How to find the oncology terms

Help & Support
1

Hi, I’m trying to follow the instruction of predicting gene expressionaccording to “Predict outputs for a genome interval (reference genome)” part in “quick start” part. For the step using “dna_model.predict_interval“, ontology_terms should be specified. I changed into “CLO:0050107“ for a test, but it failed, indicating that
_MultiThreadedRendezvous: <_MultiThreadedRendezvous of RPC that terminated with: status = StatusCode.INVALID_ARGUMENT details = "Unsupported ontology: "CLO:0050107"" debug_error_string = "UNKNOWN:Error received from peer ipv4:142.250.101.95:443 {grpc_status:3, grpc_message:"Unsupported ontology: \"CLO:0050107\""}"

I noticed that in oncology.py,

"""Supported ontology types.



  CLO: Cell Line Ontology.

  UBERON: Uber-anatomy ontology.

  CL: Cell Ontology.

  EFO: Experimental Factor Ontology.

  NTR: New Term Requested.

  """

Could you please tell me if there is some repertoir for the supported cell lines and terms I didn’t find? Or, is there some oncology term database besides Ontology Lookup Service (OLS)? Thank you!

2

Hi @Lei_Xia,

The easiest way to view the available ontologies is using the tissue ontology colab. This lets you browse all the different output metadata to find supported tissues by output type.

Hope that helps!