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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Innate immune response MFs? #18459

Open RLovering opened 4 years ago

RLovering commented 4 years ago

From 2 tickets https://github.com/geneontology/go-ontology/issues/18370 https://github.com/geneontology/go-ontology/issues/18458

RLovering commented 4 years ago

Different receptors are involved in the innate immune response to bacteria v fungi v viruses v parasites.

In addition to the papers associated with the GO term GO:0140376 innate immune receptor activity which I don't have access to right now https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6379837/ does seem to confirm that L-ficolin can recognise all potential pathogens much of this is emerging data. As some people are more susceptible to different types of pathogens it is likely that although there is a range of innate systems available to deal with pathogens some of the processes are better at dealing with specific types of pathogens than others. For infectious disease and auto-immune disease research know the preferred targets of these receptors in very important. However, I agree that once detected there are common pathways involved.

Note that many of these receptors also detect molecules from cell debris, in order to raise an inflammatory response and stimulate repair and clearance of cell debris.

I think the new GO term GO:0140376 innate immune receptor activity helps with this but I think this new term should have additional instructions for curators to use the interacting taxon field and the AE field if the data is available.

Or create MF child terms bacterial molecule recognising innate immune receptor activity Cell debris recognising innate immune receptor activity

Then remove the specific process terms, so that we don't end up with all innate proteins having to be associated with all types of innate response terms.

The new term GO:0140376 innate immune receptor activity should however have a link to the BP term GO:0045087 innate immune response And/Or GO:0002768 immune response-regulating cell surface receptor signaling pathway

Although I am not convinced about the term GO:0002768 immune response-regulating cell surface receptor signaling pathway. There should be similar terms to this but without the regulating aspect because many signaling pathways are 'part-of' the immune response not regulating it. I think this term needs more descriptions so that possibly cytokines can be associated with this term but Toll-like receptors and antibodies can be associate with immune response signaling pathway.

Ruth

ValWood commented 4 years ago

I'm not keen to have the organism encoded into the receptor either. This would introduce the same issues. Most receptors recognise 'molecules' not 'species' ( for example pattern recognition receptors that recognise 'chitin' ).

Whatever the outcome, this ticket should be considered with https://github.com/geneontology/go-ontology/issues/16616 which addresses the mispositioning of existing innate immune receptors

There are possibly other tickets which discuss "innate immune receoptors' too.

pgaudet commented 3 years ago

@addiehl