ICDO Topography + Morphology pairing to Oncotree translation

[Anurag Saxena]

Hello. I have studies with mixed cancer types that have ICD-O-3 Topography and Morphology code pairs per sample. We'd like to convert them to Oncotree codes and annotate them with Cancer Type and Cancer Type Detailed values to load them into our cBioPortal instance. I am aware of the Ontology to Ontology mapping tool: https://github.com/cBioPortal/oncotree/tree/master/scripts/ontology_to_ontology_mapping_tool

How do I use this when I have a list of ICDO Topography + Morphology Codes?

For example see file attached that has a list of topography and morphology pairings. 

Thank you for your help!

[Vincent Laufer]

Take a look at the mapping file here:

https://github.com/cBioPortal/oncotree/tree/master/scripts/ontology_to_ontology_mapping_tool

[Anurag Saxena]

Thanks Vincent. I am aware of the mapping you mentioned. However it has a lot of codes missing. Also, the script only maps either Topography or Morphology but not Topography + Morphology which is the full ICD-O-3 code. 

[Ritika Kundra]

Hi Anurag and Vincent,

We are aware that this mapping is outdated. Currently, the mapping update is not on the immediate roadmap. Once we are done with our heme release, this will be the next priority.

Thanks,

Ritika

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