diff --git a/.github/workflows/schematic-schema-convert.yml b/.github/workflows/schematic-schema-convert.yml index 66c14ba..bf4e4e0 100644 --- a/.github/workflows/schematic-schema-convert.yml +++ b/.github/workflows/schematic-schema-convert.yml @@ -10,8 +10,6 @@ on: workflow_dispatch: -env: - schema_filename: GF.csv jobs: build: @@ -30,17 +28,18 @@ jobs: persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token. fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository - - name: Install schematic and convert schema + - name: Convert schema shell: bash run: | - pip3 install schematicpy + bash < <(curl -s https://raw.githubusercontent.com/babashka/babashka/master/install) + git clone --depth 1 https://github.com/anngvu/retold.git make - name: Commit files run: | git config user.email "github-actions@github.com" git config user.name "github-actions" - git commit -m "Build csv, jsonld" -a + git commit -m "Build jsonld" -a - name: Push changes uses: ad-m/github-push-action@master @@ -59,7 +58,7 @@ jobs: pull-requests: write strategy: matrix: - schematic-version: [23.6.1] + schematic-version: [23.9.1] steps: - uses: actions/checkout@v3 diff --git a/GF.csv b/GF.csv deleted file mode 100644 index e243ae1..0000000 --- a/GF.csv +++ /dev/null @@ -1,411 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Protocol Link,"URL to a free/open protocol resource describing 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 sample was obtained or generated.",,,,TRUE,Information Content Entity,,, -File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","HEIC, hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn",,,TRUE,,,, -Checksum,MD5 checksum of the BAM file,,,,TRUE,Information Content Entity,,, -Imaging Level 2,Raw and pre-processed image data,"","Component, Filename, File Format, Lab ID, Channel Metadata Filename, Imaging Assay Type, Protocol Link, Software and Version, Microscope, Objective, NominalMagnification, LensNA, WorkingDistance, WorkingDistanceUnit, Immersion, Pyramid, Zstack, Tseries, Passed QC, Comment, FOV number, FOVX, FOVXUnit, FOVY, FOVYUnit, Frame Averaging, Image ID, DimensionOrder, PhysicalSizeX, PhysicalSizeXUnit, PhysicalSizeY, PhysicalSizeYUnit, PhysicalSizeZ, PhysicalSizeZUnit, Pixels BigEndian, PlaneCount, SizeC, SizeT, SizeX, SizeY, SizeZ, PixelType","",FALSE,Assay,"Biospecimen, Imaging Level 2 Channels","","" -Imaging Level 2 Channels,Channel-level Metadata Attributes,"","Channel ID, Channel Name, Channel Passed QC, Cycle Number, Sub Cycle Number, Target Name, Antibody Name, RRID identifier, Fluorophore, Clone, Lot, Vendor, Catalog Number, Excitation Wavelength, Emission Wavelength, Excitation Bandwidth, Emission Bandwidth, Metal Isotope Element, Metal Isotope Mass, Oligo Barcode Upper Strand, Oligo Barcode Lower Strand, Dilution, Concentration","",FALSE,Imaging Level 2,"","","" -Imaging Assay Type,Type of imaging assay,"H&E, CyCIF, t-CyCIF, IHC, mIHC, MxIF, SABER, IMC, CODEX, GeoMX-DSP, MIBI, MERFISH, ExSeq, Not Applicable","","",TRUE,Imaging Level 2,"","","" -Channel Metadata Filename,Full path of uploaded companion CSV file containing channel-level metadata details,"","","",TRUE,Imaging Level 2,"","","" -Image Acquisition Date,Date of image acquisition,"","","",FALSE,Imaging Level 2,"","","" -Microscope,"Microscope type (manufacturer, model, etc) used for this experiment","","","",TRUE,Imaging Level 2,"",http://purl.obolibrary.org/obo/OBI_0400169,"" -Objective,Objective,"","","",FALSE,Imaging Level 2,"","","" -NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),"","","",TRUE,Imaging Level 2,"","","" -LensNA,The numerical aperture of the lens. Floating point value > 0.,"","","",FALSE,Imaging Level 2,"","","" -WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.","",WorkingDistanceUnit,"",FALSE,Imaging Level 2,"","","" -WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å","","",FALSE,Imaging Level 2,"","","" -Immersion,Immersion medium,"Air, Oil, Water, Other","","",FALSE,Imaging Level 2,"","","" -Pyramid,Does data file contain pyramid of images,"Yes, No","","",TRUE,Imaging Level 2,"","","" -Zstack,Does data file contain a Z-stack of images,"Yes, No","","",TRUE,Imaging Level 2,"","","" -Tseries,Does data file contain a time-series of images,"Yes, No","","",TRUE,Imaging Level 2,"","","" -Passed QC,Did all channels pass QC (if not add free text Comment),"Yes, No - Channels QC","","",TRUE,Imaging Level 2,"","","" -No - Channels QC,Not all channels passed QC,"",Comment,"",FALSE,Imaging Level 2,"","","" -Comment,Free text field (generally for QC comment),"","","",FALSE,Imaging Level 2,"","","" -FOV number,Index of FOV (as it pertains to its sequence order). Integer >= 1,"","","",FALSE,Imaging Level 2,"","","" -FOVX,Field of view X dimension. Floating point,"",FOVXUnit,"",FALSE,Imaging Level 2,"","","" -FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å","","",FALSE,Imaging Level 2,"","","" -FOVY,Field of view Y dimension. Floating point value,"",FOVYUnit,"",FALSE,Imaging Level 2,"","","" -FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å","","",FALSE,Imaging Level 2,"","","" -Frame Averaging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1","","","",FALSE,Imaging Level 2,"","","" -Image ID,"Unique internal image identifier. eg """"Image:0"""". (To be extracted from OME-XML)","","","",TRUE,Imaging Level 2,"","","" -DimensionOrder,The order in which the individual planes of data are interleaved.,"XYZCT, XYZTC, XYCTZ, XYCZT, XYTZC, ZYX","","",TRUE,Imaging Level 2,"","","" -PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,"",PhysicalSizeXUnit,"",TRUE,Imaging Level 2,"","","" -PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å","","",TRUE,Imaging Level 2,"","","" -PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,"",PhysicalSizeYUnit,"",TRUE,Imaging Level 2,"","","" -PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å","","",TRUE,Imaging Level 2,"","","" -PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,"",PhysicalSizeZUnit,"",TRUE,Imaging Level 2,"","","" -PhysicalSizeZUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å","","",TRUE,Imaging Level 2,"","","" -Pixels BigEndian,Boolean (True/False),"True, False","","",TRUE,Imaging Level 2,"","","" -PlaneCount,"Number of Z-planes (not to be confused with downsampled """"pyramid""""). Integer >=1","","","",TRUE,Imaging Level 2,"","","" -SizeC,Number of channels. Integer >= 1,"","","",TRUE,Imaging Level 2,"","","" -SizeT,Number of time points. Integer >= 1,"","","",TRUE,Imaging Level 2,"","","" -SizeX,Size of image: X dimension (in pixels). Integer >= 1,"","","",TRUE,Imaging Level 2,"","","" -SizeY,Size of image: Y dimension (in pixels). Integer >= 1,"","","",TRUE,Imaging Level 2,"","","" -SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,"","","",TRUE,Imaging Level 2,"","","" -PixelType,"Data type for each pixel value. E.g. """"uint16""""","int8, int16, int32, uint8, uint16, uint32, float, double, bit","","",TRUE,Imaging Level 2,"","","" -Sequencing,Module for next generation sequencing assays,"","","",FALSE,Assay,"",http://example.org/htan/Sequencing,"" -Sequencing Platform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,"Illumina Next Seq 500, Illumina Next Seq 550, Illumina Next Seq 2500, Illumina NovaSeq 6000, Illumina MiSeq, 454 GS FLX Titanium, AB SOLiD 4 AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, NovaSeq 6000, NovaSeqS4, Ultima Genomics UG100, Oxford Nanopore minION, GridION, PromethION, PacBio Sequel2, Revio, Other, unknown, Not Reported",,,TRUE,Device,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Library Construction Method,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],"Smart-seq2, Smart-SeqV4, 10xV1.0, 10xV1.1, 10xV2, 10xV3,10xV3.1, CEL-seq2, Drop-seq, inDropsV2, inDropsV3, TruDrop, sci-ATAC-seq",,,TRUE,Sequencing,,http://purl.obolibrary.org/obo/OBI_0000711, -Nucleic Acid Source,The source of the input nucleic molecule,"Single Cell, Bulk Whole Cell, Single Nucleus, Bulk Nuclei",,,TRUE,Sequencing,,http://example.org/htan/NucleicAcidSource, -Read1,Read 1 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert, DNA Insert, Sample Index, Cell Barcode","","",TRUE,Sequencing,"","","" -Read2,Read 2 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert, DNA Insert, Sample Index, Cell Barcode","","",TRUE,Sequencing,"","","" -Technical Replicate Group,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),,,,FALSE,Sequencing,,, -Sequencing Batch ID,Links samples to a specific local sequencer run. Can be string or 'null',,,,TRUE,Sequencing,,, -Total Reads,Total number of reads per sample. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, -Dissociation Method,The tissue dissociation method used for scRNASeq or scATAC-seq assays,"gentleMACS, Dounce, Enzymatic Digestion, Not Applicable",,,TRUE,Single_Cell_Sequencing,,, -Cryopreserved Cells in Sample,Indicate if library preparation was based on revived frozen cells.,"Yes, No",,,TRUE,Single_Cell_Sequencing,,, -Single Cell Isolation Method,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)","Microfluidics Chip, Droplets, FACS, Plates, 10x, Nuclei Isolation",,,TRUE,Single_Cell_Sequencing,,, -Total Number of Input Cells,Number of cells loaded/placed on plates,,,,TRUE,Single_Cell_Sequencing,,, -Input Cells and Nuclei,"Number of cells and number of nuclei input; entry format: number, number",,,,TRUE,Single_Cell_Sequencing,,, -scATAC-seq Level 1,"scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files",,"Component, Filename, File Format, Participant ID, Sample ID, Detailed Sample ID,Nucleic Acid Source, Dissociation Method, Single Nucleus Buffer, Single Cell Isolation Method, Transposition Reaction, scATACseq Library Layout, Nucleus Identifier, Nuclei Barcode Length, Nuclei Barcode Read, scATACseq Read1, scATACseq Read2, scATACseq Read3, Library Construction Method, Sequencing Platform, Threshold for Minimum Passing Reads, Total Number of Passing Nuclei, Median Fraction of Reads in Peaks, Median Fraction of Reads in Annotated cis DNA Elements, Median Passing Read Percentage, Median Percentage of Mitochondrial Reads per Nucleus,Technical Replicate Group, Total Reads, Protocol Link",,FALSE,Single_Cell_Sequencing,,, -Transposition Reaction,"Name of the transposase, transposon sequences","Tn5, EZ-Tn5, Tn5-059, Nextera Tn5, Diagenode-unloaded Apex-Bio, Diagenode-loaded Apex-Bio, In-House",,,TRUE,scATAC-seq Level 1,,, -Single Nucleus Buffer,Nuclei isolation buffer,"NIB, 10x, Omni",,,TRUE,scATAC-seq Level 1,,, -scATACseq Library Layout,Sequencing read type,scATACseq Paired End,,,TRUE,scATAC-seq Level 1,,, -Nucleus Identifier,Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from,Nuclei Barcode,,,TRUE,scATAC-seq Level 1,,, -Nuclei Barcode Read,Nuclei Barcode Read,,,,TRUE,scATAC-seq Level 1,,, -Nuclei Barcode Length,Nuclei Barcode Length,,,,TRUE,scATAC-seq Level 1,,, -scATACseq Paired End,A library layout type,"scATACseq Read1, scATACseq Read2",,,FALSE,scATAC-seq Level 1,,, -scATACseq Read1,Read 1 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert, DNA Insert, Sample Index, Cell Barcode",,,TRUE,scATAC-seq Level 1,,, -scATACseq Read2,Read 2 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert, DNA Insert, Sample Index, Cell Barcode",,,TRUE,scATAC-seq Level 1,,, -scATACseq Read3,Read 3 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert, DNA Insert, Sample Index, Cell Barcode",,,FALSE,scATAC-seq Level 1,,, -Threshold for Minimum Passing Reads,Threshold for calling cells,,,,TRUE,scATAC-seq Level 1,,, -Total Number of Passing Nuclei,Number of nuclei sequenced,,,,TRUE,scATAC-seq Level 1,,, -Median Fraction of Reads in Peaks,Median fraction of reads in peaks (FRIP),,Peaks Calling Software,,TRUE,scATAC-seq Level 1,,, -Median Fraction of Reads in Annotated cis DNA Elements,Median fraction of reads in annotated cis-DNA elements (FRIADE),,Peaks Calling Software,,TRUE,scATAC-seq Level 1,,, -Median Passing Read Percentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,,,,TRUE,scATAC-seq Level 1,,, -Median Percentage of Mitochondrial Reads per Nucleus,Contamination from mitochondrial sequences,,,,TRUE,scATAC-seq Level 1,,, -scRNA-seq Level 1,Single-cell RNA-seq [EFO_0008913],,"Component, Filename, File Format, Participant ID, Sample ID, Detailed Sample ID, Cryopreserved Cells in Sample, Single Cell Isolation Method, Dissociation Method, Library Construction Method, Read Indicator, Read1, Read2, End Bias, Reverse Transcription Primer, Spike In, Sequencing Platform, Total Number of Input Cells, Input Cells and Nuclei,Protocol Link, Technical Replicate Group",,FALSE,Single_Cell_Sequencing,Biospecimen,http://www.ebi.ac.uk/efo/EFO_0008913, -Cell Barcode and UMI,Cell and transcript identifiers,"","UMI Barcode Offset, UMI Barcode Length, Median UMIs per Cell Number, Cell Barcode Offset, Cell Barcode Length, Valid Barcodes Cell Number","",FALSE,scRNA-seq Level 1,"","","" -Cell Barcode Offset,Offset in sequence for cell barcode read (in bp): number,"","","",TRUE,scRNA-seq Level 1,"","","" -Cell Barcode Length,Length of cell barcode read (in bp): number,"","","",TRUE,scRNA-seq Level 1,"","","" -Valid Barcodes Cell Number,Number,"","","",TRUE,scRNA-seq Level 1,"","","" -UMI Barcode Offset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read","","","",TRUE,scRNA-seq Level 1,"",https://www.ebi.ac.uk/arrayexpress/help/single-cell_submission_guide.html,"" -UMI Barcode Length,Length of UMI barcode read (in bp): number,"","","",TRUE,scRNA-seq Level 1,"","","" -Median UMIs per Cell Number,Number,"","","",TRUE,scRNA-seq Level 1,"","","" -Input Cells and Nuclei,"Number of cells and number of nuclei input; entry format: number, number","","","",TRUE,scRNA-seq Level 1,"","","" -CEL-seq2,Highly-multiplexed plate-based single-cell RNA-Seq assay,"","Empty Well Barcode, Well Index","",FALSE,scRNA-seq Level 1,"","","" -Empty Well Barcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,"","","",TRUE,scRNA-seq Level 1,"","","" -Well Index,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,"Yes, No","","",FALSE,scRNA-seq Level 1,"","","" -Single Cell Dissociation Days from Index,Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number],"","","",TRUE,scRNA-seq Level 1,"","","" -End Bias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript","3 Prime, 5 Prime, Full Length Transcript","","",TRUE,scRNA-seq Level 1,"","","" -Reverse Transcription Primer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA","Oligo-dT, Poly-dT, Feature barcoding, Random","","",TRUE,scRNA-seq Level 1,"",http://www.sequenceontology.org/so_wiki/index.php/Category:SO:0000112_!