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A centralized location for storing curated data from cBioPortal
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Propose new front-end names (profile_name field) and assoc metadata #1777

Open mtanggg opened 1 year ago

mtanggg commented 1 year ago

Added new columns and data to previous table in issue#445

File Category Old Data Filename New Data Filename Meta Filename Proposed profile_name field stable_id
Clinical data_bcr_clinical_data_patient.txt data_clinical_patient.txt meta_clinical_patient.txt
Clinical data_bcr_clinical_data_sample.txt data_clinical_sample.txt meta_clinical_sample.txt
CNA data_CNA.txt data_cna.txt meta_cna.txt Copy Number Alterations - Discrete gistic
CNA data_linear_CNA.txt data_linear_cna.txt meta_linear_cna.txt Copy Number Alterations - Linear linear_CNA
CNA data_log2_CNA.txt data_log2_cna.txt meta_log2_cna.txt Copy Number Alterations - Log2 log2CNA
CNA data_log2CNA.txt data_log2_cna.txt meta_log2_cna.txt Copy Number Alterations - Log2 log2CNA
CNA data_CNA_consensus.txt data_cna_consensus.txt meta_cna_consensus.txt Copy Number Alterations - Consensus cna_consensus
CNA data_CNA_RAE.txt data_cna_rae.txt meta_cna_rae.txt Copy Number Alterations - Rae cna_rae
CNA data_cna_hg19.seg data_segment.txt meta_segment.txt
CNA data_armlevel_CNA.txt data_armlevel_cna.txt meta_armlevel_cna.txt Copy Number Alterations - Arm Level
GISTIC data_gistic_genes_amp.txt data_gistic_genes_amp.txt meta_gistic_genes_amp.txt gistic_genes_amp
GISTIC data_gistic_genes_del.txt data_gistic_genes_del.txt meta_gistic_genes_del.txt gistic_genes_del
Protein Level data_rppa.txt data_rppa.txt meta_rppa.txt Protein - RPPA rppa
Protein Level data_rppa_Zscores.txt data_rppa_zscores.txt meta_rppa_zscores.txt Protein - RPPA Z-Scores rppa_Zscores
Protein Level data_protein_quantification.txt data_protein_quantification.txt meta_protein_quantification.txt Protein - Quantification protein_quantification
Protein Level data_protein_quantification_Zscores.txt data_protein_quantification_zscores.txt meta_protein_quantification_zscores.txt Protein - Quantification Z-Scores protein_quantification_zscores
MAF data_mutations_extended.txt FILE REMOVED
MAF data_mutations_mskcc.txt data_mutations.txt meta_mutations.txt Mutations mutations
Mutation Significance data_mutsig.txt data_mutsig.txt meta_mutsig.txt mutsig
Gene Panel data_gene_matrix.txt data_gene_panel_matrix.txt meta_gene_panel_matrix.txt
Generic Assay data_drug_treatment_AUC.txt data_drug_treatment_auc.txt meta_drug_treatment_auc.txt Drug Treatment AUC drug_treatment_auc
Generic Assay data_drug_treatment_IC50.txt data_drug_treatment_ic50.txt meta_drug_treatment_ic50.txt Drug Treatment IC50 drug_treatment_ic50
Generic Assay data_drug_treatment_ZSCORE.txt data_drug_treatment_zscore.txt meta_drug_treatment_zscore.txt Drug Treatment Z-Scores drug_treatment_zscore
mRNA data_expression.txt data_mrna_affymetrix_microarray.txt meta_mrna_affymetrix_microarray.txt mRNA - Affymetrix Microarray mrna_U133
mRNA data_expression_Zscores.txt data_mrna_affymetrix_microarray_zscores_ref_diploid_samples.txt meta_mrna_affymetrix_microarray_zscores_ref_diploid_samples.txt mRNA - Affymetrix Microarray Z-Scores Ref Diploid Samples mrna_U133_Zscores
mRNA data_expression_all_sample_Zscores.txt data_mrna_affymetrix_microarray_zscores_ref_all_samples.txt meta_mrna_affymetrix_microarray_zscores_ref_all_samples.txt mRNA - Affymetrix Microarray Z-Scores Ref All Samples mrna_U133_all_sample_Zscores
mRNA data_expression_median.txt data_mrna_agilent_microarray.txt meta_mrna_agilent_microarray.txt mRNA - Agilent Microarray mrna
mRNA data_mRNA_median_Zscores.txt data_mrna_agilent_microarray_zscores_ref_diploid_samples.txt meta_mrna_agilent_microarray_zscores_ref_diploid_samples.txt mRNA - Agilent Microarray Z-Scores Ref Diploid Samples mrna_median_Zscores
