From aa16024e1ee76e1acdb0159c5b3895f25810666a Mon Sep 17 00:00:00 2001 From: CollectorsCorner Date: Wed, 13 Mar 2024 16:01:19 -0400 Subject: [PATCH] Update cds-model-props.yml --- model-desc/cds-model-props.yml | 321 +++++++++++++++++++++++++-------- 1 file changed, 245 insertions(+), 76 deletions(-) diff --git a/model-desc/cds-model-props.yml b/model-desc/cds-model-props.yml index f21a6ef..c82b855 100644 --- a/model-desc/cds-model-props.yml +++ b/model-desc/cds-model-props.yml @@ -4,6 +4,7 @@ PropDefinitions: Req: true Term: - Code: '14612683' + Origin: caDSR Value: Imaging Technique CTDI Phantom Type Sequence of Items Text Type: string CTAquisitionProtocolElement_ctdiVol: @@ -11,6 +12,7 @@ PropDefinitions: Req: true Term: - Code: '3882991' + Origin: caDSR Value: Computed Tomography Dose Index Volume Quantity 8 Byte Number Type: string CTAquisitionProtocolElement_exposureModulationType_Code: @@ -27,6 +29,7 @@ PropDefinitions: Term: - Code: '2656117' Origin: caDSR + Original Source: caDSR Value: Image Gantry Detector Tilt 16 Character Number Type: string CTAquisitionProtocolElement_kVp: @@ -34,12 +37,14 @@ PropDefinitions: Req: true Term: - Code: '2904496' + Origin: caDSR Value: Image Kilovolt Peak Float 16 Number Type: string CTAquisitionProtocolElement_singleCollimationWidth: Desc: The width of a single row of acquired data. The units are of linear distince, e.g. mm. Term: - Code: '2903347' + Origin: caDSR Value: Image Single Collimation Width 8 Byte Millimeter Number Type: string CTAquisitionProtocolElement_spiralPitchFactor: @@ -47,6 +52,7 @@ PropDefinitions: Req: true Term: - Code: '2414556' + Origin: caDSR Value: Computed Tomography Pitch Factor Number Type: string CTAquisitionProtocolElement_tableSpeed: @@ -54,24 +60,28 @@ PropDefinitions: Req: true Term: - Code: Pending + Origin: caDSR Type: string CTAquisitionProtocolElement_totalCollimationWidth: Desc: The width of the total collimation over the area of active x-ray detection. The units are of linear distince, e.g. mm. Req: true Term: - Code: '2903328' + Origin: caDSR Value: Image Total Collimation Width 8 Byte Millimeter Number Type: string CTImageReconstructionProtocolElement_convolutionKernel: Desc: A label describing the mathematical operations used to reconstruct images from the acquired data. The values for this attribute are vendor specific and not coded. Term: - Code: '2656119' + Origin: caDSR Value: Image Convolution Kernel 16 Character Text Type: string CTImageReconstructionProtocolElement_convolutionKernelGroupCode: Desc: A coded value specifying the family of mathematical operations to use to reconstruct images from the acquired data Term: - Code: '14617525' + Origin: caDSR Value: Imaging Technique Convolution Kernel Group Name Type: string MRImageAcquisitionProtocolElement_acquisitionContrastCode: @@ -90,17 +100,20 @@ PropDefinitions: - TOF_Time Of Flight weighted contrast Term: - Code: '14616428' + Origin: caDSR Value: Image Acquisition Contrast Type MRImageAcquisitionProtocolElement_arterialSpinLabelingContrastCode: Desc: A coded value specifying how arterial water is used as a diffusable tracer. Term: - Code: '14616429' + Origin: caDSR Value: Imaging Technique Arterial Spin Labeling Contrast Name Type: string MRImageAcquisitionProtocolElement_diffusionBValue: Desc: The factor by which the acquisition is sensitized to the Brownian motion of water molecules. The units are of time/area, e.g. s/mm2 Term: - Code: '14607706' + Origin: caDSR Value: Imaging Technique MR Diffusion B Value Number Type: string MRImageAcquisitionProtocolElement_diffusionDirectionalityCode: @@ -112,11 +125,13 @@ PropDefinitions: - NONE Term: - Code: '14616426' + Origin: caDSR Value: Imaging Technique Diffusion Directionality Type MRImageAcquisitionProtocolElement_echoPlanarPulseSequenceIndicator: Desc: Specifies whether multiple echos of different phase steps are acquired using rephasing gradients instead of repeated 180-degree pulses. Term: - Code: '14612651' + Origin: caDSR Value: Image Acquisition Echo Planar Pulse Sequence Indicator Type: string MRImageAcquisitionProtocolElement_echoPulseSequenceCategoryCode: @@ -127,36 +142,42 @@ PropDefinitions: - BOTH Term: - Code: '14645641' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Image Acquisition Spin-Echo Pulse Sequence Code Category MRImageAcquisitionProtocolElement_inversionRecoveryIndicator: Desc: Specifies whether an inversion recovery preparatory sequence is used in the acquisition. Term: - Code: '14607722' + Origin: caDSR Value: Image Acquisition Inversion Recovery Indicator Type: string MRImageAcquisitionProtocolElement_magneticFieldStrength: