gocentral
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Just to clarify the very first problem at hand as mentioned by Alexander, which is "Despite the unnamed expert's opinion as quoted in Suparna's post on my preceding SF entry ("Pathogenic Terms," 1013068, now closed),.... "
The quote was from Shauna Somerville, who was also at the content meeting. There was another quote from Dr. Xinnian Dong from MSU, which was also on the similar line of thoughts.
So, plant pathogen experts need to review this proposal and come up with a reasonable solution for the problem and this task is not going to be easy as it may involve lot of the experts who are geographically dispersed and thus may take some time.
Suparna
Original comment by: smundodi
Reorganization of Response and Detection Terms
This proposal grows out of the GO Content Meeting discussion of the Sourceforge item "Pathogenic Terms" (1013068, now closed), taking into account some of the concerns raised at the meeting, and going a bit further to fix a wider array of problems in the GO. I would appreciate comments that go beyond simple rejection as I believe there is much to discuss of value here.
The proposal is a major reorganization of "response to . . .", "detection of . . .", and "defense response to . . ." terms.
The major goal is to systematize the terms describing how a given organism responds to the stimulus provided by other organisms, so that the types of other organisms providing the stimulus are treated more or less the same, with basic "response to . . .", "detection of . . .", and "defense response to . . ." terms. The perspective for the terms is that of the principal organism doing the responding; thus defense responses to particular organisms, bacteria, fungi, protozoa, and viruses (not quite an organism, of course), are grouped under "defense response to potential pathogen," both to please those who would like to have the concept of pathogenicity retained in the GO, and those who believe that pathogenicity ought to be viewed from the perspective of the threatened organism.
A) The Problem at Hand
Despite the unnamed expert's opinion as quoted in Suparna's post on my preceding SF entry ("Pathogenic Terms," 1013068, now closed), the fact remains that we have a plethora of redundant or partially overlapping terms describing the response to various organisms. For an example of this problem (before I get to the overall reorganization in part B), we can consider bacteria:
This is the current DAG (+ indicates child terms not shown for sake of simplicity):
response to bacteria ; GO:0009617 --% defense response to bacteria ; GO:0042742 ----% antibacterial humoral response ; GO:0019731 + ----% defense response to Gram-negative bacteria ; GO:0050829 + ----% defense response to Gram-positive bacteria ; GO:0050830+ ----% defense response to pathogenic bacteria ; GO:0042830 ------% defense response to pathogenic bacteria, incompatible interaction ; GO:0009816 ----% male-specific defense response to bacteria ; GO:0050831 + --< detection of bacteria ; GO:0016045 ----% detection of non-pathogenic bacteria ; GO:0009598 ----% detection of pathogenic bacteria ; GO:0009598 ------< detection of bacterial lipoprotein ; GO:0042494 + ----% detection of symbiotic bacteria ; GO:0009604 --% response to non-pathogenic bacteria ; GO:0009680 ----% induced systemic resistance ; GO:0009682 --% response to pathogenic bacteria ; GO:0009618 ----% defense response to pathogenic bacteria ; GO:0042830 ------% defense response to pathogenic bacteria, incompatible interaction ; GO:0009816 ----< detection of pathogenic bacteria ; GO:0009598 ------< detection of bacterial lipoprotein ; GO:0042494 + --% response to symbiotic bacteria ; GO:0009609 ----< detection of symbiotic bacteria ; GO:0009604
While representing plant biology is important in the GO, these terms are also of use to the annotation of both vertebrate and invertebrate animal genes, and the excess of terms confuses the annotation process as well as the meaning of the biology the terms are intended to represent (I wouldn't be surprised if even the plant annotators get confused in their work). Plants and animals respond to bacteria and other organisms for two main reasons: to acquire sustenance (and this includes symbiosis) and to defend themselves from the potential pathogenic effects of the bacteria living near or in an organism. "Response to bacteria" thus is a high-level term covering these two concepts, and the child term "defense response to bacteria" covers the second of the two.
