'innate immune response'. Is it OK to change the terms to that string instead, e.g. modulation of host innate immune response
At the moment our terms refer to 'innate immunity', whereas in the main GO, they talk about 'innate immune response'. Is it OK to change the terms to that string instead, e.g. modulation of host innate immune response
===Trudy===
I see no reason why we cannot use “innate immune response” in place of innate immunity.
Web definitions of immune response:
a physiological response in humans and higher animals to defend the body against the introduction of foreign material.
Web definitions of immunity:
unsusceptibility-the state of not being susceptible or a condition in which an organism can resist disease.
The word "immunity" connotes the state and "immune responses" refer to the reactions triggered by the foreign body to get the host into a state of immunity so it really depends on the context in which the phrase is being used.
I think whichever one is chosen, the other should be made a synonym or better still be included in the definition as in “innate immune response (sensu Viridiplantae)” in the main GO which is copied below:
innate immune response (sensu Viridiplantae) GO:0002226
Definition:The process of the innate immunity as in, but not restricted to, green plants and algae (Viridiplantae, ncbi_taxonomy_id:33090). Innate immune responses are defense responses mediated by germline encoded components that, in plants, directly recognize components of potential pathogens.
Any other thoughts???
===Candace===
7/17/07
Yes - I think it would be best to keep the term "innate immunity" rather than "innate immune response."  I have been reading through the program for the International meeting of MPMI (7/07, in Sorrento, Italy) and the term "innate immunity" seems to be used frequently in titles, but not "innate immune response" in terms of all the plant-microbe papers.


== Acquisition of nutrients from host ==
== Acquisition of nutrients from host ==
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Well, it seems an example of two things that fall under the parent term would be haustoria formation and hemolysin.  The haustoria is a structure for gaining nutrients, while hemolysin is a molecule produced by the pathogen which causes nutrients to be dumped into the environment which the pathogen then slurps up - no specialized structures needed.  So I think the "formation by organism of specialized...." term is correctly a more specific child of the parent.  There could also be "cytolysis of host cells for the purpose of nutrient acquisition" as another child.  I don't think we necessarily need such a term, and concurrent annotations should be able to handle it, but I am just trying to illustrate what I mean.
Well, it seems an example of two things that fall under the parent term would be haustoria formation and hemolysin.  The haustoria is a structure for gaining nutrients, while hemolysin is a molecule produced by the pathogen which causes nutrients to be dumped into the environment which the pathogen then slurps up - no specialized structures needed.  So I think the "formation by organism of specialized...." term is correctly a more specific child of the parent.  There could also be "cytolysis of host cells for the purpose of nutrient acquisition" as another child.  I don't think we necessarily need such a term, and concurrent annotations should be able to handle it, but I am just trying to illustrate what I mean.
===Trudy===
Acquisition of nutrients from host
I see this term as the process of acquiring nutrients which is different from the formation of the structures through which the symbionts acquire the nutrients but then the latter is incorporated in the definition of the term thus fusing two separate processes into one.
The primary role of most of these structures, the haustorium, syncytium, arbuscules etc is to acquire nutrients from the hosts so I see why in an earlier term development effort, even though the term name is specified as the acquisition of nutrients from host, the definition was made to include the formation of the structures.
In my opinion, which was further supported from discussions with Brett, Marcus and Tsa-Tsieng, we should have “Formation of specialized nutrient absorption structures and macromolecules” housed under two parents as detailed below:
Modification of host morphology and physiology
        Formation of specialized nutrient absorption structures and macromolecules
                    Formation of arbuscules for nutrient absorption/acquisition from host
                    Formation of haustoria for nutrient absorption/acquisition from host
                    Formation of haustoria for nutrient absorption/acquisition from host sensu Viridiplantae
                    Formation of syncytium for nutrient absorption/acquisition from host
                    Formation of symbiosome for nutrient absorption/acquisition from host
                    Formation of siderophore for nutrient absorption/acquisition from host
Acquisition of nutrients
        Formation of specialized nutrient absorption structures and macromolecules
                  Formation of arbuscules for nutrient absorption/acquisition from host
                  Formation of haustoria for nutrient absorption/acquisition from host (sensu oomycetes and
                  Formation of haustoria sensu for nutrient absorption/acquisition from host (sensu Viridiplantae)
                  Formation of syncytium for nutrient absorption/acquisition from host
                  Formation of symbiosome for nutrient absorption/acquisition from host
                  Formation of siderophore for nutrient absorption/acquisition from host
'''Definitions:'''
*Formation of specialized nutrient absorption structures and macromolecules
Defn: ''The production of structures and/or molecules in an organism that are required for the acquisition and/or utilization of nutrients obtained from its host. The host is defined as the larger of the organisms involved in a symbiotic interaction''
(note: are siderophores produced in the host)
*Acquisition of nutrients from host
Defn:''The process of acquisition and/or utilization of nutrients by symbionts from its host. The host is defined as the larger of the organisms involved in a symbiotic interaction.''
*Formation of arbuscules:
Source: Wikipedia, Harrison M.J. Annu. Rev Microb:
Defn:''The formation of highly branched structures in the parenchyma of plant cells by symbionts for acquisition of nutrients  from the host.''
*Formation of haustoria:
Defn:''The formation of specialized feeding structures in host characterized by invaginations inside the plasma membrane of the host cell resulting in the formation of an extrahaustorial membrane, the region between this and the fungal membrane referred  to as the extrahaustorial matrix.''
*Formation of haustoria (sensu Viridiplantae):
''The formation of globular shaped organs developed in parasitic plants for acquiring nutrients from the host; as in, but not restricted to, parasitic plants (Viridiplantae, ncbi_taxonomy_id:33090).''
*Formation of syncytium:
Source: Niblack et al . Annu Rev Phytopath 2006:44:283-303
Defn: ''The formation of a system of highly modified host cells from which the symbiont (cyst nematode) feeds within the host (plant root).''
*Formation of symbiosome:
Source:Taken from component term symbiosome in main GO ontology and modified to a process term
''The formation of a double-enveloped cell compartment, composed of an endosymbiont with its plasmalemma (as inner envelope) and a non-endosymbiotic outer envelope (the perisymbiontic membrane).''
           