_primer,"" -Feature barcoding,A method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc],"",Feature Reference Id,"",FALSE,scRNA-seq Level 1,"",https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc,"" -Feature Reference Id,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]","","","",TRUE,scRNA-seq Level 1,"","","" -Spike In,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,"ERCC, Other Spike In, No Spike In, PhiX","","",TRUE,scRNA-seq Level 1,"","","" -scRNA-seq Level 2,Alignment workflows downstream of scRNA-seq Level 1,,"Component, Filename, File Format, Participant ID, Sample ID, Detailed Sample ID, scRNAseq Workflow Type, Workflow Version, scRNAseq Workflow Parameters Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Whitelist Cell Barcode File Link, Cell Barcode Tag, UMI Tag, Applied Hard Trimming",,FALSE,Single_Cell_Sequencing,scRNA-seq Level 1,, -scRNA-seq Level 3,Gene and Isoform expression files,,"Component, Filename, File Format, Participant ID, Sample ID, Detailed Sample ID, Data Category, Matrix Type, Linked Matrices, Cell Median Number Reads, Cell Median Number Genes, Cell Total, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Link, Workflow Version",,FALSE,Single_Cell_Sequencing,,, -Cell Median Number Reads,Median number of reads per cell. Number,"","","",TRUE,scRNA-seq Level 3,"","","" -Cell Median Number Genes,Median number of genes detected per cell. Number,"","","",TRUE,scRNA-seq Level 3,"","","" -Cell Total,Number of sequenced cells. Applies to raw counts matrix only.,"","","",TRUE,scRNA-seq Level 3,"","","" -scRNA-seq Level 4,"Gene and Isoform expression files",,"Component, Filename, File Format, Participant ID, Sample ID, Detailed Sample ID,Data Category, Matrix Type, Linked Matrices, Cell Median Number Reads, Cell Median Number Genes, Cell Total, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Link, Workflow Version",,FALSE,Single_Cell_Sequencing,,, -Biospecimen,"Biological entity; this can be tissue, blood, analyte and subsamples of those","","Biospecimen ID, Parent ID, Parent Biospecimen ID, Adjacent Biospecimen IDs,Biospecimen Type,Timepoint Label,Specimen Laterality","",FALSE,Patient,"","","" -Sample ID, ID associated with a biosample,"","","",TRUE,Biospecimen,"",,"" -Biospecimen ID, Alias for Sample ID,"","","",TRUE,Biospecimen,"",,"" -Detailed Sample ID, Additional alternative ID associated with a biosample,"","","",TRUE,Biospecimen,"",,"" -Parent ID, ID of parent biospecimen,"","","",TRUE,Biospecimen,"",https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,"" -Parent Biospecimen ID, Biospecimen identifier indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,"","","",TRUE,Biospecimen,"",https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,"" -Biospecimen Type,Biospecimen Type,"Tissue Biospecimen Type, Blood Biospecimen Type, Analyte Biospecimen Type, Mouth Rinse Biospecimen Type, Stool Biospecimen Type, Urine Biospecimen Type, Ascites Biospecimen Type, Sputum Biospecimen Type, Fluids Biospecimen Type, Bone Marrow Biospecimen Type, Cells Biospecimen Type","","",TRUE,Biospecimen,"","","" -Analyte Biospecimen Type,A molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,"","Analyte Type, Fixation Duration, Slide Charge Type, Section Thickness Value, Sectioning Days from Index, Shipping Condition Type, Ischemic Time, Ischemic Temperature","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2513915&version=2.0,"" -Tissue Biospecimen Type,Tissue biospecimen,"","Ischemic Time, Ischemic Temperature, Site of Resection or Biopsy, Specimen Laterality, Portion Weight, Total Volume, Tumor Tissue Type, Histologic Morphology Code, Preservation Method, Biospecimen Dimension 1, Biospecimen Dimension 2, Biospecimen Dimension 3, Section Number in Sequence","",FALSE,Biospecimen,"","","" -Bone Marrow Biospecimen Type,Bone Marrow biospecimen,"","Ischemic Time, Ischemic Temperature, Site of Resection or Biopsy, Specimen Laterality, Portion Weight, Total Volume, Tumor Tissue Type, Histologic Morphology Code, Preservation Method, Biospecimen Dimension 1, Biospecimen Dimension 2, Biospecimen Dimension 3, Section Number in Sequence","",FALSE,Biospecimen,"","","" -Urine Biospecimen Type,Urine biospecimen,"","Ischemic Time, Ischemic Temperature, Site of Resection or Biopsy, Specimen Laterality, Portion Weight, Total Volume, Tumor Tissue Type, Histologic Morphology Code, Preservation Method","",FALSE,Biospecimen,"","","" -Blood Biospecimen Type,Blood biospecimen,"",Shipping Condition Type,"",FALSE,Biospecimen,"","","" -Timepoint Label,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.","","","",TRUE,Biospecimen,"","","" -Collection Days from Index,Number of days from the research participant's index date that the biospecimen was obtained.,"","","",TRUE,Biospecimen,"","","" -Adjacent Sample IDs,"List of Identifiers (separated by commas) of adjacent biospecimens cut from the same sample","","","",FALSE,Biospecimen,"","","" -Mounting Medium,"The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media","Aqueous water based, Non-Aqueous Solvent based, Xylene,Toluene,Antifade with DAPI,Antifade without DAPI,PBS,unknown,Not Reported","","",FALSE,Biospecimen,"","","" -Analyte Type,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,"cfDNA Analyte, DNA Analyte, RNA Analyte, Total RNA Analyte, Tissue Block Analyte, Tissue Section Analyte, PBMCs or Plasma or Serum Analyte, cDNA Libraries Analyte, PBMCs, Plasma, Serum Analyte","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2513915&version=2.0,"" -Acquisition Method Type,Records the method of acquisition or source for the specimen under consideration.,"Autopsy, Biopsy, Fine Needle Aspirate, Surgical Resection, Punch Biopsy, Shave Biopsy, Excision, Re-excision, Sentinel Node Biopsy, Lymphadenectomy - Regional Nodes, Other Acquisition Method, Non induced sputum, Induced sputum, BAL (bronchial alveolar lavage), Cytobrush, Blood draw, Fluid collection, Forceps biopsy, Core needle biopsy, Endoscopic biopsy, Not specified","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6626651&version=1.0,"" -Other Acquisition Method,A custom acquisition method,"",Acquisition Method Other Specify,"",FALSE,Biospecimen,"","","" -Acquisition Method Other Specify,A custom acquisition method [Text - max length 100 characters],"","","",TRUE,Biospecimen,"","","" -Preservation Method,Text term that represents the method used to preserve the sample.,"Archival,Cryopreserved, Cryopreservation in liquid nitrogen - dead tissue, Cryopreservation in dry ice - dead tissue, Cryopreservation in liquid nitrogen - live cells, Formalin fixed paraffin embedded - FFPE, Formalin fixed-unbuffered, Formalin fixed-buffered, Fresh, Fresh dissociated and single cell sorted into plates in NP40 buffer, OCT, Snap Frozen, Frozen, Negative 80 Deg C, Liquid Nitrogen, Fresh dissociated, Fresh dissociated and single cell sorted, Fresh dissociated and single cell sorted into plates, Methacarn fixed paraffin embedded - MFPE, unknown, Not Reported","","",TRUE,Biospecimen,"","","" -Fixative Type,Text term to identify the type of fixative used to preserve a tissue specimen,"Acetone, Alcohol, Formalin, Glutaraldehyde, OCT media, RNAlater, Saline, 95% Ethanol, Dimidoester, Carbodiimide, Dimethylacetamide, Para-benzoquinone, PAXgene tissue, TCL lysis buffer, NP40 lysis buffer, Methacarn, Cryo-store, Carnoy's Fixative, Polaxamer, Other, None, unknown","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=65078&version=3.0,"" -Fixation Duration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)","","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5230144&version=1.0,"" -Ischemic Time,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.","","","",FALSE,Biospecimen,"",https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-state_of_specimen-gross_description,"" -Ischemic Temperature,Specify whether specimen experienced warm or cold ischemia.,"Warm Ischemia, Cold Ischemia, Ambient air, 4C wet ice, Negative -20C, Dry Ice, Liquid Nitrogen, unknown","","",FALSE,Biospecimen,"",https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-state_of_specimen-gross_description,"" -Collection Media,Material Specimen is collected into post procedure,"DMEM, DMEM+Serum, RPMI, RPMI+Serum, PBS, PBS+Serum, None","","",FALSE,Biospecimen,"","","" -Specimen Laterality,"For samples in paired organs, designates the side from which obtained.","Bilateral, Left, Right, unknown, Not Reported, Not Applicable","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2007875&version=1.0,"" -Portion Weight,"Numeric value that represents the sample portion weight, measured in milligrams.","","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5432593&version=1.0,"" -Total Volume,Numeric value for the total amount of sample or specimen,"",Total Volume Unit,"",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3005019&version=1.0,"" -Total Volume Unit,Unit of measurement used for the total amount of sample or specimen,"mL, mm^3, cm^2","","",FALSE,Biospecimen,"","","" -Tumor Tissue Type,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),"Additional Primary, Local recurrence, Metastatic, Premalignant, Primary, Recurrent, Normal, Normal adjacent, Normal distant, Post therapy, Post therapy neoadjuvant, Post therapy adjuvant, Not Otherwise Specified, Premalignant - in situ, Atypia - hyperplasia","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3288124&version=1.0,"" -Histologic Morphology Code,"Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510","","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3226275&version=1.0,"" -Preinvasive Morphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the ","Melanocytic hyperplasia, Atypical melanocytic proliferation, Melanoma in situ - superficial spreading, Melanoma in situ - lentigo maligna type, Melanoma in situ - acral-lentiginous, Melanoma in situ - arising in a giant congenital nevus, Persistent melanoma in situ, Melanoma in situ - not otherwise classified, Scar - no residual melanoma, Invasive melanoma - superficial spreading, Invasive melanoma - nodular type, Invasive melanoma - lentigo maligna, Invasive melanoma - acral lentiginous, Invasive melanoma - desmoplastic, Invasive melanoma - nevoid, Invasive melanoma - other, Normal WDA, Reserve cell hyperplasia, Squamous metaplasia - mature, Squamous metaplasia - immature, Mild dysplasia, Moderate dysplasia, Severe dysplasia, Squamous Carcinoma in situ, Atypical adenomatous hyperplasia, Adenocarcinoma in situ - non mucinous, Adenocarcinoma in situ - mucinous, Benign tumor NOS, Hamartoma, Carcinoma NOS, No diagnosis possible","","",FALSE,Biospecimen,"","","" -Slide Charge Type,A description of the charge on the glass slide.,"Uncharged, Charged, Coverslip, Not applicable, Other","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5227611&version=1.0,"" -Section Thickness Value,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).","","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3024951&version=1.0,"" -Sectioning Days from Index,Number of days from the research participant's index date that the biospecimen was sectioned after collection,"","","",TRUE,Biospecimen,"","","" -Storage Method,The method by which a biomaterial was stored after preservation or before another protocol was used.,"Ambient temperature, Cut slide, Fresh, Frozen at -70C, Frozen at -80C, Frozen at -150C, Frozen in liquid nitrogen, Frozen in vapor phase, Paraffin block, RNAlater at 4C, RNAlater at 25C, RNAlater at -20C, Refrigerated at 4 degrees, Refrigerated vacuum chamber, 4C in vacuum chamber, Desiccant at 4C, Not Applicable, unknown","","",TRUE,Biospecimen,"",https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-preservation_storage-storage_method,"" -Processing Days from Index,Number of days from the research participant's index date that the biospecimen was processed,"","","",TRUE,Biospecimen,"","","" -Shipping Condition Type,Text descriptor of the shipping environment of a biospecimen.,"Ambient Pack, Cold Pack, Dry Ice, Ice Pack, Liquid Nitrogen, Specimen at Room Temperature, Other Shipping Environment, Not Shipped","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5495533&version=1.0,"" -Site Data Source,"Text to identify the data source for the specimen/sample from within the center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.","","","",FALSE,Biospecimen,"","","" -Processing Location,"Site with an center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.","","","",FALSE,Biospecimen,"","","" -Histology Assessment By,Text term describing who (in what role) made the histological assessments of the sample,"Pathologist, Research Scientist, Other, unknown","","",FALSE,Biospecimen,"","","" -Histology Assessment Medium,The method of assessment used to characterize histology,"Digital, Microscopy, Other, unknown","","",FALSE,Biospecimen,"","","" -Tumor Infiltrating Lymphocytes,Measure of Tumor-Infiltrating Lymphocytes [Number],"","","",FALSE,Biospecimen,"","","" -Degree of Dysplasia,Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.,"Normal or basal cell hyperplasia or metaplasia, Mild dysplasia, Moderate dysplasia, Severe dysplasia, Carcinoma in Situ, unknown","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5543188&version=1.0,"" -Dysplasia Fraction,Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5],"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2390593&version=1.0,"" -Number Proliferating Cells,Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5432636&version=1.0,"" -Percent Eosinophil Infiltration,Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897700&version=2.0,"" -Percent Granulocyte Infiltration,Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897705&version=2.0,"" -Percent Inflam Infiltration,"Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.","","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897695&version=1.0,"" -Percent Lymphocyte Infiltration,Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897710&version=2.0,"" -Percent Monocyte Infiltration,Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5455535&version=1.0,"" -Percent Necrosis,Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841237&version=1.0,"" -Percent Neutrophil Infiltration,Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841233&version=1.0,"" -Percent Normal Cells,Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841233&version=1.0,"" -Percent Stromal Cells,"Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.","","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841241&version=1.0,"" -Percent Tumor Cells,Numeric value that represents the percentage of infiltration by tumor cells in a sample.