For the concept of detection of bacteria, following the discussion at the GO content meeting and my own reading of reviews on the topic, I decided that "detection of pathogenic bacteria" was acceptable to allow for the direct detection of the products of so-called "avr" genes by "R" gene products in the plant parlance, but as a mammalian geneticist and immunologist I don't think I would use this term myself, and I wonder if a more specific type of term, such as "detection of bacterial avirulence factors" might not serve the needs of the plant biologists better in being more specific and less tied to the perspective problems involved in labeling particular organisms "pathogenic" or not. I'll leave it to the plant folks to consider that one.
I also would like point out the function terms GO:0001871 pattern binding and GO:0008329 pattern recognition activity which are very useful for annotating gene products associated with the recognition of so-called PAMP's, pathogen associated molecular patterns, and suggest some related process terms below.
The following represents my proposal for simplifying this hierarchy.
response to bacteria ; GO:0009617 --% defense response to bacteria ; GO:0042742 ----% antibacterial humoral response ; GO:0019731 + ----% defense response to Gram-negative bacteria ; GO:0050829 + ----% defense response to Gram-positive bacteria ; GO:0050830 + ----% defense response to bacteria, incompatible interaction ; GO:0009816 (as renamed) ----% induced systemic resistance ; GO:0009682 ----% male-specific defense response to bacteria c + --< detection of bacteria ; GO:0016045 ----% detection of pathogenic bacteria ; GO:0009598 ------< detection of bacterial lipoprotein ; GO:0042494 + ----% detection of symbiotic bacteria ; GO:0009604 --% response to symbiotic bacteria ; GO:0009609 ----< detection of symbiotic bacteria ; GO:0009604
Obsoleted terms 1) GO:0009680 ; response to non-pathogenic bacteria With the recognition that "induced systemic resistance" is a type of defense response (see below) to bacteria, there appears to be no need for this term. There are no annotations in Amigo directly to this term, only to its single child and that term's two children. GO:0009680 is not a grouping term, only a redundant term containing information that is already in the definition of its only child, "induced systemic resistance," which I deal with below.
2) GO:0009681 ; detection of non-pathogenic bacteria Along with GO:0009680, this term, which has never been used, has no purpose. The terms "detection of bacteria," "detection of pathogenic bacteria," and "detection of symbiotic bacteria" cover all necessary situations.
3) GO:0042830 ; defense response to pathogenic bacteria As the majority of participants at the GO content meeting appeared to agree, defense responses occur to bacteria, and other things, because they are potential pathogens, things that are perceived through evolutionarily selected mechanisms to be a threat to the responding organism; thus "defense response to pathogenic bacteria" is redundant with its parent term GO:0042742 defense response to bacteria.
4) GO:0009618 ; response to pathogenic bacteria Any organismal response based on perception of potential pathogenicity is by definition a defense response; thus GO:0009618 is redundant with GO:0042742 defense response to bacteria and GO:0042742 is the more appropriate term.
Depending on the viewpoint of the GO editorial office, it may be simpler to merge GO:0042830 and GO:0009618 to GO:0042742 defense reponse to bacteria.
Change of name: GO:0009816 should be renamed "defense response to bacteria, incompatible interaction." The word "pathogenic" is superfluous in this term name. The term then becomes a direct child of defense response to bacteria ; GO:0042742.
Induced Systemic Resistance and why the term is moved: The definition of "induced systemic resistance" is most curious: "A response to non-pathogenic bacteria that confers broad spectrum systemic resistance to disease that does not depend upon salicylic acid signaling." If the bacteria is non-pathogenic, in the absence of the induced systemic response, would disease therefore result, and thus the bacteria would be pathogenic. In other words, does the plant's response define the bacteria as being non-pathogenic or does the bacteria's lack of pathogenicity define the plant's response? If the bacteria were pathogenic in some sense that the plant detects, does the plant then not produce the induced systemic response? From my knowledge of other, non-plant, multicellular organisms, I find hard to believe that plants in general bother to distinguish between pathogenic and non-pathogenic bateria in this regard, and are rather simply responding to the presence of any bacteria as a potential pathogen and making a generalized defense response. Furthermore, because this indeed sounds like a bone fide defense response (the inclusion of the word "resistance" in both the term name and definition suggests this), "induced systemic resistance " ought to be a child of "defense response to bacteria" to avoid an obvious a true- path violation.