Desc: "A vector quantity indicating the ability of a magnetic field to exert a force on moving electric charges. [The American Heritage\xAE Science Dictionary]. The units are of magnetic flux density, e.g. tesla." Term: - Code: '14607707' + Origin: caDSR Value: Imaging Technique Magnetic Field Strength Number Type: string MRImageAcquisitionProtocolElement_multipleSpinEchoIndicator: Desc: Specifies whether different lines in k-space are collected for a single frame. Term: - Code: '14608595' + Origin: caDSR Value: Imaging Technique Multiple Spin Echo Indicator Type: string MRImageAcquisitionProtocolElement_phaseContrastIndicator: Desc: Specifies whether this is a pulse sequence in which the flowing spins are velocity encoded in phase. Term: - Code: '14608601' + Origin: caDSR Value: Image Phase Contrast Indicator Type: string MRImageAcquisitionProtocolElement_pulseSequenceName: Desc: Name of the pulse sequence that is used for the acquisition. This is usually a vendor-specific name. Term: - Code: '14608594' + Origin: caDSR Value: Image Acquisition Pulse Sequence Name Text Type: string MRImageAcquisitionProtocolElement_resonantNucleusCode: @@ -172,11 +193,13 @@ PropDefinitions: - 129XE Term: - Code: '14616427' + Origin: caDSR Value: Image Acquisition Resonant Nucleus Type MRImageAcquisitionProtocolElement_saturationRecoveryIndicator: Desc: Specifies whether a saturation recovery pulse sequence is used Term: - Code: '14612652' + Origin: caDSR Value: Imaging Technique Saturation Recovery Indicator Type: string MRImageAcquisitionProtocolElement_spectrallySelectedSuppressionCode: @@ -189,6 +212,7 @@ PropDefinitions: - NONE Term: - Code: '14616431' + Origin: caDSR Value: Imaging Technique Spectrally Selected Suppression Type MRImageAcquisitionProtocolElement_steadyStatePulseSequenceCode: Desc: A coded value specifying how residual transverse magnetization is maintained during the acquisition. @@ -200,11 +224,13 @@ PropDefinitions: - NONE Term: - Code: '14616430' + Origin: caDSR Value: Image Acquisition Steady State Pulse Sequence Type MRImageAcquisitionProtocolElement_timeOfFlightContrastIndicator: Desc: Specifies whether contrast is created by the inflow of blood in the saturated plane. Term: - Code: '14608649' + Origin: caDSR Value: Imaging Technique Time of Flight Contrast Indicator Type: string MRImageReconstructionProtocolElement_complexImageComponentCode: @@ -216,31 +242,36 @@ PropDefinitions: - MAGNITUDE Term: - Code: '14616432' + Origin: caDSR Value: Imaging Technique Complex Image Component Type PETImagingAcquisitionProtocolElement_gantryDetectorTilt: Desc: Nominal angle of tilt in degrees of the scanning gantry. The units are of plane angle , e.g. degrees. Zero degrees means the gantry is not tilted, negative degrees are when the top of the gantry is tilted away from where the table enters the gantry. Term: - Code: '2656117' + Origin: caDSR Value: Image Gantry Detector Tilt 16 Character Number Type: string Radiopharmaceutical_radionuclideCode: Desc: A coded value that specifies the radioactive isotope in the radiophamaceutical. Term: - Code: '14612653' + Origin: caDSR Value: Imaging Technique Radionuclide Code Text Type: string acl: Desc: open or restricted access to data Term: - Code: '11555664' - Origin: DSS + Origin: caDSR + Original Source: DSS Value: Electronic Data File Access Level Text Type: string acquisition_method_type: Desc: Records the method of acquisition or source for the specimen under consideration Term: - Code: '6626651' - Origin: MCL/HTAN + Origin: caDSR + Original Source: MCL/HTAN Value: Biospecimen Acquisition Method Type Type: string adult_or_childhood_study: @@ -251,31 +282,36 @@ PropDefinitions: Req: Preferred Term: - Code: '11524549' + Origin: caDSR Value: Study Subject Legal Adult Or Pediatric Participant Type age_at_diagnosis: Desc: Participant age at relevant diagnosis Term: - Code: '10609539' - Origin: DSS + Origin: caDSR + Original Source: DSS Value: Subject Age at Diagnosis Integer Type: integer antibody_name: Desc: short descriptive name for this antibody Term: - Code: '4588605' + Origin: caDSR Value: Tissue Slide IHC Antibody Used Type Type: string authz: Desc: multifactor authorization Term: - Code: Pending - Origin: CDS + Origin: caDSR + Original Source: CDS Type: string avg_read_length: Desc: Average sequence read length Req: Preferred Term: - Code: '12426615' + Origin: caDSR Value: Nucleotide Sequence Average Read Length Count Type: number bases: @@ -283,6 +319,7 @@ PropDefinitions: Req: Preferred Term: - Code: '12373573' + Origin: caDSR Value: Sequencing Library Unique Basecalling Count