PhiBabs935
commented
3 years ago Heads up that I will be replacing this pull request with a newer one soon. Made some more tweaks including adding vaccine terms from the Vaccine Ontology.
The same for VIDO and IDO pull requests.
Added to IDO-COVID-19
-Add negative regulation classes for SARS-CoV-2 generative stages, but my classification scheme still needs vetting.
-added SYMP subclasses of ‘symptom’ (fever, dry cough, taste alteration, smell alteration)
severe acute respiratory syndrome coronavirus 2 protein
Addressed comments from Darren Natale email: -Replaced CHEBI:protein with PRO:protein in all three ontologies
-moved epitope to a subclass of material entity (which is in line with OBI). Updated the textual and logical definition to reflect this change. Also updated the textual definition of ‘epitope role’ to reflect the change.
-added ‘preceded by’ axioms to SARS-CoV-2 generative stages
-Added textual definitions for those that were undefined, based on your slides. But you will need to vet them—not sure if you wanted to update these.
-replaced the Uniprot SARS-Cov-2 protein classes with their PRO equivalents. But I retained the axioms that you added. -But also added further SARS-Cov-2 proteins: spike glycoprotein, signal peptide removed form (SARS-CoV-2), spike protein S1 (SARS-CoV-2), spike protein S2 (SARS-CoV-2), spike protein S2' (SARS-CoV-2), ORF3a protein (SARS-CoV-2), ORF10 protein (SARS-CoV-2), ORF6 protein (SARS-CoV-2), ORF7a protein (SARS-CoV-2), ORF7a protein, signal peptide removed form (SARS-CoV-2), ORF8 protein (SARS-CoV-2), ORF8 protein, signal peptide removed form (SARS-CoV-2), ORF9b protein (SARS-CoV-2), uncharacterized protein 14 (SARS-CoV-2), protein non-structural 7b (SARS-CoV-2)
-and other relevant proteins from PRO: transmembrane protease serine 2