mRNA data_mRNA_median_all_sample_Zscores.txt data_mrna_agilent_microarray_zscores_ref_all_samples.txt meta_mrna_agilent_microarray_zscores_ref_all_samples.txt mRNA - Agilent Microarray Z-Scores Ref All Samples mrna_median_all_sample_Zscores
mRNA data_RNA_Seq_expression_median.txt data_mrna_seq_rpkm.txt meta_mrna_seq_rpkm.txt mRNA - RPKM rna_seq_mrna
mRNA data_rna_seq_mrna.txt data_mrna_seq_rpkm.txt meta_mrna_seq_rpkm.txt mRNA - RPKM
mRNA data_rna_seq_mrna_median_Zscores.txt data_mrna_seq_rpkm_zscores_ref_diploid_samples.txt meta_mrna_seq_rpkm_zscores_ref_diploid_samples.txt mRNA - RPKM Z-Scores Ref Diploid Samples
mRNA data_RNA_Seq_mRNA_median_Zscores.txt data_mrna_seq_rpkm_zscores_ref_diploid_samples.txt meta_mrna_seq_rpkm_zscores_ref_diploid_samples.txt mRNA - RPKM Z-Scores Ref Diploid Samples rna_seq_mrna_median_Zscores
mRNA data_expression_zscores_file.txt data_mrna_seq_rpkm_zscores_ref_diploid_samples.txt meta_mrna_seq_rpkm_zscores_ref_diploid_samples.txt mRNA - RPKM Z-Scores Ref Diploid Samples
mRNA data_RNA_Seq_mRNA_median_all_sample_Zscores.txt data_mrna_seq_rpkm_zscores_ref_all_samples.txt meta_mrna_seq_rpkm_zscores_ref_all_samples.txt mRNA - RPKM Z-Scores Ref All Samples rna_seq_mrna_median_all_sample_Zscores
mRNA data_RNA_Seq_v2_expression_median.txt data_mrna_seq_v2_rsem.txt meta_mrna_seq_v2_rsem.txt mRNA - RSEM Median v2 rna_seq_v2_mrna
mRNA data_RNA_Seq_v2_expression_RSEM_UQ_Log2.txt data_mrna_seq_v2_rsem.txt meta_mrna_seq_v2_rsem.txt mRNA - RSEM Median v2
mRNA data_RNA_Seq_v2_mRNA_median_Zscores.txt data_mrna_seq_v2_rsem_zscores_ref_diploid_samples.txt meta_mrna_seq_v2_rsem_zscores_ref_diploid_samples.txt mRNA - RSEM Median v2 Z-Scores Ref Diploid Samples rna_seq_v2_mrna_median_Zscores
mRNA data_RNA_Seq_v2_mRNA_median_all_sample_Zscores.txt data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt meta_mrna_seq_v2_rsem_zscores_ref_all_samples.txt mRNA - RSEM Median v2 Z-Scores Ref All Samples rna_seq_v2_mrna_median_all_sample_Zscores
mRNA data_mRNA_seq_fpkm_capture.txt data_mrna_seq_fpkm_capture.txt meta_mrna_seq_fpkm_capture.txt mRNA - FPKM Capture mrna_seq_fpkm_capture
mRNA data_mRNA_seq_fpkm_capture_Zscores.txt data_mrna_seq_fpkm_capture_zscores_ref_diploid_samples.txt meta_mrna_seq_fpkm_capture_zscores_ref_diploid_samples.txt mRNA - FPKM Capture Z-Scores Ref Diploid Samples mrna_seq_fpkm_capture_Zscores
mRNA data_mRNA_seq_fpkm_capture_all_sample_Zscores.txt data_mrna_seq_fpkm_capture_zscores_ref_all_samples.txt meta_mrna_seq_fpkm_capture_zscores_ref_all_samples.txt mRNA - FPKM Capture Z-Scores Ref All Samples mrna_seq_fpkm_capture_all_sample_Zscores
mRNA data_mRNA_seq_fpkm_polya.txt data_mrna_seq_fpkm_polya.txt meta_mrna_seq_fpkm_polya.txt mRNA - FPKM PolyA mrna_seq_fpkm_polya
mRNA data_mRNA_seq_fpkm_polya_Zscores.txt data_mrna_seq_fpkm_polya_zscores_ref_diploid_samples.txt meta_mrna_seq_fpkm_polya_zscores_ref_diploid_samples.txt mRNA - FPKM PolyA Z-Scores Ref Diploid Samples mrna_seq_fpkm_polya_Zscores
mRNA data_mRNA_seq_fpkm_polya_all_sample_Zscores.txt data_mrna_seq_fpkm_polya_zscores_ref_all_samples.txt meta_mrna_seq_fpkm_polya_zscores_ref_all_samples.txt mRNA - FPKM PolyA Z-Scores Ref All Samples mrna_seq_fpkm_polya_all_sample_Zscores
mRNA data_RNA_Seq_expression_cpm.txt data_mrna_seq_cpm.txt meta_mrna_seq_cpm.txt mRNA - RNA Seq Expression CPM mrna_seq_cpm
mRNA data_RNA_Seq_expression_cpm_Zscores.txt data_mrna_seq_cpm_zscores_ref_diploid_samples.txt meta_mrna_seq_cpm_zscores_ref_diploid_samples.txt mRNA - RNA Seq Expression CPM Z-Scores Ref Diploid Samples
mRNA data_RNA_Seq_expression_cpm_all_sample_Zscores.txt data_mrna_seq_cpm_zscores_ref_all_samples.txt meta_mrna_seq_cpm_zscores_ref_all_samples.txt mRNA - RNA Seq Expression CPM Z-Scores Ref All Samples mrna_seq_cpm_all_sample_Zscores
