NCIt to OncoTree Mapping

[Suhasini Lulla]

Hello,

I am trying to annotate COSMIC Phenotype IDs (which are already annotated with NCIt code) with OncoTree codes . I used the ontology to ontology mapping tool to convert from NCIt to OncoTree codes but only 2923 NCIt codes got mapped to OncoTree codes. 4024 NCIt codes remained unmapped. I appreciate any help in trying to figure this out- thanks!

Suhasini

[rima.w.alhamad]

Hi Suhasini,

Thanks for reaching out! I replicated the mapping using COSMIC v103 and the ontology-to-ontology mapping tool, and your results are correct- it’s not an issue with the tool. 

The unmapped codes are due to a coverage gap between COSMIC and OncoTree. COSMIC covers a broader range of tumor types than OncoTree currently has nodes for, so many NCIt codes simply have no OncoTree equivalent to map to yet.

We are currently working on major updates that will help:

1. Adding more cancer types to OncoTree: we have a couple of updates in progress that will significantly increase the number of mappable tumor types

2. Filling in missing NCIt codes for existing OncoTree nodes, which will also improve mapping

Once these updates are released, you should see a much higher number of successful mappings when you rerun the tool.

Hope this helps! Please let us know if you have any other questions

Best, 

Rima