*Formation of siderophore
Source: Wikipedia
Defn: ''The formation of iron chelating compounds, many of which are nonribosomal petides  secreted by the symbiont to dissolve Fe3+ ions as soluble Fe3+ complexes.''
'''Notes:'''
1.Syncytium formation is already in the main ontology: GO:0006949
Definition:The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division.
2.Note that there are other kinds of syncytium formation but these have been accommodated under different terms in the main ontology namely:
            GO:0006949 : syncytium formation ( 2 )
                    GO:0000768 : syncytium formation by plasma membrane fusion ( 1 )
            GO:0006949 : syncytium formation  ( 2 )
                  GO:0000769 : syncytium formation by mitosis without cell division ( 0 )
3. The process of  haustoria formation  in fungi and oomycetes is different from that in parasitic plants thus a sensu designation was incorporated.
4. Where passage of nutrients is from symbionts to host, the term acquisition of nutrients from symbionts (which is already in the ontology)  can be used but the definition of that term should also be changed to infer acquiring and utilizing nutrients only.
***Could work on the definitions a bit more but thought to throw the general idea out there
===Michelle_Candace_Trudy_@PAG_Jan 29, 2007===
In  a recent discussion with Candace and Michelle, a better definition was formulated for the term “Acquisition of nutrients”
“Any process that results in the acquisition and/or utilization of nutrients obtained from its host, including, but not limited to, the formation of specialized structures for that purpose. The host is defined as the larger of the organisms involved in a symbiotic interaction."
In an earlier response  I had proposed a second parent “Modification of host morphology or physiology”  for  “Formation by organism of specialized structure for nutrient acquisition from  host” but  I realized now that in the draft ,  “Formation by organism of specialized structure for nutrient acquisition from  host” has a second parentage under  “Growth and development during symbiotic interaction” (an introduced term which is probably okay. So the tree structure should be:                   
(1) Acquisition of nutrients from other organism during symbiotic interaction
      Acquisition of nutrients from host
            Formation by symbiont of specialized structure for nutrient acquisition from host
                    Acquisition by organism of nutrients from host via siderophore
                    Formation by organism of specialized structure for nutrient acquisition…
                    Formation of arbuscule for nutrient acquisition from host
                    Formation of haustorium for nutrient acquisition from host (sensu
                    oomycete and fungi) 
                    Formation of haustorium for nutrient acquisition from host (sensu
                    viridiplantae)   
                    Formation of syncytium for nutrient acquisition from host
                    Formation of symbiosome for nutrient acquisition from host
(2) Growth or development during symbiotic interaction
        Formation of specialized structure for nutrient acquisition from other organism during symbiotic interaction
            Formation by symbiont of specialized structure for nutrient acquisition from host 
                    Formation by organism of specialized structure for nutrient acquisition from
                    host
                    Formation of arbuscule for nutrient acquisition from host
                    Formation of haustorium for nutrient acquisition from host (sensu
                    oomycete and fungi) 
                    Formation of haustorium for nutrient acquisition from host (sensu
                    viridiplantae)   
                    Formation of syncytium for nutrient absorption/acquisition from host
                    Formation of symbiosome for nutrient absorption/acquisition from host
===Jane 26th March 2007===
Quick query:
*We are currently removing all of the sensu strings from GO - they're just too confusing for everyone. We've been changing the names so that rather than saying e.g. 'cell wall (sensu Fungi)' we base it on something like compositional differences, so it would change to 'peptidoglycan-based cell wall'. So can we change the names of the two haustorium sensu terms? Maybe something like 'formation of hyphal tip haustorium for nutrient acquisition from host' v/s 'formation of root haustorium for nutrient acquisition from host' (I'm sure these are wrong, I know nothing about the biology, just to give you an idea!)


== Entry of organism into host cell by promotion of host phagocytosis ==
== Entry of organism into host cell by promotion of host phagocytosis ==
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Yes, at least that was my understanding.
Yes, at least that was my understanding.
===Candace_Trudy@PAG_Jan 28, 2007===
We wouldn’t say “upregulates” the whole process, but it promotes phagocytosis at the site of contact with the organism, so the organism gets taken up by the host cell.  This definitely is a “modulation” of host phagocytosis, but we wouldn’t say it’s actually an up-regulation (positive reg.) of phagocytosis  Hope this helps….


== Recognition of other organism during symbiotic interaction ==
== Recognition of other organism during symbiotic interaction ==
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response to other organism
response to other organism
*detection of other organism
*detection of other organism
===Candace_Trudy@PAG_Jan 28, 2007===
We actually prefer our definition, because it will be more understandable to people working in this area, but if it’s really important to keeping some internal consistency in GO that is essential in your mind, then you could change it.  But, we’d prefer to keep it as is, if possible.


== Induction terms ==
== Induction terms ==
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I seem to recall that for the induction terms we meant "kicking off an inactive process" and for upregulating we used "enhancement" however, I am not sure that we put in "enhancement" terms everywhere we needed them.  We may need to create analagous enhancement terms for many of the induction terms.
I seem to recall that for the induction terms we meant "kicking off an inactive process" and for upregulating we used "enhancement" however, I am not sure that we put in "enhancement" terms everywhere we needed them.  We may need to create analagous enhancement terms for many of the induction terms.
===Candace_Trudy@PAG_Jan 28, 2007===
INDUCTION TERMS
Could we make all “induction” terms (and terms that were formerly “activation of”) have this type of definition: “The activation or enhancement by an organism of the defense response of a second organism, where the two organisms are in a symbiotic interaction.”
Add the synonym, to all of these, “positive regulation.”
Do NOT at this time make any special “enhancement of” terms.


== Protein secretion systems ==
== Protein secretion systems ==
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Ref: Abramovitch et al (2006) Nature Reviews Molecular Cell Biology, 7:601-611.
Ref: Abramovitch et al (2006) Nature Reviews Molecular Cell Biology, 7:601-611.
===Trudy===
I would like to suggest the use of macromolecules instead of substance. Substance is too general a word. To support my stance on this, the definition of macromolecules and its usage in the context of the T4SS which Donghui rightly said secretes proteins and DNA can be found below:
Source: Wikipedia
Macromolecule is defined as: A macromolecule is a large molecule with a large molecular mass, but generally the use of the term is restricted to polymers and molecules which structurally include polymers. Many examples come from biology and in particular biochemistry. In case of "biomacromolecules" or biopolymers, there are proteins, carbohydrates, nucleic acids (such as DNA), and lipids (fat).
In the literature nucleic acids and proteins are jointly referred to as macromolecules.
For eg. Christie et al: 2005. Annu. Rev. Microbiol.2005. 59:451-485
            PMID:16153176
“In the T4SS , VirB11 is a member of a large family of ATPases associated with systems dedicated to secretion of macromolecules” (proteins and DNA).


== Protein secretion systems (again) ==
== Protein secretion systems (again) ==
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At the moment, we have regulation of the defense-related MAPK signalling pathways as an is-a of regulation of ethylene-mediated defense response. I vaguely remember discussing that but I just want to check it's correct.
At the moment, we have regulation of the defense-related MAPK signalling pathways as an is-a of regulation of ethylene-mediated defense response. I vaguely remember discussing that but I just want to check it's correct.
===Trudy===
Having "regulation of the defense-related MAPK signalling pathways" as a child of "regulation of ethylene-mediated defense response" violates the true path rule.
Suggestion as to how these terms ought to be placed in the hierachy can be found below.
Modulation of host morphology and physiology
  Modulation by symbiont of host signal transduction pathway
      Modulation by symbiont of host protein kinases
Modulation of host morphology and physiology
  Modulation by symbiont of host defense responses
      Modulation by symbiont of defense related signalling pathways
        Modulation by symbiont of defense-related protein kinases
            Regulation/Modulation by symbiont of the defense-related MAPK signalling pathways
            Regulation/Modulation by symbiont of ethylene-mediated signalling pathways
All other types of protein kinases besides MAPK induced during the host-microbe intearction can be listed as children of  "Modulation by symbiont of defense-related protein kinases".


== Avoidance, Evasion and Tolerance, oh my! ==
== Avoidance, Evasion and Tolerance, oh my! ==
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I really need to know, for the 'avoidance' and the 'evasion or tolerance' terms, exactly what is being meant. I am wondering if the 'avoidance' terms could themselves be avoided. Hmmmm.
I really need to know, for the 'avoidance' and the 'evasion or tolerance' terms, exactly what is being meant. I am wondering if the 'avoidance' terms could themselves be avoided. Hmmmm.
===Trudy===
Amelia, this is what I ended up with in response to the above issue after discussions with Brett and Marcus
Altering the effectiveness of host defenses
  Reducing effectiveness of host defenses
        Avoidance of host defenses
            Evasion of host defenses
            Suppression of host defenses
        Tolerance of host defenses
        Modification of host defenses
            Modification of defensive structures
                Physical modification of defensive structures
                Biochemical modification of defensive structures
            Modification of defensive compounds and chemicals
                Biochemical modification of defensive structures
  Enhancing effectiveness of host defenses
Definitions and other child terms can be provided later but this will serve as the basic structure. Note that