mRNA data_RNA_Seq_expression_tpm.txt data_mrna_seq_tpm.txt meta_mrna_seq_tpm.txt mRNA - RNA Seq Expression TPM mrna_seq_tpm
mRNA data_RNA_Seq_expression_tpm_Zscores.txt data_mrna_seq_tpm_zscores_ref_diploid_samples.txt meta_mrna_seq_tpm_zscores_ref_diploid_samples.txt mRNA - RNA Seq Expression TPM Z-Scores Ref Diploid Samples
mRNA data_RNA_Seq_expression_tpm_all_sample_Zscores.txt data_mrna_seq_tpm_zscores_ref_all_samples.txt meta_mrna_seq_tpm_zscores_ref_all_samples.txt mRNA - RNA Seq Expression TPM Z-Scores Ref All Samples mrna_seq_tpm_all_sample_Zscores
mRNA data_RNA_Seq_v2_mRNA_median_normals.txt data_mrna_seq_v2_rsem_normal_samples.txt meta_mrna_seq_v2_rsem_normal_samples.txt mRNA - RNA Seq Expression Median v2 Normals rna_seq_v2_mrna_median_normals
mRNA data_RNA_Seq_v2_mRNA_median_Zscores_normals.txt data_mrna_seq_v2_rsem_normal_samples_zscores_ref_normal_samples.txt meta_mrna_seq_v2_rsem_normal_samples_zscores_ref_normal_samples.txt mRNA - RNA Seq Expression Median v2 Normals Z-Scores Ref Normal Samples rna_seq_v2_mrna_median_normals_Zscores
mRNA data_RNA_Seq_v2_mRNA_median_all_sample_ref_normal_Zscores.txt data_mrna_seq_v2_rsem_zscores_ref_normal_samples.txt meta_mrna_seq_v2_rsem_zscores_ref_normal_samples.txt mRNA - RNA Seq Expression Median v2 Normals Z-Scores Ref All Samples rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores
mRNA data_expression_merged.txt data_mrna_affymetrix_microarray_merged.txt meta_mrna_affymetrix_microarray_merged.txt mRNA - Affymetrix Microarray Merged
mRNA data_expression_merged_Zscores.txt data_mrna_affymetrix_microarray_merged_zscores_ref_diploid_samples.txt meta_mrna_affymetrix_microarray_merged_zscores_ref_diploid_samples.txt mRNA - Affymetrix Microarray Merged Z-Scores Ref Diploid Samples
mRNA data_expression_merged_median_Zscores.txt data_mrna_mirna_merged_zscores.txt meta_mrna_mirna_merged_zscores.txt mRNA - miRNA Merged Z-Scores mrna_merged_median_Zscores
mRNA data_mRNA_outliers.txt data_mrna_outliers.txt meta_mrna_outliers.txt mRNA Outliers mrna_outliers
miRNA data_expression_miRNA.txt data_mirna.txt meta_mirna.txt miRNA mirna
miRNA data_miRNA_median_Zscores.txt data_mirna_zscores.txt meta_mirna_zscores.txt miRNA Z-Scores mirna_median_Zscores
SV data_SV.txt data_sv.txt meta_sv.txt Structural Variants structural_variants
Methylation data_methylation_promoters_hmEPIC.txt data_methylation_promoters_hmepic.txt meta_methylation_promoters_hmepic.txt Methylation - Promoters HMEpic
Methylation data_methylation_genebodies_hmEPIC.txt data_methylation_genebodies_hmepic.txt meta_methylation_genebodies_hmepic.txt Methylation - Genebodies HMEpic
Methylation data_methylation_hm27.txt data_methylation_hm27.txt meta_methylation_hm27.txt Methlytation - HM27 methylation_hm27
Methylation data_methylation_hm450.txt data_methylation_hm450.txt meta_methylation_hm450.txt Methlytation - HM450 methylation_hm450 
         Mapping of old to new naming patterns: (only the files with name changes, doesn't include the files to be removed as specified in the above comments)
File Category Old Data Filename New Data Filename
Clinical data_bcr_clinical_data_patient.txt data_clinical_patient.txt
Clinical data_bcr_clinical_data_sample.txt data_clinical_sample.txt
CNA data_CNA.txt data_cna.txt
CNA data_linear_CNA.txt data_linear_cna.txt
CNA data_log2_CNA.txt data_log2_cna.txt
CNA data_log2CNA.txt data_log2_cna.txt
CNA data_CNA_consensus.txt data_cna_consensus.txt
CNA data_CNA_RAE.txt data_cna_rae.txt
CNA data_armlevel_CNA.txt data_armlevel_cna.txt
RPPA data_rppa_Zscores.txt data_rppa_zscores.txt
Protein Quantification data_protein_quantification_Zscores.txt data_protein_quantification_zscores.txt
