Jax CKB disease terms incorrect

Question

Jax CKB disease terms incorrect

ahwagner opened this issue 6 years ago · comments

Alex H. Wagner, PhD commented 6 years ago

Currently, 87% of associations from Jax CKB have DOID:162 - Cancer. This isn't correct. Other resources are much more reasonable at 0-7%.

Alex H. Wagner, PhD · Answer 1 · Thu Apr 19 2018 06:50:32 GMT+0800 (China Standard Time)

On reloading with the most recent data release, this number is closer to 24%--I'm not sure why this changed so dramatically (possible error in my original query?), but it is still far above our other resources.

Brian · Answer 2 · Wed Apr 25 2018 00:16:57 GMT+0800 (China Standard Time)

The following terms are mapped to the generic term cancer

$ grep "\tCancer" disease_alias.tsv
Advanced Solid Tumor	Cancer
Solid tumor	Cancer
All Solid Tumors	Cancer
Any cancer type	Cancer
Solid tumors	Cancer
Malignant neoplastic disease	Cancer
All Tumors	Cancer

Brian · Answer 3 · Wed Apr 25 2018 00:27:26 GMT+0800 (China Standard Time)

Regarding jax:

$ cat  jax.json | jq '.jax | .indication.name' | grep 'Advanced Solid Tumor' | wc -l
    1330

Brian · Answer 4 · Wed Apr 25 2018 00:34:30 GMT+0800 (China Standard Time)

That is 1330 out of 5754.

$ cat  jax.json | jq '.jax | .indication.name'  | wc -l
    5754

Alex H. Wagner, PhD · Answer 5 · Wed Apr 25 2018 03:04:38 GMT+0800 (China Standard Time)

These numbers are accurate per discussion with Sara Patterson at CKB. Resolving.