detection of muramyl dipeptide?

[gocentral]

PMID: 16973131 How is detection and response different from one another?

GO has terms for response and detection of muramyl dipeptide - a peptidoglycan derived molecule that NOD2 gene product binds. But is detection really a process? Detection of this and other bacterially derived molecules represents binding of these molecules by NOD2 and Toll-like receptors. Binding triggers several events associated with innate immunity. This would be the response to. GO:0032495 (response to muramyl dipeptide) is defined as the 'a change in state or [...] as a result of the detection of muramyl dipeptide'. But if response is the result of detection (which actually is the binding event), then it should be the child not the parent.

Detection - 127 biological process terms - generally defined as 'the series of events in which an [...] stimulus is received by a cell and converted into a molecular signal' perhaps may be an appropriate term for certain processes, but when in fact it represents a molecular function (binding), like for muramyl and all other bacteria-derived molecules, I find it a rather forced approach. The process is the response to, what that binding triggers - the definition of detection is pretty much what a response can be thought of.

I'm not sure what the correct thing to do should be, but this detection/response issue, relationships and definitions are rather counterintuitive. I was looking up lit for the NOD2 gene - see PubMed ID above, and in the process of curation I was looking up terms related to muramyl dipeptide when I found detection vs response. I thought I'd bring up the issue. Since this gene is on the December list for the Ref Genome project, I may e-mail to that list also and see what people think about.

Victoria

Reported by: vpetri

Original Ticket: "geneontology/ontology-requests/4606":https://sourceforge.net/p/geneontology/ontology-requests/4606

[gocentral]

Logged In: YES user_id=436423 Originator: NO

Well, the background is mostly in SF 1290786 ...

https://sourceforge.net/tracker/index.php?func=detail&aid=1290786&group\_id=36855&atid=440764

Original comment by: mah11

[gocentral]

Logged In: YES user_id=865072 Originator: NO

Victoria,

As Midori has pointed out, both the definitions and structure of these terms have been discussed at length, both in the SF item Midori referenced as well as in numerous other forums, not least at the GO Immunology Content meeting, where outside experts were in attendance and which also covered "response and detection" terms in addition to pure immunology terms. Numerous response and detection terms were introduced with the immunology revision and structural rearrangements were made as well. Additional response and detection terms have been added since the immunology revision using this established paradigm.

Binding is not in of itself always part of a detection event. Many proteins bind ligands without cellular signal transduction events occurring. Detection is the initial response to a binding event, the proximal processes occurring upon binding carried out typically by the receptor and its immediate signal transduction partners. Detection is thus a type of response to a stimulus, but responses to stimuli include larger or more distant processes as well, such as activation of transcription factors, production of reactive oxygen species, release of cytokines, etc.

The arrangement of the terms in the GO does not represent temporal order. If I were to change anything here, I would remove the word "detection" from the response to definition (some of the other response term defs already follow this pattern):

A change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a muramyl dipeptide stimulus. Muramyl dipeptide is derived from peptidoglycan.

I hope this is helpful,

Alex

Original comment by: addiehl

[gocentral]

Logged In: YES user_id=436423 Originator: NO

I have changed the definition of GO:0032494 (and six others that had 'detection'). Given that all response to/detection of pairs will be kept consistent (even if we change from the present relationship pattern), I'll close this.

m

Original comment by: mah11

[gocentral]

• status: open --> closed-works-for-me

Original comment by: mah11