Type: integer bioproject_accession: @@ -295,6 +332,7 @@ PropDefinitions: Req: Preferred Term: - Code: '2230047' + Origin: caDSR Value: Specimen Accession Number Type: pattern: ^SAMN[0-9]+$ @@ -302,6 +340,7 @@ PropDefinitions: Desc: catalog number from vendor Term: - Code: Pending + Origin: caDSR Type: string cds_primary_bucket: Desc: The primary bucket for depositing data @@ -321,13 +360,15 @@ PropDefinitions: Req: true Term: - Code: Pending + Origin: caDSR Type: string channel_metadata_file_url_in_cds: Desc: '' Req: true Term: - Code: '11556141' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Electronic File Pathname Text Type: string channel_metadata_filename: @@ -335,7 +376,8 @@ PropDefinitions: Req: true Term: - Code: '7787678' - Origin: HTAN + Origin: caDSR + Original Source: HTAN Value: Channel Analysis Metadata Electronic File Name Text Type: string channel_name: @@ -343,18 +385,21 @@ PropDefinitions: Req: true Term: - Code: Pending + Origin: caDSR Type: string citation_or_DOI: Desc: Publication and/or digital object identifier of the publication for open access studies Req: true Term: - Code: '7787673' - Origin: CDS + Origin: caDSR + Original Source: CDS Type: string clinical_trial_arm: Desc: Arm of clinical trial, if appropriate Term: - Code: '11524548' + Origin: caDSR Value: Clinical Trial Treatment Arm Text Type: string clinical_trial_identifier: @@ -363,6 +408,7 @@ PropDefinitions: ' Term: - Code: '14673514' + Origin: caDSR Value: Clinical Trial Study Protocol Unique Identifier Type: string clinical_trial_system: @@ -376,6 +422,7 @@ PropDefinitions: Desc: Unique clone identifier Term: - Code: Pending + Origin: caDSR Type: string co_investigator_email: Desc: Email of co-principal investigator @@ -387,12 +434,14 @@ PropDefinitions: Desc: Final concentration used in experiment Term: - Code: Pending + Origin: caDSR Type: string coverage: Desc: Average depth of coverage on reference used Req: Preferred Term: - Code: '11556322' + Origin: caDSR Value: Genome Assembly Sequence Depth of Coverage Number Type: number crdc_id: @@ -403,12 +452,14 @@ PropDefinitions: Req: Preferred Term: - Code: '11636299' + Origin: caDSR Value: Genome Assembly Custom FASTA File Name Type: string cycle_number: Desc: 'the cycle # in which the co-listed reagent(s) was(were) used' Term: - Code: Pending + Origin: caDSR Type: string data_access_level: Desc: Is data open, controlled, or mixed? @@ -426,7 +477,8 @@ PropDefinitions: Desc: Days to last participant followup, relative to study index date Term: - Code: '12426616' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Subject Initial Cancer Diagnosis To Last Followup Day Count Type: integer days_to_last_known_status: @@ -436,14 +488,16 @@ PropDefinitions: Desc: Days to disease recurrence, relative to study index date Term: - Code: '12432576' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Subject First Treatment Date To Recurrence Day Count Type: integer days_to_treatment: Desc: Days to start of treatment, relative to index date Term: - Code: '12447194' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Subject Initial Cancer Diagnosis To Treatment Day Count Type: integer dbGaP_subject_id: @@ -451,7 +505,8 @@ PropDefinitions: Req: Preferred Term: - Code: '11524544' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Research Activity dbGaP Accession Number Identifier Type: string de_identification_method_description: @@ -467,7 +522,8 @@ PropDefinitions: Req: true Term: - Code: 14607284 - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Deidentification Method Type de_identification_software: Desc: Software that was used to de-identify the images (if used) @@ -476,7 +532,8 @@ PropDefinitions: Desc: Identier of the parent specimen of this sample Term: - Code: '5581201' - Origin: HTAN + Origin: caDSR + Original Source: HTAN Value: Parent Specimen Label Identifier Type: string design_description: @@ -484,6 +541,7 @@ PropDefinitions: Req: Preferred Term: - Code: '11529028' + Origin: caDSR Value: Sequencing Library Platform Model Name Type: string diagnosis_id: @@ -493,6 +551,7 @@ PropDefinitions: Desc: Final dilution ratio used in experiment Term: - Code: Pending + Origin: caDSR Type: string disease_type: Desc: Type of disease [?] @@ -538,7 +597,8 @@ PropDefinitions: - Wolffian Tumor Term: - Code: '13471160' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Diagnosis Disease or Disorder Morphology Disease embedding_medium: Desc: A material that infiltrates and supports a specimen and preserves its shape and structure for sectioning and microscopy. @@ -556,17 +616,20 @@ PropDefinitions: Req: true Term: - Code: '8037927' - Origin: HTAN + Origin: caDSR + Original Source: HTAN Value: Biospecimen Collection Medium Type emission_bandwidth: Desc: nominal width of emission spectrum (nm) Term: - Code: Pending + Origin: caDSR Type: string emission_wavelength: Desc: center/peak of the emission spectrum (nm) Term: - Code: Pending + Origin: caDSR Type: string ethnicity: Desc: OMB Ethinicity designator @@ -579,17 +642,20 @@ PropDefinitions: Req: Preferred Term: - Code: '2192217' - Origin: NCI Std + Origin: caDSR + Original Source: NCI Std Value: Ethnic Group Category Text excitation_bandwidth: Desc: nominal width of excitation spectrum (nm) Term: - Code: Pending + Origin: caDSR Type: string excitation_wavelength: Desc: center/peak of the excitation spectrum (nm) Term: - Code: Pending + Origin: caDSR Type: string experimental_strategy_and_data_subtypes: Desc: 'What is the experimental strategy used for the study (or what @@ -619,7 +685,8 @@ PropDefinitions: Desc: Human-readable description of file Term: - Code: '11280338' - Origin: DSS + Origin: caDSR + Original Source: DSS Value: Electronic Data File Description Text Type: string file_id: @@ -632,7 +699,8 @@ PropDefinitions: Req: true Term: - Code: '11284037' - Origin: DSS + Origin: caDSR + Original Source: DSS Value: Electronic Data File Name Type: string file_size: @@ -640,7 +708,8 @@ PropDefinitions: Req: false Term: - Code: '11479876' - Origin: DSS + Origin: caDSR + Original Source: DSS Value: Electronic Data File Size Integer Type: integer file_type: @@ -664,7 +733,8 @@ PropDefinitions: Req: true Term: - Code: '11416926' - Origin: DSS + Origin: caDSR + Original Source: DSS Value: Electronic Data File Format Type file_types: Desc: File types for storage @@ -684,19 +754,22 @@ PropDefinitions: Req: Preferred Term: - Code: '11556141' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Electronic File Pathname Text Type: string fluorophore: Desc: Fluorescent dye label Term: - Code: Pending + Origin: caDSR Type: string funding_agency: Desc: Funding agency of the requestor study Req: Preferred Term: - Code: '11524545' + Origin: caDSR Value: Funding Agency Organization Name Text Type: string funding_source_program_name: @@ -704,6 +777,7 @@ PropDefinitions: Req: Preferred Term: - Code: '11524546' + Origin: caDSR Value: Funding Agency Program Name Text Type: string gender: @@ -717,7 +791,8 @@ PropDefinitions: Req: true Term: - Code: '2200604' - Origin: NCI Std + Origin: caDSR + Original Source: NCI Std Value: Person Gender Text Type genomic_info_id: Desc: Genomic info identifier, the ID property for the ndoe genomic_info. @@ -729,6 +804,7 @@ PropDefinitions: Req: Preferred Term: - Code: '3434057' + Origin: caDSR Value: Grant Funding Identifier Number Type: string image_modality: @@ -788,14 +864,16 @@ PropDefinitions: Req: true Term: - Code: '12137353' - Origin: DSS + Origin: caDSR + Original Source: DSS Value: Imaging Technology DICOM Modality Type imaging_assay_type: Desc: Type of imaging assay Req: true Term: - Code: '7789196' - Origin: HTAN + Origin: caDSR + Original Source: HTAN Value: Imaging Assay Technology Type Type: string imaging_equipment_manufacturer: @@ -803,35 +881,40 @@ PropDefinitions: Req: true Term: - Code: '2866141' - Origin: NCI Standard + Origin: caDSR + Original Source: NCI Standard Value: Equipment Manufacturer Name Text Type: string imaging_equipment_model: Desc: The words used to describe the specific model of the instrument used to carry out an imaging experiment. Term: - Code: '2413274' - Origin: NCI Standard + Origin: caDSR + Original Source: NCI Standard Value: Equipment Manufacturer Model Name Text Type: string imaging_protocol: Desc: A rule which guides how an activity should be performed. Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the image was obtained or generated. Term: - Code: '7787673' - Origin: HTAN + Origin: caDSR + Original Source: HTAN Value: Raw Data Protocol Or Digital Object Identifier Text Type: string imaging_sofware: Desc: The name of the software package that was used to capture, generate, and process the image. Term: - Code: '2413278' - Origin: NCI Standard + Origin: caDSR + Original Source: NCI Standard Value: Equipment Software Version Text Type: string immersion: Desc: Immersion medium Term: - Code: '8058286' - Origin: HTAN + Origin: caDSR + Original Source: HTAN Value: Microscope Device Immersion Medium Type Type: string incidence_type: @@ -922,6 +1005,7 @@ PropDefinitions: Req: Preferred Term: - Code: '6352164' + Origin: caDSR Value: Sequencing Library Platform Model Name last_known_disease_status: Desc: Last known disease incidence for this