Closed jseager7 closed 7 months ago
Issue is fixed and deployed.
@sahujashobanta I've confirmed that this is fixed for most cases, but there are still some pathogen genotypes that seem to be missing in the UI:
@sahujashobanta Here's a walkthrough of the JSON export for one of the missing multi-allele genotypes listed above.
The example below is for PHIG:324 (the rhlI gene).
Here is how the genotype name currently appears in the PHI-base 5 UI:
And here is how it should appear:
This annotation in the JSON export is as follows:
{
"checked": "no",
"conditions": [
"PECO:0000102"
],
"creation_date": "2019-09-11",
"curator": {
"community_curated": false
},
"evidence_code": "Cell growth assay",
"extension": [],
"figure": "Fig S3",
"genotype": "11fa7733063e791c-genotype-10",
"publication": "PMID:28715477",
"status": "new",
"submitter_comment": "",
"term": "PHIPO:0001057",
"type": "pathogen_phenotype"
},
The genotype object referenced in the genotype
property is:
"11fa7733063e791c-genotype-10": {
"loci": [
[
{
"id": "P54291:11fa7733063e791c-1"
}
],
[
{
"expression": "Not assayed",
"id": "Q51559:11fa7733063e791c-1"
}
]
],
"organism_strain": "PA14",
"organism_taxonid": 287
}
Note that the loci
array links to two allele objects. The first allele is rhlIdelta:
"P54291:11fa7733063e791c-1": {
"allele_type": "deletion",
"gene": "Pseudomonas aeruginosa P54291",
"name": "rhlIdelta",
"primary_identifier": "P54291:11fa7733063e791c-1",
"synonyms": []
}
And the second allele is rhlAC11STOP:
"Q51559:11fa7733063e791c-1": {
"allele_type": "nonsense_mutation",
"description": "aaC11->stop",
"gene": "Pseudomonas aeruginosa Q51559",
"name": "rhlAC11STOP",
"primary_identifier": "Q51559:11fa7733063e791c-1",
"synonyms": []
}
Both these alleles need to be listed in the genotype name, not just the first one.
The multi-allele genotype name also has to be displayed on the PHIG:331 gene page (the rhlA gene), since that gene is the other allele in the genotype.
Currently, the genotype name on PHIG:331 looks like this:
But it should look like this:
Note that the expression level [Not assayed] is also missing in that genotype name on the current PHIG:331 gene page.
@sahujashobanta I've confirmed that the display of multi-allele genotypes is fixed, but the expression level is still missing from some genotypes with the nonsense_mutation allele type.
Currently, the genotype name on PHIG:331 looks like this:
But it should look like this:
Note that the expression [Not assayed] is missing in the first example.
Here's the genotype object in the JSON export for this genotype, showing the expression:
"11fa7733063e791c-genotype-10": {
"loci": [
[
{
"id": "P54291:11fa7733063e791c-1"
}
],
[
{
"expression": "Not assayed",
"id": "Q51559:11fa7733063e791c-1"
}
]
],
"organism_strain": "PA14",
"organism_taxonid": 287
}
As a reminder, any time the expression
property is present in the array of allele objects in the genotype object, then the expression value should be shown in square brackets next to the corresponding allele in the genotype display name.
Confirmed this is fixed for every gene page.
Many genotypes in PHI-base 5 have more than one allele, but the PHI-base 5 UI is only showing one allele for many of these genotypes. Here's an example from PHIG:277:
Currently, both metagenotype display names are the same, but this is incorrect: one of these metagenotype display names should have two alleles in the pathogen genotype.
The correct display names would appear as follows:
ATR1-delta51-K92E (amino acid deletion and mutation) [Not assayed] H. arabidopsidis (Emoy2)
ATR1-delta51-K92E (amino acid deletion and mutation) [Not assayed] ATR1-delta51-G191D (amino acid deletion and mutation) [Not assayed] H. arabidopsidis (Emoy2)
Here is how the genotypes appear in the JSON export:
The multi-allele display will have to be applied to all sections that display genotypes and metagenotypes (e.g. PHI Phenotype, Gene for Gene Phenotype, Pathogen Phenotype, Host Phenotype, and Disease name).
This bug might be caused by the fact that multi-allele display was only enabled for host genotypes.
Currently, multi-allele genotypes are only displayed correctly on the following gene pages:
Here's an example of multi-allele genotypes being correct displayed from PHIG:285:
See below for a list of multi-allele genotypes grouped by PHI ID.