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5432686&version=1.0,"" -Percent Tumor Nuclei,Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841225&version=1.0,"" -Fiducial Marker,Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.,"Nuclear Stain - DAPI, Fluorescent Beads, Grid Slides - Hemocytometer, Adhesive Markers, Other, unknown, Not Reported","","",FALSE,Biospecimen,"",https://data.humancellatlas.org/metadata/dictionary/protocol/imaging/imaging_preparation_protocol#imaging_preparation_protocol-protocol_core-protocols_io_doi,"" -Slicing Method,Imaging specific: the method by which the tissue was sliced.,"Vibratome, Cryosectioning, Tissue molds, Sliding microtome, Sectioning, Other, unknown, Not Reported","","",FALSE,Biospecimen,"",https://data.humancellatlas.org/metadata/dictionary/protocol/imaging/imaging_preparation_protocol#imaging_preparation_protocol-protocol_core-protocols_io_doi,"" -Antigen Retrieval,"Imaging specific: information on antigen retrieval when it is used for a pathology specimen. E.g. pH 6 (Citric Acid), pH 8 (tris), or pH 10. [Text - max length 100] ","","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64676&version=3.0,"" -Biospecimen Slide Location,Imaging specific: text term to capture the relative position and orientation of the core location within a piece of tissue on the slide relative to the region of interest slide coordinates. use https://docs.openmicroscopy.org/ome-model/6.0.1/developers/roi.html#shape-concrete-implementations if applciable,"","","",FALSE,Biospecimen,"","","" -Staining Markers,Imaging specific: text to identify proteins/ antibodies selected for staining,"","","",FALSE,Biospecimen,"","","" -Lysis Buffer,scRNA-seq specific: Type of lysis buffer used,"","","",FALSE,Biospecimen,"","","" -Method of Nucleic Acid Isolation,"Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]","","","",FALSE,Biospecimen,"","","" -Biospecimen Dimension 1,"First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the """"dimensions_unit"""" CDE","",Dimensions Unit,"",FALSE,Biospecimen,"","","" -Biospecimen Dimension 2,"Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the """"dimensions_unit"""" CDE","","","",FALSE,Biospecimen,"","","" -Biospecimen Dimension 3,"Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the """"dimensions_unit"""" CDE","","","",FALSE,Biospecimen,"","","" -Dimensions Unit,"Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)","mm, cm","","",FALSE,Biospecimen,"","","" -Section Number in Sequence,"Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)","","","",FALSE,Biospecimen,"","","" -Sample Core Template,Minimal required set of sample-level clinical data,"","Participant ID, Sample ID, Detailed Sample ID, Adjacent Sample IDs, Sample Site, ER Status, PR Status, HER2 Status",,FALSE,Sample,Sample,"","" -Morphology,"The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.","","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3226275&version=1.0,"" -Gross Tumor Weight,"Numeric value used to describe the gross pathologic tumor weight, measured in grams.","","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6133606&version=1.0,"" -Classification of Tumor,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.,"Primary, Metastasis, Recurrence, Other, unknown, Not Reported, Not Allowed To Collect","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3288124&version=1.0,"" -Breslow Thickness,"The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.","","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64809&version=3.0,"" -Tumor Depth,"Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).","","","",FALSE,Diagnosis,"","","" -Tumor Grade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.","G1, G2, G3, G4, GX, GB, High Grade, Intermediate Grade, Low Grade, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Publication Template,Publication entity.,,"Publication DOI, Title, Authors, Linked Project, Linked Datasets",,FALSE,Publication,Publication,, -Breast Carcinoma Detection Method Type,"The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.","Clinical Exam, Data not available, Nipple Discharge, Other, Screening Mammography, Screening MRI, Self exam, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma Histology Category,Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.,"Infiltrating ductal carcinoma, Infiltrating lobular carcinoma, Invasive mammary carcinoma NOS, Invasive mixed ductal and lobular carcinoma, Other","","",FALSE,Breast Cancer Tier 3,"","","" -Invasive Lobular Breast Carcinoma Histologic Category,The histologic subtype for an infiltrating lobular carcinoma of the breast.,"Alveolar type, Classical type, Data not available, Pleomorphic type, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Invasive Ductal Breast Carcinoma Histologic Category,The histologic subtype for the most common type of invasive breast carcinoma.,"Classical type, Invasive carcinoma-type cannot be determined, Invasive cribriform carcinoma, Invasive micropapillary carcinoma, Invasive papillary carcinoma, Invasive tubular carcinoma, Medullary carcinoma, Mucinous carcinoma, Tubulolobular carcinoma, Other, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Biopsy Procedure Finding Type,Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease.,"Atypical hyperplasia, DCIS, LCIS, Cancer, No cancer, Other","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Quadrant Site,The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.,"Upper outer quadrant, Lower outer quadrant, Upper inner quadrant, Lower inner quadrant, Central, Nipple, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Cancer Assessment Tests,Text term to identify assessment tests done in participants during diagnosis,"Estrogen receptor IHC, Progesterone receptor IHC, HER2 IHC, HER2 FISH-CISH, HER2 FISH, Other, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Cancer Genomic Test Performed,Text term that represents the name of the genomic test performed for breast cancer.,"Oncotype, MammaPrint, Other, Data not available, unknown, Not performed","","",FALSE,Breast Cancer Tier 3,"","","" -Mammaprint Risk Group,Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.,"High risk, Intermediate risk, Low risk, Data not available, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Oncotype Risk Group,Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.,"High risk, Intermediate risk, Low risk, Data not available, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma Estrogen Receptor Status,Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer,"Borderline, Equivocal, Indeterminate, Negative, Not Performed, Performed but Not Available, Positive, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma Progesteroner Receptor Status,Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer,"Borderline, Equivocal, Indeterminate, Negative, Not Performed, Performed but Not Available, Positive, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Cancer Allred Estrogen Receptor Score,"The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.","0, 1, 2, 3, 4, 5, 6, 7, 8, 10, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Prior Invasive Breast Disease,Text term to indicate prior invasive breast condition in the participant,"DCIS, LCIS, Invasive breast cancer (unrelated to the current cancer), Other, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma ER Status Percentage Value,A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer,"","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma PR Status Percentage Value,A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer,"","","",FALSE,Breast Cancer Tier 3,"","","" -HER2 Breast Carcinoma Copy Number Total,"Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values.","","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma Centromere 17 Copy Number,"Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.","","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma HER2 Centromere17 Copynumber Total,Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer,"","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma HER2 Chromosome17 Ratio,HER2 chromosome 17 ratio in participants with breast cancer,"","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma Surgical Procedure Name,Text name of a surgical procedure performed for a person with a diagnosis of breast cancer,"Lumpectomy, Radical mastectomy, Modified radical mastectomy, Other, Partial mastectomy, Re-excision, Simple mastectomy, Surgery not performed, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma HER2 Ratio Diagnosis,HER2 ratio of the participant at diagnosis,"","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma HER2 Status,Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 in a participant with breast cancer,"Positive, Negative, Amplified, Non-amplified, Equivocal, Indeterminate, Not Performed, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Hormone Therapy Breast Cancer Prevention Indicator,Did the patient receive hormonal therapy for prevention of breast cancer?,"Yes, No, unknown, Not Applicable","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma ER Staining Intensity,Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer,"Strong, Moderate, Weak, Weak-Moderate, Moderate-Strong, Weak-Strong, Other, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma PR Staining Intensity,Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer,"Strong, Moderate, Weak, Weak-Moderate, Moderate-Strong, Weak-Strong, Other, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Oncotype Score,OncotypeDX recurrence score,"","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Imaging Performed Type,"The kind of technology or method performed for screening, diagnosis, surgical procedures or therapy that aids in the visualization of the breast(s).","Mammogram, Ultrasound, MRI, PET/CT, CT, Multiple imaging modalities, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -Multifocal Breast Carcinoma Present Indicator,A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from the same clone and usually located in the same quadrant of the breast.,"Yes, No, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -Multicentric Breast Carcinoma Present Indicator,A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from different clones and usually located in different quadrants of the breast.,"Yes, No, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -BIRADS Mammography Breast Density Category,The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines.,"Predominantly fatty, Scattered fibroglandular densities, Heterogeneously dense, Extremely dense, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -BIRADS Score,Score within the BI-RADS system to characterize abnormal findings,"0,1,2,3,4,4A,4B,4C,5,6","","",FALSE,Breast Cancer Tier 3,"","","" -Cohort Core Template,Set of individual-level clinical data across different cohort collections,"","Participant ID,Age,Sex,BMI,Race,Ethnicity,Vital Status,Height,Weight,Gravidity,Parity,Age At Menarche,Menstrual Cycle Phase,Menopause Status,Primary Diagnosis,Age at Diagnosis,Diagnosis Status Type,Class BRCA1,Class BRCA2,Tobacco Use,Pack Years Smoked,Alcohol Use,Number of Drinks Per Week,Antibiotic Use,Sample Collection Center,Sample Collection Year,ER Status, PR Status, HER2 Status","",FALSE,Patient,,"","" -Ethnicity,"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.","hispanic or latino, not hispanic or latino, unknown, Not Reported, not allowed to collect","","",TRUE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2192217&version=2.0,"" -Gender,"Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]","female, male, unknown, unspecified, Not Reported","","",TRUE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2200604&version=3.0,"" -Race,"An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.","white, american indian or alaska native, black or african american, asian, native hawaiian or other pacific islander, other, unknown, Not Reported, not allowed to collect","","",TRUE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2192199&version=1.0,"" -Vital Status,The survival state of the person registered on the protocol.,"Alive, Dead, unknown, Not Reported","","",TRUE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5&version=5.0,"" -Dead,This indicates the participant is dead and defines further required metadata,"","Year of Death, Cause of Death, Cause of Death Source, Days to Death","",FALSE,Demographics,"","","" -Days to Birth,Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days.,"","","",FALSE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154723&version=1.0,"" -Year of Death,Numeric value to represent the year of the death of an individual.,"","","",TRUE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897030&version=1.0,"" -Country of Residence,Country of Residence at enrollment,"Afghanistan,Albania,Algeria,Andorra,Angola,Anguilla,Antigua and Barbuda,Argentina,Armenia,Aruba,Australia,Austria,Azerbaijan,Bahamas,Bahrain,Bangladesh,Barbados,Belarus,Belgium,Belize,Benin,Bermuda,Bhutan,Bolivia,Bosnia and Herzegovina,Botswana,Brazil,Brunei,Bulgaria,Burkina