TCGA patient variable data dictionary
Hi, I downloaded miRNA seq and patient data from TCGA-PRAD. Is there a way to find out the explanation /dictionary on patient/clinical variable
colnames(tcga-prad)
[1] "bcr_patient_barcode" "additional_studies"
[3] "tumor_tissue_site" "other_dx"
[5] "gender" "vital_status"
[7] "days_to_birth" "days_to_death"
[9] "days_to_last_followup" "race_list"
[11] "tissue_source_site" "patient_id"
[13] "bcr_patient_uuid" "history_of_neoadjuvant_treatment"
[15] "informed_consent_verified" "icd_o_3_site"
[17] "icd_o_3_histology" "icd_10"
[19] "tissue_prospective_collection_indicator" "tissue_retrospective_collection_indicator"
[21] "days_to_initial_pathologic_diagnosis" "age_at_initial_pathologic_diagnosis"
[23] "year_of_initial_pathologic_diagnosis" "person_neoplasm_cancer_status"
[25] "ethnicity" "day_of_form_completion"
[27] "month_of_form_completion" "year_of_form_completion"
[29] "histological_type" "histological_type_other"
[31] "zone_of_origin" "laterality"
[33] "tumor_levels" "initial_pathologic_diagnosis_method"
[35] "days_to_bone_scan_performed" "bone_scan_results"
[37] "diagnostic_ct_abd_pelvis_performed" "days_to_diagnostic_computed_tomography_performed"
[39] "diagnostic_ct_abd_pelvis_results" "diagnostic_mri_performed"
[41] "days_to_diagnostic_mri_performed" "diagnostic_mri_results"
[43] "lymphnodes_examined" "number_of_lymphnodes_examined"
[45] "number_of_lymphnodes_positive_by_he" "residual_tumor"
[47] "patient_death_reason" "source_of_patient_death_reason"
[49] "postoperative_rx_tx" "radiation_therapy"
[51] "primary_therapy_outcome_success" "biochemical_recurrence"
[53] "days_to_first_biochemical_recurrence" "has_new_tumor_events_information"
[55] "has_drugs_information" "has_radiations_information"
[57] "has_follow_ups_information" "stage_event_system_version"
[59] "stage_event_clinical_stage" "stage_event_pathologic_stage"
[61] "stage_event_tnm_categories" "stage_event_psa"
[63] "stage_event_gleason_grading" "stage_event_ann_arbor"
[65] "stage_event_serum_markers" "stage_event_igcccg_stage"
[67] "stage_event_masaoka_stage"
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Kevin Blighe
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Björn •
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Björn •
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There are different ways to do this.
first way
First, see my previous answers, here:
- A: How to get CDE ID corresponds to each column feature of clinical data from TCGA
- A: TCGA clinical feature meaning of "pct_tumor_invasion" for TCGA-UCEC project (Ute
In a nutshell, if you want more comprehensive information on these terms, you should go by the Common Data Elements (CDE) ID of each. You should have the CDE ID, which likely appears in the third row of the data that you downloaded.
With the CDE ID, do the following:
- Go to CDE Browser
- Go to Public ID Search tab
- Put the numerical CDE ID into the Public ID search box
- Click on Search
second way
Just go to the GDC Data Dictionary (in particular, the Viewer), and you can find descriptions there, too).
Kevin
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