I suspect the genesis of this term is based on the fact that most studies of ISR as defined as SA-independent systemic resistance are based on studies of the interaction of non- pathogenic rhizobacteria in the model organism Arabidopsis with certain crop species. There is naturally a strong interest in the literature in studying ISR as a mechanism of crop protection, which has had the side effect that few studies of the range of pathogens that induce ISR style systemic resistance vs. SAR, systemic acquired resistance, have been performed. However the fact that isolated bacterial LPS can induce ISR directly suggests very strongly that ISR is a response to bacteria in general and not just to "non-pathogenic" bacteria. Indeed ISR and SAR are phenotypically similar at several levels, not least of which is the involvement of the NPR1 gene product in triggering both pathways. To insist that ISR-type responses are limited to "non-pathogenic" bacteria strikes me as a false dogma due the lack of experimental inquiry. I expect in the relatively near future SAR and ISR responses will defined better in terms of both their triggering pathways as well as their effector pathways and both will be seen as part of a larger range of defense responses in plants to microorganisms and pests expressing a variety of triggering ligands.
Thus I suggest that GO:0009682 induced systemic resistance be moved to a child of GO:0042742 defense response to bacteria as its sole parent, and that either the term "non- pathogenic" be stricken from the definition or the word "typically" be inserted in front of "non-pathogenic."
Reference: van Loon LC, Bakker PA, Pieterse CM. Annu Rev Phytopathol. 1998;36:453-83.
Systemic resistance induced by rhizosphere bacteria.
Department of Plant Ecology and Evolutionary Biology, Utrecht University, TB Utrecht, The Netherlands. L.C.vanloon@bio.uu.nl
Nonpathogenic rhizobacteria can induce a systemic resistance in plants that is phenotypically similar to pathogen-induced systemic acquired resistance (SAR). Rhizobacteria-mediated induced systemic resistance (ISR) has been demonstrated against fungi, bacteria, and viruses in Arabidopsis, bean, carnation, cucumber, radish, tobacco, and tomato under conditions in which the inducing bacteria and the challenging pathogen remained spatially separated. Bacterial strains differ in their ability to induce resistance in different plant species, and plants show variation in the expression of ISR upon induction by specific bacterial strains. Bacterial determinants of ISR include lipopolysaccharides, siderophores, and salicylic acid (SA). Whereas some of the rhizobacteria induce resistance through the SA-dependent SAR pathway, others do not and require jasmonic acid and ethylene perception by the plant for ISR to develop. No consistent host plant alterations are associated with the induced state, but upon challenge inoculation, resistance responses are accelerated and enhanced. ISR is effective under field conditions and offers a natural mechanism for biological control of plant disease.
(The pdf of this review is available online or from me.)
Thus, I am proposing the obsoletion of four terms, the renaming of one, and the relocation of two within the DAG.
If there are genuine problems with this, I would like to hear of specific examples of gene products (with references) that cannot be annotated correctly within the new scheme.
Please read the rest of the proposal to see how the changes to the "response to bacteria" DAG fit in with the other changes proposed.
