PMID: 33203871 Two nuclear effectors of the rice blast fungus modulate host immunity via transcriptional reprogramming

[CuzickA]

Curation of this paper may need some new PHIPO terms as the pathogen effector protein is binding to host gene promoter. Therefore will probably need some pathogen protein - host DNA binding terms under PHI molecular function group.

[smvelasquez]

https://canto.phi-base.org/curs/81de82780f1e9d83

[smvelasquez]

I need new terms: normal localization to the biotrophic interfacial complex (BIC), normal vegetative growth, V8 agar, +9dpi

[ValWood]

speckles is quite vague and does not relate to a specific structure. Speckles tend to be a generic terms for inclusion bodies if authors are not sure of the exact structure. I would not annotate this without additional info.

Re

Tricky to know whether to annotate essentially WT protein localization data as a phenotype or a GO CC (or both!).

If it is WT, GO annotation for the cellular component only.
You don't need to make normal locations phenotypes for WT (that is a given).

[ValWood]

Ideally it would be cytoplasm part_of https://www.ebi.ac.uk/ols/ontologies/fao/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFAO_0000024

[ValWood]

ideally it would be cytoplasm part_of conidium from fungal anatomy ontology https://www.ebi.ac.uk/ols/ontologies/fao/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFAO_0000024

[CuzickA]

Thanks @ValWood :-)

I have now used 'edit as text' to add in 'part_of(conidium)', deleted the WT normal location phenotypes in favour of GO and omitted the vague 'speckles' observation.

[CuzickA]

Hi @smvelasquez,

We don't need to curate the WT pathogen phenotype controls for normal number of spores here. I will delete these entries.

In the case of PHI phenotype annotations we DO curate the WT controls where possible as this makes the PHI phenotype annotations to altered metagenotypes easier to interpret (also using the AE compared_to). I have made a note of this on our Documentation tracker. Do you feel this is information missing from the Help documentation?

[smvelasquez]

@alayne I think it would be good to added because I always added the Wt phenotype. I wouldn't have though to make that distinction.

…

________________________________ From: CuzickA ***@***.***> Sent: Monday, November 21, 2022 3:01:22 PM To: PHI-base/curation ***@***.***> Cc: Melina Velasquez ***@***.***>; Mention ***@***.***> Subject: Re: [PHI-base/curation] PMID: 33203871 Two nuclear effectors of the rice blast fungus modulate host immunity via transcriptional reprogramming (Issue #104) CAUTION: This email originated from outside of the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. Hi @smvelasquez<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsmvelasquez&data=05%7C01%7Cmelina.velasquez%40rothamsted.ac.uk%7C70f25dc9f0e74b802d2508dacbd14210%7Cb688362589414342b0e37b8cc8392f64%7C1%7C0%7C638046396855913206%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LS6Arwh7vJZY%2F%2BWFoo1b76m0PraliTxsN8bFpFiHATY%3D&reserved=0>, We don't need to curate the WT pathogen phenotype controls for normal number of spores here. I will delete these entries. [image]<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F11753634%2F203085940-98b75e59-1531-4012-8d54-7ecd7d172d12.png&data=05%7C01%7Cmelina.velasquez%40rothamsted.ac.uk%7C70f25dc9f0e74b802d2508dacbd14210%7Cb688362589414342b0e37b8cc8392f64%7C1%7C0%7C638046396855913206%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=bdJi27eDUbq3zrtwZ1zH%2FpeqhfvI4A0nwV%2FXwIQ%2B5mY%3D&reserved=0> In the case of PHI phenotype annotations we DO curate the WT controls where possible as this makes the PHI phenotype annotations to altered metagenotypes easier to interpret (also using the AE compared_to). I have made a note of this on our Documentation tracker. Do you feel this is information missing from the Help documentation? — Reply to this email directly, view it on GitHub<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FPHI-base%2Fcuration%2Fissues%2F104%23issuecomment-1322195610&data=05%7C01%7Cmelina.velasquez%40rothamsted.ac.uk%7C70f25dc9f0e74b802d2508dacbd14210%7Cb688362589414342b0e37b8cc8392f64%7C1%7C0%7C638046396855913206%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=lBUd3qr3EUlD3eIyvE2%2BFkWl%2F9E%2FQgluF3prWr8v%2FxQ%3D&reserved=0>, or unsubscribe<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAYCFUF2DRZIPKSZV762GJL3WJOFEFANCNFSM5SBSD4SA&data=05%7C01%7Cmelina.velasquez%40rothamsted.ac.uk%7C70f25dc9f0e74b802d2508dacbd14210%7Cb688362589414342b0e37b8cc8392f64%7C1%7C0%7C638046396855913206%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=d5ctYZ%2F8ueI0fMDHYLvtUdJm5EKrL2eXiQt33g%2FF1MQ%3D&reserved=0>. You are receiving this because you were mentioned.Message ID: ***@***.***> Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.