Faso,Burundi,Cambodia,Cameroon,Canada,Cape Verde,Cayman Islands,Central African Republic,Chad,Chile,China,Colombia,Comoros,Congo,Cook Islands,Costa Rica,Cote d'Ivoire,Croatia,Cuba,Curacao,Cyprus,Czech Republic (Czechia),Democratic Republic of the Congo,Denmark,Djibouti,Dominica,Dominican Republic,Ecuador,Egypt,El Salvador,Equatorial Guinea,Eritrea,Estonia,Eswatini,Ethiopia,Falkland Islands (Malvinas),Faroe Islands,Federated States of Micronesia,Fiji,Finland,France,French Guiana,French Polynesia,Gabon,Gambia,Georgia,Germany,Ghana,Gibraltar,Greece,Greenland,Grenada,Guadeloupe,Guam,Guatemala,Guernsey,Guinea,Guinea-Bissau,Guyana,Haiti,Holy See,Honduras,Hong Kong,Hungary,Iceland,India,Indonesia,Iran,Iraq,Ireland,Isle of Man,Israel,Italy,Jamaica,Japan,Jersey,Jordan,Kazakhstan,Kenya,Kiribati,Kosovo,Kuwait,Kyrgyzstan,Laos,Latvia,Lebanon,Lesotho,Liberia,Libya,Liechtenstein,Lithuania,Luxembourg,Macau,Madagascar,Malawi,Malaysia,Maldives,Mali,Malta,Marshall Islands,Martinique,Mauritania,Mauritius,Mayotte,Mexico,Moldova,Monaco,Mongolia,Montenegro,Montserrat,Morocco,Mozambique,Myanmar,Namibia,Nauru,Nepal,Netherlands,New Caledonia,New Zealand,Nicaragua,Niger,Nigeria,Niue,North Korea,North Macedonia,Northern Mariana Islands,Norway,Oman,Pakistan,Palau,Panama,Papua New Guinea,Paraguay,Peru,Philippines,Poland,Portugal,Puerto Rico,Qatar,Reunion,Romania,Russia,Rwanda,Saint Helena Ascension and Tristan da Cunha,Saint Kitts and Nevis,Saint Lucia,Saint Pierre and Miquelon,Saint Vincent and the Grenadines,Samoa,San Marino,Sao Tome and Principe,Saudi Arabia,Senegal,Serbia,Seychelles,Sierra Leone,Singapore,Slovakia,Slovenia,Solomon Islands,Somalia,South Africa,South Korea,South Sudan,Spain,Sri Lanka,State of Palestine,Sudan,Suriname,Svalbard & Jan Mayen Islands,Sweden,Switzerland,Syria,Taiwan,Tajikistan,Tanzania,Thailand,Timor-Leste,Togo,Tokelau,Tonga,Trinidad and Tobago,Tunisia,Turkey,Turkmenistan,Tuvalu,Uganda,Ukraine,United Arab Emirates,United Kingdom,United States,Uruguay,Uzbekistan,Vanuatu,Venezuela,Vietnam,Virgin Islands British,Virgin Islands U.S.,Wallis and Futuna,Western Sahara,Yemen,Zambia,Zimbabwe","","",FALSE,Demographics,"","","" -Age at Index,For GDC submission only - this is going to be always 0 since 's index is the date of birth,"","","",FALSE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6028530&version=1.0,"" -Age Is Obfuscated,The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.,"true, false","","",FALSE,Demographics,"","","" -Year Of Birth,Numeric value to represent the calendar year in which an individual was born.,"","","",FALSE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2896954&version=1.0,"" -Cause of Death,The cause of death,"Cancer Related, Cardiovascular Disorder NOS, End-stage Renal Disease, Infection, Not Cancer Related, Renal Disorder NOS, Spinal Muscular Atrophy, Surgical Complications, Toxicity, Not Reported, unknown, Not Applicable","","",TRUE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2554674&version=3.0,"" -Days to Death,Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days.,"","","",FALSE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154724&version=1.0,"" -Sex,Sex of individual,"female, male, unknown, unspecified, Not Reported",,,FALSE,Demographics Extended,,, -Age,Age of individual,,,,FALSE,Demographics Extended,,, -Age at Menarche,Age at first period,,,,FALSE,Demographics Extended,,, -Age at Menopause,Age at menopause,,,,FALSE,Demographics Extended,,, -Menopause Cause,Causal history of menopause,"Natural, Surgically induced, unknown",,,FALSE,Demographics Extended,,, -Obstetric History,Obstetric history notation such as “G1 P1”,,,,FALSE,Demographics Extended,,, -Parity,Number of pregnancies carried over the threshold of viability,,,,FALSE,Demographics Extended,,, -Gravidity,Total number of pregnancies regardless of outcome,,,,FALSE,Demographics Extended,,, -Age at First Birth,Age when individual gave first birth,,,,FALSE,Demographics Extended,,, -Yes - Given Birth,Has given birth,"Yes, No, unknown",,,FALSE,Demographics Extended,,, -Number of Live Births,Number of live births,,,,FALSE,Demographics Extended,,, -Yes - Issues With Pregnancy,Whether there was an issue with any pregnancy,,,,FALSE,Demographics Extended,,, -Years of Contraceptive Use,Years of contraceptive use,,,,FALSE,Demographics Extended,,, -Days to Progression,Number of days between the date used for index and the date the patient's disease progressed.,"","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154730&version=1.0,"" -Days to Progression Free,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free.,"","","",FALSE,Diagnosis,"","","" -Progression or Recurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,"Yes - Progression or Recurrence, No, unknown, Not Reported","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3121376&version=1.0,"" -Yes - Progression or Recurrence,The patient has had a new tumor event after initial treatment,"","Progression or Recurrence Type, Days to Progression, Days to Progression Free, Days to Recurrence, Days to Recurrence, Progression or Recurrence Anatomic Site","",FALSE,Diagnosis,"","","" -Sentinel Lymph Node Count,Numeric count of sentinel lymph nodes.,"","","",FALSE,Diagnosis,"","","" -Sentinel Node Positive Assessment Count,The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.,"","","",FALSE,Diagnosis,"","","" -Tumor Extranodal Extension Indicator,The indicator to determine extranodal involvement or extent of the disease.,"Absent,Indeterminate,NO, YES, No source documentation,Not applicable,Not sampled or dissected,Present,Present - extensive,Present - minimal,UNKNOWN,Unspecified","","",FALSE,Diagnosis,"","","" -Satellite Metastasis Present Indicator,A yes/no indicator to ask if intransit metastases or satellite lesions are present.,"Yes, No, unknown","","",FALSE,Diagnosis,"","","" -Other Biopsy Resection Site,A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under Clinical Data Tier 1),"","","",FALSE,Diagnosis,"","","" -Extent of Tumor Resection,"The degree to which the lesion has been cut out, or resected.","Gross Total Resection, Open Biopsy, Subtotal Resection, Extensive Subtotal, Minor, Optimal debulking, Other, Partial debulking, Segmental, Suboptimal, Suboptimal debulking, NTR, unknown, Not Reported, Not Applicable ","","",FALSE,Diagnosis,"","","" -Precancerous Condition Type,The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).,"Ductal Carcinoma In Situ,Pancreatic Intraductal Papillary-Mucinous Neoplasm,Atypical Adenomatous Lung Hyperplasia,Other,Pancreatic Intraepithelial Neoplasia,Prostatic Intraepithelial Neoplasia,Melanocytic hyperplasia,Atypical melanocytic proliferation,Melanoma in situ,Superficial spreading,Melanoma in situ,Lentigo maligna type,Melanoma in situ,Acral-lentiginous,Melanoma in situ arising in a giant congenital nevus,Persistent melanoma in situ,Melanoma in situ not otherwise classified,Scar - no residual melanoma,Invasive melanoma - superficial spreading,Invasive melanoma - nodular type,Invasive melanoma - lentigo maligna,Invasive melanoma - acral lentiginous,Invasive melanoma - desmoplastic,Invasive melanoma - nevoid,Invasive melanoma,Normal WDA,Reserve cell hyperplasia,Squamous metaplasia - mature,Squamous metaplasia - immature,Mild dysplasia,Moderate dysplasia,Severe dysplasia,Atypical adenomatous hyperplasia,Adenocarcinoma in situ - non mucinous,Adenocarcinoma in situ - mucinous,Benign tumor NOS,Hamartoma,Carcinoma NOS,No diagnosis possible","","",FALSE,Diagnosis,"","","" -Mode of Cancer Detection,"Text term used to describe the mode of cancer detection, like standard of care screening or random detection","Standard of Care Screening, Clinical Examination of unrelated cancer symptoms, Incidentaloma, Interval Cancer, Data not available","","",FALSE,Diagnosis,"","","" -Gleason Grade Group,"The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.","Group 1, Group 2, Group 3, Group 4, Group 5","","",FALSE,Diagnosis,"","","" -Gleason Grade Tertiary,The text term used to describe the tertiary pattern as described by the Gleason Grading System.,"Pattern 4, Pattern 5","","",FALSE,Diagnosis,"","","" -Gleason Patterns Percent,"Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.","","","",FALSE,Diagnosis,"","","" -Greatest Tumor Dimension,Numeric value that represents the measurement of the widest portion of the tumor in centimeters.,"","","",FALSE,Diagnosis,"","","" -Lymph Node Involved Site,The text term used to describe the anatomic site of lymph node involvement.,"Axillary,Cervical,Epitrochlear,Femoral,Hilar,Iliac-common,Iliac-external,Iliac, NOS,Inguinal,Mediastinal,Mesenteric,None,Occipital,Paraaortic,Parotid,Popliteal,Retroperitoneal,Splenic,Submandibular,Supraclavicular,unknown,Not Reported","","",FALSE,Diagnosis,"","","" -Margin Distance,Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.,"","","",FALSE,Diagnosis,"","","" -Margins Involved edulloblastoma Molecular ClassificationSite,The text term used to describe the anatomic sites that were involved in the survival margins.,"Gerota Fascia, Parenchyma, Perinephric Fat, Renal, Renal Capsule, Renal Sinus, Renal Vein, Ureter","","",FALSE,Diagnosis,"","","" -M,The text term used to describe the classification of medulloblastoma tumors based on molecular features.,"Not Determined, Non-WNT/non-SHH Activated, SHH-Activated, WNT-Activated, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Micropapillary Features,The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.,"Absent, Present, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Non Nodal Regional Disease,The text term used to describe whether the patient had non-nodal regional disease.,"Absent, Indeterminate, Present, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Non Nodal Tumor Deposits,The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.,"Yes, No, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Ovarian Specimen Status,The text term used to describe the physical condition of the involved ovary.,"Ovarian Capsule Intact, Ovarian Capsule Ruptured, Ovarian Capsule Fragmented, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Ovarian Surface Involvement,The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.,"Absent, Present, Indeterminate, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Pregnant at Diagnosis,The text term used to indicate whether the patient was pregnant at the time they were diagnosed.,"Yes, No, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Primary Gleason Grade,"The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.","Pattern 1, Pattern 2, Pattern 3, Pattern 4, Pattern 5","","",FALSE,Diagnosis,"","","" -Secondary Gleason Grade,"The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.","Pattern 1, Pattern 2, Pattern 3, Pattern 4, Pattern 5","","",FALSE,Diagnosis,"","","" -WHO CNS Grade,WHO CNS Grade,"Grade I, Grade II, Grade III, Grade IV, Grade Not Assigned, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -WHO NTE Grade,WHO NTE Grade,"G1, G2, G3, GX, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Age at Diagnosis,Age at the time of diagnosis expressed in number of days since birth.,"","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3225640&version=2.0,"" -Days to Last Follow up,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.","","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3008273&version=1.0,"" -Days to Last Known Disease Status,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.","","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3008273&version=1.0,"" -Last Known Disease Status,Text term that describes the last known state or condition of an individual's neoplasm.,"Distant met recurrence/progression, Loco-regional recurrence/progression, Biochemical evidence of disease without structural correlate, Tumor free, unknown tumor status, With tumor, Not Reported, Not Allowed To Collect, Not Applicable","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2759550&version=1.0,"" -Primary Diagnosis,"Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).","Acinar cell carcinoma,Acute basophilic leukaemia,Acute leukemia Burkitt type,Acute leukemia NOS,Acute lymphatic leukemia,Acute lymphoblastic leukemia-lymphoma NOS,Acute lymphoblastic leukemia mature B-cell type,Acute lymphoblastic leukemia NOS,Acute lymphoblastic leukemia precursor cell type,Acute lymphocytic leukemia,Acute lymphoid leukemia,Acute myeloid leukemia minimal differentiation,Acute myeloid leukemia MLL,Acute myeloid leukemia NOS,Acute myelomonocytic leukemia,Acute promyelocytic leukemia NOS,Adenocarcinoid tumor,Adenocarcinoma combined with other types of carcinoma,Adenocarcinoma in a polyp NOS,Adenocarcinoma in adenomatous polyp,Adenocarcinoma in polypoid adenoma,Adenocarcinoma in situ in a polyp NOS,Adenocarcinoma in situ in adenomatous polyp,Adenocarcinoma in situ in tubular adenoma,Adenocarcinoma in situ mucinous,Adenocarcinoma in situ non-mucinous,Adenocarcinoma in situ NOS,Adenocarcinoma in tubular adenoma,Adenocarcinoma in villous adenoma,Adenocarcinoma of anal ducts,Adenocarcinoma of anal glands,Adenocarcinoma diffuse type,Adenocarcinoma endocervical type,Adenocarcinoma intestinal type,Adenocarcinoma metastatic NOS,Adenocarcinoma NOS,Adenocarcinoma pancreatobiliary type,Adult rhabdomyoma,Adult T-cell lymphoma,Adult T-cell lymphoma/leukemia,Astrocytoma anaplastic,Astrocytoma low grade,Astrocytoma NOS,B cell lymphoma NOS,B lymphoblastic leukemia/lymphoma with hyperdiploidy,B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL),B lymphoblastic leukemia/lymphoma NOS,B-ALL,B-cell lymphocytic leukemia/small lymphocytic lymphoma,Basal cell adenocarcinoma,Basal cell adenoma,Basal cell carcinoma NOS,Basal cell epithelioma,Basal cell tumor,Basophil adenocarcinoma,Basophil adenoma,Basophil carcinoma,Bile duct adenocarcinoma,Bile duct adenoma,Bile duct carcinoma,Bile duct cystadenocarcinoma,Bile duct cystadenoma,Bronchial adenoma carcinoid,Bronchial adenoma cylindroid,Bronchial adenoma NOS,Bronchial-associated lymphoid tissue lymphoma,Bronchio-alveolar carcinoma mixed mucinous and non-mucinous,Bronchio-alveolar carcinoma mucinous,Bronchiolar