B) The Big Picture
Here I present a proposed DAG for all of the "response to . . .", "detection of . . .", and "defense response to . . ." terms:
Gene_Ontology --< biological_process ; GO:0008150 ----% physiological process ; GO:0007582 ------% response to stimulus ; GO:0007582 --------% response to biotic stimulus ; GO:0009607 ----------% response to oxidative stress ; GO:0006979 ----------< detection of biotic stimulus ; GO:0009595 ------------% detection of endogenous biotic stimulus ; GO:NewTerm ---------------% detection of ER-overloading ; GO:NewTerm ---------------% detection of unfolded protein ; GO:NewTerm ------------% detection of foreign biotic stimulus ; GO:NewTerm --------------% detection of bacteria ; GO:0016045 ----------------% detection of pathogenic bacteria ; GO:0009598 ------------------% detection of bacterial lipoprotein ; GO:0042494 + ----------------% detection of symbiotic bacteria ; GO:0009604 --------------% detection of fungi ; GO:0016046 ----------------% detection of pathogenic fungi ; GO:0009599 ----------------% detection of symbiotic fungi ; GO:0009603 ----------------% detection of yeast ; GO:0001879 --------------% detection of insect ; GO:0009601 --------------% detection of nematode ; GO:0009600 --------------% detection of potential pathogen ; GO:0009596 (as renamed) ----------------% detection of pathogenic bacteria ; GO:0009598 + ----------------% detection of pathogenic fungi ; GO:0009599 ----------------% detection of pathogenic protozoa ; GO:NewTerm ----------------% detection of virus ; GO:0009597 --------------% detection of protozoa ; GO:0001563 ----------------% detection of pathogenic protozoa ; GO:NewTerm --------------% detection of symbiont ; GO:0009602 ----------------% detection of symbiotic bacteria ; GO:0009604 ----------------% detection of symbiotic fungi ; GO:0009604 (new parentage) ----------% response to endogenous biotic stimulus ; GO:NewTerm ------------% ER-overload response ; GO:0006983 (note term move) ---------------% detection of ER-overloading ; GO:NewTerm ------------% response to unfolded protein ; GO:0006986 (note term move) ---------------% detection of unfolded protein ; GO:NewTerm ----------% response to foreign biotic stimulus ; GO:0043207 (as renamed) ------------% response to bacteria ; GO:0009617 --------------% defense response to bacteria ; GO:0042742 ----------------% antibacterial humoral response ; GO:0019731 + ----------------% defense response to Gram-negative bacteria ; GO:0050829 + ----------------% defense response to Gram-positive bacteria ; GO:0050830 + ----------------% defense response to bacteria, incompatible interaction ; GO:0009816 (as renamed) ----------------% induced systemic resistance ; GO:0009682 ----------------% male-specific defense response to bacteria ; GO:0050831 + --------------< detection of bacteria ; GO:0016045 ----------------% detection of pathogenic bacteria ; GO:0009598 ------------------% detection of bacterial lipoprotein ; GO:0042494+ ----------------% detection of symbiotic bacteria ; GO:0009604 --------------% response to symbiotic bacteria ; GO:0009609 ----------------< detection of symbiotic bacteria ; GO:0009604 ------------% response to fungi ; GO:0009620 --------------% defense response to fungi ; GO:0050832 ----------------% defense response to fungi, incompatible interaction ; GO:0009817 (as renamed) ----------------% antifungal humoral responsec --------------< detection of fungi ; GO:0016046 ----------------% detection of pathogenic fungi ; GO:0009599 ----------------% detection of symbiotic fungi ; GO:0009603 ----------------% detection of yeast ; GO:0001879 --------------% response to symbiotic fungi ; GO:0009610 ----------------< detection of symbiotic fungi ; GO:0009603 --------------% response to yeast ; GO:0001878 ----------------< detection of yeast ; GO:0001879 ------------% response to insect ; GO:0009625 --------------% defense response to insect ; GO:NewTerm --------------< detection of insect ; GO:0009601 ------------% response to nematodes ; GO:0009624 --------------% defense response to nematode ; GO:NewTerm --------------< detection of nematodes ; GO:0009600 ------------% response to protozoa ; GO:0001562 --------------% defense response to protozoa ; GO:0042832 (as renamed) ----------------% defense response to protozoa, incompatible interaction ; GO:0009818 (as renamed) --------------< detection of protozoa ; GO:0001563 ----------------% detection of pathogenic protozoa ; GO:NewTerm ------------% response to symbiont ; GO:0009608 --------------% response to symbiotic bacteria ; GO:0009609 ----------------< detection of symbiotic bacteria ; GO:0009609 --------------% response to symbiotic fungi ; GO:0009610 ----------------< detection of symbiotic fungi ; GO:0009603 --------------< detection of symbiont ; GO:0009602 ----------------% detection of symbiotic bacteria ; GO:0009609 ----------------% detection of symbiotic fungi ; GO:0009603 (new parentage) ------------% response to virus ; GO:0009615 --------------< detection of virus ; GO:0009597 --------------% defense response to virus ; GO:NewTerm ----------------% phage shock ; GO:0009271 (good term, but needs definition) ----------------% virus induced gene silencing ; GO:0009616 ----------------< regulation of antiviral response ; GO:0050688 + (children here could be improved) ------------% defense response ; GO:0006952 --------------% defense response to insect ; GO:NewTerm --------------% defense response to nematode ; GO:NewTerm --------------% defense response to potential pathogen ; GO:0042829 (as renamed) ----------------% defense response signaling pathway, resistance gene-dependent ; GO:0009870 ----------------% defense response signaling pathway, activated by recognition of pathogen-associated molecular patterns via pattern recognition receptors ; GO:0010204 (as renamed) ----------------% defense response, incompatible interaction ; GO:0009814 (as renamed) ------------------% defense response to bacteria, incompatible interaction ; GO:0009816 (as renamed) ------------------% defense response to fungi, incompatible interaction ; GO:0009817 (as renamed) ------------------% defense response to protozoa, incompatible interaction ; GO:0009818 (as renamed) ----------------% defense response to bacteria ; GO:0042742 ------------------% antibacterial humoral response ; GO:0019731 + ------------------% defense response to Gram-negative bacteria ; GO:0050829 + ------------------% defense response to Gram-positive bacteria ; GO:0050830 + ------------------% defense response to bacteria, incompatible interaction ; GO:0009816 (as renamed) ------------------% induced systemic resistance ; GO:0009682 ------------------% male-specific defense response to bacteria ; GO:0050831 + ----------------% defense response to fungi ; GO:0050832 ------------------% defense response to fungi, incompatible interaction ; GO:0009817 (as renamed) ------------------% antifungal humoral response ; GO:0019732 ----------------% defense response to protozoa ; GO:0042832 (as renamed) ------------------% defense response to protozoa, incompatible interaction ; GO:0009818 (as renamed) ----------------% defense response to virus ; GO:NewTerm ------------------% phage shock ; GO:0009271 (good term, but needs definition) ------------------% virus induced gene silencing ; GO:0009616 ------------------< regulation of antiviral response ; GO:0050688 + (children here could be improved) --------------% evasion of host defense response ; GO:0030682+ --------------% immune response ; GO:0006955 + --------------% melanization defense response ; GO:0035006 + --------------% virus induced gene silencing ; GO:0035006
As a consequence of this streamlining and standardization the following obsoletions are necessary: 1) Obsolete: GO:0009621 response to pathogenic fungi Any organismal response based on perception of potential pathogenicity is by definition a defense response; thus GO:0009621 is redundant with GO:0050832 defense response to fungi and GO:0050832 is the more appropriate term.
2) Obsolete: GO:0042831 defense response to pathogenic fungi As the majority of participants at the GO content meeting appeared to agree, defense responses occur to fungi, and other things, because they are potential pathogens, things that are perceived through evolutionarily selected mechanisms to be a threat to the responding organism; thus "defense response to pathogenic fungi" is redundant with its parent term GO:0050832 defense response to fungi.
3) Obsolete: GO:0016047 detection of parasitic fungi This terms has never been used, and its definition and meaning overlaps both with GO:0009599 detection of pathogenic fungi and GO:0009603 detection of symbiotic fungi. It is thus superfluous.
4) Obsolete: GO:0042833 response to pathogenic protozoa Any organismal response based on perception of potential pathogenicity is by definition a defense response; thus GO:0042833 is redundant with GO:0042832 defense response to protozoa (as renamed below) and GO:0042832 is the more appropriate term.
5) Obsolete: GO:0043019 response to pathogenic insects This term has never been used, and is more or less nonsensical. I propose replacing it with "defense response to insect," as defined below (under New Terms).
6) Obsolete: GO:0009613 response to pest, pathogen or parasite This is an interesting term, but a response to something that is, by definition, perceived to be bad by the responding organism, is by implication a defense response of some kind, and thus this term should be obsoleted. Its children all have other parents, and direct annotations to this term could be shifted to defense response or one of its children.
