HTAN Dashboard Auto-generated by the HTAN Data Coordinating Center (DCC)

HTA13: TNP SARDANA

Total File Size
6.7 TB

Total size of all files submitted to the DCC.

Total Number of Files
35,792

Total number of files submitted to the DCC.

Validation Errors
16

Total number of validation errors detected by the DCC dashboard.

Percent Metadata Complete
50.9%

Total percent of metadata fields completed.

This tab provides a complete list of all metadata files submitted by the atlas.
Synapse ID Category Num Records Percent Complete Metadata
syn41745520 Biospecimen 402 38.16%
syn41745688 Demographics 2 23.33%
syn41745802 Diagnosis 2 16.28%
syn41745888 Exposure 2 13.79%
syn41745941 FamilyHistory 2 14.29%
syn41745973 FollowUp 2 5.45%
syn41746037 ImagingLevel2 232 77.07%
syn41746051 ImagingLevel2 7 74.53%
syn41746067 ImagingLevel2 12 74.09%
syn47878101 ImagingLevel3Segmentation 25 76.92%
syn48015494 ImagingLevel4 25 73.33%
syn41746009 MolecularTest 3 10.26%
syn41745996 Therapy 2 15.00%
This tab provides a complete list of all validation errors detected by the dashboard.

Validation Passed.

Validation Passed.

Validation Passed.

Validation Passed.

Validation Passed.

Validation Passed.

Validation Passed.

In folder: imaging_level_2/WD-76847_Stanford/Processed/Segmented/compensated, file name: Normal colon_FFPE_CODEX_02262020_reg001_compensated.txt contains unsupported characters.
In folder: imaging_level_2/WD-76847_Stanford/Processed/Segmented/compensated, file name: Normal colon_FFPE_CODEX_02262020_reg001_compensated.csv contains unsupported characters.
In folder: imaging_level_2/WD-76847_Stanford/Processed/Segmented/compensated, file name: Normal colon_FFPE_CODEX_02262020_reg001_compensated.fcs contains unsupported characters.
In folder: imaging_level_2/WD-76846_Stanford/Processed/Segmented/Segmented/compensated, file name: Normal colon_FF_CODEX_03122020_reg001_compensated.txt contains unsupported characters.
In folder: imaging_level_2/WD-76846_Stanford/Processed/Segmented/Segmented/compensated, file name: Normal colon_FF_CODEX_03122020_reg001_compensated.fcs contains unsupported characters.
In folder: imaging_level_2/WD-76847_Stanford/Processed/Stitched, file name: Normal colon_FFPE_CODEX_02262020_reg001.tif contains unsupported characters.
In folder: imaging_level_2/WD-76846_Stanford/Processed/Segmented/Segmented/compensated, file name: Normal colon_FF_CODEX_03122020_reg001_compensated.csv contains unsupported characters.
In folder: imaging_level_2/WD-76846_Stanford/Processed/Stitched, file name: Normal colon_FF_CODEX_03122020_reg001.tif contains unsupported characters.
In folder: imaging_level_2/WD-76845_Stanford/Processed, file name: Normal colon_FFPE_CODEX_02262020_reg001_compensated.csv contains unsupported characters.
In folder: imaging_level_2/WD-76845_Stanford/Processed, file name: Normal colon_FFPE_CODEX_02262020_reg001_compensated.txt contains unsupported characters.
In folder: imaging_level_2/WD-76845_Stanford/Processed, file name: Normal colon_FFPE_CODEX_02262020_reg001_compensated.fcs contains unsupported characters.
In folder: imaging_level_2/WD-76845_Stanford/Processed/Segmented/compensated, file name: Normal colon_FFPE_CODEX_02262020_reg001_compensated.fcs contains unsupported characters.
In folder: imaging_level_2/WD-76845_Stanford/Processed/Segmented/compensated, file name: Normal colon_FFPE_CODEX_02262020_reg001_compensated.csv contains unsupported characters.
In folder: imaging_level_2/WD-76845_Stanford/Processed/Segmented/compensated, file name: Normal colon_FFPE_CODEX_02262020_reg001_compensated.txt contains unsupported characters.
In folder: imaging_level_2/WD-76845_Stanford/Processed, file name: Normal colon_FFPE_CODEX_02262020_reg001.tif contains unsupported characters.
In folder: imaging_level_2/WD-76845_Stanford/Processed/Stitched, file name: Normal colon_FFPE_CODEX_02262020_reg001.tif contains unsupported characters.
These plots are designed to visually summarize the data completeness of an HTAN atlas.

