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(TAIR)\r\n@ebakker2 (TAIR)\r\n@tberardini (TAIR)\r\n@CuzickA  (PHI_Base)\r\n\r\nAs part  of the PHI-Base project we are  building and ontology to represent  and annotate pathogen host interaction phenotypes. These terms will be logically defined using GO terms to describe 'normal' processes . We will also provide GO annotations for pathogen species and occasionaly for host species.\r\n\r\nAs part of the tool development I was curating this paper:\r\nPMID:20601497 Activation of an Arabidopsis resistance protein is specified by the in planta association of its leucine-rich repeat domain with the cognate oomycete effector.\r\nAuthors | Krasileva KV, Dahlbeck D, Staskawicz BJ\r\n\r\nAnd  we encounterd a few problems with the GO terms we would to use to describe the Arabidopsis protein.\r\n\r\nBackground for GO editors\r\nPlants have evolved a multilevel innate immune system to protect them against infection by a diverse range of pathogens, including viruses, bacteria, fungi, oomycetes, and nematodes. Despite the great evolutionary distance among phytopathogens, the out- come of the plant–pathogen interactions is controlled by the same principles: the ability of the pathogen to suppress the plant immune system to establish infection, and the ability of plants to recognize the presence of a pathogen and to induce immune responses that restrict pathogen growth.\r\n\r\nPlants  innate immune systems have 2 main components:\r\n1. First line of defense: PAMP- triggered immunity (PTI)\r\nUpon association with PAMPs, the pattern-recognition receptors activate a downstream mitogen-activated protein kinase signaling cascade that culminates in transcriptional activation and generation of the innate immune responses\r\nTo interfere with PTI effector proteins that are delivered into and function within the host plant cells\r\n\r\n2. Second  line of defense: Effector-triggered immunity\r\nhttps://en.wikipedia.org/wiki/Effector-triggered_immunity\r\nThe second layer of plant immunity depends on the ability of the plant to recognize these pathogen- derived effectors and trigger a robust resistance response that normally culminates in a hypersensitive cell death response (HR)\r\nEffector-triggered immunity is mediated by a large group of structurally related intracellular innate immune receptors encoded by resistance (R) genes. \r\n\r\nRPP1, MOLECULAR FUNCTION\r\n\r\nSo RPP1 is an  \"intracellular signalling receptor\" for the  \"pathogen-derived effectors\"\r\nWe couldn't find anything suitable for this under \"signaling receptor activity\" \r\nhttps://www.ebi.ac.uk/QuickGO/term/GO:0038023\r\nSUGGEST\r\nNTR:\r\nintracellular innate receptor activity\r\nsynonym related  resistance gene\r\nsynonym related receptor recognition\r\nCombining with an effector entity produced by a pathogen in order to activate effector-triggered immunity in a host.\r\nPMID: 21490299 is one paper that uses this  term to describe such receptors, however the term might not be specific enough to describe  effector-triggered immunity.\r\nIt would be OK to make the activity definition more general if necessary (we can link the activity to the process to capture this detail).\r\n\r\nNotes/Comments: \r\n-  \"intracellular innate receptor activity\" may exist in other contexts, in which case this would need to be revised?\r\n- It seems reasonable to describe receptors based on their ligands (i.e specifically a 'pathogen effector' , but  note that  pathogen 'effectors are fairly heterogeneous).\r\n- we tried to make this generic  for effector-triggered immunity \r\n- \"intracellular innate receptor activity\" most slosely matched the community descriptions we could find. Generally these types of receptors are just called \"resistance genes\" which is not informative about the function.\r\n\r\nRPP1 BIOLOGICAL PROCESS\r\n\r\n~We looked for the term to describe the process \r\n\"Effector-triggered immunity\" and eventually located \r\nGO:0080185    effector dependent induction by symbiont of host immune response\r\nwhich is *very nicely defined*\r\nAny process that involves recognition of an effector, and by which an organism activates, maintains or increases the frequency, rate or extent of the immune response of the host organism; the immune response is any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. The host is defined as the larger of the organisms involved in a symbiotic interaction. Effectors are proteins secreted into the host cell by pathogenic microbes, presumably to alter host immune response signaling. The best characterized effectors are bacterial effectors delivered into the host cell by type III secretion system (TTSS). Effector-triggered immunity (ETI) involves the direct or indirect recognition of an effector protein by the host (for example through plant resistance or R proteins) and subsequent activation of host immune response. PMID:16497589\r\nbut is there any reason why the primary term name can't be\r\n\"Effector-triggered immunity\"? 2,440,000 results \r\n\"effector dependent induction by symbiont of host immune response\" About 223 results\r\npresumably all from GO.\r\nI very nearly missed this term. And it only has 5 annotations which is no surprise!~\r\n\r\ntransferred to \r\nhttps://github.com/geneontology/go-ontology/issues/17014\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n"}}
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