subject and diagnosis @@ -938,19 +1022,22 @@ PropDefinitions: - Tumor free Term: - Code: '12447172' - Origin: DSS + Origin: caDSR + Original Source: DSS Value: Subject Last Known Disease Status lens_numerical_aperture: Desc: The numerical aperture of the lens. Floating point value > 0. Term: - Code: '7788942' - Origin: HTAN + Origin: caDSR + Original Source: HTAN Value: Microscope Device Lens Numerical Aperture Float Value Type: string library_id: Desc: Library identifier as submitted by requestor Term: - Code: '11555660' + Origin: caDSR Value: Sequencing Library Unique Identifier Text Type: string library_layout: @@ -962,6 +1049,7 @@ PropDefinitions: Req: Preferred Term: - Code: '11527735' + Origin: caDSR Value: Sequencing Library Read Layout Type library_selection: Desc: Library selection method @@ -1003,6 +1091,7 @@ PropDefinitions: Req: Preferred Term: - Code: '6347743' + Origin: caDSR Value: Sequencing Library Creation Method Type library_source: Desc: Source material used to create library @@ -1022,6 +1111,7 @@ PropDefinitions: Req: Preferred Term: - Code: '6285979' + Origin: caDSR Value: Sequencing Library Specimen Source library_strategy: Desc: Nucleic acid capture or processing strategy for this library @@ -1064,6 +1154,7 @@ PropDefinitions: Req: Preferred Term: - Code: '6273393' + Origin: caDSR Value: Sequencing Library Technique Type license: Desc: Official or legal permission to do or own a specified thing. @@ -1076,24 +1167,28 @@ PropDefinitions: Req: true Term: - Code: Pending + Origin: caDSR longitudinal_temporal_event_offset: Desc: An offset in days from a particular event of significance. May be fractional. In the context of a clinical trial, this is often the days since enrollment, or the baseline imaging Study. Term: - Code: '14612661' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Longitudinal Study Temporal Offset Number Type: number longitudinal_temporal_event_type: Desc: The type of event to which Longitudinal Temporal Offset from Event is relative. Term: - Code: '14670294' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Longitudinal Study Temporal Event Type Type: number lot: Desc: lot number from vendor Term: - Code: Pending + Origin: caDSR Type: string md5sum: Desc: MD5 hex digest for this file @@ -1104,6 +1199,7 @@ PropDefinitions: Desc: Element mass number Term: - Code: Pending + Origin: caDSR Type: string morphology: Desc: ICD-O-3 Morphology term associated with this diagnosis @@ -2262,13 +2358,15 @@ PropDefinitions: - Not Reported Term: - Code: '13594090' - Origin: CCDI (DDE) + Origin: caDSR + Original Source: CCDI (DDE) Value: Disease Morphology ICD-O-3 Code Label Text nominal_magnification: Desc: The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units) Term: - Code: '7788940' - Origin: HTAN + Origin: caDSR + Original Source: HTAN Value: Microscope Device Nominal Magnification Float Value Type: string number_of_participants: @@ -2276,7 +2374,8 @@ PropDefinitions: Req: 'Yes' Term: - Code: '11555662' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Research Activity Unique Subjects Count Type: number number_of_reads: @@ -2284,6 +2383,7 @@ PropDefinitions: Req: Preferred Term: - Code: '11529035' + Origin: caDSR Value: Sequencing Library Sequence Read Count Type: integer number_of_samples: @@ -2291,30 +2391,35 @@ PropDefinitions: Req: 'Yes' Term: - Code: '11555663' + Origin: caDSR Value: Research Activity Sample Size Count Type: number objective: Desc: "An\_objective\_is an optical element that gathers light from an object being observed and\_focuses\_the\_light rays\_from it to produce a\_real image\_of the object." Term: - Code: '7788935' + Origin: caDSR Value: Microscope Device Objective Lens Text Type: string oligo_barcode_lower_strand: Desc: DNA barcode used for labeling Term: - Code: Pending + Origin: caDSR Type: string oligo_barcode_upper_strand: Desc: DNA barcode used for labeling Term: - Code: Pending + Origin: caDSR Type: string organ_or_tissue: Desc: Site where images are associated Req: true Term: - Code: 6161035 - Origin: CDS + Origin: caDSR + Original Source: CDS Value: ICD-O Origin of Disease Anatomic Site Type: string organism_species: @@ -2330,20 +2435,23 @@ PropDefinitions: Req: true Term: - Code: '12220014' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Subject Data Origin Identifier Type: string passes_qc: Desc: Identify stains that did not pass QC but are included in the dataset. Term: - Code: Pending + Origin: caDSR Type: string performed_imaging_study_acquisitionTypeCode: Desc: A coded value specifying spatial aspects of the mechanism of data collection. Req: true Term: - Code: '14670301' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Image Study Spatial Acquisition Type Code Type: string performed_imaging_study_admittingDiagnosisCode: @@ -2351,7 +2459,8 @@ PropDefinitions: Req: true Term: - Code: '2902328' - Origin: DICOM + Origin: caDSR + Original Source: DICOM Value: Image Study Admitting Diagnosis Description 64 Character Text Type: string performed_imaging_study_algorithmCode: @@ -2359,6 +2468,7 @@ PropDefinitions: Req: true Term: - Code: '14617557' + Origin: caDSR Value: Imaging Reconstruction Protocol Algorithm Code Text Type: string performed_imaging_study_bodyPositionCode: @@ -2369,7 +2479,8 @@ PropDefinitions: - Standing Term: - Code: '14617523' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Image Study Body Position Name performed_imaging_study_cardiacSynchronizationTechniqueCode: Desc: The means used to coordinate the collection or reconstruction of data with the cardiac cycle. @@ -2381,14 +2492,16 @@ PropDefinitions: - NONE Term: - Code: '14617521' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Image Study Cardiac Synchronization Technique Code Name performed_imaging_study_dataCollectionDiameter: Desc: The diameter of the region over which information is acquired. Req: true Term: - Code: '14612665' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Image Acquisition Data Collection Location Diameter Number Type: string performed_imaging_study_description: @@ -2396,7 +2509,8 @@ PropDefinitions: Req: true Term: - Code: '2182389' - Origin: DICOM + Origin: caDSR + Original Source: DICOM Value: Image Study Description 64 Character Text Type: string performed_imaging_study_imageTypeCode: @@ -2407,7 +2521,8 @@ PropDefinitions: - RCBV Term: - Code: Pending - Origin: CDS + Origin: caDSR + Original Source: CDS performed_imaging_study_lossyImageCompressionIndicator: Desc: Specifies whether any images in the study are irreversibly altered during encoding at any time during its life. Req: true @@ -2417,7 +2532,8 @@ PropDefinitions: Req: true Term: - Code: '12137353' - Origin: DSS + Origin: caDSR + Original Source: DSS Value: Imaging Technology DICOM Modality Type Type: string performed_imaging_study_primaryAnatomicSiteCode: @@ -2425,7 +2541,8 @@ PropDefinitions: Req: true Term: - Code: '14612662' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Image Study Primary Anatomic Site Sequence of Items Text Type: string performed_imaging_study_reconstructionDiameter: @@ -2433,6 +2550,7 @@ PropDefinitions: Req: true Term: - Code: '2182085' + Origin: caDSR Value: Reconstruction Diameter in Millimeter(s) Type: string performed_imaging_study_reconstructionFieldOfViewHeight: @@ -2440,6 +2558,7 @@ PropDefinitions: Req: true Term: - Code: '14612672' + Origin: caDSR Value: Imaging Reconstruction Protocol Field of View Height Number Type: string performed_imaging_study_reconstructionFieldOfViewWidth: @@ -2447,6 +2566,7 @@ PropDefinitions: Req: true Term: - Code: '14612674' + Origin: caDSR Value: Imaging Reconstruction Protocol Field of View Width Number Type: string performed_imaging_study_reconstructionInterval: @@ -2454,6 +2574,7 @@ PropDefinitions: Req: true Term: - Code: '14612682' + Origin: caDSR Value: Imaging Reconstruction Protocol Reconstruction Interval Millimeter Number Type: string performed_imaging_study_respiratoryMotionTechniqueCode: @@ -2469,13 +2590,15 @@ PropDefinitions: Req: true Term: - Code: '14617522' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Image Study Respiratory Motion Technique Code Name performed_imaging_study_sliceThickness: Desc: The cross plane dimension of the reconstructed image. Req: true Term: - Code: '3113185' + Origin: caDSR Value: Image Plane Slice Thickness Float or Fixed-point Millimeter Number Type: string performed_imaging_study_summary: @@ -2483,7 +2606,8 @@ PropDefinitions: Req: true Term: - Code: '14670299' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Imaging Study Process Protocol Element Summary Text Type: string performed_imaging_study_typeCode: @@ -2491,6 +2615,7 @@ PropDefinitions: Req: true Term: - Code: Pending + Origin: caDSR Type: string phs_accession: Desc: PHS accession number (a.k.a dbGaP accession) @@ -2498,7 +2623,8 @@ PropDefinitions: Req: true Term: - Code: '11524544' - Origin: DSS CDE + Origin: caDSR + Original Source: DSS CDE Value: Research Activity dbGaP Accession Number Identifier Type: pattern: ^phs[0-9]+([.]v[0-9]+)*$ @@ -2506,21 +2632,24 @@ PropDefinitions: Desc: Physical size (X-dimension) of a pixel. Floating point value > 0. Size needs to be specified in microns (um) Term: - Code: '7786584' - Origin: HTAN + Origin: caDSR + Original Source: HTAN Value: Image Processing Pyramid Representation True False Indicator Type: string physical_size_y: Desc: Physical size (Y-dimension) of a pixel. Floating point value > 0. Size needs to be specified in microns (um) Term: - Code: '7786585' - Origin: HTAN + Origin: caDSR + Original Source: HTAN Value: Pixel Y-Dimension Float Value Type: string physical_size_z: Desc: Physical size (Z-dimension) of a pixel. Floating point value > 0. Size needs to be specified in microns (um) Term: - Code: '7786586' - Origin: HTAN + Origin: caDSR + Original Source: HTAN Value: Pixel Z-Dimension Float Value Type: string platform: @@ -2546,6 +2675,7 @@ PropDefinitions: Req: Preferred Term: - Code: '6347771' + Origin: caDSR Value: Sequencing Library Platform Name primary_diagnosis: Desc: Primary disease diagnosed for this diagnosis and subject @@ -3059,7 +3189,8 @@ PropDefinitions: Req: true Term: - Code: 13606067 - Origin: CDS + Origin: caDSR + Original Source: CDS Value: ICD Label/Name primary_investigator_email: Desc: Email of principal investigator @@ -3135,7 +3266,8 @@ PropDefinitions: - Vulva Term: - Code: '13279286' - Origin: PCDC + Origin: caDSR + Original Source: PCDC Value: Diagnosis Primary Anatomic Site ICD-O-3 Name program_acronym: Desc: The name of the program under which related studies will be grouped, expressed in the form of the acronym by which it will identified within the UI.
This property is used as the key via which study records can be associated with the appropriate program during data loading, and to identify the correct records during data updates. @@ -3159,7 +3291,8 @@ PropDefinitions: Src: Internally-curated Term: - Code: '11444542' - Origin: DSS + Origin: caDSR + Original Source: DSS Value: Program Name Text Type: string program_short_description: @@ -3182,13 +3315,15 @@ PropDefinitions: - Not Allowed To Collect Term: - Code: 13529783 - Origin: DSS + Origin: caDSR + Original Source: DSS Value: Disease Progression Or Recurrence Indicator pyramid: Desc: The data file contains an image pyramid Term: - Code: '7788945' - Origin: HTAN + Origin: caDSR + Original Source: HTAN Value: Image Processing Pyramid Representation True False Indicator Type: string race: @@ -3205,7 +3340,8 @@ PropDefinitions: Req: Preferred Term: - Code: '2192199' - Origin: NCI Std + Origin: caDSR + Original Source: NCI Std Value: Race Category Text reference_genome_assembly: Desc: Accession or name of genome reference or assembly used for alignment @@ -3216,16 +3352,19 @@ PropDefinitions: Req: Preferred Term: - Code: '11529031' + Origin: caDSR Value: Genome Assembly NCBI Genetic Reference Sequence Identifier rrid_identifier: Desc: Research Resource Identifier Term: - Code: Pending + Origin: caDSR Type: string sample_age_at_collection: Desc: Number of days to collection, relative to index date Term: - Code: '11253404' + Origin: caDSR Value: Days from Specimen Collection To Initial Pathologic Diagnosis Day Count Type: integer sample_anatomic_site: @@ -3573,6 +3712,7 @@ PropDefinitions: - Not Reported Term: - Code: '12083894' + Origin: caDSR Value: Specimen Original Anatomic Site Uberon Identifier sample_id: Desc: Sample identifier as submitted by requestor @@ -3580,6 +3720,7 @@ PropDefinitions: Req: 'Yes' Term: - Code: '6921892' + Origin: caDSR Value: Biospecimen Source Laboratory Identifier Type: string sample_tumor_status: @@ -3593,7 +3734,8 @@ PropDefinitions: Req: 'Yes' Term: - Code: '14688604' - Origin: DSS + Origin: caDSR + Original Source: DSS Value: Specimen Neoplasm Category sample_type: Desc: Tissue type of this sample @@ -3668,12 +3810,14 @@ PropDefinitions: Req: 'Yes' Term: - Code: '13255982' + Origin: caDSR Value: Specimen Material Type sequence_alignment_software: Desc: Name of software program used to align nucleotide sequence data Req: Preferred Term: - Code: '11529072' + Origin: caDSR Value: Nucleotide Sequence Alignment Software Name Text Type: string short_description: @@ -3690,6 +3834,7 @@ PropDefinitions: Desc: Number of channels. Integer >= 1 Term: - Code: '7794859' + Origin: caDSR Value: OME TIFF Channel Count Type: string size_of_data_being_uploaded: @@ -3705,24 +3850,28 @@ PropDefinitions: Desc: Number of time points. Integer >= 1 Term: - Code: '7794860' + Origin: caDSR Value: OME TIFF Timepoint Count Type: string size_x: Desc: 'Size of image: X dimension (in pixels). Integer >= 1' Term: - Code: '7788567' + Origin: caDSR Value: OME TIFF X-Dimension Pixel Measurement Type: string size_y: Desc: 'Size of image: Y dimension (in pixels). Integer >= 1' Term: - Code: '7788568' + Origin: caDSR Value: OME TIFF Y-Dimension