Using Oncotree Mappings Api for ICD-O-3 histology code

[Kevin]

Hi,

I am interested in mapping a set of ICD-O-3 topography and morphology code to Oncotree ontoly. However, I'm having trouble making the API work at http://oncotree.mskcc.org/#/home?tab=api and can't seem to find documentation to understand what I'm doing wrong. All my requests return a 404 status with "org.mskcc.oncotree.error.CrosswalkConceptNotFoundException" exception raised and message  "No OncoTree codes were mapped to your query". 

This is an example or Request URL of mine :

http://oncotree.mskcc.org/api/crosswalk?vocabularyId=ICD-O-3&histologyCode=8140%2F3&siteCode=C77

I have tried a few different combinations of histology codes and site codes (and changing vocabularyId to ICDO, ICD-O or ICDO10CM) but they return the same errors.

I've found this other google group discussion from a year ago where it was said that the tool had fallen behind on mapping with other ontologies. Is it still the case and ICD-O-3 mapping is not easily possible ? Or am I doing it the wrong way as I admit I am confused on how to fill vocabulartId and conceptId fields ? Note that I have tried working combinations of histology and morphology code in the 2018 post and they didn't work for me

Thanks in advance,
Kevin

[Benjamin Gross]

Hi Kevin,

We took down the web page providing the UI to the crosswalk endpoint because the mapping were not complete and when a mapping was provided, we were not always happy with the results.  Unfortunately, we forgot to remove the endpoint from the API tab.

We have talked about revisiting this feature, but we currently have no plans to do this.

Sorry for any inconvenience this has caused.

Regards,

Benjamin

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[Hassan Ghani]

Hi, I understand why the mapping was taken down and appreciate the desire for both accuracy and completeness. Would you be willing to provide the mapping with the express understanding of these shortcomings? I have spent some effort on making a map, and would simply like to compare the two.

Sincerely,

Hassan

[Ritika Kundra]

Hi Hassan,

We do have an initial mapping we did from our side logged here:

https://github.com/cBioPortal/oncotree/blob/master/scripts/ontology_to_ontology_mapping_tool/ontology_mappings.txt

Let me know if you have any questions.

Thanks,

Ritika

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