MAF data_mutations_extended.txt FILE REMOVED
MAF data_mutations_mskcc.txt data_mutations.txt
Gene Panel data_gene_matrix.txt data_gene_panel_matrix.txt
Generic Assay data_drug_treatment_AUC.txt data_drug_treatment_auc.txt
Generic Assay data_drug_treatment_IC50.txt data_drug_treatment_ic50.txt
Generic Assay data_drug_treatment_ZSCORE.txt data_drug_treatment_zscore.txt
mRNA data_expression.txt data_mrna_affymetrix_microarray.txt
mRNA data_expression_Zscores.txt data_mrna_affymetrix_microarray_zscores_ref_diploid_samples.txt
mRNA data_expression_all_sample_Zscores.txt data_mrna_affymetrix_microarray_zscores_ref_all_samples.txt
mRNA data_expression_median.txt data_mrna_agilent_microarray.txt
mRNA data_mRNA_median_Zscores.txt data_mrna_agilent_microarray_zscores_ref_diploid_samples.txt
mRNA data_mRNA_median_all_sample_Zscores.txt data_mrna_agilent_microarray_zscores_ref_all_samples.txt
mRNA data_RNA_Seq_expression_median.txt data_mrna_seq_rpkm.txt
mRNA data_rna_seq_mrna.txt data_mrna_seq_rpkm.txt
mRNA data_rna_seq_mrna_median_Zscores.txt data_mrna_seq_rpkm_zscores_ref_diploid_samples.txt
mRNA data_RNA_Seq_mRNA_median_Zscores.txt data_mrna_seq_rpkm_zscores_ref_diploid_samples.txt
mRNA data_expression_zscores_file.txt data_mrna_seq_rpkm_zscores_ref_diploid_samples.txt
mRNA data_RNA_Seq_mRNA_median_all_sample_Zscores.txt data_mrna_seq_rpkm_zscores_ref_all_samples.txt
mRNA data_RNA_Seq_v2_expression_median.txt data_mrna_seq_v2_rsem.txt
mRNA data_RNA_Seq_v2_expression_RSEM_UQ_Log2.txt data_mrna_seq_v2_rsem.txt
mRNA data_RNA_Seq_v2_mRNA_median_Zscores.txt data_mrna_seq_v2_rsem_zscores_ref_diploid_samples.txt
mRNA data_RNA_Seq_v2_mRNA_median_all_sample_Zscores.txt data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt
mRNA data_mRNA_seq_fpkm_capture.txt data_mrna_seq_fpkm_capture.txt
mRNA data_mRNA_seq_fpkm_capture_Zscores.txt data_mrna_seq_fpkm_capture_zscores_ref_diploid_samples.txt
mRNA data_mRNA_seq_fpkm_capture_all_sample_Zscores.txt data_mrna_seq_fpkm_capture_zscores_ref_all_samples.txt
mRNA data_mRNA_seq_fpkm_polya.txt data_mrna_seq_fpkm_polya.txt
mRNA data_mRNA_seq_fpkm_polya_Zscores.txt data_mrna_seq_fpkm_polya_zscores_ref_diploid_samples.txt
mRNA data_mRNA_seq_fpkm_polya_all_sample_Zscores.txt data_mrna_seq_fpkm_polya_zscores_ref_all_samples.txt
mRNA data_RNA_Seq_expression_cpm.txt data_mrna_seq_cpm.txt
mRNA data_RNA_Seq_expression_cpm_Zscores.txt data_mrna_seq_cpm_zscores_ref_diploid_samples.txt
mRNA data_RNA_Seq_expression_cpm_all_sample_Zscores.txt data_mrna_seq_cpm_zscores_ref_all_samples.txt
mRNA data_RNA_Seq_expression_tpm.txt data_mrna_seq_tpm.txt
mRNA data_RNA_Seq_expression_tpm_Zscores.txt data_mrna_seq_tpm_zscores_ref_diploid_samples.txt
mRNA data_RNA_Seq_expression_tpm_all_sample_Zscores.txt data_mrna_seq_tpm_zscores_ref_all_samples.txt
mRNA data_RNA_Seq_v2_mRNA_median_normals.txt data_mrna_seq_v2_rsem_normal_samples.txt
mRNA data_RNA_Seq_v2_mRNA_median_Zscores_normals.txt data_mrna_seq_v2_rsem_normal_samples_zscores_ref_normal_samples.txt
mRNA data_RNA_Seq_v2_mRNA_median_all_sample_ref_normal_Zscores.txt data_mrna_seq_v2_rsem_zscores_ref_normal_samples.txt
mRNA data_expression_merged.txt data_mrna_affymetrix_microarray_merged.txt
mRNA data_expression_merged_Zscores.txt data_mrna_affymetrix_microarray_merged_zscores_ref_diploid_samples.txt
mRNA data_expression_merged_median_Zscores.txt data_mrna_mirna_merged_zscores.txt
mRNA data_mRNA_outliers.txt data_mrna_outliers.txt
miRNA data_expression_miRNA.txt data_mirna.txt
miRNA data_miRNA_median_Zscores.txt data_mirna_zscores.txt
SV data_SV.txt data_sv.txt
Methylation data_methylation_promoters_hmEPIC.txt data_methylation_promoters_hmepic.txt
Methylation data_methylation_genebodies_hmEPIC.txt data_methylation_genebodies_hmepic.txt

