Add term 'restored pathogenicity'

[jseager7]

@Hsinyugithub I've drafted a version of the PHIPO term for 'restored pathogenicity' that will be used in the 'infective ability' annotation extension. The name, definition and comment fields are shown below.

Note that the comment field follows the existing format used for other infective ability terms, like 'gain of pathogenicity'.

Please can you review this to make sure it's what you wanted? Once you've confirmed you're happy with it, I'll merge these changes into PHIPO.

Also, I've used 'changh' as your username in the 'created by' field. I assume based on previous terms you've created that this is the username you're now using for ontology editing.

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Name

restored pathogenicity

Definition

A phenotype where the ability of a pathogen to produce an infectious disease in another organism is restored (pathogenicity was present, then absent, and now present).

Comment

For use in the annotation extension infective ability. Can only apply to changes in the pathogen. Note that this ability to cause pathogenicity is a feature of the pathogen. Therefore restoration of pathogenicity should never be dependent on changes to the host genotype, only on changes to the pathogen genotype. If you are annotating changes in disease presence or absence dependent on the changes to the host consider increased/decreased virulence phenotypes.

[Hsinyugithub]

Hi James, Looks good to me. Thanks! Best, Hsin-Yu

…

________________________________ From: James Seager ***@***.***> Sent: 14 July 2025 14:39 To: PHI-base/phipo ***@***.***> Cc: Hsinyugithub ***@***.***>; Mention ***@***.***> Subject: [PHI-base/phipo] Add term 'restored pathogenicity' (PR #438) @Hsinyugithub<https://github.com/Hsinyugithub> I've drafted a version of the PHIPO term for 'restored pathogenicity' that will be used in the 'infective ability' annotation extension. The name, definition and comment fields are shown below. Note that the comment field follows the existing format used for other infective ability terms, like 'gain of pathogenicity'. Please can you review this to make sure it's what you wanted? Once you've confirmed you're happy with it, I'll merge these changes into PHIPO. Also, I've used 'changh' as your username in the 'created by' field. I assume based on previous terms you've created that this is the username you're now using for ontology editing.

________________________________ Name restored pathogenicity Definition A phenotype where the ability of a pathogen to produce an infectious disease in another organism is restored (pathogenicity was present, then absent, and now present). Comment For use in the annotation extension infective ability. Can only apply to changes in the pathogen. Note that this ability to cause pathogenicity is a feature of the pathogen. Therefore restoration of pathogenicity should never be dependent on changes to the host genotype, only on changes to the pathogen genotype. If you are annotating changes in disease presence or absence dependent on the changes to the host consider increased/decreased virulence phenotypes.

________________________________ You can view, comment on, or merge this pull request online at: #438 Commit Summary * b4cabf0<b4cabf0> Add term 'restored pathogenicity' File Changes (1 file<https://github.com/PHI-base/phipo/pull/438/files>) * M src/ontology/phipo-edit.owl<https://github.com/PHI-base/phipo/pull/438/files#diff-e376eee280534a54f9bb4cd4d85f00cabe4526ae668d49ac0ef865f02419529b> (18) Patch Links: * https://github.com/PHI-base/phipo/pull/438.patch * https://github.com/PHI-base/phipo/pull/438.diff — Reply to this email directly, view it on GitHub<#438>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BDHCILL7UISXR7GDXVXHGU33IOXKHAVCNFSM6AAAAACBPC7THGVHI2DSMVQWIX3LMV43ASLTON2WKOZTGIZDQOBRG42TKNY>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[jseager7]

@Hsinyugithub Thanks. Merging this now. The term should be available in PHI-Canto tomorrow.