We should replace the term "Sequenced Tumors" in case lists

[jjgao]

@schultzn commented on Fri Oct 19 2018

The term sequenced tumors is misleading. To be consistent with what we use in the study view, we should rename these lists to:

"Tumors with mutation data" and "Tumors with mutation and CNA data"

[jjgao]

• [x] let's only change the name, not the case list ID (since _sequenced is used in code)
• [x] fix files of cases_sequenced.txt and cases_cnaseq.txt on datahub
• [x] run an SQL to fix the database
• [ ] fix the pipeline for future import
• [ ] update google spreadsheet

[jjgao]

@rmadupuri asked if we should use "Samples with..." instead of "Tumors with...". I think it's a good idea.

[schultzn]

+1

On Feb 25, 2019, at 11:03 AM, JianJiong Gao notifications@github.com wrote:

@rmadupuri https://github.com/rmadupuri asked if we should use "Samples with..." instead of "Tumors with...". I think it's a good idea.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/cBioPortal/datahub/issues/444#issuecomment-467068735, or mute the thread https://github.com/notifications/unsubscribe-auth/ALV34EcQc2H6sWZ52Mg5LU26MmohneRMks5vRAldgaJpZM4YTChZ.

[rmadupuri]

@jjgao @schultzn @ritikakundra here is the table of current case_list_names and their normalized values. Could you let me know if the normalized names are correct or require any changes? Thank you!

case file name	current case_list_name	new normalized case_list_name
cases_all.txt	All tumors	All samples
cases_sequenced.txt	Sequenced Tumors / Sequenced Samples / All Seq Tumors / All sequenced samples / All Sequenced Tumors	Samples with mutation data
cases_cna.txt	Tumor Samples with CNA data / Tumors CNA	Samples with CNA data
cases_cnaseq.txt	Tumor Samples with sequencing and CNA data / Tumors with sequencing and CNA data	Samples with mutation and CNA data
cases_log2CNA.txt	Tumor Samples with log2 copy-number / Tumors log2 copy-number	Samples with log2 copy-number
cases_methylation_all.txt	All tumor samples with methylation data	All samples with methylation data
cases_methylation_hm27.txt	Tumor Samples with methylation data (HM27) / Tumors with methylation data	Samples with methylation data (HM27)
cases_methylation_hm450.txt	Tumor Samples with methylation data (HM450) / Tumors with methylation data (HM450)	Samples with methylation data (HM450)
cases_miRNA.txt	Tumor Samples with microRNA data (microRNA-Seq) / Tumors with microRNA	Samples with microRNA data (microRNA-Seq)
cases_mRNA_U133.txt	Tumor Samples with mRNA data (U133 microarray only)	Samples with mRNA data (U133 microarray only)
cases_mRNA.txt	Tumor Samples with mRNA data (Agilent microarray) / Tumors with mRNA	Samples with mRNA data (Agilent microarray)
cases_protein_quantification.txt	Tumor Samples with Protein Quantification (Mass Spec) / Protein Quantification (Mass Spec)	Samples with Protein Quantification (Mass Spec)
cases_RNA_Seq_mRNA.txt	Tumor Samples with mRNA data (RNA Seq) / Tumors with mRNA data (RNA Seq)	Samples with mRNA data (RNA Seq)
cases_RNA_Seq_v2_mRNA.txt	Tumor Samples with mRNA data (RNA Seq V2) / Tumors with mRNA data (RNA Seq V2)	Samples with mRNA data (RNA Seq V2)
cases_rppa.txt	Tumor Samples with RPPA data / Tumors with RPPA data	Samples with RPPA data

[schultzn]

Thanks. See my edits in red below.

Niki.

On Feb 25, 2019, at 4:34 PM, Ramya Madupuri notifications@github.com wrote:

@jjgao https://github.com/jjgao @schultzn https://github.com/schultzn @ritikakundra https://github.com/ritikakundra here is the table of current case_list_names and their normalized values. Could you let me know if the normalized names are correct or require any changes? Thank you!