== all is_a relationships ==
== all is_a relationships ==


I'm interested in the rationale for building this portion of the ontology with terms that represent collections of processes rather than global processes that are then broken down into part_of subprocesses. Is there a plan to break these terms down into parts at some point? It seems for the nervous system development portion of the ontology we took the converse approach. We considered global processes and broke them down into parts. We are now going back and adding the is_a parents that will eventually have is_a relationships to the more 'primitive' terms in the process ontology.
I'm interested in the rationale for building this portion of the ontology with terms that represent collections of processes rather than global processes that are then broken down into part_of subprocesses. Is there a plan to break these terms down into parts at some point? It seems for the nervous system development portion of the ontology we took the converse approach. We considered global processes and broke them down into parts. We are now going back and adding the is_a parents that will eventually have is_a relationships to the more 'primitive' terms in the process ontology.
==Terms recommended  for obsoletion ==
===Trudy===
Since the new terms have not been committed to the GO yet, I am assuming terms that are marked for obsoletion can be eliminated completly... Am I right Amelia?? I created this section to put any such terms I come across as I go through all the new terms in the obo file Amelia posted on Sourceforge for download.
GO:0052435  modulation by organism of symbiont phytoalexin production
Reason: The implies that the is modulating phytoalexin production  in the symbiont. This is not biologically true. In some cases, such as "acquisition of nutrients from host", the reverse occurs. For example, in the mutualistic relationship formed between arbuscular mycorrhizal (AM) fungi and vascular flowering plants, the host receives all its phosphorous from the fungal symbiont whilst the fungus obtains its carbon source from the plant. This is not the case for:
GO:0052435 modulation by organism of symbiont phytoalexin production
Similar terms for obsoletion include:
*GO:0052395  induction by organism of defense-related symbiont nitric oxide production
*GO:0052401  induction by organism of defense-related symbiont reactive oxygen species production
These are just a few examples but there are a lot more in the draft...instead of listing them, I am sure Amelia can fish them out in the obo file with a keyword or with a script.
===Trudy===
These terms have been recommended for elimination from the new set of PAMGO terms. The terms were script generated as reciprocal terms for the host from the proposed symbiont terms. I used the "keyword" symbiont to pull them out from the obo file and separated out the ones that do not make biological sense to be eliminated.
active evasion of symbiont immune response GO:0051846
active evasion of symbiont immune response via regulation of symbiont antigen processing and presentation GO:0051849
active evasion of symbiont immune response via regulation of symbiont complement system GO:0051847
active evasion of symbiont immune response via regulation of symbiont cytokine network GO:0051848
evasion or tolerance by organism of symbiont-produced nitric oxide GO:0052375
evasion or tolerance by organism of symbiont-produced phytoalexins GO:0052377
evasion or tolerance by organism of symbiont-produced reactive oxygen species GO:0052384
evasion or tolerance of symbiont defense response GO:0051843
evasion or tolerance of symbiont immune response GO:0051842
induction by organism of defense-related symbiont calcium ion flux GO:0052392
induction by organism of defense-related symbiont cell wall thickening GO:0052394
induction by organism of defense-related symbiont nitric oxide production GO:0052395
induction by organism of defense-related symbiont reactive oxygen species production GO:0052401
induction by organism of induced systemic resistance in symbiont GO:0052350
induction by organism of symbiont apoptosis GO:0052387
induction by organism of symbiont non-apoptotic programmed cell death GO:0052396
induction by organism of symbiont immune response GO:0052560
induction by organism of symbiont innate immunity GO:0052383
induction by organism of symbiont phytoalexin production GO:0052398
induction by organism of symbiont programmed cell death GO:0052399
induction by organism of symbiont resistance gene-dependent defense response GO:0052402
induction by organism of systemic acquired resistance in symbiont GO:0052351
induction in symbiont of tumor, nodule, or growth GO:0051853
induction in symbiont of tumor, nodule, or growth containing transformed cells GO:005185
interaction with symbiont via protein secreted by type II secretion system GO:0052327
interaction with symbiont via protein secreted by type III secretion system GO:0052328
interaction with symbiont via protein secreted by type IV secretion system GO:0052326
modification by organism of symbiont morphology or physiology via protein secreted by type II secretion system GO:0052425
modification by organism of symbiont morphology or physiology via protein secreted by type III secretion system GO:0052424
modification by organism of symbiont morphology or physiology via substance secreted by type IV secretion system GO:0052426
modulation by organism of defense-related symbiont calcium ion flux GO:0052437
modulation by organism of defense-related symbiont calcium-dependent protein kinase pathway GO:0052436
modulation by organism of defense-related symbiont callose deposition GO:0052438
modulation by organism of defense-related symbiont cell wall callose deposition GO:005243
modulation by organism of defense-related symbiont cell wall thickening GO:0052446
modulation by organism of defense-related symbiont ethylene-mediated signal transduction pathway GO:0052440
modulation by organism of defense-related symbiont jasmonic acid-mediated signal transduction pathway GO:0052442
modulation by organism of defense-related symbiont nitric oxide production GO:0052457
modulation by organism of defense-related symbiont reactive oxygen species production GO:0052465
modulation by organism of defense-related symbiont salicylic acid-mediated signal transduction pathway GO:0052444
modulation by organism of ethylene levels in symbiont GO:0052448
modulation by organism of induced systemic resistance in symbiont GO:0052450
modulation by organism of jasmonic acid levels in symbiont GO:0052455
modulation by organism of pathogen-associated molecular pattern-induced symbiont innate immunity GO:0052461
modulation by organism of salicylic acid levels in symbiont GO:0052468
modulation by organism of symbiont apoptosis GO:0052432
modulation by organism of symbiont B-cell mediated immune response GO:0052429
modulation by organism of symbiont cell-mediated immune response GO:0052434
modulation by organism of symbiont ethylene-mediated defense response GO:0052447
modulation by organism of symbiont hormone or growth regulator levels GO:0052184
modulation by organism of symbiont immune response GO:0052308
modulation by organism of symbiont inflammatory response GO:0052451
modulation by organism of symbiont innate immunity GO:0052452
modulation by organism of symbiont intracellular transport GO:0052453
modulation by organism of symbiont jasmonic acid-mediated defense response GO:0052454
modulation by organism of symbiont non-apoptotic programmed cell death GO:0052458
modulation by organism of symbiont phytoalexin production GO:0052463
modulation by organism of symbiont programmed cell death GO:0052464
modulation by organism of symbiont resistance gene-dependent defense response GO:0052466
modulation by organism of symbiont salicylic acid-mediated defense response GO:0052467
modulation by organism of symbiont T-cell mediated immune response GO:0052431
modulation by organism of systemic acquired resistance in symbiont GO:0052466
negative regulation by organism of defense-related symbiont callose deposition GO:0052504
negative regulation by organism of defense-related symbiont cell wall callose deposition GO:0052477
negative regulation by organism of defense-related symbiont ethylene-mediated signal transduction pathway GO:0052479
negative regulation by organism of defense-related symbiont jasmonic acid-mediated signal transduction pathway GO:0052480
negative regulation by organism of defense-related symbiont salicylic acid-mediated signal transduction pathway GO:0052481
negative regulation by organism of pathogen-associated molecular pattern-induced symbiont innate immunity GO:0052488
negative regulation by organism of symbiont B-cell mediated immune response GO:0052473
negative regulation by organism of symbiont cell-mediated immune response GO:0052475
negative regulation by organism of symbiont ethylene-mediated defense response GO:0052484
negative regulation by organism of symbiont immune response GO:0052563
negative regulation by organism of symbiont inflammatory response GO:0052485
negative regulation by organism of symbiont innate immunity GO:0052486
negative regulation by organism of symbiont jasmonic acid-mediated defense response GO:0052487
negative regulation by organism of symbiont salicylic acid-mediated defense response GO:0052491
negative regulation by organism of symbiont T-cell mediated immune response GO:0052474
passive evasion of symbiont immune response GO:0051845
pathogen-associated molecular pattern dependent induction by organism of symbiont innate immunity GO:0052498
pathogen-associated molecular pattern dependent modulation by organism of symbiont innate immunity GO:0052499
positive regulation by organism of defense-related symbiont calcium ion flux GO:0052531
positive regulation by organism of defense-related symbiont calcium-dependent protein kinase pathway GO:0052503
positive regulation by organism of defense-related symbiont callose deposition GO:0052504
positive regulation by organism of defense-related symbiont cell wall callose deposition GO:0052505
positive regulation by organism of defense-related symbiont cell wall thickening GO:0052540
positive regulation by organism of defense-related symbiont ethylene-mediated signal transduction pathway GO:0052506
positive regulation by organism of defense-related symbiont jasmonic acid-mediated signal transduction pathway GO:0052507
positive regulation by organism of defense-related symbiont nitric oxide production GO:0052346
positive regulation by organism of defense-related symbiont reactive oxygen species production GO:0052349
positive regulation by organism of defense-related symbiont salicylic acid-mediated signal transduction pathway GO:0052508
positive regulation by organism of hormone or growth regulator levels in symbiont GO:0052512
positive regulation by organism of induced systemic resistance in symbiont GO:0052534
positive regulation by organism of symbiont apoptosis GO:0052500
positive regulation by organism of symbiont ethylene-mediated defense response GO:0052511
positive regulation by organism of symbiont immune response GO:0052557
positive regulation by organism of symbiont inflammatory response GO:0052514
positive regulation by organism of symbiont innate immunity GO:0052515
positive regulation by organism of symbiont jasmonic acid-mediated defense response GO:0052516
positive regulation by organism of symbiont non-apoptotic programmed cell death GO:0052517
positive regulation by organism of symbiont phytoalexin production GO:0052343
positive regulation by organism of symbiont programmed cell death GO:0052523
positive regulation by organism of symbiont resistance gene-dependent defense response GO:0052530
positive regulation by organism of symbiont salicylic acid-mediated defense response GO:0052524
positive regulation by organism of systemic acquired resistance in symbiont GO:0052536
response to defense-related symbiont nitric oxide production GO:0052569
response to defense-related symbiont reactive oxygen species production GO:0052570
response to symbiont immune response GO:0052571
response to symbiont phytoalexin production GO:0052568
translocation of DNA into symbiont GO:0051863
upregulation by organism of symbiont programmed cell death GO:0052528
== Modify definitions of these terms????? ==
== New Terms ==
===Michelle_Trudy_Candace@PAG===
Commensalism, Mutualism: Add as siblings to pathogenesis
===Jane===
Can we have some defs for these terms please?
===Candace===
7/17/07
Commensalism = a symbiotic relationship between two living organisms of different species in which one derives some benefit while the other is unaffected, or affected very little.
A child of GO:0044403 : symbiosis;  a sibling to GO:0009405 : pathogenesis   
No children terms
Mutualism = an interaction between organisms of two or more species, where both species derive benefit.
Note a change here from our original request in terms of parentage.
This term should be a child of GO:0044419 : interspecies interaction between organisms;  a sibling to GO:0044403 : symbiosis
No children terms

