Data release v21

[kgaonkar6]

Purpose/implementation Section

What scientific question is your analysis addressing?

Updated data download script for v21 along with documentation.

What was your approach?

• Updated broad_histology and short_histology in pbta-histologies-base.tsv as per #1155
• Added pathology_diagnosis == Subependymal Giant Cell Astrocytoma (SEGA) to LGAT subtyping #1154
• cancer_group and harmonized_diagnosis updated in pbta-histologies.tsv as per #1149
  - Ganglioglioma and Glial-neuronal tumors were added to LGAT subtyping but integrated_diagnosis was not accurately updated in previous release
  - Additionally latest mapping file for pathology_diagnosis == "Other" was used to correspond to terms in files used in #1155
  - Updated CNV interpretation as per Updated data-formats.md #1160

Finally, uploaded pbta-histologies.tsv and pbta-histologies-base.tsv and release-notes.md to release-v21-20210820 and testing s3 buckets.

What GitHub issue does your pull request address?

#1052

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Are all changes documented?

Is there anything that you want to discuss further?

NA

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes

Results

What types of results are included (e.g., table, figure)?

documentation

What is your summary of the results?

• v21 release with updated Glial-neuronal( total 24) , Ganglioglioma ( total 95) and SEGA(6 from updated pathology_diagnosis inclusion ) molecular_subtypes, integrated_diganosis, harmonized_diagnosis and cancer_groups.

Data Release Checklist

• Is the table in doc/data-file-descriptions.md up to date?
• Is doc/data-format.md up to date?
• Is doc/release-notes.md up to date?
• Is download-data.sh up to date?
• Was download-data.sh tested and did it complete without error?

[jharenza]

@kgaonkar6 now that #1150 is in, looks like this one needs the histology file update on s3.

[kgaonkar6]

Updated in release-v21-20210820 and testing folder on s3.

[jharenza]

This looks correct now. Thank you @kgaonkar6 !