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knowledgesystems / curation-scrum

Used for issue tracking of data curation efforts.
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Breast TCGA published study - missing clinical data? #156

Open schultzn opened 8 years ago

schultzn commented 8 years ago

We seem to be missing clinical annotation for the TCGA Breast paper: http://www.cbioportal.org/study.do?cancer_study_id=brca_tcga_pub2015#summary

There should be annotation on ductal vs lobular, as well as PAM50 subtypes...

schultzn commented 8 years ago

We should add the categories below from this file: http://www.cell.com/cms/attachment/2041387239/2055163323/mmc2.xlsx

Final Pathology PAM50 TumorPurity ProliferationScore ER IHC PR IHC HER2 IHC

schultzn commented 8 years ago

The number of samples in the study should also match the manuscript: 817 samples...

ritikakundra commented 8 years ago

@schultzn : I think the data is there in the public portal screen shot 2016-06-21 at 5 24 13 pm

schultzn commented 8 years ago

Yes, but we need to import them as clinical attributes too.

On Jun 21, 2016, at 5:24 PM, ritikakundra notifications@github.com wrote:

@schultzn https://github.com/schultzn : I think the data is there in the public portal https://cloud.githubusercontent.com/assets/12007862/16246846/03f91e72-37d5-11e6-9728-01612ebf325c.png — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/knowledgesystems/curation/issues/156#issuecomment-227576893, or mute the thread https://github.com/notifications/unsubscribe/ALV34Iz53vYX8nfbR0YITGuxyOwvieV_ks5qOFaRgaJpZM4I7FZh.

ritikakundra commented 8 years ago

I sent the screen shot before you dropped by. Will redo the clinical. Thanks!

schultzn commented 8 years ago

I know. Just wanted to keep a record in case anybody else ever looks at this :-)

On Jun 21, 2016, at 6:41 PM, ritikakundra notifications@github.com wrote:

I sent the screen shot before you dropped by. Will redo the clinical. Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/knowledgesystems/curation/issues/156#issuecomment-227594141, or mute the thread https://github.com/notifications/unsubscribe/ALV34C2SYEAhzwM0CV1ql8TZA2Pc6ZKfks5qOGingaJpZM4I7FZh.