Latest revision as of 15:52, 17 July 2007

Some issues I'm encountering whilst working through the file. Please put your thoughts on the matter underneath each issue. Also see the PAMGO terms to be defined page for a list of PAMGO terms which need definitions.


The first draft of the ontology changes can be found in this SourceForge item:

https://sourceforge.net/tracker/index.php?func=detail&aid=1546635&group_id=36855&atid=440764

It would be great if we could discuss any points on the wiki here, since it allows you to organise things much better than SourceForge.


If you want to leave a comment, click on the "edit" tag for that section, and add your comment at the bottom, starting it with your name as a subheader (put three equals signs in front of and after your name, i.e.

===The Invisible Hulk===

). This will automatically create a link at the top of the page, making it easy to navigate to.

If the point you want to talk about isn't already in the list here, just click the + sign at the top of the page; that creates a new comment section.


Thanks!

The 'other organism' string

See PAMGO The Other Organism String

Hypersensitive response

See PAMGO Hypersensitive Response

Modification of host protein function

At the moment, modification of host protein function is a child of 'modification ... via secreted substance'. This seems OK to me, but are there any ways in which host protein function can be modified directly or via some other method?


Candace_Michelle_Trudy@PAG

In the literature, most of the macromolecules involved in the modification of host protein function are secreted so it is safe to conclude for now that host protein functions are modified mainly via secreted proteins and as such would be a child of 'modification ... via secreted substance" without creating a sibling term "modification ... via non-secreted substance".


However, we modified the definition....find below:

The process by which an organism effects a change in the function of a host protein via a direct interaction. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Jane

Done.

Modification/modulation of host defenses

Host defenses consist of the induced defenses - the defense response mounted by the host - and the preexisting defenses, such as the cell wall and other defensive structures. We've got modification of host structure and modulation of host defense response, but nothing to encapsulate both - logically it seems like a term we should have since elsewhere we have structures like this:

  • evasion or tolerance of host defenses
    • evasion or tolerance of host defense response

Currently, we've got the term 'response to host defenses ; GO:0044413' (was 'avoidance of host defenses' but we renamed it), which is defined thus:

Any process, either constitutive or induced, by which an organism evades, suppresses or tolerates the effects of its host organism's defense(s). Host defenses may be induced by the presence of the organism or may be preformed (e.g. physical barriers). The host is defined as the larger of the organisms involved in a symbiotic interaction.

I am no longer sure that this term is correctly named, as there are situations where the symbiont induces host defenses, but the def of 'response to host defenses' only covers the "negative" aspects of the response. Perhaps 'response to host defenses' should be used as a term to encapsulate modification/modulation of host defenses?

As yet I don't have any suggestion for a new name for 'response to host defenses', unfortunately!





Trudy_Candace_Michelle@PAG

We think it is okay to replace "avoidance of host defences" with response to "response to [org] defenses". We have other suggestions to merge what were previously child terms of "avoidance of host defences" to the new parent term "response to [org] defenses" (See details below)



response to [org] defenses

  evasion or tolerance of [org] defenses (merge to the parent term “response to [org] defenses”

(MAKE AS MORE NARROW SYNONYMS OF THIS TERM: “evasion of [org] defenses,” “suppression of [org] defenses,” “tolerance of [org] defenses.

 response to [org] oxidative burst  (child of “response to [org] defenses”)
 response to [org] phytoalexins (child of “response to [org] defenses”)
 response to [org] nitric oxide (child of “response to [org] defenses”)
 evasion by virus of host defenses (obsolete this term)
 evasion of host defense response (GO:0030682) (merge to parent “response to [org] defenses”)
 evasion of host immune response (GO:0020012) (child of “response to [org] de fenses”)
 suppression of [org] defenses (merge to parent term “response to [org] defenses”

child terms include suppression of host processes (merged into terms up above)

We do not need to add terms about “passive” and “active” evasion, etc.; on the other hand, having the words “constitutive” and “induced” in the definition is fine and desirable.

Symbiont defenses

I am just contemplating adding terms for the following:

  • modulation by organism of symbiont defense response
    • modulation by organism of symbiont inflammatory response
    • modulation by organism of symbiont innate immunity

The first one is OK, but I'm not sure about the second and third. Are there/might there be symbioses out there where the smaller partner is a multicellular organism with inflammatory responses and innate immunity which the host species regulates in some way? Most of the symbioses between larger organisms seem to be more behavioural...


===Candace_Michelle_Trudy

We would rather not have those children terms added under “modulation by organism of symbiont defense response”. Just keep the parent term

Innate immunity

At the moment our terms refer to 'innate immunity', whereas in the main GO, they talk about 'innate immune response'. Is it OK to change the terms to that string instead, e.g. modulation of host innate immune response

Trudy

I see no reason why we cannot use “innate immune response” in place of innate immunity.

Web definitions of immune response: a physiological response in humans and higher animals to defend the body against the introduction of foreign material.

