Hello,
I’m using PHIPO for describing phenotypes correlated with SARS-CoV-2 mutations. I’ve run across a few (4-5) cases where a phenotype I’m looking for doesn’t exist in PHIPO yet, but can be found in another ontology, and I’m wondering about the preferred way to resolve these cases.
For example, a certain mutation in SARS-COV-2 is correlated with increased viral gene expression. “Gene expression phenotype” is already a term in the Ontology of Microbial Phenotypes that might also fit under “single species phenotype” in PHIPO.
A second example is that a certain mutation in SARS-COV-2 is correlated with increased viral load in some host tissue, compared to wild type. “Altered viral load” might be a “pathogen-host interaction phenotype”. “Viral load” is a term in VIDO, as a subclass of “quality”.
What is the preferred way to sort this out? Is it all right to suggest merging terms from other ontologies into PHIPO in GitHub issues? Or, would it be better to suggest brand new PHIPO terms, or to just use terms from each ontology separately without trying to align them?
Thank you,
Madeline Iseminger
MSc. student
Centre for Infectious Disease Genomics and One Health
Simon Fraser University
https://orcid.org/0000-0002-0548-891X
Hello,
I’m using PHIPO for describing phenotypes correlated with SARS-CoV-2 mutations. I’ve run across a few (4-5) cases where a phenotype I’m looking for doesn’t exist in PHIPO yet, but can be found in another ontology, and I’m wondering about the preferred way to resolve these cases.
For example, a certain mutation in SARS-COV-2 is correlated with increased viral gene expression. “Gene expression phenotype” is already a term in the Ontology of Microbial Phenotypes that might also fit under “single species phenotype” in PHIPO.
A second example is that a certain mutation in SARS-COV-2 is correlated with increased viral load in some host tissue, compared to wild type. “Altered viral load” might be a “pathogen-host interaction phenotype”. “Viral load” is a term in VIDO, as a subclass of “quality”.
What is the preferred way to sort this out? Is it all right to suggest merging terms from other ontologies into PHIPO in GitHub issues? Or, would it be better to suggest brand new PHIPO terms, or to just use terms from each ontology separately without trying to align them?
Thank you,
Madeline Iseminger
MSc. student
Centre for Infectious Disease Genomics and One Health
Simon Fraser University
https://orcid.org/0000-0002-0548-891X