case file name current case_list_name new normalized case_list_name cases_all.txt All tumors All samples cases_sequenced.txt Sequenced Tumors / Sequenced Samples / All Seq Tumors / All sequenced samples / All Sequenced Tumors Samples with mutation data cases_cna.txt Tumor Samples with CNA data / Tumors CNA Samples with CNA data cases_cnaseq.txt Tumor Samples with sequencing and CNA data / Tumors with sequencing and CNA data Samples with mutation and CNA data cases_log2CNA.txt Tumor Samples with log2 copy-number / Tumors log2 copy-number Samples with log2 copy-number data cases_methylation_all.txt All tumor samples with methylation data All Samples with methylation data cases_methylation_hm27.txt Tumor Samples with methylation data (HM27) / Tumors with methylation data Samples with methylation data (HM27) cases_methylation_hm450.txt Tumor Samples with methylation data (HM450) / Tumors with methylation data (HM450) Samples with methylation data (HM450) cases_miRNA.txt Tumor Samples with microRNA data (microRNA-Seq) / Tumors with microRNA Samples with microRNA data (microRNA-Seq) cases_mRNA_U133.txt Tumor Samples with mRNA data (U133 microarray only) Samples with mRNA data (U133 microarray only) cases_mRNA.txt Tumor Samples with mRNA data (Agilent microarray) / Tumors with mRNA Samples with mRNA data (Agilent microarray) cases_protein_quantification.txt Tumor Samples with Protein Quantification (Mass Spec) / Protein Quantification (Mass Spec) Samples with protein Quantification data (Mass Spec) cases_RNA_Seq_mRNA.txt Tumor Samples with mRNA data (RNA Seq) / Tumors with mRNA data (RNA Seq) Samples with mRNA data (RNA Seq) cases_RNA_Seq_v2_mRNA.txt Tumor Samples with mRNA data (RNA Seq V2) / Tumors with mRNA data (RNA Seq V2) Samples with mRNA data (RNA Seq V2) cases_rppa.txt Tumor Samples with RPPA data / Tumors with RPPA data Samples with protein RPPA data (RPPA) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/cBioPortal/datahub/issues/444#issuecomment-467192577, or mute the thread https://github.com/notifications/unsubscribe-auth/ALV34FXy-yPAwc1kAZxsvH217eUOL9O7ks5vRFb7gaJpZM4YTChZ.

[schultzn]

Edits did not come through. Here is an image.

[rmadupuri]

Summary table of normalized case list names and descriptions - (for reference)

case list file	normalized name	normalized description
cases_all.txt	All samples	All samples (# samples)
cases_sequenced.txt	Samples with mutation data	Samples with mutation data (# samples)
cases_cna.txt	Samples with CNA data	Samples with CNA data (# samples)
cases_cnaseq.txt	Samples with mutation and CNA data	Samples with mutation and CNA data (# samples)
cases_log2CNA.txt	Samples with log2 copy-number data	Samples with log2 copy-number data (# samples)
cases_methylation_all.txt	Samples with methylation data	Samples with methylation data (# samples)
cases_methylation_hm27.txt	Samples with methylation data (HM27)	Samples with methylation (HM27) data (# samples)
cases_methylation_hm450.txt	Samples with methylation data (HM450)	Samples with methylation (HM450) data (# samples)
cases_miRNA.txt	Samples with microRNA data (microRNA-Seq)	Samples with microRNA data (# samples)
cases_mRNA_U133.txt	Samples with mRNA data (U133 microarray)	Samples with mRNA expression data (# samples)
cases_mRNA.txt	Samples with mRNA data (Agilent microarray)	Samples with mRNA expression data (# samples)
cases_protein_quantification.txt	Samples with protein data (Mass Spec)	Samples with protein data (Mass Spec) (# samples)
cases_RNA_Seq_mRNA.txt	Samples with mRNA data (RNA Seq)	Samples with mRNA expression data (# samples)
cases_RNA_Seq_v2_mRNA.txt	Samples with mRNA data (RNA Seq V2)	Samples with mRNA expression data (# samples)
cases_rppa.txt	Samples with protein data (RPPA)	Samples protein data (RPPA) (# samples)
cases_complete.txt	Complete samples	Samples with mutation, CNA and expression data (# samples)

[yichaoS]

@jjgao @schultzn Do we want to rename these case lists as well? They are only used in the poetic study:

cases_methylation_promoters_hmEPIC.txt cases_methylation_genebodies_hmEPIC.txt cases_methylation_promoters_wgbs.txt cases_methylation_genebodies_wgbs.txt

And this one in gbm_tcga only: cases_GSVA.txt

[jjgao]

@yichaoS I think these are fine.