For example:

  • how much Tier 1 clinical data has the atlas provided?
  • for sequencing or imaging data, has the atlas provided Level 1-4 data?

Clinical Data Matrix: Tiers 1 and 2





ParticipantID Demographics Exposure FamilyHistory FollowUp Diagnosis Therapy MolecularTest ClinicalDataTier2 SRRSClinicalDataTier2
HTA13_1 1 1 1 1 1 1 1 0 0
HTA13_2 1 1 1 1 1 1 1 0 0
Counts
Demographics 2
Exposure 2
FamilyHistory 2
FollowUp 2
Diagnosis 2
Therapy 2
MolecularTest 2
ClinicalDataTier2 0
SRRSClinicalDataTier2 0

Clinical Data Matrix: Tier 3

No data available.

ParticipantID AcuteLym.. Neurobla.. BreastCa.. Colorect.. LungCanc.. Melanoma.. OvarianC.. Pancreat.. Prostate.. SarcomaT..
HTA13_1 0 0 0 0 0 0 0 0 0 0
HTA13_2 0 0 0 0 0 0 0 0 0 0
Counts
AcuteLym.. 0
Neurobla.. 0
BreastCa.. 0
Colorect.. 0
LungCanc.. 0
Melanoma.. 0
OvarianC.. 0
Pancreat.. 0
Prostate.. 0
SarcomaT.. 0