Pixel Measurement Type: string size_z: Desc: 'Size of image: Z dimension (in pixels). Integer >= 1' Term: - Code: '7788569' + Origin: caDSR Value: OME TIFF Z-Dimension Pixel Measurement Type: string species: @@ -3730,7 +3879,8 @@ PropDefinitions: Req: true Term: - Code: '10543100' - Origin: DSS + Origin: caDSR + Original Source: DSS Value: NCBI Taxonomy ID Type: string specimen_id: @@ -3742,7 +3892,8 @@ PropDefinitions: Req: true Term: - Code: '7789196' - Origin: HTAN + Origin: caDSR + Original Source: HTAN Value: Imaging Assay Technology Type Type: string study_access: @@ -3755,7 +3906,8 @@ PropDefinitions: Desc: Short acronym or other study desginator Term: - Code: '11459812' - Origin: DSS + Origin: caDSR + Original Source: DSS Value: Study Short Name Text Type: string study_data_types: @@ -3767,6 +3919,7 @@ PropDefinitions: Req: 'Yes' Term: - Code: '12571096' + Origin: caDSR Value: Data Collection Scientific Data Type Category study_description: Desc: Human-readable study description @@ -3791,13 +3944,15 @@ PropDefinitions: Req: true Term: - Code: New CDE + Origin: caDSR Type: string study_name: Desc: Official name of study Req: 'Yes' Term: - Code: '11459810' - Origin: DSS + Origin: caDSR + Original Source: DSS Value: Study Name Type: string study_participant_id: @@ -3819,6 +3974,7 @@ PropDefinitions: Desc: 'sub-cycle #' Term: - Code: Pending + Origin: caDSR Type: string submission_version: Desc: Raw data file submission @@ -3828,6 +3984,7 @@ PropDefinitions: Desc: short descriptive name (abbreviation) for this target (antigen) Term: - Code: Pending + Origin: caDSR Type: string therapeutic_agents: Desc: Text identification of the individual agent(s) used as part of a treatment regimen. @@ -8309,7 +8466,8 @@ PropDefinitions: - Not Reported Term: - Code: '13579886' - Origin: CDS + Origin: caDSR + Original Source: CDS Value: Therapeutic Procedure Agent Name tissue_fixative: Desc: A compound that preserves tissues and cells for microscopic study. @@ -8339,7 +8497,8 @@ PropDefinitions: Req: true Term: - Code: '65078' - Origin: NCI Standard + Origin: caDSR + Original Source: NCI Standard Value: Specimen Fixative Type treatment_id: Desc: Internal identifier @@ -8363,7 +8522,8 @@ PropDefinitions: - Very Good Partial Response Term: - Code: '5102383' - Origin: TCGA + Origin: caDSR + Original Source: TCGA Value: Treatment Outcome Type treatment_type: Desc: Text term that describes the kind of treatment administered @@ -8435,7 +8595,8 @@ PropDefinitions: - Not Reported Term: - Code: '14737565' - Origin: TCGA + Origin: caDSR + Original Source: TCGA Value: Therapeutic Procedure Performed Type tumor_grade: Desc: Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness. @@ -8453,7 +8614,8 @@ PropDefinitions: - Not Reported Term: - Code: '11325685' - Origin: DSS + Origin: caDSR + Original Source: DSS Value: Diagnosis Tumor Grade tumor_stage_clinical_m: Desc: Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment. @@ -8469,7 +8631,8 @@ PropDefinitions: - Not Reported Term: - Code: '3440331' - Origin: TCGA + Origin: caDSR + Original Source: TCGA Value: Neoplasm American Joint Committee on Cancer Clinical Distant Metastasis M Stage tumor_stage_clinical_n: Desc: Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment. @@ -8502,7 +8665,8 @@ PropDefinitions: - Not Reported Term: - Code: '3440330' - Origin: TCGA + Origin: caDSR + Original Source: TCGA Value: Neoplasm American Joint Committee on Cancer Clinical Regional Lymph Node N Stage tumor_stage_clinical_t: Desc: Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment. @@ -8545,19 +8709,22 @@ PropDefinitions: - Not Reported Term: - Code: '3440328' - Origin: TCGA + Origin: caDSR + Original Source: TCGA Value: Neoplasm American Joint Committee on Cancer Clinical Primary Tumor T Stage tumor_tissue_type: Desc: Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints) Term: - Code: '3288124' - Origin: HTAN + Origin: caDSR + Original Source: HTAN Value: Tumor Tissue Disease Description Type Type: string vendor: Desc: Vendor name Term: - Code: Pending + Origin: caDSR Type: string vital_status: Desc: Vital status as of last known follow up @@ -8568,12 +8735,14 @@ PropDefinitions: - Not Reported Term: - Code: '2847330' - Origin: NCI Std + Origin: caDSR + Original Source: NCI Std Value: Participant Vital Status Type working_distance: Desc: The working distance of the lens, expressed as a floating point number. Floating point > 0. Size needs to be specified in microns (um) Term: - Code: '7788943' - Origin: HTAN + Origin: caDSR + Original Source: HTAN Value: Microscope Device Working Distance Float Value Type: string