adenocarcinoma,Bronchiolar carcinoma,Bronchiolo-alveolar adenocarcinoma NOS,Bronchiolo-alveolar carcinoma Clara cell,Bronchiolo-alveolar carcinoma Clara cell and goblet cell type,Bronchiolo-alveolar carcinoma goblet cell type,Bronchiolo-alveolar carcinoma indeterminate type,Bronchiolo-alveolar carcinoma non-mucinous,Bronchiolo-alveolar carcinoma NOS,Burkitt cell leukemia,Burkitt lymphoma NOS (Includes all variants),Burkitt tumor,Burkitt-like lymphoma,c-ALL,Cancer,Capillary hemangioma,Capillary lymphangioma,Carcinoma in a polyp NOS,Carcinoma in adenomatous polyp,Carcinoma in pleomorphic adenoma,Carcinoma in situ in a polyp NOS,Carcinoma in situ in adenomatous polyp,Carcinoma in situ NOS,Carcinoma anaplastic NOS,Carcinoma diffuse type,Carcinoma intestinal type,Carcinoma metastatic NOS,Carcinoma NOS,Carcinosarcoma NOS,Carcinoma undifferentiated NOS,Cementoma NOS,Central neuroblastoma,Central neurocytoma,Cerebellar liponeurocytoma,Cerebellar sarcoma NOS,Cervical intraepithelial neoplasia grade III,Cervical intraepithelial neoplasia low grade,Chondroma NOS,Chondrosarcoma grade 2/3,Chronic granulocytic leukemia BCR/ABL,Chronic granulocytic leukemia NOS,Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive,Chronic leukemia NOS,Chronic lymphatic leukemia,Chronic lymphocytic leukemia,Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL),Chronic lymphoid leukemia,Chronic monocytic leukemia,Chronic myelocytic leukemia NOS,Chronic myelogenous leukemia BCR-ABL positive,Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive,Chronic myeloid leukemia NOS,Chronic myelomonocytic leukemia in transformation,Chronic myelomonocytic leukemia NOS,Chronic myelomonocytic leukemia Type 1,Chronic myelomonocytic leukemia Type II,Chronic myeloproliferative disease NOS,Chronic myeloproliferative disorder,Chronic neutrophilic leukemia,Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis,Classical Hodgkin lymphoma lymphocyte depletion NOS,Classical Hodgkin lymphoma lymphocyte depletion reticular,Classical Hodgkin lymphoma lymphocyte-rich,Classical Hodgkin lymphoma mixed cellularity NOS,Classical Hodgkin lymphoma nodular sclerosis cellular phase,Classical Hodgkin lymphoma nodular sclerosis grade 1,Classical Hodgkin lymphoma nodular sclerosis grade 2,Classical Hodgkin lymphoma nodular sclerosis NOS,Combined hepatocellular carcinoma and cholangiocarcinoma,Combined large cell neuroendocrine carcinoma,Combined small cell carcinoma,Combined small cell-adenocarcinoma,Combined small cell-large carcinoma,Combined small cell-squamous cell carcinoma,Combined/mixed carcinoid and adenocarcinoma,Composite Hodgkin and non-Hodgkin lymphoma,Dermal nevus,Dermatofibroma NOS,Diffuse astrocytoma IDH-mutant,Diffuse astrocytoma IDH-wildtype,Diffuse astrocytoma low grade,Diffuse large B-cell lymphoma NOS,Diffuse melanocytosis,Duct adenocarcinoma NOS,Duct adenoma NOS,Duct carcinoma desmoplastic type,Duct carcinoma NOS,Duct cell carcinoma,Ductal carcinoma in situ NOS,Ductal carcinoma NOS,Dysplastic nevus,Endometrial sarcoma NOS,Endometrioid adenocarcinoma NOS,Endometrioid adenofibroma NOS,Endometrioid adenoma NOS,Endometrioid carcinoma NOS,Eosinophil adenocarcinoma,Eosinophil adenoma,Eosinophil carcinoma,Eosinophilic granuloma,Eosinophilic leukemia,Ependymoma NOS,Epidermoid carcinoma in situ NOS,Epidermoid carcinoma NOS,Epithelial tumor benign,Epithelial tumor malignant,Esophageal glandular dysplasia (intraepithelial neoplasia) high grade,Esophageal glandular dysplasia (intraepithelial neoplasia) low grade,Esophageal intraepithelial neoplasia high grade,Esophageal squamous intraepithelial neoplasia (dysplasia) high grade,Esophageal squamous intraepithelial neoplasia (dysplasia) low grade,Ewing sarcoma,Ganglioglioma NOS,Familial adenomatous polyposis,Gastrin cell tumor,Gastrin cell tumor malignant,Gastrinoma malignant,Gastrinoma NOS,Gastrointestinal stromal tumor malignant,Glioblastoma,Glioma malignant,Glioma NOS,Haemangioblastoma,Haemangiosarcoma,Hepatocarcinoma,Hepatocellular adenoma,Hepatocellular carcinoma NOS,Hepatocholangiocarcinoma,Hepatoid adenocarcinoma,Hepatoid carcinoma,Hodgkin disease NOS,Hodgkin granuloma,Hodgkin lymphoma mixed cellularity NOS,Hodgkin lymphoma nodular sclerosis NOS,Hodgkin lymphoma NOS,Hodgkin paragranuloma NOS,Hodgkin sarcoma,Infiltrating basal cell carcinoma NOS, Infiltrating duct carcinoma NOS, Infiltrating duct and colloid carcinoma,Infiltrating duct and cribriform carcinoma,Inflammatory adenocarcinoma,Inflammatory carcinoma,Interstitial cell tumor benign,Interstitial cell tumor malignant,Interstitial cell tumor NOS,Intracystic papilloma,Intradermal nevus,Intraductal adenocarcinoma noninfiltrating NOS,Intraductal and lobular carcinoma,Intraductal carcinoma and lobular carcinoma in situ,Intraductal carcinoma clinging,Intraductal carcinoma noninfiltrating NOS,Intraductal carcinoma NOS,Intraductal carcinoma solid type,Intraductal micropapillary carcinoma,Intraductal papillary adenocarcinoma with invasion,Intraductal papillary adenocarcinoma NOS,Intraductal papillary carcinoma,Intraductal tubular-papillary neoplasm high grade,Intraductal tubular-papillary neoplasm low grade,Intraductal tubulopapillary neoplasm,Intraepidermal carcinoma NOS,Intraepidermal squamous cell carcinoma Bowen type,Intravascular B-cell lymphoma,Juvenile myelomonocytic leukemia,Kaposi sarcoma,Large cell carcinoma NOS,Liposarcoma differentiated,Liposarcoma NOS,Liposarcoma well differentiated,Liver cell adenoma,Liver cell carcinoma,Lobular adenocarcinoma,Lobular and ductal carcinoma,Lobular carcinoma in situ NOS,Lobular carcinoma noninfiltrating,Lobular carcinoma NOS,Lymphatic leukemic NOS,Lymphoblastic leukemia NOS,Lymphoblastoma,Lymphocytic leukemia NOS,Lymphoma NOS,Malignancy,Malignant lymphoma diffuse NOS,Malignant lymphoma Hodgkin,Malignant lymphoma immunoblastic NOS,Malignant lymphoma large B-cell diffuse NOS,Malignant lymphoma large B-cell NOS,Malignant lymphoma large cell NOS,Malignant lymphoma lymphoblastic NOS,Malignant lymphoma lymphocytic diffuse NOS,Malignant lymphoma lymphocytic nodular NOS,Malignant lymphoma lymphocytic NOS,Malignant lymphoma mixed cell type diffuse,Malignant lymphoma mixed cell type follicular,Malignant lymphoma mixed cell type nodular,Malignant lymphoma nodular NOS,Malignant lymphoma non-Hodgkin NOS,Malignant lymphoma NOS,Malignant lymphoma small B lymphocytic NOS,Malignant melanoma in congenital melanocytic nevus,Malignant melanoma in giant pigmented nevus,Malignant melanoma in Hutchinson melanotic freckle,Malignant melanoma in junctional nevus,Malignant melanoma in precancerous melanosis,Malignant melanoma NOS,Malignant melanoma regressing,Mammary carcinoma in situ,Medullary adenocarcinoma,Medullary carcinoma NOS,Medullary osteosarcoma,Medulloblastoma NOS,Melanoameloblastoma,Melanocytic nevus,Melanocytoma eyeball,Melanocytoma NOS,Melanoma in situ,Melanoma malignant of soft parts,Melanoma NOS,Melanotic medulloblastoma,Melanotic MPNST,Melanotic neuroectodermal tumor,Melanotic neurofibroma,Melanotic progonoma,Melanotic psammomatous MPNST,Melanotic schwannoma,Meningeal melanocytoma,Meningeal melanoma,Meningioma anaplastic,Meningioma malignant,Meningioma NOS,Micropapillary carcinoma NOS,Mixed adenocarcinoma and epidermoid carcinoma,Mixed adenocarcinoma and squamous cell carcinoma,Mixed medullary-follicular carcinoma,Mixed medullary-papillary carcinoma,Mixed pancreatic endocrine and exocrine tumor malignant,Mixed pineal tumor,Mixed small cell carcinoma,Mixed squamous cell and glandular papilloma,Mixed tumor malignant NOS,Mixed tumor NOS,Monocytic leukemia NOS,Mucosal-associated lymphoid tissue lymphoma,Mucous adenocarcinoma,Multiple myeloma,Myelocytic leukemia NOS,Myeloid leukemia NOS,Myeloma NOS,Myoepithelioma,Neoplasm benign,Neoplasm malignant,Neoplasm malignant uncertain whether primary or metastatic,Neoplasm metastatic,Neoplasm NOS,Neoplasm secondary,Neoplasm uncertain whether benign or malignant,Nephroblastoma NOS,Neuroblastoma NOS,Neuroendocrine carcinoma NOS,Neuroepithelioma NOS,Neurofibroma NOS,Neurofibromatosis NOS,Neurofibrosarcoma,Neurosarcoma,Nevus NOS,Non-Hodgkin lymphoma NOS,Non-invasive low grade serous carcinoma,Non-lymphocytic leukemia NOS,Non-small cell carcinoma,Nonpigmented nevus,Not Reported,Oat cell carcinoma,Osteoblastoma malignant,Osteoblastoma NOS,Osteosarcoma NOS,Paget disease and infiltrating duct carcinoma of breast,Paget disease and intraductal carcinoma of breast,Paget disease of breast,Paget disease extramammary,Paget disease mammary,Pagetoid reticulosis,Pancreatic endocrine tumor benign,Pancreatic endocrine tumor malignant,Pancreatic endocrine tumor nonfunctioning,Pancreatic endocrine tumor NOS,Pancreatic microadenoma,Pancreatobiliary neoplasm non-invasive,Pancreatobiliary-type carcinoma,Pancreatoblastoma,Papillary adenocarcinoma follicular variant,Papillary adenocarcinoma NOS,Papillary adenofibroma,Papillary adenoma NOS,Papillary and follicular carcinoma,Papillary carcinoma in situ,Papillary carcinoma NOS,Papillary cystadenoma NOS,Papillary epidermoid carcinoma,Papillary glioneuronal tumor,Papillary meningioma,Papillary microcarcinoma,Papillary renal cell carcinoma,Papillary serous adenocarcinoma,Papillary serous cystadenocarcinoma,Papillary serous cystadenoma NOS,Papillary squamous cell carcinoma,Papillary squamous cell carcinoma in situ,Papillary transitional cell carcinoma,Papillary tumor of the pineal region,Papillary urothelial carcinoma,Papilloma of bladder,Papilloma NOS,Papillomatosis glandular,Papillomatosis NOS,Papillotubular adenocarcinoma,Papillotubular adenoma,Paraganglioma benign,Paraganglioma malignant,Paraganglioma NOS,Peripheral T-cell lymphoma large cell,Peripheral T-cell lymphoma NOS,Pigmented adenoma,Pigmented basal cell carcinoma,Pigmented nevus NOS,Pituitary adenoma NOS,Pituitary carcinoma NOS,Pleomorphic adenoma,Pleomorphic carcinoma,Pleomorphic lipoma,Pleomorphic liposarcoma,Pleomorphic lobular carcinoma,Pleomorphic lobular carcinoma in situ,Precancerous melanosis NOS,Precursor B-cell lymphoblastic leukemia,Precursor B-cell lymphoblastic lymphoma,Precursor cell lymphoblastic leukemia NOS,Precursor T-cell lymphoblastic leukemia,Precursor T-cell lymphoblastic lymphoma,Preleukemia,Preleukemic syndrome,Primary amyloidosis,Pro-B ALL,Pro-T ALL,Prostatic intraepithelial neoplasia grade III,Pulmonary adenomatosis,Pulmonary artery intimal sarcoma,Pulmonary blastoma,Renal carcinoma collecting duct type,Renal cell adenocarcinoma,Renal cell carcinoma chromophobe type,Renal cell carcinoma NOS,Renal cell carcinoma sarcomatoid,Renal cell carcinoma spindle cell,Renal cell carcinoma unclassified,Renal medullary carcinoma,Rhabdoid meningioma,Rhabdoid sarcoma,Rhabdoid tumor NOS,Rhabdomyoma NOS,Rhabdomyosarcoma with ganglionic differentiation,Rhabdomyosarcoma NOS,Rhabdosarcoma,Rodent ulcer,Sarcoma NOS,Sclerosing hemangioma,Sclerosing hepatic carcinoma,Secondary carcinoma,Secretory carcinoma of breast,Serous cystadenocarcinoma NOS,Serous surface papillary carcinoma,High-grade serous carcinoma,Skin appendage carcinoma,Small cell carcinoma NOS,Small cell neuroendocrine carcinoma,Small cell osteosarcoma,Small cell sarcoma,Small congenital nevus,Spindle cell carcinoma NOS,Spindle cell melanoma NOS,Splenic B-cell lymphoma/leukemia unclassifiable,Splenic diffuse red pulp small B-cell lymphoma,Splenic lymphoma with villous lymphocytes,Splenic marginal zone B-cell lymphoma,Splenic marginal zone lymphoma NOS,Squamous cell carcinoma in situ NOS,Squamous cell carcinoma adenoid,Squamous cell carcinoma clear cell type,Squamous cell carcinoma NOS,T lymphoblastic leukemia/lymphoma,T-cell large granular lymphocytic leukemia,T-cell large granular lymphocytosis,T-cell lymphoma NOS,Teratoma malignant NOS,Teratoma NOS,Therapy related myeloid neoplasm,Transitional carcinoma,Transitional cell carcinoma,Transitional cell carcinoma in situ,Tubular adenocarcinoma,Tubular adenoma NOS,Tubular androblastoma with lipid storage,Tubular androblastoma NOS,Tubular carcinoid,Tubular carcinoma,Tubulo-papillary adenoma,Tubulocystic renal cell carcinoma,Tubulolobular carcinoma,Tubulopapillary adenocarcinoma,Tubulovillous adenoma NOS,Tumor cells benign,Tumor cells malignant,Tumor cells NOS,Tumor cells uncertain whether benign or malignant,Tumor embolus,Tumor benign,Tumor malignant NOS,Tumor metastatic,Tumor NOS,Tumor secondary,Tumorlet benign,Typical carcinoid,Unclassified tumor benign,Unclassified tumor borderline malignancy,Unclassified tumor malignant,Unclassified tumor malignant uncertain whether primary or metastatic,Unclassified tumor uncertain whether benign or malignant,Undifferentiated epithelioid sarcoma,Undifferentiated high-grade pleomorphic sarcoma,Undifferentiated leukaemia,Undifferentiated pleomorphic sarcoma,Undifferentiated round cell sarcoma,Undifferentiated sarcoma,Undifferentiated spindle cell sarcoma,Undifferentiated uterine sarcoma,unknown","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161032&version=1.0,"" -Prior Malignancy,The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.,"Yes, No, unknown, Not Reported, Not Allowed To Collect","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3382736&version=2.0,"" -Prior Treatment,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.,"Yes, No, unknown, Not Reported, Not Allowed To Collect","","",FALSE,Diagnosis,"","","" -Site of Resection or Biopsy,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).","Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Paraspinal,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,unknown,Not Reported","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161034&version=1.0,"" -Tissue or Organ of Origin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).","Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Paraspinal,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,unknown,Not Reported","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161035&version=1.0,"" -Tumor Grade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.","G1, G2, G3, G4, GX, GB, High Grade, Low Grade, unknown, Not Reported, Not Applicable","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2785839&version=2.0,"" -AJCC Clinical