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Wrong allele names displayed for MGG_08054 gene #37

Closed jseager7 closed 2 years ago

jseager7 commented 2 years ago

Many of the PHI Phenotype annotations on the gene page for MGG_08054 of Magnaporthe oryzae (PHIG:294) have the wrong allele name in the pathogen genotype. Most of these errors have 'Chia1-NSP' as the allele name, instead of 'Chia1+'. For example:

image

According to the data in JSON export, the pathogen genotype should be displayed as follows:

Chia1+ (wild_type) M. oryzae (Guy11)

Mocked up as it would appear in the user interface:

image

This bug may have occurred elsewhere in the interface, but so far I have only recorded seeing it on this page.

The metagenotype identifier for this annotation can be seen in the JSON export:

{
  ...
  "metagenotype": "79c56f92435923ab-metagenotype-25",
  "publication": "PMID:30610168",
  "status": "new",
  "submitter_comment": "...",
  "term": "PHIPO:0000368",
  "type": "pathogen_host_interaction_phenotype"
},

The pathogen genotype identifier can be retrieved from the metagenotype object:

"79c56f92435923ab-metagenotype-25": {
  "host_genotype": "79c56f92435923ab-genotype-13",
  "pathogen_genotype": "79c56f92435923ab-genotype-17",
  "type": "pathogen-host"
},

The pathogen genotype object contains the identifier for each allele, as the id property:

"79c56f92435923ab-genotype-17": {
  "loci": [
    [
      {
        "expression": "Wild type product level",
        "id": "G4MXR2:79c56f92435923ab-24"
      }
    ]
  ],
  "organism_strain": "Guy11",
  "organism_taxonid": 318829
},

And the object corresponding to the allele identifier is as follows:

"G4MXR2:79c56f92435923ab-24": {
  "allele_type": "wild_type",
  "gene": "Magnaporthe oryzae G4MXR2",
  "name": "Chia1+",
  "primary_identifier": "G4MXR2:79c56f92435923ab-24",
  "synonyms": []
},

Where it can be seen that the allele name is in fact 'Chia1+'.

Molecular-Connections commented 2 years ago

The issue has been fixed .

image

jseager7 commented 2 years ago

The allele names look correct now, many thanks.

CuzickA commented 2 years ago

There is still a problem here as the current displayed data does not make biological sense

image image image

There are three different phenotypes annotated to the same WT metagenotype. Also the AE compared to is usually only annotated to an altered metagenotype comparing it to a (WT) control.

jseager7 commented 2 years ago

@CuzickA Thanks for checking this. I'll have to compare all the data on this page against the JSON export to see what's going wrong.

Molecular-Connections commented 2 years ago

@jseager7 Please provide us some guidance so that we can fix it soon . Thanks .

jseager7 commented 2 years ago

@Molecular-Connections Sorry for the delay, but I had to figure out what the problem was first.

It looks like the allele names are missing from the host genotypes. Some of the host genotypes should have alleles specified, for example 'TPR1+' and 'TPR1-OE'.

Shown below is a table of all the PHI phenotype annotations in the JSON export (from 7 July 2021) for the UniProtKB accession number G4MXR2 (MGG_08054, PHIG:294).

Another potential problem is that the export I checked has 41 PHI phenotypes for this gene, whereas the PHI-base 5 gene page only seems to display 27. This might be because the host genotypes with alleles aren't being displayed properly.

