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kumc-bmi / naaccr-tumor-data

using NAACCR tumor registry data in i2b2, PCORNet CDM
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re-publishing list of primary sites, morphologies from WHO #6

Open dckc opened 5 years ago

dckc commented 5 years ago

I'd like to openly release the HERON NAACCR Ontology in .csv format, but it includes lists of primary sites and morphologies from WHO, and their license "expressly excludes: ... incorporation of the Classifications in any publicly accessible computer-based information system or public electronic bulletin board including the Internet; distribution of the Classifications on a stand-alone basis, publishing or translating or creating derivative works; ..."

dckc commented 5 years ago

via https://en.wikipedia.org/wiki/International_Classification_of_Diseases_for_Oncology I found this material in spreadsheet form: https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20190618.xls from https://seer.cancer.gov/icd-o-3/

Unless otherwise indicated, all text within NCI products is free of copyright and may be reused without our permission. -- https://www.cancer.gov/policies/copyright-reuse

dckc commented 4 years ago

nice: https://github.com/WerthPADOH/naaccr/blob/master/inst/COPYRIGHTS

dckc commented 4 years ago

primary site: https://staging.seer.cancer.gov/cs/input/02.05.50/breast/site/?breadcrumbs=(~view_schema~,~breast~) https://github.com/imsweb/staging-algorithm-cs/blob/master/src/main/resources/algorithms/cs/02.05.50/tables/primary_site.json

dckc commented 4 years ago

@ctmay4 , thanks for the primary_site.json table in https://github.com/imsweb/staging-algorithm-cs .

Do you know of a corresponding openly published table of morphology codes? Something like https://en.wikipedia.org/wiki/International_Classification_of_Diseases_for_Oncology#Morphology_Codes_(ICD-O-3)[1] but with a more clear license and straightforward data format?

dckc commented 4 years ago

@ctmay4 https://github.com/imsweb/staging-algorithm-cs/blob/master/src/main/resources/algorithms/cs/02.05.50/tables/ajcc6_exclusions_paf.json has a large number of morphology codes with lables but doesn't seem to be exhaustive. Do you know of an exhaustive table?

ctmay4 commented 4 years ago

Sorry, I don't have a good source for you. The library you mentioned is for cancer staging. It does use morphology as an input however it is not exclusive and defines them as ranges many times. I would think the SEER website has this information somewhere, but I'm not sure where.

ctmay4 commented 4 years ago

Randomly, I just ran across this on the NAACCR website. Maybe it will help you.

https://www.naaccr.org/icdo3/#1582820761121-27c484fc-46a7

There is an "Annotated Histology List" spreadsheet there that I think is what you are looking for.