Closed CuzickA closed 3 years ago
I have changed names of alleles to 'RALF' overexpression allele was made incorrectly. Author had selected allele type 'other' and overexpression, I have updated this to allele type 'wild type' with overexpression.
No mention of 'peptidase' in paper Fig 3 and 5
Continue checking from Fig 6 next
Tricky issues in curating this paper 1) no obvious disease phenotype for Fig 3 Fg on wheat text uses language like 'diseased' and 'FHB disease' I have decided to record this phenotype as 'host lesions' 2) transgenic hosts have been created with a pathogen gene I have made these into metagenotypes. It is not possible to curate WT controls in some cases as we cannot create a metagenotype with an empty vector (EV) control 3) conditions recording the 'age' of the transgenic plant is not straight forward with the conditions. eg '2 weeks post inoculation', would it be better to have '2 weeks old?' Here we are looking at a metagenotype of transgenic host carrying pathogen gene. Follow on expts then inoculate with a WT pathogen so we can use condition '+ wild type pathogen inoculation' but it is still tricky to capture the age of transgenic plant vs timing after inoculation that observation was made. Need NTR for PHI-ECO 'pathogen gene expressed by transgenic host'
author created allele
I have changed to
Similar author error as above in not using allele type 'wild type' and adding the gene/uniprot name to the description section
Fig 8 wheat gene silencing
I think WT genotypes need to be made for each wheat homeologue and then combined as a multi-allele to indicate FER1 silencing and FER2 silencing
Note all of these wheat UniProt ids are in UniParc
Following are current screenshots of session
Just to note I have not yet deleted orginal annotations by author.
Yes, might be useful to see why they were confused if anything can be tweaked.
Need NTR for PHI-ECO 'pathogen gene expressed by transgenic host'
I have
i) Deleted the incorrect old annotations recorded above.
ii) Noted that it is difficult to annotate many of the metagenotype controls in this session
iii) still have a query on whether we need PHI-ECO terms for age of plants rather than time after inoculation
@ValWood please could you have a check through of this session and let me know what you think about point iii) thanks.
Removed AE causes_disease Added Disease name curation type
Synonyms see https://github.com/PHI-base/phido/issues/4
Hi @ValWood, please could you check this session. looks like I just have a query about the conditions (text from above)
iii) still have a query on whether we need PHI-ECO terms for age of plants rather than time after inoculation
and then this should be ready to approve thanks.
I checked this session and it looks fine to me. I agree it is tricky about the conditions for 'age' as it will be another bunch of conditions. However, if this is something you think you need to capture I guess you will need to add them? Otherwise this one looks complete to me. v
Thanks @ValWood For the conditions do you think I should add 'host' to the label? Otherwise it may not be clear if we are referring to the age of the pathogen or the host. eg 'host: one week old' Definition: Host organisms were observed or treated at one week old.
I guess so...
PHI-ECO terms created - just waiting for loading into PHI-Canto.
PHI-ECO terms now added, session approved, closing ticket.
https://canto.phi-base.org/curs/925be40b9263f9e8/ro/
Trial curation by Ana of her own paper into PHI-Canto.
Here are a few screen shots of her annotations
I need to read the publication and look at the annotations that have been made. Initial thoughts - should there be a metagenotype with annotations in this session??