[CuzickA]

Session now checked.
Waiting on loading of PHI-ECO and PHIPO terms.

[CuzickA]

Summary of curation issues and tips to document from this session

1. Highlight the importance of making a GO BP 'effector-mediated...' annotation where appropriate so enable high level 'effector' term to be displayed in PHI5. https://canto.phi-base.org/docs/phipo_annotation#pathogen_host_interaction_phenotypes
2. When connecting GO MF to GO BP 'effector-mediated...' use AE 'involved in biological process/part_of' rather than 'has function during/happens_during' (it is a stronger statement than during which is only saying happens at this time). https://canto.phi-base.org/docs/phipo_annotation#pathogen_host_interaction_phenotypes
3. Make it clear when to make a GO annotation vs a phenotype annotation. Make it clear that some WT annotations can be covered by GO annotations and do not need additional phenotype annotations canto-docs#26
4. Careful use of terms 'presence of pathogen-associated host lesions' vs 'presence of pathogen-associated host defense induced lesions' and 'presence of host-defense induced lesion by host hypersensitive response'.
5. No need to curate complementation control expts. It is a given that the author has done these expts.
6. How to curate 'Transgenic host plant expressing pathogen effector and then inoculated with same WT pathogen' using conditions 'delivery mechanism: pathogen gene expressed by transgenic host', '+ wild type pathogen inoculation'.
7. It is NOT possible to curate 'Transgenic host plant expressing pathogen effector and then inoculated with a different WT pathogen.'
8. AE 'penetrance' does not mean penetration of pathogen into host. https://canto.phi-base.org/docs/phipo_annotation#annotation_extensions
9. Don't curate Pathogen or host phenotype controls. Do curate WT metagenotype controls where possible to aid interpretation of altered metagenotype phenotypes. Check documentation is clear on when to add WT control phenotype annotations canto-docs#27 https://canto.phi-base.org/docs/genotypes#metagenotype_management
10. Trying to keep genotypes simple. We may need to provide a few example genotypes from different publications.

[CuzickA]

Existing documentation in the main Help document covering the above issues
@smvelasquez, please can you review to see if you think it is adequate

1. and 2. https://canto.phi-base.org/docs/phipo_annotation#pathogen_host_interaction_phenotypes
   

8 https://canto.phi-base.org/docs/phipo_annotation#annotation_extensions

9. https://canto.phi-base.org/docs/genotypes#metagenotype_management
   

Issues 3, 4, 6, 10 could be documented with examples in the FAQ document (to be combined with curation tips document). Issues 5, 7, 9 could be added to a section on 'Information not to curate'.

[smvelasquez]

@CuzickA I think what you wrote clarifies those points and I do agree with diving the items into FAQ and a new section 'Information not to curate'

[CuzickA]

PHI-ECO and PHIPO terms now loaded so approving session.

Keeping ticket open until 'curations issues' noted above have been fully documented.

[CuzickA]

Added AE 'with host species'

I don't think its possible to add GO CC for "biotrophic interfacial complex (BIC)"

Consider adding https://www.ebi.ac.uk/QuickGO/term/GO:0085039

[CuzickA]

Added BIC / hyphal membrane term to GO CC. Reapproved session

[CuzickA]

Closing ticket for now as session complete and approved. May need to be referred back to when writing up the FAQ document.