Originally posted by @rmadupuri in https://github.com/cBioPortal/datahub/issues/445#issuecomment-882855032

mtanggg commented 1 year ago

Summarized names here: cBio: Propose new front-end names

arup1221 commented 1 year ago

Summarized names here: https://docs.google.com/spreadsheets/d/1hsLgj4OXJ5AmVJSI0K_SC5-bCyfofwZRgH2KYAY9nFo/edit?usp=sharing

It is empty. Please update it. I want to work on the issue.

mtanggg commented 1 year ago

Sorry I have updated it, please try again

arup1221 commented 1 year ago

now It is ok, Can I work on this issue ?

mtanggg commented 1 year ago

I'm not sure what is best, the link to the table above (via google doc to be more readable, wasn't working previously; I have just updated it, the link should work now)

rmadupuri commented 1 year ago

@arup1221 @mtanggg thanks for your effort to standardize the profile names. Are you working on the datahub studies that should go to cBioPortal? If so, we need the teams approval since this is a big change that impacts all the studies.

arup1221 commented 1 year ago

@arup1221 @mtanggg are you working on the datahub studies that should go to cBioPortal? If so, we need the teams approval since this is a big change that impacts all the studies.

@rmadupuri Mam, Currently I am not working on it, first I need conformation about it, Then I can start work on it.

arup1221 commented 1 year ago

@rmadupuri mam can I work on the issue?