M,"Extent of the distant metastasis for the cancer based on evidence obtained from clinical - assessment parameters determined prior to treatment.","M0, M1, M1a, M1b, M1c, MX, cM0 (i+), unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440331&version=1.0,"" -AJCC Clinical N,"Extent of the regional lymph node involvement for the cancer based on evidence obtained from - clinical assessment parameters determined prior to treatment.","N0, N0 (i+), N0 (i-), N0 (mol+), N0 (mol-), N1, N1a, N1b, N1bI, N1bII, N1bIII, N1bIV, N1c, N1mi, N2, N2a, N2b, N2c, N3, N3a, N3b, N3c, N4, NX, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440330&version=1.0,"" -AJCC Clinical Stage,"Stage group determined from clinical information on the tumor (T), regional node (N) and - metastases (M) and by grouping cases with similar prognosis for cancer.","Stage 0, Stage 0a, Stage 0is, Stage I, Stage IA, Stage IA1, Stage IA2, Stage IB, Stage IB1, Stage IB2, Stage IC, Stage II, Stage IIA, Stage IIA1, Stage IIA2, Stage IIB, Stage IIC, Stage IIC1, Stage III, Stage IIIA, Stage IIIB, Stage IIIC, Stage IIIC1, Stage IIIC2, Stage IS, Stage IV, Stage IVA, Stage IVB, Stage IVC, Stage Tis, Stage X, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440332&version=1.0,"" -AJCC Clinical T,"Extent of the primary cancer based on evidence obtained from clinical assessment parameters - determined prior to treatment.","T0, T1, T1a, T1a1, T1a2, T1b, T1b1, T1b2, T1c, T1mi, T2, T2a, T2a1, T2a2, T2b, T2c, T2d, T3, T3a, T3b, T3c, T3d, T4, T4a, T4b, T4c, T4d, T4e, TX, Ta, Tis, Tis (DCIS), Tis (LCIS), Tis (Paget's), unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440328&version=1.0,"" -AJCC Pathologic M,"Code to represent the defined absence or presence of distant spread or metastases (M) to - locations via vascular channels or lymphatics beyond the regional lymph nodes, using - criteria established by the American Joint Committee on Cancer (AJCC).","M0, M1, M1a, M1b, M1c, MX, cM0 (i+), unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3045439&version=1.0,"" -AJCC Pathologic N,"The codes that represent the stage of cancer based on the nodes present (N stage) according - to criteria based on multiple editions of the AJCC's Cancer Staging Manual.","N0, N0 (i+), N0 (i-), N0 (mol+), N0 (mol-), N1, N1a, N1b, N1bI, N1bII, N1bIII, N1bIV, N1c, N1mi, N2, N2a, N2b, N2c, N3, N3a, N3b, N3c, N4, NX, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3203106&version=1.0,"" -AJCC Pathologic Stage,"The extent of a cancer, especially whether the disease has spread from the original site to - other parts of the body based on AJCC staging criteria.","Stage 0, Stage 0a, Stage 0is, Stage I, Stage IA, Stage IA1, Stage IA2, Stage IB, Stage IB1, Stage IB2, Stage IC, Stage II, Stage IIA, Stage IIA1, Stage IIA2, Stage IIB, Stage IIC, Stage IIC1, Stage III, Stage IIIA, Stage IIIB, Stage IIIC, Stage IIIC1, Stage IIIC2, Stage IS, Stage IV, Stage IVA, Stage IVB, Stage IVC, Stage Tis, Stage X, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3203222&version=1.0,"" -AJCC Pathologic T,"Code of pathological T (primary tumor) to define the size or contiguous extension of the - primary tumor (T), using staging criteria from the American Joint Committee on Cancer - (AJCC).","T0, T1, T1a, T1a1, T1a2, T1b, T1b1, T1b2, T1c, T1mi, T2, T2a, T2a1, T2a2, T2b, T2c, T2d, T3, T3a, T3b, T3c, T3d, T4, T4a, T4b, T4c, T4d, T4e, TX, Ta, Tis, Tis (DCIS), Tis (LCIS), Tis (Paget's), unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3045435&version=1.0,"" -AJCC Staging System Edition,"The text term used to describe the version or edition of the American Joint Committee on Cancer - Staging Handbooks, a publication by the group formed for the purpose of developing a system of - staging for cancer that is acceptable to the American medical profession and is compatible with - other accepted classifications.","1st, 2nd, 3rd, 4th, 5th, 6th, 7th, 8th, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2722309&version=1.0,"" -Anaplasia Present,"Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.","Yes - Anaplasia Present, No, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6059599&version=1.0,"" -Yes - Anaplasia Present,Indicates anaplasia is present,"",Anaplasia Present Type,"",FALSE,Diagnosis,"","","" -Anaplasia Present Type,"The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.","Absent, Diffuse, Equivocal, Focal, Present, Sclerosis, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4925534&version=1.0,"" -Best Overall Response,The best improvement achieved throughout the entire course of protocol treatment.,"AJ-Adjuvant Therapy, CPD-Clinical Progression, CR-Complete Response, CRU-Complete Response Unconfirmed, DU-Disease Unchanged, IMR-Immunoresponse, IPD-Immunoprogression, MR-Minimal/Marginal Response, MX-Mixed Response, Non-CR/Non-PD-Non-CR/Non-PD, NPB-No Palliative Benefit, NR-No Response, PA-Palliative Therapy, PB-Palliative Benefit, PD-Progressive Disease, PPD-Pseudoprogression, PR-Partial Response, PSR-Pseudoresponse, RD-Responsive Disease, RP-Response, RPD-Radiographic Progressive Disease, sCR-Stringent Complete Response, SD-Stable Disease, SPD-Surgical Progression, TE-Too Early, VGPR-Very Good Partial Response","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2003324&version=4.0,"" -Days to Diagnosis,Number of days between the date used for index and the date the patient was diagnosed with the malignant disease.,"","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154733&version=1.0,"" -Pathology from Left Breast,"Pathology description for left breast.","","","",FALSE,Diagnosis,"",,"" -Pathology from Right Breast,"Pathology description for right breast.","","","",FALSE,Diagnosis,"",,"" -Laterality,"For paired organs, designates the side on which the cancer originates.","Bilateral, Left, Midline, Right, Unilateral, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=827&version=3.0,"" -Lymph Nodes Positive,The number of lymph nodes involved with disease as determined by pathologic examination.,"","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=89&version=3.0,"" -Lymph Nodes Tested,The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.,"","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3&version=3.0,"" -Lymphatic Invasion Present,"A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement","Yes, No, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64171&version=3.0,"" -Metastasis at Diagnosis,The text term used to describe the extent of metastatic disease present at diagnosis.,"Distant Metastasis, Metastasis NOS, No Metastasis, Regional Metastasis, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6133614&version=1.0,"" -Metastasis at Diagnosis Site,Text term to identify an anatomic site in which metastatic disease involvement is found.,"Abdomen, Adrenal Gland, Ascites, Bone, Bone Marrow, Brain, Cerebrospinal Fluid, Central Nervous System, Colon, Distant Nodes, Distant Organ, Groin, Kidney, Liver, Lung, Lymph Node, Axillary, Lymph Node, Inguinal, Lymph Node NOS, Mediastinum, Omentum, Ovary, Pelvis, Peritoneal Cavity, Peritoneum, Pleura, Scalp, Skin, Small Intestine, Soft Tissue, Spinal Cord, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3029815&version=1.0,"" -Method of Diagnosis,Text term used to describe the method used to confirm the patients malignant diagnosis.,"Autopsy,Biopsy,Blood Draw,Bone Marrow Aspirate,Core Biopsy,Cytology,Cystoscopy,Debulking,Diagnostic Imaging,Dilation and Curettage Procedure,Enucleation,Excisional Biopsy,Fine Needle Aspiration,Imaging,Incisional Biopsy,Laparoscopy,Laparotomy,Other,Pap Smear,Physical Exam,Pathologic Review,Surgical Resection,Thoracentesis,Ultrasound Guided Biopsy,unknown,Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161031&version=1.0,"" -Mitotic Count,"The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.","","","",FALSE,Diagnosis,"","","" -Percent Tumor Invasion,The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.,"","","",FALSE,Diagnosis,"","","" -Peritoneal Fluid Cytological Status,The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.,"Atypical, Malignant, Non-Malignant, Unsatisfactory, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6690681&version=1.0,"" -Perineural Invasion Present,A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.,"Yes, No, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64181&version=3.0,"" -Residual Disease,Text terms to describe the status of a tissue margin following surgical resection.,"R0, R1, R2, RX, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2608702&version=1.0,"" -Synchronous Malignancy,"A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.","Yes, No, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6142390&version=1.0,"" -Tumor Confined to Organ of Origin,The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.,"Yes, No, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4925494&version=1.0,"" -Tumor Focality,The text term used to describe whether the patient's disease originated in a single location or multiple locations.,"Multifocal, Unifocal, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3174022&version=1.0,"" -Tumor Largest Dimension Diameter,"Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.","","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64215&version=3.0,"" -Vascular Invasion Present,The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.,"Yes - Vascular Invasion Present, No, unknown, Not Reported, Not Allowed To Collect","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64358&version=3.0,"" -Yes - Vascular Invasion Present,Indicates venous invasion was detected by surgery or presence in a tumor specimen,"",Vascular Invasion Type,"",FALSE,Diagnosis,"","","" -Vascular Invasion Type,Text term that represents the type of vascular tumor invasion.,"Extramural, Intramural, Macro, Micro, No Vascular Invasion, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3168001&version=1.0,"" -Year of Diagnosis,Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.,"","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2896960&version=1.0,"" -Topography Code,"Topography Code, indicating site within the body, based on ICD-O-3.","","","",FALSE,Diagnosis,"","","" -Additional Topography,Topography not included in the ICD-O-3 Topography codes.,"Skin of scalp, Skin of eye lid, Skin of nose, Skin of lip, Skin of ear, Skin of neck, Skin of other parts of face, Skin of chest, Skin of back, Skin of abdomen, Skin of trunk, Skin of breast, Skin of upper limb and shoulder, Skin of palm, Skin of lower limb and hip, Skin of sole, Skin of penis, Skin of scrotum, Skin of vulva, Skin NOS, Hilar Airway, Peri-tumoral Airway, Not Reported","","",FALSE,Diagnosis,"","","" -Smoking Exposure,Indicate if individual has smoking exposure,"Yes - Smoking Exposure, No - Smoking Exposure, Not Reported","","",TRUE,Exposure,"","","" -Yes - Smoking Exposure,Individual has been exposed to smoke; requires additional metadata,"","Years Smoked, Pack Years Smoked, Cigarettes per Day, Smoking Frequency, Type of Smoke Exposure, Time between Waking and First Smoke, Tobacco Smoking Onset Year, Tobacco Smoking Quit Year, Tobacco Smoking Status, Type of Tobacco Used, Secondhand Smoke as Child, Smoke Exposure Duration, Tobacco Use per Day, Smokeless Tobacco Quit Age","",FALSE,Exposure,"","","" -Pack Years Smoked,Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.,"","","",TRUE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2955385&version=1.0,"" -Years Smoked,Numeric value (or unknown) to represent the number of years a person has been smoking.,"","","",TRUE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3137957&version=1.0,"" -Smoking Frequency,The text term used to generally decribe how often the patient smokes.,"Every day, Some days, unknown","","",FALSE,Exposure,"","","" -Secondhand Smoke as Child,The text term used to indicate whether the patient was exposed to secondhand smoke as a child.,"Yes, No, unknown, Not Reported","","",FALSE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6841888&version=1.0,"" -Tobacco Use per Day,Numeric value that represents the number of times the patient uses tobacco each day.,"","","",FALSE,Exposure,"","","" -Tobacco Smoking Status,Category describing current smoking status and smoking history as self-reported by a patient,"Lifelong Non-Smoker, Current Smoker, Current Reformed Smoker for > 15 yrs, Current Reformed Smoker for < or = 15 yrs, Current Reformed Smoker, Duration Not Specified, Smoking history not documented, unknown, Not Reported","","",FALSE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2181650&version=1.0,"" -Alcohol Exposure,Indicate if individual has alcohol exposure,"Yes - Alcohol Exposure, No - Alcohol Exposure, Not Reported","","",TRUE,Exposure,"","","" -Yes - Alcohol Exposure,"","","Alcohol Days Per Week, Alcohol Drinks Per Day, Alcohol History, Alcohol Intensity, Alcohol Type","",FALSE,Exposure,"","","" -Alcohol Days Per Week,Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.,"","","",FALSE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3114013&version=1.0,"" -Alcohol Drinks Per Day,Numeric value used to describe the average number of alcoholic beverages a person consumes per day.,"","","",FALSE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3124961&version=1.0,"" -Alcohol History,A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.,"Yes, No, unknown, Not Reported","","",FALSE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2201918&version=1.0,"" -Alcohol Intensity,Category to describe the patient's current level of alcohol use as self-reported by the patient.,"Drinker, Heavy Drinker, Lifelong Non-Drinker, Non-Drinker, Occasional Drinker, unknown, Not Reported","","",FALSE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3457767&version=1.0,"" -Alcohol Type,Type of alcohol use,"Beer, Liquor, Other, Wine, unknown, Not Reported","","",FALSE,Exposure,"","","" -Cigarettes per Day,The average number of cigarettes smoked per day.,"","","",FALSE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2001716&version=4.0,"" -Environmental Tobacco