Grouping terms for PHI level terms of host RNA / Protein

[CuzickA]

Hi @ValWood,

As more terms are made I am having to request AE 'assayed_using' for individual terms. @jseager7 has suggested we create grouping terms for this so that the AE option can just be added to the parent terms.

Do you think we could group all the host defense protein terms under 'host defense-induced protein phenotype'

[ValWood]

You can add to the configuration file at the level of "host-defense induced phenotype" and the extension will become available for all of the children of this term?

~@kimrutherford do we have any documention on the wiki for managing the Canto config for which extensions are available?~

[ValWood]

https://github.com/pombase/canto/wiki/AnnotationExtensionConfig

[CuzickA]

You can add to the configuration file at the level of "host-defense induced phenotype" and the extension will become available for all of the children of this term?

You can add to the configuration file at the level of "host-defense induced phenotype" and the extension will become available for all of the children of this term?

Do you mean add the AE configuration to 'host-defense induced substance level protein phenotype'?

The children of this term also include 'callose', 'phenolic compound' etc terms which won't need the 'assayed _using' AE.

[ValWood]

Edited to corect to protein

[CuzickA]

We currently don't have a term for 'host-defense induced protein phenotype'. The above is a mock suggestion made by James.

Sounds like you agree that I should make this grouping term.

[CuzickA]

NTR: host defense-induced protein level phenotype Term creation 5353cbf moving children under term 0b4a7eb

NTR: host defense-induced RNA level phenotype Term creation 03c9101 moving children under term a3497ce

[CuzickA]

@jseager7, Please could you add the AE assayed_using to the new grouping terms NTR: host defense-induced protein level phenotype NTR: host defense-induced RNA level phenotype

[CuzickA]

Would it be useful to mirror these new protein and RNA grouping terms for the 'level of pathogen produced substance within host phenotype' or wait until there are more child terms to group?

[CuzickA]

Parent term 'level of pathogen produced substance within host phenotype'

I will also group

NTR: level of pathogen produced RNA within host phenotype 248eac5 moving child terms 8b18d6a

@jseager7, please also add the AE assayed_using to the new grouping term 'NTR: level of pathogen produced RNA within host phenotype '

The corresponding pathogen induced protein within host terms only currently consist of one term 'decreased level of pathogen protein within host' so there is probably no need to create a grouping parent term for now.

[jseager7]

@CuzickA I've added assayed_using on the following terms:

• host defense-induced protein level phenotype (PHIPO:0001262)
• host defense-induced RNA level phenotype (PHIPO:0001263)
• level of pathogen produced RNA within host phenotype (PHIPO:0001267)

The changes still need to be applied on the PHI-Canto servers.