Is there a list of supported ontologies? Getting error for "UBERON:0001826"

Help & Support
1

Hi folks, I’m going through the Quick start – Predict variant effects. I’m entering my own variant and trying to use UBERON:0001826 for nasal mucosa, but getting an error: details = "Unsupported ontology: "UBERON:0001826"". The default ['UBERON:0001157'] works ok for me.

Is there a list clarifying which ontologies are currently supported? In the docs, I only found supported ontology types. Thank you. Best, Dave.

2

Hi! I encountered a similar problem and it was to do with specifying the species in the predict_sequence / predict_interval. I think all available ontology can be found in the output_metadata:

#Load metadata objects for human.
output_metadata_hs = model.output_metadata(
organism=dna_client.Organism.HOMO_SAPIENS
).concatenate()

#Load metadata objects for mouse.
output_metadata_mm = model.output_metadata(
organism=dna_client.Organism.MUS_MUSCULUS
).concatenate()

In my case, I wanted to predict in the mouse and this needed to be specified in the function:

output = model.predict_interval(
interval=interval,
organism=dna_client.Organism.MUS_MUSCULUS,
requested_outputs={
dna_client.OutputType.CHIP_HISTONE,
dna_client.OutputType.RNA_SEQ,
dna_client.OutputType.ATAC,
},
ontology_terms=output_metadata_mm.ontology_curie.unique().tolist(),#ontology_terms,
)

This worked for me and hope it helps.

Best,
Ken

3

Please find the following tutorial for navigating data ontologies: