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Pathogen-Host Interaction Phenotype Ontology
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Correct errors found in OBO Foundry PHIPO dashboard report #353

Open CuzickA opened 2 years ago

CuzickA commented 2 years ago

http://dashboard.obofoundry.org/dashboard/index.html , http://dashboard.obofoundry.org/dashboard/phipo/dashboard.html and http://dashboard.obofoundry.org/dashboard/phipo/robot_report.html.

CuzickA commented 2 years ago

@ValWood

jseager7 commented 1 year ago

Since the dashboard seems out of date, I can just run robot report on the ontology to get a list of problems.

jseager7 commented 1 year ago

@CuzickA I've run the reports for PHIPO and no errors are currently reported, although I suspect that's because I disabled one check related to subset properties that was causing errors. See issue https://github.com/PHI-base/phipo/issues/383 for more details.

I disabled the check so that we could make a PHIPO release. I only meant for the check to be disabled temporarily, but we then forgot to fix the underlying problem. It's been six months since then.

The WARN and INFO level messages from the report are shown below. The lowercase definition ones are a bit misleading: the warning is due to starting the definition with a left bracket.

Level Rule Name Subject Property Value
WARN duplicate_scoped_synonym normal hyphal growth oboInOwl:hasBroadSynonym normal colony morphology
WARN duplicate_scoped_synonym normal hyphal growth oboInOwl:hasBroadSynonym normal hyphal colony morphology
WARN duplicate_scoped_synonym normal hyphal growth oboInOwl:hasExactSynonym normal filament formation
WARN duplicate_scoped_synonym normal hyphal growth oboInOwl:hasExactSynonym normal filamentous formation
WARN duplicate_scoped_synonym normal hyphal growth oboInOwl:hasExactSynonym normal hyphae formation
WARN duplicate_scoped_synonym normal hyphal growth oboInOwl:hasRelatedSynonym normal colony morphology
WARN duplicate_scoped_synonym normal hyphal growth oboInOwl:hasRelatedSynonym normal filament formation
WARN duplicate_scoped_synonym normal hyphal growth oboInOwl:hasRelatedSynonym normal filamentous formation
WARN duplicate_scoped_synonym normal hyphal growth oboInOwl:hasRelatedSynonym normal hyphae formation
WARN duplicate_scoped_synonym normal hyphal growth oboInOwl:hasRelatedSynonym normal hyphal colony morphology
WARN duplicate_scoped_synonym abnormal hyphal growth oboInOwl:hasBroadSynonym abnormal hyphal colony morphology
WARN duplicate_scoped_synonym abnormal hyphal growth oboInOwl:hasRelatedSynonym abnormal hyphal colony morphology
WARN duplicate_scoped_synonym effector-mediated suppression of host PAMP-triggered immunity absent oboInOwl:hasExactSynonym abolished pathogen suppression of host PTI
WARN duplicate_scoped_synonym effector-mediated suppression of host PAMP-triggered immunity absent oboInOwl:hasExactSynonym abolished suppression of host MAMP-triggered immunity
WARN duplicate_scoped_synonym effector-mediated suppression of host PAMP-triggered immunity absent oboInOwl:hasExactSynonym abolished suppression of host PAMP-triggered immunity
WARN duplicate_scoped_synonym effector-mediated suppression of host PAMP-triggered immunity absent oboInOwl:hasExactSynonym abolished suppression of host PTI
WARN duplicate_scoped_synonym effector-mediated suppression of host PAMP-triggered immunity absent oboInOwl:hasNarrowSynonym abolished pathogen suppression of host PTI
WARN duplicate_scoped_synonym effector-mediated suppression of host PAMP-triggered immunity absent oboInOwl:hasNarrowSynonym abolished suppression of host MAMP-triggered immunity
WARN duplicate_scoped_synonym effector-mediated suppression of host PAMP-triggered immunity absent oboInOwl:hasNarrowSynonym abolished suppression of host PAMP-triggered immunity
WARN duplicate_scoped_synonym effector-mediated suppression of host PAMP-triggered immunity absent oboInOwl:hasNarrowSynonym abolished suppression of host PTI
WARN invalid_xref obsolete pathogen host interaction metabolic process phenotype oboInOwl:hasDbXref GO_0008152
WARN invalid_xref metabolic process phenotype oboInOwl:hasDbXref GO_0008152
WARN missing_definition qualifier IAO:0000115  
INFO lowercase_definition obsolete effector of pathogenicity phenotype IAO:0000115 (Required for successful infection of the host species). The ability of an organism to activate or suppress host defenses to enable infectious disease. (Irrespective of the host genotype).
INFO lowercase_definition obsolete effector of virulence phenotype IAO:0000115 (gene for gene relationships) or defined from the phenotype described in the published study. The pathogen has the ability to cause infectious disease dependent upon the gene for gene relationship between the pathogen and host genotype.
INFO missing_superclass phenotype rdfs:subClassOf