search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
216 stars 39 forks source link

MP immune system process #14262

Closed ValWood closed 4 years ago

ValWood commented 6 years ago

Any reason why this is not under "system process"?

ValWood commented 6 years ago

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?

pgaudet commented 6 years ago

That seems odd to me. cellular process (GO:0009987) and multicellular organism process (GO:0032501) are not mutually exclusive; ie all (or at least most) processes that occur in multicellular organisms do occur at the cellular level. I would say that the immune cells, even when they float around in the blood (or whereever they may be), are part of a system that acts in a coordinated manner.

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: UniProtKB:P75960 protein-lysine deacetylase/desuccinylase defense response to virus GO:0051607 EcoCyc NCBITaxon:83333 IMP PMID:25516616 20161221 UniProtKB:Q8GED7 Cyclo(L-leucyl-L-phenylalanyl) synthase antibacterial peptide biosynthetic process GO:0002780 UniProt NCBITaxon:1971 IDA PMID:19430487 20130617 UniProtKB:B8X8Z0 Endoribonuclease ToxN defense response to virus GO:0051607 UniProt NCBITaxon:29471 IDA PMID:19124776 20150227 UniProtKB:Q2YLF3 4-hydroxyproline epimerase macrophage activation GO:0042116 CACAO NCBITaxon:359391 IDA PMID:23720774 20141123 UniProtKB:A4VWH9 Enolase antibacterial humoral response GO:0019731 CAFA NCBITaxon:391295 IDA PMID:19848587 20160712 UniProtKB:Q46901 Cascade subunit A defense response to virus GO:0051607 EcoCyc NCBITaxon:83333 IMP PMID:18703739 20110725 UniProtKB:Q46899 Cascade subunit C defense response to virus GO:0051607 EcoCyc NCBITaxon:83333 IMP PMID:18703739 20110725 UniProtKB:Q46898 Cascade subunit D defense response to virus GO:0051607 EcoCyc NCBITaxon:83333 IDA PMID:18703739 20110725 UniProtKB:Q46897 pre-CRISPR RNA endonuclease defense response to virus GO:0051607 EcoCyc NCBITaxon:83333 IMP PMID:18703739 20110725 UniProtKB:P76632 Cascade subunit B defense response to virus GO:0051607 EcoCyc NCBITaxon:83333 IMP PMID:18703739 20110725 UniProtKB:P52126 CP4-57 prophage; putative helicase YfjK defense response to virus GO:0051607 EcoCyc NCBITaxon:83333 IMP PMID:25224971 20141009 UniProtKB:P38036 Cas3 nuclease/helicase defense response to virus GO:0051607 EcoCyc NCBITaxon:83333 IMP PMID:21699496 20110706 UniProtKB:P38036 Cas3 nuclease/helicase defense response to virus GO:0051607 EcoCyc NCBITaxon:83333 IDA PMID:18703739 20080910 UniProtKB:P52127 CP4-57 prophage; anti-bacteriophage protein defense response to virus GO:0051607 EcoCyc NCBITaxon:83333 IMP PMID:25224971 20141009

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

tberardini commented 6 years ago

@pgaudet : yes, 'systemic acquired resistance' is a multicellular organism process. Classic paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2634024/

cmungall commented 6 years ago

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?

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/geneontology/go-ontology/issues/14262#issuecomment-331942220

ukemi commented 6 years ago

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.

ValWood commented 6 years ago

OK close?

pgaudet commented 6 years ago

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

ValWood commented 4 years ago

hi, @pgaudet is this might be relevant to current work. Added multi-species label

pgaudet commented 4 years ago

@addiehl thoughts?

pgaudet commented 4 years ago

There is a comment that explains why immune system process is not under "system process": "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)."

I am closing this - @ValWood reopen if you have a suggestion as to how to fix this.