jychien
commented
2 years ago | I've tested using the following cases, looks good to me! | Test Case | Expected Result |
Obtained Result | Test File |
Needs attention |
|---|---|---|---|---|---|
| have ontology terms that used to be in cxg but is no longer valid in pinned ontologies | Fail validation | Failed validation Logging: ERROR: 'CL:0008029' in 'cell_type_ontology_term_id' is a deprecated term id of 'CL'. |
adata_ontologies_exp.h5ad | ||
| have an ontology terms that have updated term names (CL:0000653, podocyte) | Pass validation run --add-labels |
Passed validation, term name was the updated name of "podocyte" | adata_ontologies_updated.h5ad adata_ontologies_updated_labeled.h5ad |
||
| have ontology terms that are new to pinned ontologies (EFO:0030062, Slide-seqV2) | Pass validation | Passed validation | adata_ontologies_new.h5ad | ||
| have disease term that is new (MONDO:0800029) in MONDO | Pass validation | Passed validation | adata_ontologies_mondo_new.h5ad | ||
| have disease term that is deprecated (MONDO:0008345) | Fail validation | Failed validation Logging: ERROR: 'MONDO:0008345' in 'disease_ontology_term_id' is a deprecated term id of 'MONDO'. Only 'PATO:0000461' is allowed for 'PATO' term ids. |
adata_ontologies_mondo_exp.h5ad | ||
| have disease terms that is new (UBERON:8410081) in UBERON | Pass validation | Passed validation | adata_ontologies_uberon.h5ad |
Note: HsapDv and MmusDV releases are neither documented nor tagged in their repositories.
Their downloads include release metadata:
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mmusdv/releases/2020-03-10/mmusdv.owl"/>`
`
Both match the current pinned versions in the schema so these ontologies do not need to be refreshed.
Required Ontologies
The following ontology dependencies are pinned for this version of the schema.