Web definitions of immunity: unsusceptibility-the state of not being susceptible or a condition in which an organism can resist disease.

The word "immunity" connotes the state and "immune responses" refer to the reactions triggered by the foreign body to get the host into a state of immunity so it really depends on the context in which the phrase is being used.

I think whichever one is chosen, the other should be made a synonym or better still be included in the definition as in “innate immune response (sensu Viridiplantae)” in the main GO which is copied below:

innate immune response (sensu Viridiplantae) GO:0002226 Definition:The process of the innate immunity as in, but not restricted to, green plants and algae (Viridiplantae, ncbi_taxonomy_id:33090). Innate immune responses are defense responses mediated by germline encoded components that, in plants, directly recognize components of potential pathogens.

Any other thoughts???



Candace

7/17/07

Yes - I think it would be best to keep the term "innate immunity" rather than "innate immune response." I have been reading through the program for the International meeting of MPMI (7/07, in Sorrento, Italy) and the term "innate immunity" seems to be used frequently in titles, but not "innate immune response" in terms of all the plant-microbe papers.

Acquisition of nutrients from host

...is defined as

"The production of structures and/or molecules in an organism that are required for the acquisition and/or utilization of nutrients obtained from its host. The host is defined as the larger of the organisms involved in a symbiotic interaction."

How are we going to differentiate "formation by organism of specialized structure for nutrient acquisition from host" from this term? Is the def for "acquisition of nutrients from host" too detailed?

Michelle

Well, it seems an example of two things that fall under the parent term would be haustoria formation and hemolysin. The haustoria is a structure for gaining nutrients, while hemolysin is a molecule produced by the pathogen which causes nutrients to be dumped into the environment which the pathogen then slurps up - no specialized structures needed. So I think the "formation by organism of specialized...." term is correctly a more specific child of the parent. There could also be "cytolysis of host cells for the purpose of nutrient acquisition" as another child. I don't think we necessarily need such a term, and concurrent annotations should be able to handle it, but I am just trying to illustrate what I mean.

Trudy

Acquisition of nutrients from host

I see this term as the process of acquiring nutrients which is different from the formation of the structures through which the symbionts acquire the nutrients but then the latter is incorporated in the definition of the term thus fusing two separate processes into one.


The primary role of most of these structures, the haustorium, syncytium, arbuscules etc is to acquire nutrients from the hosts so I see why in an earlier term development effort, even though the term name is specified as the acquisition of nutrients from host, the definition was made to include the formation of the structures.

In my opinion, which was further supported from discussions with Brett, Marcus and Tsa-Tsieng, we should have “Formation of specialized nutrient absorption structures and macromolecules” housed under two parents as detailed below:


Modification of host morphology and physiology

        Formation of specialized nutrient absorption structures and macromolecules
                   Formation of arbuscules for nutrient absorption/acquisition from host
                   Formation of haustoria for nutrient absorption/acquisition from host
                   Formation of haustoria for nutrient absorption/acquisition from host sensu Viridiplantae
                   Formation of syncytium for nutrient absorption/acquisition from host
                   Formation of symbiosome for nutrient absorption/acquisition from host
                   Formation of siderophore for nutrient absorption/acquisition from host


Acquisition of nutrients

       Formation of specialized nutrient absorption structures and macromolecules
                  Formation of arbuscules for nutrient absorption/acquisition from host
                  Formation of haustoria for nutrient absorption/acquisition from host (sensu oomycetes and 
                  Formation of haustoria sensu for nutrient absorption/acquisition from host (sensu Viridiplantae)
                  Formation of syncytium for nutrient absorption/acquisition from host
                  Formation of symbiosome for nutrient absorption/acquisition from host
                  Formation of siderophore for nutrient absorption/acquisition from host


Definitions:

  • Formation of specialized nutrient absorption structures and macromolecules

Defn: The production of structures and/or molecules in an organism that are required for the acquisition and/or utilization of nutrients obtained from its host. The host is defined as the larger of the organisms involved in a symbiotic interaction (note: are siderophores produced in the host)

  • Acquisition of nutrients from host

Defn:The process of acquisition and/or utilization of nutrients by symbionts from its host. The host is defined as the larger of the organisms involved in a symbiotic interaction.

  • Formation of arbuscules:

Source: Wikipedia, Harrison M.J. Annu. Rev Microb:

Defn:The formation of highly branched structures in the parenchyma of plant cells by symbionts for acquisition of nutrients from the host.

  • Formation of haustoria:

Defn:The formation of specialized feeding structures in host characterized by invaginations inside the plasma membrane of the host cell resulting in the formation of an extrahaustorial membrane, the region between this and the fungal membrane referred to as the extrahaustorial matrix.

  • Formation of haustoria (sensu Viridiplantae):

The formation of globular shaped organs developed in parasitic plants for acquiring nutrients from the host; as in, but not restricted to, parasitic plants (Viridiplantae, ncbi_taxonomy_id:33090).

  • Formation of syncytium:

Source: Niblack et al . Annu Rev Phytopath 2006:44:283-303

Defn: The formation of a system of highly modified host cells from which the symbiont (cyst nematode) feeds within the host (plant root).

  • Formation of symbiosome:

Source:Taken from component term symbiosome in main GO ontology and modified to a process term

The formation of a double-enveloped cell compartment, composed of an endosymbiont with its plasmalemma (as inner envelope) and a non-endosymbiotic outer envelope (the perisymbiontic membrane).


  • Formation of siderophore

Source: Wikipedia Defn: The formation of iron chelating compounds, many of which are nonribosomal petides secreted by the symbiont to dissolve Fe3+ ions as soluble Fe3+ complexes.


Notes:

1.Syncytium formation is already in the main ontology: GO:0006949

Definition:The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division.


2.Note that there are other kinds of syncytium formation but these have been accommodated under different terms in the main ontology namely:

            GO:0006949 : syncytium formation ( 2 )
                   GO:0000768 : syncytium formation by plasma membrane fusion ( 1 )
            GO:0006949 : syncytium formation  ( 2 )
                  GO:0000769 : syncytium formation by mitosis without cell division ( 0 )


3. The process of haustoria formation in fungi and oomycetes is different from that in parasitic plants thus a sensu designation was incorporated.

4. Where passage of nutrients is from symbionts to host, the term acquisition of nutrients from symbionts (which is already in the ontology) can be used but the definition of that term should also be changed to infer acquiring and utilizing nutrients only.

      • Could work on the definitions a bit more but thought to throw the general idea out there


Michelle_Candace_Trudy_@PAG_Jan 29, 2007

In a recent discussion with Candace and Michelle, a better definition was formulated for the term “Acquisition of nutrients”

“Any process that results in the acquisition and/or utilization of nutrients obtained from its host, including, but not limited to, the formation of specialized structures for that purpose. The host is defined as the larger of the organisms involved in a symbiotic interaction."