7) Obsolete: GO:0042828 response to pathogen This is an another interesting term, nearly synonymous with GO:0009613. Again, a response to something that is, by definition, perceived to be bad by the responding organism, is by implication a defense response of some kind, and thus this term should be obsoleted. Its children all have other parents, and direct annotations to this term could be shifted to defense response or one of its children.
Depending on the viewpoint of the GO editorial office, it may be simpler to merge GO:0009613 and GO:0042828 to GO:0042829 defense reponse to potential pathogen (as renamed).
With these obsoletions (or merging) of GO:0009613 and GO:0042828, I worry a little about the linkage to "response to stress" that was provided by GO:0009613. I would argue that the best solution to this is to make GO:0006952 defense response a child of GO:0006950 response to stress, because any defense response is inherently a response to a what can only be termed a stressed condition: "Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack" (the definition of GO:0006950).
Renamings 1) Rename GO:0043207 (formerly "response to external biotic stimulus") I propose that GO:0043207 be renamed "response to foreign biotic stimulus" reflect the nature of what is being responded to, which is a stimulus from a separate, non-self organism.
The revised definition is "A change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the perception of a stimulus caused by, or produced by a separate non-self organism." The original term name should be kept as a synonym. The usage of "foreign" here is in accordance with the common usage of the word in immunology meaning something that is of non-self origin, not originating from the responding organism. This includes responses to other organisms of the same species (think of some of the nasty sequelae of organ transplantation, for instance, or mouse mothers eating their young because of stress). The use of "foreign" also allows for response to things that are not external in the strict literal sense, such as the intracellular detection of dsRNA during viral infection that triggers an anti-viral response, or the detection of avr products intracellularly by R gene products in plants.
2) Rename and redefine GO:0042829 (formerly "defense response to pathogen") I propose that GO:0042829 be renamed "defense response to potential pathogen" in light of the fact that organisms make evolutionarily selected responses to pathogens based on specific receptors for microbial and fungal gene products without necessarily knowing the degree of virulence of the source of the stimulus or the outcome of continued infection ahead of time. Thus, from the perspective of the responding organism, the specific stimulus indicates the presence of a potential pathogen. Also, the definition should include the word "potential" in front of the word "pathogen," to clarify the issue.
Since defense response to bacteria, fungi, protozoa, and virus, which are sometimes referred to as "pathogens" in the sense that they can make an organism diseased (from the human perspective), I am placing GO:0042742, GO:0050832, GO:0042832, and the new term "defense response to virus" (see below), as is-a children of this term.
I also recommend that GO:0009870 defense response signaling pathway, resistance gene-dependent, become a direct child of this term, because the R genes of plants exist to detect the presence or effects of avr gene products of potential pathogens.
3) Rename and redefine GO:0010204 (formerly "defense response signaling pathway, resistance gene-independent") This term has never been used, but the concept behind it has the potential to be of great use in annotation genes involved in innate immunity in both plants and animals.
New Name: defense response signaling pathway, activated by recognition of pathogen-associated molecular patterns via pattern recognition receptors
New Definition: A series of molecular signals that is activated during defense response dependent upon by recognition of pathogen-associated molecular patterns (PAMP's) via pattern recognition receptors (PRR's).
Such a term allows for the annotation of a large number of genes from plants, invertebrates, and vertebrate species, such as TLRs in mammals and many other species, and, for instance, FLS2 in Arabadopsis (which not only is homologous to TLR5 in its extracellular domain, but activates a similar signaling pathway [Gsmez-Gsmez, 2004, "Plant perception systems for pathogen recognition and defense," Molecular Immunology in press]).
It is much better for the GO to have a general term for this concept, than a plant-specific term.
The renamed and redefined GO:0010204 then becomes a child of GO:0042829 defense response to potential pathogen.
4) Rename and redefine GO:0009596 (formerly "detection of pest, pathogen or parasite") New Name: detection of potential pathogen
New Definition: The series of events by which a stimulus from a potential pathogen is received and converted into a molecular signal.
