CuzickA
commented
1 year ago Hello @miseminger, many thanks for your message and for using PHIPO.
We use PHIPO for annotations in the Pathogen-Host Interactions database (PHI-base, http://www.phi-base.org/) which currently does not curate viruses.
We would be happy to consider adding viral specific terms to PHIPO, however, since this is out of scope for PHI-base if it is more than a small number of terms then the viral community would need to train a dedicated ontology developer to develop and maintain this aspect.
You could add the suggested new PHIPO terms, and any relevant cross-reference information from other ontologies, to the PHIPO GitHub issue tracker and we will try to include those that are in scope.
Tagging @ValWood and @jseager7 for any follow up discussions.
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