In an earlier response I had proposed a second parent “Modification of host morphology or physiology” for “Formation by organism of specialized structure for nutrient acquisition from host” but I realized now that in the draft , “Formation by organism of specialized structure for nutrient acquisition from host” has a second parentage under “Growth and development during symbiotic interaction” (an introduced term which is probably okay. So the tree structure should be:


(1) Acquisition of nutrients from other organism during symbiotic interaction 
      Acquisition of nutrients from host
           Formation by symbiont of specialized structure for nutrient acquisition from host
                   Acquisition by organism of nutrients from host via siderophore
                   Formation by organism of specialized structure for nutrient acquisition… 
                   Formation of arbuscule for nutrient acquisition from host
                   Formation of haustorium for nutrient acquisition from host (sensu 
                    oomycete and fungi)   
                   Formation of haustorium for nutrient acquisition from host (sensu 
                    viridiplantae)    
                   Formation of syncytium for nutrient acquisition from host
                   Formation of symbiosome for nutrient acquisition from host

(2) Growth or development during symbiotic interaction
        Formation of specialized structure for nutrient acquisition from other organism during symbiotic interaction 
            Formation by symbiont of specialized structure for nutrient acquisition from host  
                    Formation by organism of specialized structure for nutrient acquisition from 
                    host
                    Formation of arbuscule for nutrient acquisition from host
                    Formation of haustorium for nutrient acquisition from host (sensu 
                    oomycete and fungi)   
                    Formation of haustorium for nutrient acquisition from host (sensu 
                    viridiplantae)    
                    Formation of syncytium for nutrient absorption/acquisition from host
                    Formation of symbiosome for nutrient absorption/acquisition from host

Jane 26th March 2007

Quick query:

  • We are currently removing all of the sensu strings from GO - they're just too confusing for everyone. We've been changing the names so that rather than saying e.g. 'cell wall (sensu Fungi)' we base it on something like compositional differences, so it would change to 'peptidoglycan-based cell wall'. So can we change the names of the two haustorium sensu terms? Maybe something like 'formation of hyphal tip haustorium for nutrient acquisition from host' v/s 'formation of root haustorium for nutrient acquisition from host' (I'm sure these are wrong, I know nothing about the biology, just to give you an idea!)

Entry of organism into host cell by promotion of host phagocytosis

def: "The invasion by an organism of a cell of its host organism by utilizing the host phagocytosis mechanism."

Just to check - does this term mean that the organism upregulates host phagocytosis?


Michelle

Yes, at least that was my understanding.



Candace_Trudy@PAG_Jan 28, 2007

We wouldn’t say “upregulates” the whole process, but it promotes phagocytosis at the site of contact with the organism, so the organism gets taken up by the host cell. This definitely is a “modulation” of host phagocytosis, but we wouldn’t say it’s actually an up-regulation (positive reg.) of phagocytosis Hope this helps….

Recognition of other organism during symbiotic interaction

This is defined as "The specific processes that allow an organism to detect the presence of a second organism via physical or chemical signals, where the two organisms are in a symbiotic interaction.".

Could this be a standard detection term? The std def for detection terms is:

The series of events in which a [...] stimulus is received by a cell and converted into a molecular signal.

or is recognition more of an organismal-level process?

I was just wondering as it would be nice to have a structure that mimics the main ontology, i.e.

response to other organism

  • detection of other organism


Candace_Trudy@PAG_Jan 28, 2007

We actually prefer our definition, because it will be more understandable to people working in this area, but if it’s really important to keeping some internal consistency in GO that is essential in your mind, then you could change it. But, we’d prefer to keep it as is, if possible.

Induction terms

At the moment, under positive regulation, we have various 'induction' and 'activation' terms. What specifically should these terms mean? Are they induction as in kicking off an inactive process, or are the induction meaning general positive regulation, i.e. activating an inactive process and perpetuating or upregulating an existing process? The terms in question are:

  • GO:0052103 activation by organism of induced systemic resistance in host
  • GO:0052104 activation by organism of systemic acquired resistance in host
  • GO:0052030 induction by organism of host apoptotic programmed cell death
  • GO:0052065 induction by organism of host calcium ion flux
  • GO:0044416 induction by organism of host defense response
  • GO:0052105 induction by organism of host defensive cell wall thickening
  • GO:0052063 induction by organism of host nitric oxide production
  • GO:0012504 induction by organism of host non-apoptotic programmed cell death
  • GO:0052062 induction by organism of host phytoalexin production
  • GO:0052044 induction by organism of host programmed cell death
  • GO:0052064 induction by organism of host reactive oxidative species production
  • GO:0052101 induction by organism of host resistance gene-dependent defense response
  • GO:0052033 pathogen-associated molecular pattern dependent induction by organism of host innate immunity

Michelle

I seem to recall that for the induction terms we meant "kicking off an inactive process" and for upregulating we used "enhancement" however, I am not sure that we put in "enhancement" terms everywhere we needed them. We may need to create analagous enhancement terms for many of the induction terms.

Candace_Trudy@PAG_Jan 28, 2007

INDUCTION TERMS

Could we make all “induction” terms (and terms that were formerly “activation of”) have this type of definition: “The activation or enhancement by an organism of the defense response of a second organism, where the two organisms are in a symbiotic interaction.”

Add the synonym, to all of these, “positive regulation.”

Do NOT at this time make any special “enhancement of” terms.

Protein secretion systems

We've got the terms for modification of morphology and physiology using substances secreted by various types of secretion systems. Are these systems only found in symbionts, or might there be symbioses where the host organism had type II / III / IV (i.e. a bacterium was the host)? Also, we've got the term names as follows:

  • GO:0052049 interaction with host via protein secreted by type III secretion system
  • GO:0052050 interaction with host via substance secreted by type IV secretion system
  • GO:0052051 interaction with host via protein secreted by type II secretion system

Should these all be "... *protein* secreted by type ..."? Do other substances ever get secreted by these systems?

T4SS secretes protein and DNA (Donghui Li)

Three distinct secretion pathyways have been studied in plant pathogens.

The Type II secretion systems (T2SS) exports enzymes that are involved in degrading the plant cell wall, including pectinases, endo-glucanases and cellulases.

T3SS is the most widely studied secretion system in plant pathogens. Pathogens use T3SS to inject effectors (proteins) into the host cell. There is a great diversity of effectors; they have diverse enzymatic activities. Bacterial effectors have a prominent role in promoting the virulence in plants.

The T4SS has a critical role in the pathogenesis of Argobacterium and its capacity to form galls on plants. The T4SS mediates the trafficking of bacterial proteins and DNA into the plant cell. The bacterial DNA is integrated into the host genome to produce hormones that modify the phsyiology of plants.

Many pathogens rely on multiple secretion systems. For example, several strains of Xanthomonas have T2SS, T3SS and T4SS.

Based on the above discussion, it is clear that the use of 'substance' instead of 'protein' for T4SS is appropriate: T4SS secretes both protein and DNA, while T2SS and T3SS only secrete proteins.

Ref: Abramovitch et al (2006) Nature Reviews Molecular Cell Biology, 7:601-611.


Trudy

I would like to suggest the use of macromolecules instead of substance. Substance is too general a word. To support my stance on this, the definition of macromolecules and its usage in the context of the T4SS which Donghui rightly said secretes proteins and DNA can be found below:

Source: Wikipedia Macromolecule is defined as: A macromolecule is a large molecule with a large molecular mass, but generally the use of the term is restricted to polymers and molecules which structurally include polymers. Many examples come from biology and in particular biochemistry. In case of "biomacromolecules" or biopolymers, there are proteins, carbohydrates, nucleic acids (such as DNA), and lipids (fat).

In the literature nucleic acids and proteins are jointly referred to as macromolecules. For eg. Christie et al: 2005. Annu. Rev. Microbiol.2005. 59:451-485

           PMID:16153176

“In the T4SS , VirB11 is a member of a large family of ATPases associated with systems dedicated to secretion of macromolecules” (proteins and DNA).

Protein secretion systems (again)

Def of "modification by organism of host morphology or physiology via secreted substance":

The process by which an organism effects a change in the structure or function of its host organism, mediated by a substance secreted by one of the organisms.

Is this supposed to be suitable for referring to either host- or symbiont-secreted substances, or is it supposed to be specific to the organism secreting the substance (i.e. the symbiont in this case)?

MAPK pathways

At the moment, we have regulation of the defense-related MAPK signalling pathways as an is-a of regulation of ethylene-mediated defense response. I vaguely remember discussing that but I just want to check it's correct.

Trudy

Having "regulation of the defense-related MAPK signalling pathways" as a child of "regulation of ethylene-mediated defense response" violates the true path rule. Suggestion as to how these terms ought to be placed in the hierachy can be found below.