With these changes this term complements the renamed term GO:0042829 defense response to potential pathogen.
I can imagine two new children of GO:0009596 (analogous to GO:0009870, and the reformulated GO:0010204): "detection of pathogen associated avr gene products" and "detection of pathogen associated molecular patterns," although I will wait to see if others are interested in such terms before including them in the DAG.
5) Rename: GO:0042832 ; defense response to pathogenic protozoa As there is no "defense response to protozoa" term, I propose GO:0042832 be renamed "defense response to protozoa" in parallel with the similar terms GO:0042742 defense response to bacteria, and GO:0050832 defense response to fungi. And as the majority of participants at the GO content meeting appeared to agree, defense responses occur to protozoa, and other things, because they are potential pathogens, things that are perceived through evolutionarily selected mechanisms to be a threat to responding organism; thus the word "pathogenic" is redundant in the term "defense response to pathogenic protozoa."
New Terms 1) GO:NewTerm, "detection of foreign biotic stimulus"
Definition: The series of events by which a stimulus from a foreign biotic stimulus is received and converted into a molecular signal.
Parentage: is-a to GO:0009595 detection of biotic stimulus, part-of to GO:0043207 response to foreign biotic stimulus
This term is being created to be analogous to the (renamed) GO:0043207 response to foreign biotic stimulus. All the current children of GO:0009595 detection of biotic stimulus are detection terms for foreign biotic stimuli, and therefore should become children of the new term. Furthermore I recommend that a term "detection of endogenous biotic stimulus" be created as a child of GO:0009595 detection of biotic stimulus for processes that detect things like ER- overloading (see GO:0006983, ER-overload response), unfolded proteins, etc.
2) GO:NewTerm, "detection of pathogenic protozoa" Definition: The series of events by which a stimulus from a potentially pathogenic protozoa is received and converted into a molecular signal.
Parentage: is-a to GO:0001563 detection of protozoa, is-a to GO:0009596 detection of potential pathogen (as renamed)
This term is being created to be analogous to the terms GO:0009598 detection of pathogenic bacteria and GO:0009599 detection of pathogenic fungi, both of which should also have the word "potential" inserted into their definitions.
3) GO:NewTerm, "defense response to insect" Definition: Reactions triggered in response to the presence of an insect or insects that act to protect the cell or organism.
Parentage: is-a to GO:0009625 response to insect
This term is being created to be analogous to the other defense response to organism terms (bacteria, fungi, etc.) for the sake of consistency in the GO.
4) GO:NewTerm, "defense response to nematode" Definition: Reactions triggered in response to the presence of a nematode or nematodes that act to protect the cell or organism.
Parentage: is-a to GO:0009624 response to nematodes
This term is being created to be analogous to the other defense response to organism terms (bacteria, fungi, etc.) for the sake of consistency in the GO.
5) GO:NewTerm, "defense response to virus"
Parentage: is-a to GO:0009615 response to virus
This term is being created to be analogous to the other defense response to organism terms (bacteria, fungi, etc.) for the sake of consistency in the GO. (Yeah, I know viruses are not quite the same, but it's hard to imagine a response to virus that isn't a defense response.)
The following four terms seem like obvious additions based on the exisiting structure of the ontology, and I included them above, but I will leave their suggested definitions to others for the moment. GO:NewTerm, "detection of endogenous biotic stimulus" GO:NewTerm, "detection of ER-overloading" GO:NewTerm, "detection of unfolded protein" GO:NewTerm, "response to endogenous biotic stimulus"
One large issue that remains unresolved here is that many of the defense response terms refer to types of innate immune responses, which is a usage that is common even in describing plant defense. Because innate immune response is a child of immune response which itself is a child of defense response, I will probably end up proposing additional parentage for certain terms as part of my anticipated revisions to the immune response process ontology.
Thank you for your comments,
Alex
Reported by: addiehl
Original Ticket: "geneontology/ontology-requests/2020":https://sourceforge.net/p/geneontology/ontology-requests/2020