Assay Matrix: Core Imaging





BiospecimenID ImagingLevel1 ImagingLevel2 ImagingLevel3Image ImagingLevel3Channels ImagingLevel3Segmentation ImagingLevel4 SRRSImagingLevel2
HTA13_1_5 0 1 0 0 0 0 0
HTA13_1_6 0 1 0 0 1 1 0
HTA13_1_7 0 1 0 0 0 0 0
HTA13_1_9 0 1 0 0 0 0 0
HTA13_1_10 0 1 0 0 0 0 0
HTA13_1_11 0 1 0 0 1 1 0
HTA13_1_17 0 1 0 0 0 0 0
HTA13_1_18 0 1 0 0 1 1 0
HTA13_1_23 0 1 0 0 0 0 0
HTA13_1_24 0 1 0 0 1 1 0
HTA13_1_28 0 1 0 0 0 0 0
HTA13_1_29 0 1 0 0 1 1 0
HTA13_1_32 0 1 0 0 0 0 0
HTA13_1_33 0 1 0 0 1 1 0
HTA13_1_37 0 1 0 0 0 0 0
HTA13_1_38 0 1 0 0 1 1 0
HTA13_1_42 0 1 0 0 0 0 0
HTA13_1_43 0 1 0 0 1 1 0
HTA13_1_47 0 1 0 0 0 0 0
HTA13_1_48 0 1 0 0 1 1 0
HTA13_1_49 0 1 0 0 0 0 0
HTA13_1_50 0 1 0 0 0 0 0
HTA13_1_51 0 1 0 0 0 0 0
HTA13_1_52 0 1 0 0 0 0 0
HTA13_1_53 0 1 0 0 1 1 0
HTA13_1_54 0 1 0 0 1 1 0
HTA13_1_55 0 1 0 0 1 1 0
HTA13_1_56 0 1 0 0 1 1 0
HTA13_1_57 0 1 0 0 0 0 0
HTA13_1_58 0 1 0 0 1 1 0
HTA13_1_62 0 1 0 0 0 0 0
HTA13_1_63 0 1 0 0 1 1 0
HTA13_1_67 0 1 0 0 0 0 0
HTA13_1_68 0 1 0 0 1 1 0
HTA13_1_72 0 1 0 0 0 0 0
HTA13_1_73 0 1 0 0 1 1 0
HTA13_1_77 0 1 0 0 0 0 0
HTA13_1_78 0 1 0 0 1 1 0
HTA13_1_79 0 1 0 0 0 0 0
HTA13_1_80 0 1 0 0 0 0 0
HTA13_1_81 0 1 0 0 0 0 0
HTA13_1_82 0 1 0 0 1 1 0
HTA13_1_83 0 1 0 0 0 0 0
HTA13_1_86 0 1 0 0 0 0 0
HTA13_1_87 0 1 0 0 0 0 0
HTA13_1_88 0 1 0 0 1 1 0
HTA13_1_89 0 1 0 0 0 0 0
HTA13_1_90 0 1 0 0 1 1 0
HTA13_1_93 0 1 0 0 0 0 0
HTA13_1_94 0 1 0 0 0 0 0
HTA13_1_95 0 1 0 0 1 1 0
HTA13_1_100 0 1 0 0 0 0 0
HTA13_1_101 0 1 0 0 1 1 0
HTA13_1_105 0 1 0 0 0 0 0
HTA13_1_106 0 1 0 0 1 1 0
HTA13_1_109 0 1 0 0 0 0 0
HTA13_1_110 0 1 0 0 1 1 0
HTA13_1_117 0 1 0 0 0 0 0
HTA13_1_118 0 1 0 0 0 0 0
HTA13_1_130 0 1 0 0 0 0 0
HTA13_1_133 0 1 0 0 0 0 0
HTA13_1_134 0 1 0 0 0 0 0
HTA13_1_139 0 1 0 0 0 0 0
HTA13_1_141 0 1 0 0 0 0 0
HTA13_1_208 0 1 0 0 0 0 0
HTA13_1_212 0 1 0 0 0 0 0
HTA13_1_215 0 1 0 0 0 0 0
HTA13_1_216 0 1 0 0 0 0 0
HTA13_1_223 0 1 0 0 0 0 0
HTA13_1_225 0 1 0 0 0 0 0
HTA13_1_265 0 1 0 0 0 0 0
HTA13_1_266 0 1 0 0 0 0 0
HTA13_2_7 0 1 0 0 0 0 0
HTA13_2_77 0 1 0 0 0 0 0
HTA13_2_78 0 1 0 0 0 0 0
HTA13_2_81 0 1 0 0 0 0 0
HTA13_2_82 0 1 0 0 0 0 0
HTA13_2_91 0 1 0 0 0 0 0
HTA13_2_131 0 1 0 0 0 0 0
HTA13_2_132 0 1 0 0 0 0 0
Counts
ImagingLevel1 0
ImagingLevel2 80
ImagingLevel3Image 0
ImagingLevel3Channels 0
ImagingLevel3Segmentation 25
ImagingLevel4 25
SRRSImagingLevel2 0

gantt dateFormat X axisFormat %s section HTA13_1 Cecum Right Surgical Resection (4):milestone,0,0 section HTA13_2 Tonsil NOS Bilateral Surgical Resection (2):milestone,0,0

This tab is for HTAN DCC debugging purposes only. It reviews all paths in the atlas, and summarizes:
  • the number of files annotated via an existing metadata file.
  • the number of files upload to the cloud, but not yet annotated with any metadata.
Root Path Num Annotated Files Num Unannotated Files
imaging_level_2 232 35472
imaging_level_3_segmentation 25 0
imaging_level_4 25 0
sardana_phase_1_ffpe_level_2 12 12
sardana_phase_1_ff_level_2 7 7
This tab is for HTAN DCC debugging purposes only. Atlases should please ignore.

@ HTAN Data Coordinating Center (DCC).