Modulation of host morphology and physiology

  Modulation by symbiont of host signal transduction pathway
     Modulation by symbiont of host protein kinases

Modulation of host morphology and physiology

  Modulation by symbiont of host defense responses
     Modulation by symbiont of defense related signalling pathways
        Modulation by symbiont of defense-related protein kinases
            Regulation/Modulation by symbiont of the defense-related MAPK signalling pathways
            Regulation/Modulation by symbiont of ethylene-mediated signalling pathways


All other types of protein kinases besides MAPK induced during the host-microbe intearction can be listed as children of "Modulation by symbiont of defense-related protein kinases".

Avoidance, Evasion and Tolerance, oh my!

I'm trying to work out a systematic way to deal with the terms under 'response to ... defenses', because at the moment, the terms have various names (evasion, evasion and tolerance, suppression, avoidance, response to, etc.) and the defs all seem to differ. This is the current structure (I've used a generic 'org' instead of spelling out all the host / symbiont / other organism terms):

  • response to [org] defenses
    • avoidance of [org] defenses
      • evasion or tolerance of [org] defenses
        • evasion by virus of host defenses
          • child terms include suppression of host processes
        • evasion or tolerance of [org] defense response
          • evasion or tolerance of [org] immune response
            • active evasion terms
            • passive evasion terms
            • evasion or tolerance of [org] oxidative burst / [org] phytoalexins / [org] NO
      • suppression of [org] defenses
    • modulation of [org] defense response

I would like to try to work out what we're actually meaning by "evasion", "tolerance" and so on.


  • "passive evasion" is defined as a process by which an organism deals with a defense response without affecting the other organism
  • "active evasion" is a process by which an organism deals with a defense response and affects the other organism into the bargain. It is not clear
  • "tolerance" isn't used on its own, so I am not sure what it represents
  • "suppression" seems to be very similar, if not identical, to "negative regulation" - i.e. stopping a process, impeding a process, or preventing an inactive process from starting.
  • "avoidance" seems to be the conjunction of "tolerance", "evasion" and "suppression"

Some of the term defs mention "constitutive" and "induced" processes (the avoidance terms), and others talk about "active" and "passive" (evasion or tolerance terms). I am not sure whether "active" and "passive" here means the same as "active evasion" and "passive evasion".


This is how I have been thinking of defenses and the defense response:

  • "defenses" applies to everything that an organism has developed over its lifespan and through evolution to deal with threats.
  • you can separate defenses into two types, structural defenses and defensive processes. I *think* this correlates with constitutive and induced defenses (aka the defense response). I can't think of any constitutive defenses that are a GO process, rather than just a protein sitting there holding the cell wall together.
  • structural defenses can't harm you, so the only thing you're likely to do to them is to attack them
  • the defense response of the other organism is likely to harm you in some way. There are three ways you could deal with this:
  1. build up fortifications to protect yourself against the effects of the other organism's process (e.g. cell wall)
  2. neutralize the effects of the other organism's process (e.g. detoxifying harmful chemicals)
  3. stop the other organism from performing the process

No. 1 is your structural defenses. They are constitutive and passive, and they can't be represented by a GO process term (I believe). No. 2 and 3 are your 'defense response'.

So your response to the defenses of the other organism could be split up thus:

response to [org] defenses
[i] modification of [org] defenses
---[i] physical modification of [org] defensive structures
---[i] modulation of [org] defense response (#3)
[i] response to [org] defense response
---[i] modulation of [org] defense response (#3)
---[i] examples of neutralizing the effects of the other org's defense response (#2)

No. 2 would include the new terms like 'evasion or tolerance of [org] phytoalexins'.

From this perspective, 'suppression of [org] defenses' doesn't make much sense, as you can't suppress a physical structure. I think it would be better to alter this term to be 'suppression of [org] defense response'.

Is 'tolerance' supposed to represent the passive / structural defenses?

[this is unfinished at the moment due to temporary loss of mind]

Later thoughts

For concepts where we have both modulation terms and evasion/tolerance terms, I've grouped them together under a 'response to' term, e.g.

response to [org] phytoalexin production
[i] evasion or tolerance of [org]-produced phytoalexins
[i] modulation of [org] phytoaxelin production
---[i] positive regulation of [org] phytoalexin production
------[i] induction of [org] phytoalexin production

I really need to know, for the 'avoidance' and the 'evasion or tolerance' terms, exactly what is being meant. I am wondering if the 'avoidance' terms could themselves be avoided. Hmmmm.

Trudy

Amelia, this is what I ended up with in response to the above issue after discussions with Brett and Marcus

Altering the effectiveness of host defenses

  Reducing effectiveness of host defenses
       Avoidance of host defenses
            Evasion of host defenses
            Suppression of host defenses
       Tolerance of host defenses
       Modification of host defenses
            Modification of defensive structures
                Physical modification of defensive structures
                Biochemical modification of defensive structures
            Modification of defensive compounds and chemicals
                Biochemical modification of defensive structures
  Enhancing effectiveness of host defenses


Definitions and other child terms can be provided later but this will serve as the basic structure. Note that

all is_a relationships

I'm interested in the rationale for building this portion of the ontology with terms that represent collections of processes rather than global processes that are then broken down into part_of subprocesses. Is there a plan to break these terms down into parts at some point? It seems for the nervous system development portion of the ontology we took the converse approach. We considered global processes and broke them down into parts. We are now going back and adding the is_a parents that will eventually have is_a relationships to the more 'primitive' terms in the process ontology.

Terms recommended for obsoletion

Trudy

Since the new terms have not been committed to the GO yet, I am assuming terms that are marked for obsoletion can be eliminated completly... Am I right Amelia?? I created this section to put any such terms I come across as I go through all the new terms in the obo file Amelia posted on Sourceforge for download.


GO:0052435 modulation by organism of symbiont phytoalexin production Reason: The implies that the is modulating phytoalexin production in the symbiont. This is not biologically true. In some cases, such as "acquisition of nutrients from host", the reverse occurs. For example, in the mutualistic relationship formed between arbuscular mycorrhizal (AM) fungi and vascular flowering plants, the host receives all its phosphorous from the fungal symbiont whilst the fungus obtains its carbon source from the plant. This is not the case for:

GO:0052435 modulation by organism of symbiont phytoalexin production


Similar terms for obsoletion include:

  • GO:0052395 induction by organism of defense-related symbiont nitric oxide production
  • GO:0052401 induction by organism of defense-related symbiont reactive oxygen species production


These are just a few examples but there are a lot more in the draft...instead of listing them, I am sure Amelia can fish them out in the obo file with a keyword or with a script.


Trudy

These terms have been recommended for elimination from the new set of PAMGO terms. The terms were script generated as reciprocal terms for the host from the proposed symbiont terms. I used the "keyword" symbiont to pull them out from the obo file and separated out the ones that do not make biological sense to be eliminated.

