NTR: 'pathogen inhibition of host defense induced acidification in phagolysome'

[CuzickA]

For https://github.com/PHI-base/curation/issues/36

@ValWood I think this section needs some re-structuring

In the WT metagenotype see 'pathogen inhibition of host defense induced acidification in phagolysome', which could not go under an 'abnormal heading'

and we discussed changing the term label for 'pathogen-induced pH decrease in host phagolysome' to 'host defense induced acidification in phagolysome'

Perhaps 'abnormal pathogen-induced host pH' should change to something more general like 'pathogen host interaction pH phenotype', remove the increase/ decreased grouping terms if they are not used (to check??) and position 'pathogen inhibition of host defense induced acidification in phagolysome' and 'host defense induced acidification in phagolysome' under ''pathogen host interaction pH phenotype'. What do you think @ValWood?

[ValWood]

this sounds good.

[CuzickA]

@jseager7 please could you check if these terms have been used in annotations? Thanks

PHIPO:0001109 abnormal pathogen-induced host pH PHIPO:0001110 pathogen-induced decrease in host pH PHIPO:0001111 pathogen-induced increase in host pH PHIPO:0001112 pathogen-induced pH decrease in host phagolysome

[jseager7]

@CuzickA None of these terms show up in the export, but the last export was made on 27 January so it's pretty out of date. Unfortunately I can't make another export at the moment because there's an error in the export script. You should be fine if you're confident that you haven't made any pH annotations since then.

[CuzickA]

Can I just rename 'abnormal pathogen-induced host pH' to 'pathogen host interaction pH phenotype'?

See https://github.com/PHI-base/phipo/issues/241 It looks like we had a term for 'pathogen host interaction pH phenotype' which was obsoleted. Does this need to be unobsoleted?

[CuzickA]

http://wiki.geneontology.org/index.php/Restoring_an_Obsolete_Ontology_Term Followed this to restore PHIPO:0001108 pathogen host interaction pH phenotype f380b2f

[CuzickA]

change term label PHIPO:0001113 pathogen-induced pH decrease in host phagolysome -> host defense induced acidification in phagolysome old def A pathogen host interaction phenotype where the pathogen induces a pH decrease within the host phagolysome. new def A pathogen host interaction phenotype where the host induces a pH decrease within the host phagolysome in response to pathogen colonization.

ea1693a

[CuzickA]

NTR: pathogen inhibition of host defense induced acidification in phagolysome

and edit to PHIPO:0001113 definition

b2f9273

[CuzickA]

Obsolete PHIPO:0001109 abnormal pathogen-induced host pH PHIPO:0001110 pathogen-induced decrease in host pH PHIPO:0001111 pathogen-induced increase in host pH

d446293

Now looks like this