term_id term_label pathogen_genotype host_genotype high_level_term
PHIPO:0000365 decreased pathogen growth within host Chia1+ (wild_type) M. oryzae (Guy11) TPR1-OE (wild_type) O. sativa (cv. Nipponbare) reduced virulence
PHIPO:0000365 decreased pathogen growth within host Dex::Chia1+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare) reduced virulence
PHIPO:0000365 decreased pathogen growth within host Chia1Δ (deletion) M. oryzae (Guy11) O. sativa (cv. Nipponbare) reduced virulence
PHIPO:0000368 increased pathogen growth within host Chia1+ (wild_type) M. oryzae (Guy11) TPR1-silenced (other) O. sativa (cv. Nipponbare) increased virulence
PHIPO:0000480 presence of pathogen-associated host lesions Chia1+ (wild_type) M. oryzae (Guy11) TPR1+ (wild_type) O. sativa (cv. Nipponbare)
PHIPO:0000480 presence of pathogen-associated host lesions Chia1+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0000927 host defense-induced reactive oxygen species present Chia1+ (wild_type) M. oryzae (Guy11) TPR1+ (wild_type) O. sativa (cv. Nipponbare)
PHIPO:0000927 host defense-induced reactive oxygen species present Chia1+ (wild_type) M. oryzae (Guy11) TPR1+ (wild_type) O. sativa (cv. Nipponbare)
PHIPO:0000927 host defense-induced reactive oxygen species present Chia1+ (wild_type) M. oryzae (Guy11) TPR1+ (wild_type) O. sativa (cv. Nipponbare)
PHIPO:0000927 host defense-induced reactive oxygen species present Chia1+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0000927 host defense-induced reactive oxygen species present Chia1+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0000927 host defense-induced reactive oxygen species present Chia1+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0000927 host defense-induced reactive oxygen species present Dex::Chia1-E137Q (amino_acid_mutation) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0000927 host defense-induced reactive oxygen species present Dex::Chia1+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0000927 host defense-induced reactive oxygen species present Chia1-E137Q (amino_acid_mutation) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0000954 presence of pathogen growth within host Chia1+ (wild_type) M. oryzae (Guy11) TPR1+ (wild_type) O. sativa (cv. Nipponbare)
PHIPO:0000954 presence of pathogen growth within host Chia1+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0000985 decreased extent of pathogen-associated host lesions Chia1+ (wild_type) M. oryzae (Guy11) TPR1-OE (wild_type) O. sativa (cv. Nipponbare) reduced virulence
PHIPO:0000985 decreased extent of pathogen-associated host lesions Chia1Δ (deletion) M. oryzae (Guy11) O. sativa (cv. Nipponbare) reduced virulence
PHIPO:0000985 decreased extent of pathogen-associated host lesions Dex::Chia1+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare) reduced virulence
PHIPO:0000986 increased extent of pathogen-associated host lesions Chia1+ (wild_type) M. oryzae (Guy11) TPR1-silenced (other) O. sativa (cv. Nipponbare) increased virulence
PHIPO:0000992 increased expression of a host defense-related protein involved in a pathogen interaction Dex::Chia1+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0001069 death of host organism with pathogen Ubi::Chia1-OE+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0001083 host defense-induced callose deposition present Chia1+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0001104 increased level of host defense-induced RNA Chia1Δ (deletion) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0001104 increased level of host defense-induced RNA Chia1Δ (deletion) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0001106 presence of pathogen host protein-protein interaction Chia1+ (wild_type) M. oryzae (Guy11) TPR1+ (wild_type) O. sativa (cv. Nipponbare)
PHIPO:0001106 presence of pathogen host protein-protein interaction Chia1-E137Q (amino_acid_mutation) M. oryzae (Guy11) TPR1+ (wild_type) O. sativa (cv. Nipponbare)
PHIPO:0001106 presence of pathogen host protein-protein interaction Chia1+ (wild_type) M. oryzae (Guy11) TPR1+ (wild_type) O. sativa (cv. Nipponbare)
PHIPO:0001107 absence of pathogen host protein-protein interaction Chia1-NSP (other) M. oryzae (Guy11) TPR1+ (wild_type) O. sativa (cv. Nipponbare)
PHIPO:0001128 effector-mediated suppression of host PAMP-triggered immunity present Chia1+ (wild_type) M. oryzae (Guy11) TPR1+ (wild_type) O. sativa (cv. Nipponbare)
PHIPO:0001192 decreased level of host defense-induced reactive oxygen species Chia1+ (wild_type) M. oryzae (Guy11) TPR1-silenced (other) O. sativa (cv. Nipponbare) increased virulence
PHIPO:0001192 decreased level of host defense-induced reactive oxygen species Chia1+ (wild_type) M. oryzae (Guy11) TPR1+ (wild_type) O. sativa (cv. Nipponbare)
PHIPO:0001193 increased level of host defense-induced reactive oxygen species Chia1+ (wild_type) M. oryzae (Guy11) TPR1-OE (wild_type) O. sativa (cv. Nipponbare)
PHIPO:0001193 increased level of host defense-induced reactive oxygen species Dex::Chia1+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0001193 increased level of host defense-induced reactive oxygen species Chia1+ (wild_type) M. oryzae (Guy11) TPR1-OE (wild_type) O. sativa (cv. Nipponbare) reduced virulence
PHIPO:0001235 host defense-related RNA involved in a pathogen interaction present Chia1+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0001235 host defense-related RNA involved in a pathogen interaction present Chia1+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0001237 effector-mediated suppression of host PAMP-triggered immunity absent Chia1+ (wild_type) M. oryzae (Guy11) TPR1+ (wild_type) O. sativa (cv. Nipponbare)
PHIPO:0001245 increased protein phosphorylation involved in host PAMP-triggered immunity (MAPK) signaling activated by pathogen Chia1+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
PHIPO:0001246 host PAMP-triggered immunity activated by pathogen present Chia1+ (wild_type) M. oryzae (Guy11) O. sativa (cv. Nipponbare)
sahujashobanta commented 2 years ago

We have grouped then while displaying in the UI w.r.t display name for a PHIPO ID . Hence the count looks mismatch . Please suggest.

jseager7 commented 2 years ago

We need further discussion to decide whether grouping by display name is the right option.

If we do choose to continue grouping by display name, then the high-level terms would need to be associated with the Additional information blocks, in order to prevent invalid combinations of high-level terms such as 'Reduced virulence' and 'Increased virulence' on the same annotation.

Note that the Entry Summary section should still aggregate all of the high level terms on the page: no changes will be required there.

jseager7 commented 2 years ago

@sahujashobanta Just to clarify, the fix for displaying the missing host genotypes for PHIG:294 doesn't need to wait for the above discussion to be resolved.

I will open a new issue for deciding whether or not we want to keep aggregating annotations by display name.

Once the host genotypes (allele names) are displayed in the display names correctly again (see https://github.com/PHI-base/PHI5_web_display/issues/37#issuecomment-1138478576), I can close this issue.

jseager7 commented 2 years ago

I've confirmed that all the PHI Phenotypes in the above table are now displayed on the page correctly.

We decided in issue https://github.com/PHI-base/PHI5_web_display/issues/48#issuecomment-1203743586 to keep the current grouping by phenotype, so no further action is needed there.