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Pathogen-Host Interaction Phenotype Ontology
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Revision of PTI vs PTI signalling terms #332

Closed CuzickA closed 3 years ago

CuzickA commented 3 years ago

Follows on from discussion on #251

Today @ValWood and I discussed the following edits

image

ID:1167 pathogen modulatio of host interaction immune system process phenotype (is modulation as includes necrotrophs) --NTR: host PAMP-triggered immunity activated by pathogen present ----NTR: host PAMP-triggered immunity signalling activated by pathogen present ------NTR: increased protein phosphorylation involved in host PAMP-triggered immunity (MAPK) signalling activated by pathogen

1116 pathogen modulation of host immune system signaling pathway activated by pathogen phenotype → host immune system signaling pathway pathogen-host interaction phenotype

-1117 host immune signaling pathway activated by pathogen MERGE with 1116 (use 116 new term label)

--1140 host PAMP-triggered immunity signaling activated by pathogen -present (edit term label) ---NTR: host PAMP-triggered immunity signalling activated by pathogen present SAME AS 1140 -----NTR: increased protein phosphorylation involved in host PAMP-triggered immunity (MAPK) signalling activated by pathogen

NTR: host PAMP-triggered immunity activated by pathogen present --1140 host PAMP-triggered immunity signaling activated by pathogen ----NTR: increased protein phosphorylation involved in host PAMP-triggered immunity (MAPK) signalling activated by pathogen

Future add comments to PTI read outs eg callose and ROS about co-annotation with PTI terms

CuzickA commented 3 years ago

From effector ticket #251 usage of abolished pathogen suppression of host PAMP-triggered immunity image

@jseager7 please could you let me know if the following terms have been used in annotation

PHIPO:0001116 pathogen modulation of host immune system signaling pathway phenotype PHIPO:0001117 host immune signaling pathway activated by pathogen PHIPO:0001140 host PAMP-triggered immunity signaling activated by pathogen

I need to check whether the annotations refer to PTI present (due to readout eg callose, ROS) or whether PTI MAPK signaling has been observed.

jseager7 commented 3 years ago

'host PAMP-triggered immunity signaling activated by pathogen' (PHIPO:0001140) has been used once in PMID:30610168.

There are no uses for 'pathogen modulation of host immune system signaling pathway phenotype' (PHIPO:0001116) or 'host immune signaling pathway activated by pathogen' (PHIPO:0001117).

CuzickA commented 3 years ago

Thanks @jseager7

CuzickA commented 3 years ago

e3bc227 edit PHIPO:0001116 ded9a26 edit PHIPO:0001140 b0d7bcc NTR: increased protein phosphorylation involved in host PAMP-triggered immunity (MAPK) signaling activated by pathogen f7a3b0e NTR: host PAMP-triggered immunity activated by pathogen present

Now looks like this image

@ValWood It may be worth reviewing the definitions within this branch next week or wait until you do the PHIPO review?

To discuss next week the term 'abolished pathogen suppression of host PAMP-triggered immunity' vs 'effector-mediated suppression of host PAMP-triggered immunity absent' see #251

CuzickA commented 3 years ago

See #251 where 'abolished pathogen suppression of host PAMP-triggered immunity' has been merged into 'effector-mediated suppression of host PAMP-triggered immunity absent'