active evasion of symbiont immune response GO:0051846

active evasion of symbiont immune response via regulation of symbiont antigen processing and presentation GO:0051849

active evasion of symbiont immune response via regulation of symbiont complement system GO:0051847

active evasion of symbiont immune response via regulation of symbiont cytokine network GO:0051848

evasion or tolerance by organism of symbiont-produced nitric oxide GO:0052375

evasion or tolerance by organism of symbiont-produced phytoalexins GO:0052377

evasion or tolerance by organism of symbiont-produced reactive oxygen species GO:0052384

evasion or tolerance of symbiont defense response GO:0051843

evasion or tolerance of symbiont immune response GO:0051842

induction by organism of defense-related symbiont calcium ion flux GO:0052392

induction by organism of defense-related symbiont cell wall thickening GO:0052394

induction by organism of defense-related symbiont nitric oxide production GO:0052395

induction by organism of defense-related symbiont reactive oxygen species production GO:0052401

induction by organism of induced systemic resistance in symbiont GO:0052350

induction by organism of symbiont apoptosis GO:0052387

induction by organism of symbiont non-apoptotic programmed cell death GO:0052396

induction by organism of symbiont immune response GO:0052560

induction by organism of symbiont innate immunity GO:0052383

induction by organism of symbiont phytoalexin production GO:0052398

induction by organism of symbiont programmed cell death GO:0052399

induction by organism of symbiont resistance gene-dependent defense response GO:0052402

induction by organism of systemic acquired resistance in symbiont GO:0052351

induction in symbiont of tumor, nodule, or growth GO:0051853

induction in symbiont of tumor, nodule, or growth containing transformed cells GO:005185

interaction with symbiont via protein secreted by type II secretion system GO:0052327

interaction with symbiont via protein secreted by type III secretion system GO:0052328

interaction with symbiont via protein secreted by type IV secretion system GO:0052326

modification by organism of symbiont morphology or physiology via protein secreted by type II secretion system GO:0052425

modification by organism of symbiont morphology or physiology via protein secreted by type III secretion system GO:0052424

modification by organism of symbiont morphology or physiology via substance secreted by type IV secretion system GO:0052426

modulation by organism of defense-related symbiont calcium ion flux GO:0052437

modulation by organism of defense-related symbiont calcium-dependent protein kinase pathway GO:0052436

modulation by organism of defense-related symbiont callose deposition GO:0052438

modulation by organism of defense-related symbiont cell wall callose deposition GO:005243

modulation by organism of defense-related symbiont cell wall thickening GO:0052446

modulation by organism of defense-related symbiont ethylene-mediated signal transduction pathway GO:0052440

modulation by organism of defense-related symbiont jasmonic acid-mediated signal transduction pathway GO:0052442

modulation by organism of defense-related symbiont nitric oxide production GO:0052457

modulation by organism of defense-related symbiont reactive oxygen species production GO:0052465

modulation by organism of defense-related symbiont salicylic acid-mediated signal transduction pathway GO:0052444

modulation by organism of ethylene levels in symbiont GO:0052448

modulation by organism of induced systemic resistance in symbiont GO:0052450

modulation by organism of jasmonic acid levels in symbiont GO:0052455

modulation by organism of pathogen-associated molecular pattern-induced symbiont innate immunity GO:0052461

modulation by organism of salicylic acid levels in symbiont GO:0052468

modulation by organism of symbiont apoptosis GO:0052432

modulation by organism of symbiont B-cell mediated immune response GO:0052429

modulation by organism of symbiont cell-mediated immune response GO:0052434

modulation by organism of symbiont ethylene-mediated defense response GO:0052447

modulation by organism of symbiont hormone or growth regulator levels GO:0052184

modulation by organism of symbiont immune response GO:0052308

modulation by organism of symbiont inflammatory response GO:0052451

modulation by organism of symbiont innate immunity GO:0052452

modulation by organism of symbiont intracellular transport GO:0052453

modulation by organism of symbiont jasmonic acid-mediated defense response GO:0052454

modulation by organism of symbiont non-apoptotic programmed cell death GO:0052458

modulation by organism of symbiont phytoalexin production GO:0052463

modulation by organism of symbiont programmed cell death GO:0052464

modulation by organism of symbiont resistance gene-dependent defense response GO:0052466

modulation by organism of symbiont salicylic acid-mediated defense response GO:0052467

modulation by organism of symbiont T-cell mediated immune response GO:0052431

modulation by organism of systemic acquired resistance in symbiont GO:0052466

negative regulation by organism of defense-related symbiont callose deposition GO:0052504

negative regulation by organism of defense-related symbiont cell wall callose deposition GO:0052477

negative regulation by organism of defense-related symbiont ethylene-mediated signal transduction pathway GO:0052479

negative regulation by organism of defense-related symbiont jasmonic acid-mediated signal transduction pathway GO:0052480

negative regulation by organism of defense-related symbiont salicylic acid-mediated signal transduction pathway GO:0052481

negative regulation by organism of pathogen-associated molecular pattern-induced symbiont innate immunity GO:0052488

negative regulation by organism of symbiont B-cell mediated immune response GO:0052473

negative regulation by organism of symbiont cell-mediated immune response GO:0052475

negative regulation by organism of symbiont ethylene-mediated defense response GO:0052484

negative regulation by organism of symbiont immune response GO:0052563

negative regulation by organism of symbiont inflammatory response GO:0052485

negative regulation by organism of symbiont innate immunity GO:0052486

negative regulation by organism of symbiont jasmonic acid-mediated defense response GO:0052487

negative regulation by organism of symbiont salicylic acid-mediated defense response GO:0052491

negative regulation by organism of symbiont T-cell mediated immune response GO:0052474

passive evasion of symbiont immune response GO:0051845

pathogen-associated molecular pattern dependent induction by organism of symbiont innate immunity GO:0052498

pathogen-associated molecular pattern dependent modulation by organism of symbiont innate immunity GO:0052499

positive regulation by organism of defense-related symbiont calcium ion flux GO:0052531

positive regulation by organism of defense-related symbiont calcium-dependent protein kinase pathway GO:0052503

positive regulation by organism of defense-related symbiont callose deposition GO:0052504

positive regulation by organism of defense-related symbiont cell wall callose deposition GO:0052505

positive regulation by organism of defense-related symbiont cell wall thickening GO:0052540

positive regulation by organism of defense-related symbiont ethylene-mediated signal transduction pathway GO:0052506

positive regulation by organism of defense-related symbiont jasmonic acid-mediated signal transduction pathway GO:0052507

positive regulation by organism of defense-related symbiont nitric oxide production GO:0052346

positive regulation by organism of defense-related symbiont reactive oxygen species production GO:0052349

positive regulation by organism of defense-related symbiont salicylic acid-mediated signal transduction pathway GO:0052508

positive regulation by organism of hormone or growth regulator levels in symbiont GO:0052512

positive regulation by organism of induced systemic resistance in symbiont GO:0052534

positive regulation by organism of symbiont apoptosis GO:0052500

positive regulation by organism of symbiont ethylene-mediated defense response GO:0052511

positive regulation by organism of symbiont immune response GO:0052557

positive regulation by organism of symbiont inflammatory response GO:0052514

positive regulation by organism of symbiont innate immunity GO:0052515

positive regulation by organism of symbiont jasmonic acid-mediated defense response GO:0052516

positive regulation by organism of symbiont non-apoptotic programmed cell death GO:0052517

positive regulation by organism of symbiont phytoalexin production GO:0052343

positive regulation by organism of symbiont programmed cell death GO:0052523

positive regulation by organism of symbiont resistance gene-dependent defense response GO:0052530

positive regulation by organism of symbiont salicylic acid-mediated defense response GO:0052524

positive regulation by organism of systemic acquired resistance in symbiont GO:0052536

response to defense-related symbiont nitric oxide production GO:0052569

response to defense-related symbiont reactive oxygen species production GO:0052570

response to symbiont immune response GO:0052571

response to symbiont phytoalexin production GO:0052568

translocation of DNA into symbiont GO:0051863

upregulation by organism of symbiont programmed cell death GO:0052528

Modify definitions of these terms?????

New Terms

Michelle_Trudy_Candace@PAG

Commensalism, Mutualism: Add as siblings to pathogenesis

Jane

Can we have some defs for these terms please?


Candace

7/17/07

Commensalism = a symbiotic relationship between two living organisms of different species in which one derives some benefit while the other is unaffected, or affected very little.

A child of GO:0044403 : symbiosis; a sibling to GO:0009405 : pathogenesis No children terms


Mutualism = an interaction between organisms of two or more species, where both species derive benefit.

Note a change here from our original request in terms of parentage.

This term should be a child of GO:0044419 : interspecies interaction between organisms; a sibling to GO:0044403 : symbiosis

No children terms