MP immune system process #14262
Comments
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Hmm, I see but isn't that true of any system process? |
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That seems odd to me. On the other hand some types of 'multicellular organism process ' and 'unicellular organism' processes may be. Isn't it? If you remove the 'regulation of immune system process' (which viruses/bacteria can do), and remove eukaryotes, there are only few EXP annotations left: The terms there should not be under immune response. Also if you remove Metazoa and look at what's annotated in lower eukaryotes:
One question I have is for @tberardini : a few plant proteins are annotated to 'systemic acquired resistance'; is this a multicellular organism process ? (it sounds like a dumb question; if the plant is multicellular then it should be a multicellular organism process.... ) Thanks, Pascale |
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@pgaudet : yes, 'systemic acquired resistance' is a multicellular organism process. Classic paper: |
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The challenge may be with single-celled organisms rather than cellular
processes per se. In CARO, anatomical system is multicellular, and GO
follows suit:
id: GO:0003008
name: system process
namespace: biological_process
def: "A multicellular organismal process carried out by any of the
organs or tissues in an organ system. An organ system is a regularly
interacting or interdependent group of organs or tissues that work
together to carry out a biological objective." [GOC:mtg_cardio]
synonym: "organ system process" EXACT []
is_a: GO:0032501 ! multicellular organismal process
So this means that CRISPR in bacteria can't be a system process, by this
definition
At the very least, it could be said that GO's nomenclature is confusing.
This class should probably be renamed something like 'anatomical system
process' or even the ugly 'gross anatomical system process'. But it's
really not clear how useful the class is. Or how useful it is having a
class for immune processes that are restricted to those that occur in
multi-cellular systems.
oh, and it looks like CRISPR-cas isn't even under immune system process:
GO:0008150 ! biological_process
is_a GO:0050896 ! response to stimulus
is_a GO:0006950 ! response to stress
is_a GO:0006952 ! defense response
is_a GO:0099046 ! clearance of foreign intracellular nucleic acids
is_a GO:0099048 ! CRISPR-cas system ***
The text definition uses the genus 'adaptive immune response':
id: GO:0099048
name: CRISPR-cas system
namespace: biological_process
def: "An **adaptive immune response** of bacteria that serves to clear
host cells of foreign DNA and RNA. It has three distinct stage:
acquisition of foreign DNA by integration into CRISPR loci in the host
chromosome, CRISPR RNA (crRNA) biogenesis, and target interference.
CISPR stands for Clustered Regularly Interspaced Short Palindromic
Repeat, which describes the nature of the loci." [PMID:23495939]
is_a: GO:0099046 ! clearance of foreign intracellular nucleic acids
Which is terminologically inconsistent with this GO class that bakes in
assumptions about the immune mechanism:
id: GO:0002250
name: adaptive immune response
namespace: biological_process
def: "An immune response mediated by cells expressing specific receptors
for antigen produced through a somatic diversification process, and
allowing for an enhanced secondary response to subsequent exposures to
the same antigen (immunological memory)." [GO_REF:0000022, GOC:add,
GOC:mtg_15nov05, ISBN:0781735149]
comment: This term was added by GO_REF:0000022.
synonym: "acquired immune response" EXACT [ISBN:068340007X]
synonym: "immune memory response" EXACT [GOC:add]
xref: Wikipedia:Adaptive_immune_system
is_a: GO:0006955 ! immune response
TL;DR - there is a lot of implicit taxonomic assumptions built in here
that will take a while to unpack. We need to axiomatize this as much as
possible to detect these issues and automate the classification.
…On 25 Sep 2017, at 9:47, Val Wood wrote:
Hmm, I see
Comments
Note that this term is a direct child of 'biological_process ;
GO:0008150' because some immune system processes are types of cellular
process (GO:0009987), whereas others are types of multicellular
organism process (GO:0032501).
but isn't that true of any system process?
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#14262 (comment)
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Seems to me that the comment here explains why this is ok. In some cases, immune system processes are cellular processes and in some cases they are multicellular processes. Therefore even though immune system process has that name, it does not fit the definition of system process. |
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OK close? |
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From PAINT's perspective, it is always useful to distinguish the multicellular organism processes vs the single organism processes. how about creating a term 'immune response' to cover adaptive immune response, that occurs in all organisms, and move 'immune system process' under 'system process'? That seems more correct at least evolutionarily. @thomaspd do you have an opinion on this one ? Thanks, Pascale |
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hi, @pgaudet is this might be relevant to current work. Added multi-species label |
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@addiehl thoughts? |
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There is a comment that explains why immune system process is not under "system process": I am closing this - @ValWood reopen if you have a suggestion as to how to fix this. |
Any reason why this is not under "system process"?
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