Add demographic fields to gdc-head-and-mouth data

cancerDHC / example-data

This repository is intended to act as a store of example data files from across the NCI Cancer Research Data Commons (CRDC) nodes in a number of formats.

MIT License

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Add demographic fields to gdc-head-and-mouth data #43

Closed jooho-lee-kim closed 2 years ago

jooho-lee-kim commented 2 years ago

This PR is updating gdc-head-and-mouth.json file to include demographic information. The query statement is also revised in Head and Mouth Cancer Datasets.ipynb

Closes #24

jooho-lee-kim commented 2 years ago

Some data fields are updated on PDC data.

The changes I've noticed in the downloaded PDC file (JSON format) are:

All the numbers are now treated as string (e.g., "days_to_birth": -22269 -> "days_to_birth": "-22268").
Change in format of some fields from integer to float (e.g., "days_to_last_follow_up": "145" -> "days_to_last_follow_up": "145.00")
Change in permitted value (e.g., "is_ffpe": "0" -> "is_ffpe": "FALSE")
Updated values in demographic_id and diagnosis_id fields.

It would be better to update PDC data as well, since the data on the repo is downloaded 7 months ago.

gaurav commented 2 years ago

Some data fields are updated on PDC data.

Good catch! Apart from the examples you provided, I notice that some values have changed as well: for example, with case df4e907e-8f98-11ea-b1fd-0aad30af8a83, "days_to_last_follow_up" and "days_to_last_known_disease_status" both changed from 772 days to 1112.00 days, and "progression_or_recurrence" changed from "No" to "Yes". I guess PDC case information continues to be updated!

It would be better to update PDC data as well, since the data on the repo is downloaded 7 months ago.

I completely agree! I've updated that file in 36d4b85 (but feel free to regenerate or delete that if you notice anything wrong with this file). Otherwise, I think this PR is good to go!

gaurav commented 2 years ago

[ ] @gaurav to open an issue describing this case that appears to have been updated after release -- do we need to learn more about PDC's release system and when we might expect their data to change in the future?