Smoke Exposure,"The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.","Yes, No, unknown","","",FALSE,Exposure,"","","" -Antibiotic Use,"Antibiotic use","No, Yes - within last monthh, Yes - within last 1-6 months, Yes - over 6 months ago,unknown","","",FALSE,Exposure,"","","" -Relationship Gender,The text term used to describe the gender of the patient's relative with a history of cancer.,"Female, Male, unknown, unspecified, Not Reported","","",FALSE,Family History,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161021&version=1.0,"" -Relationship Age at Diagnosis,The age (in years) when the patient's relative was first diagnosed.,"","","",FALSE,Family History,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5300571&version=1.0,"" -Relationship Primary Diagnosis,The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.,"Adrenal Gland Cancer, Basal Cell Cancer, Bile Duct Cancer, Bladder Cancer, Blood Cancer, Bone Cancer, Brain Cancer, Breast Cancer, Cancer, Cervical Cancer, Chondrosarcoma, CNS Cancer, Colorectal Cancer, Esophageal Cancer, Ewing Sarcoma, Gallbladder Cancer, Gastric Cancer, Glioblastoma, Gynecologic Cancer, Head and Neck Cancer, Hematologic Cancer, Kaposi Sarcoma, Kidney Cancer, Laryngeal Cancer, Leukemia, Liver Cancer, Lung Cancer, Lymph Node Cancer, Lymphoma, Melanoma, Mesothelioma, Multiple Myeloma, Neuroblastoma, Osteosarcoma, Ovarian Cancer, Pancreas Cancer, Prostate Cancer, Rectal Cancer, Rhabdomyosarcoma, Sarcoma, Skin Cancer, Spleen Cancer, Testicular Cancer, Throat Cancer, Thyroid Cancer, Tongue Cancer, Tonsillar Cancer, Uterine Cancer, Wilms Tumor, unknown, Not Reported","","",FALSE,Family History,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161022&version=1.0,"" -Relationship Type,The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.,"Adopted Daughter, Adopted Son, Adoptive Brother, Adoptive Father, Adoptive Mother, Adoptive Sister, Aunt, Brother, Brother-in-law, Child, Cousin, Daughter, Daughter-in-law, Domestic Partner, Father, Father-in-law, Female Cousin, First Cousin, First Cousin Once Removed, Foster Brother, Foster Daughter, Foster Father, Foster Mother, Foster Sister, Foster Son, Fraternal Twin Brother, Fraternal Twin Sibling, Fraternal Twin Sister, Full Brother, Full Sister, Grand Nephew, Grand Niece, Grandchild, Granddaughter, Grandfather, Grandmother, Grandparent, Grandson, Great Grandchild, Half Brother, Half Sibling, Half Sister, Husband, Identical Twin Brother, Identical Twin Sibling, Identical Twin Sister, Legal Guardian, Male Cousin, Maternal Aunt, Maternal First Cousin, Maternal First Cousin Once Removed, Maternal Grandfather, Maternal Grandmother, Maternal Grandparent, Maternal Great Aunt, Maternal Great Grandparent, Maternal Great Uncle, Maternal Half Brother, Maternal Half Sibling, Maternal Half Sister, Maternal Uncle, Mother, Mother-in-law, Natural Brother, Natural Child, Natural Daughter, Natural Father, Natural Grandchild, Natural Grandfather, Natural Grandmother, Natural Grandparent, Natural Mother, Natural Parent, Natural Sibling, Natural Sister, Natural Son, Nephew, Niece, Niece Second Degree Relative, Other, Parent, Paternal Aunt, Paternal First Cousin, Paternal First Cousin Once Removed, Paternal Grandfather, Paternal Grandmother, Paternal Grandparent, Paternal Great Aunt, Paternal Great Grandparent, Paternal Great Uncle, Paternal Half Brother, Paternal Half Sibling, Paternal Half Sister, Paternal Uncle, Refused, Sibling, Sister, Sister-in-law, Son, Son-in-law, Spouse, Step Child, Step Sibling, Stepbrother, Stepdaughter, Stepfather, Stepmother, Stepsister, Stepson, Twin Sibling, Uncle, Unrelated, Ward, Wife, unknown, Not Reported","","",FALSE,Family History,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2690165&version=2.0,"" -Relative with Cancer History,The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.,"Yes - Cancer History Relative, None, unknown, Not Reported","","",FALSE,Family History,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161023&version=1.0,"" -First or Second Degree Relatives with Breast Cancer History Count,The number of close relatives the patient has with a known history of breast cancer.,"","","",FALSE,Family History,"","","" -Third Degree Relatives with Breast Cancer History Count,The number of 3rd degree relatives the patient has with a known history of breast cancer.,"","","",FALSE,Family History,"","","" -First or Second Degree Relatives with Ovarian Cancer History Count,The number of close relatives the patient has with a known history of ovarian cancer.,"","","",FALSE,Family History,"","","" -Third Degree Relatives with Ovarian Cancer History Count,The number of 3rd degree relatives the patient has with a known history of ovarian cancer.,"","","",FALSE,Family History,"","","" -Relatives with Cancer History Count,The number of relatives the patient has with a known history of cancer.,"","","",FALSE,Family History,"","","" -Yes - Cancer History Relative,Individual has a relative with cancer history,"","Relatives with Cancer History Count, Relationship Type, Relationship Primary Diagnosis, Relationship Gender,Relationship Age at Diagnosis","",FALSE,Family History,"","","" -Family Member Vital Status Indicator,The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1),"Vital Status Alive, Vital Status Dead, unknown, Not Reported","","",FALSE,Family History,"","","" -Known Genetic Predisposition Mutation,A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.,"Yes, No, unknown","","",FALSE,Family History,"","","" -Hereditary Cancer Predisposition Syndrome,History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.,"Alpha-1 antitrypsin,Attenuated familial adenomatous polyposis,BAP1 mutant disease,Beckwith-Wiedemann,Biliary disorder,Birt-Hogg-Dube syndrome,Carney complex,Cirrhosis unknown etiology,Constitutional mismatch repair deficiency,Familial adenomatous polyposis,Familial gastrointestinal stromal tumor,Familial pancreatic cancer,Familial prostate cancer,Familial renal cancer,Fanconi anemia,Glycogen Storage Disease,Gorlin syndrome,Hereditary breast–ovarian cancer syndrome,Hereditary diffuse gastric cancer ,Hereditary leiomyoma-renal cell carcinoma,Hereditary melanoma,Hereditary mixed polyposis syndrome,Hereditary papillary RCC ,Hereditary papillary renal cell carcinoma,Hereditary paraganglioma–pheochromocytoma syndrome,Hereditary renal oncocytoma,Hereditary retinoblastoma ,Juvenile polyposis syndrome,Li-Fraumeni syndrome,Lynch syndrome,Melanoma–astrocytoma syndrome,Multiple endocrine neoplasia type I,Multiple endocrine neoplasia type II,MUTYH-associated polyposis,Nevoid basal cell carcinoma syndrome ,Not Applicable ,Not Reported,Peutz–Jeghers syndrome,Cowden syndrome,Rhabdoid tumor predisposition syndrome type I,Rhabdoid tumor predisposition syndrome type II,Rubinstein-Taybi syndrome,SDH associated renal cancer,Serrated polyposis syndrome,Tuberous sclerosis complex ,Turcot syndrome,Tyrosinemia,unknown,von Hippel-Lindau Syndrome","","",FALSE,Family History,"","","" -Cancer Associated Gene Mutations,Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history,"APC mutation,ALK mutation,ARF mutation,ATM mutation,ATRX mutation,ACVR1 mutation,BAP1 mutation,BMPR1A mutation,BLM mutation,BRCA1 mutation,BRCA1 and 2 mutation,BRCA2 mutation,BRAF mutation,CDH1 mutation,CDKN2A mutation,CDKN2A and p14ARF mutation,CHK mutation,ETV6 mutation, EGFR mutation, FH mutation,FLCN mutation,GREM1 mutation,HOXB13 mutation,H3K27M mutation,H3G34R/V mutation,IKZF1 mutation,KIT mutation, KRAS mutation, MAX mutation,MEN1 mutation,MET mutation,MLH1 mutation,MSH2 mutation,MSH6 mutation,MUTYH mutation,NF1 mutation,NF2 mutation,Not Applicable,Not Reported,p14ARF mutation,PALB2 mutation,PAX5 mutation,PDGFRA mutation,PHOX2B mutation,PMS2 mutation,PolD mutation,PolE mutation,POT1 mutation,PRKAR1A mutation,PTCH mutation,PTEN mutation,RAD51C mutation,ROS1 mutation,RB1 mutation,RET mutation,SDHAF2 mutation,SDHB mutation,SDHC mutation,SDHD mutation,SETD2 mutation,SMAD4 mutation,SMARCA4 mutation,SMARCB1 mutation,STK11 mutation,TMEM127 mutation,TP53 mutation,TSC1 mutation,TSC2 mutation,unknown,VHL mutation","","",FALSE,Family History,"","","" -Mutational Signatures,"Mutational signatures identified in the patient, includes signatures linked to selected exogenous carcinogens, endogenous and enzymatic modification of DNA or defective DNA repair. Note: Include only outputs of tests that were completed clinically for the participant and only include data from a diagnostic array that was completed prior to research sequencing was done. ","UV light induced mutations,Alkylating Agents (Temozolomide) induced mutations,Tobacco use associated mutations,age of cancer diagnosis,transcriptional strand bias,microsatellite instability (additions and deletions),methylated CpG sequences mutagenesis(deamination of 5-methyl-cytosine) ,Activation Induced Deaminases (AID) associated mutations,APOBEC enzymes associated mutations,altered activity of the error-prone polymerase POLε (POLE) ,localized substitution hypermutation (kataegis),DNA MMR Deficiency,Ig gene hypermutation,Signature 1A,Signature 1B,Signature 2,Signature 3,Signature 4,Signature 5,Signature 6,Signature 7,Signature 8,Signature 9,Signature 10,Signature 11,Signature 12,Signature 13,Signature 14,Signature 15,Signature 16,Signature 17,Signature 18,Signature 19,Signature 20,Signature 21,Other,Data not available,Not Applicable,Not Reported,unknown","","",FALSE,Molecular Test,"","","" -Mismatch Repair System Status,The text that best describes the condition or state of MMR (mismatch repair system) in the patient,"Mismatch repair deficiency MMRD, Mismatch repair proficiency MMPP, Microsatellite instability high MSIH, Microsatellite stable MSS, unknown or other","","",FALSE,Molecular Test,"","","" -Lab Tests for MMR Status,Laboratory tests used to evaluate the status of mismatch repair pathways,"IHC staining for mismatch repair proteins, PCR to evaluate microsatellite instability, MLH1 promoter methylation analysis, BRAF sequencing, Other, Not Applicable, unknown","","",FALSE,Molecular Test,"","","" -Gene Symbol,"The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","","","",TRUE,Molecular Test,"","","" -Molecular Analysis Method,The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"Comparative Genomic Hybridization,Cytogenetics NOS,FISH,Flow Cytometry,IHC,ISH,Karyotype,Microarray,Microsatellite Analysis,Nuclear Staining,Other,RNA Sequencing,RT-PCR,Sequencing NOS,Southern Blotting,Targeted Sequencing,WGS,WXS,unknown,Not Reported,Not Applicable","","",TRUE,Molecular Test,"","","" -Test Result,The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"Abnormal NOS,Copy Number Reported,Equivocal,High,Intermediate,Loss of Expression,Low,Negative,Normal,Overexpressed,Positive,Test Value Reported,unknown,Not Reported,Not Applicable","","",TRUE,Molecular Test,"","","" -AA Change,Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"","","",FALSE,Molecular Test,"","","" -Antigen,The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"BCL6, CA-125, CA19-9, CCND1, CD10, CD117, CD138, CD14, CD15, CD19, CD20, CD22, CD23, CD25, CD3, CD30, CD33, CD34, CD45, CD5, CD56, CD7, CD79A, CEA, HLA-DR, Mesothelin, NSE, Squamous Cell Carcinoma Antigen, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Clinical Biospecimen Type,"The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","Blood, Bone Marrow, Buccal Mucosa, Buffy Coat, Cerebrospinal Fluid, Connective Tissue, Embryonic Fluid, Embryonic Tissue, Feces, Granulocyte, Muscle Tissue, Nerve Tissue, Peritoneal Fluid, Plasma, Pleural Fluid, Saliva, Serum, Skin, Soft Tissue, Tissue NOS, Uninvolved Tissue NOS, Urine, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Blood Test Normal Range Upper,Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.,"","","",FALSE,Molecular Test,"","","" -Blood Test Normal Range Lower,Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.,"","","",FALSE,Molecular Test,"","","" -Cell Count,Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"","","",FALSE,Molecular Test,"","","" -Chromosome,"The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr23,chrM,chrX,chrY,unknown,Not Reported","","",FALSE,Molecular Test,"","","" -Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"Clonal, Non-clonal","","",FALSE,Molecular Test,"","","" -Copy Number,"Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","","","",FALSE,Molecular Test,"","","" -Cytoband,"Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","","","",FALSE,Molecular Test,"","","" -Exon,"Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","","","",FALSE,Molecular Test,"","","" -Histone Family,"The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.","H1, H2A, H2B, H3, H4, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Histone Variant,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.","CENP-A, H2A-Bbd, H2A.X, H2A.Z,H2A.Z.1, H2A.Z.2, H2A.Z.2.2, H3.1, H3.2, H3.3, H3.5, H3.X, H3.Y, H3t (H3.4), mH2A, mH2A.1, mH2A.2, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Intron,"Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.","","","",FALSE,Molecular Test,"","","" -Laboratory Test,"The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.","Absolute Neutrophil,Albumin,Alpha Fetoprotein,B-cell genotyping,Basophil,Beta 2 Microglobulin,Blood Urea Nitrogen,C-Reactive Protein,Calcium,Cellularity,Circulating Tumor Cells,Creatinine,Eosinophil,Epstein-Barr Virus,Glucose,Hematocrit,Hemoglobin,HPV-E6/E7,Human Chorionic Gonadotropin,Human Papillomavirus,Immunoglobulin A,Immunoglobulin G,Immunoglobulin M,Lactate Dehydrogenase,Leukocytes,Luteinizing Hormone,Lymphoblasts,Lymphocytes,M Protein,Metamyelocytes,Myeloblasts,Myelocytes,Neutrophil Bands,Platelets,Prolymphocytes,Promonocytes,Promyelocytes,Segmented Neutrophil,Serum Free Immunoglobulin Light Chain, Kappa,Serum Free Immunoglobulin Light Chain, Lambda,Serum Free Immunoglobulin Light Chain, NOS,Testosterone,Total Bilirubin,Total Protein,unknown,Not Reported","","",FALSE,Molecular Test,"","","" -Loci Abnormal Count,Numeric value used to describe the number of loci determined to be abnormal.,"","","",FALSE,Molecular Test,"","","" -Loci Count,Numeric value used to describe the number of loci tested.,"","","",FALSE,Molecular Test,"","","" -Locus,Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.,"","","",FALSE,Molecular Test,"","","" -Mismatch Repair Mutation,The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"Yes, No, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Molecular Consequence,The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"3 Prime UTR Variant, 5 Prime UTR Variant, Coding Sequence Variant, Downstream Gene Variant, Feature Elongation, Feature Truncation, Frameshift Variant, Incomplete Terminal Codon Variant, Inframe Deletion, Inframe Insertion, Intergenic Variant, Intron Variant, Mature miRNA Variant, Missense Variant, NMD Transcript Variant, Non-coding Transcript Exon Variant, Non-coding Transcript Variant, Protein Altering Variant, Regulatory Region Ablation, Regulatory Region Amplification, Regulatory Region Variant, Splice Acceptor Variant, Splice Donor Variant, Splice Region Variant, Start Lost, Stop Gain, Stop Lost, Stop Retained Variant, Synonymous Variant, TF Binding Site Variant, TFBS Ablation, TFBS Amplification, Transcript Ablation, Transcript Amplification, Upstream Gene Variant","","",FALSE,Molecular Test,"","","" -Pathogenicity,The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).,"Benign, Likely Benign, Likely Pathogenic, Pathogenic, Uncertain Significance","","",FALSE,Molecular Test,"","","" -Ploidy,Text term used to describe the number of sets of homologous chromosomes.,"Aneuploid, Diploid, Hyperdiploid, Hypodiploid, Near Diploid, Tetraploid, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Second Exon,"The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.","","","",FALSE,Molecular Test,"","","" -Second Gene Symbol,"The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","","","",FALSE,Molecular Test,"","","" -Specialized Molecular Test,Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"","","",FALSE,Molecular Test,"","","" -Test Analyte Type,The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"DNA, mRNA, miRNA, Protein Analyte, Total RNA, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Test Units,The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"","","",FALSE,Molecular Test,"","","" -Test Value,The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here,"","","",FALSE,Molecular Test,"","","" -Transcript,Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"","","",FALSE,Molecular Test,"","","" -Variant Origin,The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"Germline, Somatic, unknown","","",FALSE,Molecular Test,"","","" -Variant Type,The text term used to describe the type of genetic variation.,"Alleles, Amplification, Chrimerism, Conversion, Deletion, Deletion-Insertion, Duplication, Extension, Gain, Hypermethylation, Insertion, Inversion, Loss, Methylation, Mosaicism, Other, Partial Methylation, Rearrangement, Repeated Sequences, Splice, Substitution, Translocation, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Zygosity,The text term used to describe the zygosity of a specific genetic variant.,"Heterozygous, Hemizygous, Homozygous, Nullizygous, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Ovarian Cancer Histologic Subtype,Text term to describe the histological subtype of ovarian cancer in the participant,"High-grade serous, Low-grade serous, High-grade endometrioid, Low-grade endometrioid, Clear cell, Mucinous, Sex-cord stromal, Germ cell, Other, unknown, Data not available","","",FALSE,Ovarian Cancer Tier 3,"","","" -Ovarian Cancer Surgical Outcome,Text term that describes the kind of surgical treatment administered.,"R0 resection,Optimal cytoreduction, Sub-optimal cytoreduction, Other, unknown, Data not available","","",FALSE,Ovarian Cancer Tier 3,"","","" -Ovarian Cancer Platinum Status,Text term to indicate the status of treatment with platinum in participant with ovarian cancer,"Platinum-refractory, Platinum-sensitive, Platinum-resistant, Data not available, unknown","","",FALSE,Ovarian Cancer Tier 3,"","","" -Participant ID, ID associated with a patient,"","","",TRUE,Patient,"",,"" -Clinical Data Tier 2,Cancer related clinical data,"","Component, Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Sentinel Lymph Node Count, Sentinel Node Positive Assessment Count, Tumor Extranodal Extension Indicator, Satellite Metastasis Present Indicator, Other Biopsy Resection Site, Extent of Tumor Resection, Precancerous Condition Type, Prior Sites of Radiation, Immunosuppression, Concomitant Medication Received Type, Family Member Vital Status Indicator, COVID19 Occurrence Indicator, COVID19 Current Status, COVID19 Positive Lab Test Indicator, COVID19 Antibody Testing, COVID19 Complications Severity, COVID19 Cancer Treatment Followup, Ecig vape use, Ecig vape 30 day use num, Ecig vape times per day, Type of smoke exposure cumulative years, Chewing tobacco daily use count, Second hand smoke exposure years, Known Genetic Predisposition Mutation, Hereditary Cancer Predisposition Syndrome, Cancer Associated Gene Mutations, Mutational Signatures, Mismatch Repair System Status, Lab Tests for MMR Status, Mode of Cancer Detection, Education Level, Country of Birth, Medically Underserved Area, Rural vs Urban, Cancer Incidence, Cancer Incidence Location","",FALSE,Patient,Patient,"","" -Breast Cancer Tier 3,Breast cancer specific attributes in Clinical Data Tier 3,"","Component, Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Breast Carcinoma Detection Method Type, Breast Carcinoma Histology Category, Invasive Lobular Breast Carcinoma Histologic Category, Invasive Ductal Breast Carcinoma Histologic Category, Breast Biopsy Procedure Finding Type, Breast Quadrant Site, Breast Cancer Assessment Tests, Breast Cancer Genomic Test Performed, Mammaprint Risk Group, Oncotype Risk Group, Breast Carcinoma Estrogen Receptor Status, Breast Carcinoma Progesteroner Receptor Status, Breast Cancer Allred Estrogen Receptor Score, Prior Invasive Breast Disease, Breast Carcinoma ER Status Percentage Value, Breast Carcinoma PR Status Percentage Value, HER2 Breast Carcinoma Copy Number Total, Breast Carcinoma Centromere 17 Copy Number, Breast Carcinoma HER2 Centromere17 Copynumber Total, Breast Carcinoma HER2 Chromosome17 Ratio, Breast Carcinoma Surgical Procedure Name, Breast Carcinoma HER2 Ratio Diagnosis, Breast Carcinoma HER2 Status, Hormone Therapy Breast Cancer Prevention Indicator, Breast Carcinoma ER Staining Intensity, Breast Carcinoma PR Staining Intensity, Oncotype Score, Breast Imaging Performed Type, Multifocal Breast Carcinoma Present Indicator, Multicentric Breast Carcinoma Present Indicator, BIRADS Mammography Breast Density Category","",FALSE,Patient,Patient,"","" -Ovarian Cancer Tier 3,Ovarian cancer specific attributes in Clinical Data Tier 3,"","Component, Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Ovarian Cancer Histologic Subtype, Ovarian Cancer Surgical Outcome, Ovarian Cancer Platinum Status","",FALSE,Patient,Patient,"","" -Demographics,Individual biomedical demographics attributes,"","Component, Participant ID, Ethnicity, Gender, Race, Vital Status, Days to Birth, Country of Residence, Age Is Obfuscated, Year Of Birth","",FALSE,Patient,"","","" -Family History,Individual's family cancer history,"","Component, Participant ID, Relative with Cancer History","",FALSE,Patient,"","","" -Exposure,Individual's exposure to carcenogens,"","Component, Participant ID, Start Days from Index, Smoking Exposure, Alcohol Exposure, Environmental Tobacco Smoke Exposure","",FALSE,Patient,"","","" -Molecular Test,Individual's clinical molecular test data,"","Component, Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Gene Symbol, Molecular Analysis Method, Test Result, AA Change, Antigen, Clinical Biospecimen Type, Blood Test Normal Range Upper, Blood Test Normal Range Lower, Cell Count, Chromosome, Clonality, Copy Number, Cytoband, Exon, Histone Family, Histone Variant, Intron, Laboratory Test, Loci Abnormal Count, Loci Count, Locus, Mismatch Repair Mutation, Molecular Consequence, Pathogenicity, Ploidy, Second Exon, Second Gene Symbol, Specialized Molecular Test, Test Analyte Type, Test Units, Test Value, Transcript, Variant Origin, Variant Type, Zygosity","",FALSE,Patient,"","","" -Start Days from Index,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'","","","",TRUE,Patient,"","","" -Stop Days from Index,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'","","","",FALSE,Patient,"","","" diff --git a/GF.jsonld b/GF.jsonld index 0994f55..f22f2f0 100644 --- a/GF.jsonld +++ b/GF.jsonld @@ -1,64870 +1,35105 @@ { - "@context": { - "bts": "http://schema.biothings.io/", - "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "schema": "http://schema.org/", - "xsd": "http://www.w3.org/2001/XMLSchema#" - }, - "@graph": [ - { - "@id": "schema:Text", - "@type": [ - "schema:DataType", - "rdfs:Class" - ], - "rdfs:comment": "Data type: Text.", - "rdfs:label": "Text" - }, - { - "@id": "schema:Number", - "@type": [ - "schema:DataType", - "rdfs:Class" - ], - "rdfs:comment": "Data type: Number.", - "rdfs:label": "Number" - }, - { - "@id": "schema:Integer", - "@type": "rdfs:Class", - "rdfs:comment": "Data type: Integer.", - "rdfs:label": "Integer", - "rdfs:subClassOf": { - "@id": "schema:Number" - } - }, - { - "@id": "schema:Thing", - "@type": "rdfs:Class", - "rdfs:comment": "Thing", - "rdfs:label": "Thing", - "schema:isPartOf": { - "@id": "http://schema.org" - } - }, - { - "@id": "bts:BiologicalEntity", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "BiologicalEntity", - "rdfs:subClassOf": { - "@id": "schema:Thing" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:OntologyClass", - "@type": "rdfs:Class", - "rdfs:comment": "a concept or class in an ontology, vocabulary or thesaurus", - "rdfs:label": "OntologyClass", - "rdfs:subClassOf": { - "@id": "schema:Thing" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:RelationshipType", - "@type": "rdfs:Class", - "rdfs:comment": "The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.", - "rdfs:label": "RelationshipType", - "rdfs:subClassOf": [ - { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AdoptedDaughter" - }, - { - "@id": "bts:AdoptedSon" - }, - { - "@id": "bts:AdoptiveBrother" - }, - { - "@id": "bts:AdoptiveFather" - }, - { - "@id": "bts:AdoptiveMother" - }, - { - "@id": "bts:AdoptiveSister" - }, - { - "@id": "bts:Aunt" - }, - { - "@id": "bts:Brother" - }, - { - "@id": "bts:Brother-in-law" - }, - { - "@id": "bts:Child" - }, - { - "@id": "bts:Cousin" - }, - { - "@id": "bts:Daughter" - }, - { - "@id": "bts:Daughter-in-law" - }, - { - "@id": "bts:DomesticPartner" - }, - { - "@id": "bts:Father" - }, - { - "@id": "bts:Father-in-law" - }, - { - "@id": "bts:FemaleCousin" - }, - { - "@id": "bts:FirstCousin" - }, - { - "@id": "bts:FirstCousinOnceRemoved" - }, - { - "@id": "bts:FosterBrother" - }, - { - "@id": "bts:FosterDaughter" - }, - { - "@id": "bts:FosterFather" - }, - { - "@id": "bts:FosterMother" - }, - { - "@id": "bts:FosterSister" - }, - { - "@id": "bts:FosterSon" - }, - { - "@id": "bts:FraternalTwinBrother" - }, - { - "@id": "bts:FraternalTwinSibling" - }, - { - "@id": "bts:FraternalTwinSister" - }, - { - "@id": "bts:FullBrother" - }, - { - "@id": "bts:FullSister" - }, - { - "@id": "bts:GrandNephew" - }, - { - "@id": "bts:GrandNiece" - }, - { - "@id": "bts:Grandchild" - }, - { - "@id": "bts:Granddaughter" - }, - { - "@id": "bts:Grandfather" - }, - { - "@id": "bts:Grandmother" - }, - { - "@id": "bts:Grandparent" - }, - { - "@id": "bts:Grandson" - }, - { - "@id": "bts:GreatGrandchild" - }, - { - "@id": "bts:HalfBrother" - }, - { - "@id": "bts:HalfSibling" - }, - { - "@id": "bts:HalfSister" - }, - { - "@id": "bts:Husband" - }, - { - "@id": "bts:IdenticalTwinBrother" - }, - { - "@id": "bts:IdenticalTwinSibling" - }, - { - "@id": "bts:IdenticalTwinSister" - }, - { - "@id": "bts:LegalGuardian" - }, - { - "@id": "bts:MaleCousin" - }, - { - "@id": "bts:MaternalAunt" - }, - { - "@id": "bts:MaternalFirstCousin" - }, - { - "@id": "bts:MaternalFirstCousinOnceRemoved" - }, - { - "@id": "bts:MaternalGrandfather" - }, - { - "@id": "bts:MaternalGrandmother" - }, - { - "@id": "bts:MaternalGrandparent" - }, - { - "@id": "bts:MaternalGreatAunt" - }, - { - "@id": "bts:MaternalGreatGrandparent" - }, - { - "@id": "bts:MaternalGreatUncle" - }, - { - "@id": "bts:MaternalHalfBrother" - }, - { - "@id": "bts:MaternalHalfSibling" - }, - { - "@id": "bts:MaternalHalfSister" - }, - { - "@id": "bts:MaternalUncle" - }, - { - "@id": "bts:Mother" - }, - { - "@id": "bts:Mother-in-law" - }, - { - "@id": "bts:NaturalBrother" - }, - { - "@id": "bts:NaturalChild" - }, - { - "@id": "bts:NaturalDaughter" - }, - { - "@id": "bts:NaturalFather" - }, - { - "@id": "bts:NaturalGrandchild" - }, - { - "@id": "bts:NaturalGrandfather" - }, - { - "@id": "bts:NaturalGrandmother" - }, - { - "@id": "bts:NaturalGrandparent" - }, - { - "@id": "bts:NaturalMother" - }, - { - "@id": "bts:NaturalParent" - }, - { - "@id": "bts:NaturalSibling" - }, - { - "@id": "bts:NaturalSister" - }, - { - "@id": "bts:NaturalSon" - }, - { - "@id": "bts:Nephew" - }, - { - "@id": "bts:Niece" - }, - { - "@id": "bts:NieceSecondDegreeRelative" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Parent" - }, - { - "@id": "bts:PaternalAunt" - }, - { - "@id": "bts:PaternalFirstCousin" - }, - { - "@id": "bts:PaternalFirstCousinOnceRemoved" - }, - { - "@id": "bts:PaternalGrandfather" - }, - { - "@id": "bts:PaternalGrandmother" - }, - { - "@id": "bts:PaternalGrandparent" - }, - { - "@id": "bts:PaternalGreatAunt" - }, - { - "@id": "bts:PaternalGreatGrandparent" - }, - { - "@id": "bts:PaternalGreatUncle" - }, - { - "@id": "bts:PaternalHalfBrother" - }, - { - "@id": "bts:PaternalHalfSibling" - }, - { - "@id": "bts:PaternalHalfSister" - }, - { - "@id": "bts:PaternalUncle" - }, - { - "@id": "bts:Refused" - }, - { - "@id": "bts:Sibling" - }, - { - "@id": "bts:Sister" - }, - { - "@id": "bts:Sister-in-law" - }, - { - "@id": "bts:Son" - }, - { - "@id": "bts:Son-in-law" - }, - { - "@id": "bts:Spouse" - }, - { - "@id": "bts:StepChild" - }, - { - "@id": "bts:StepSibling" - }, - { - "@id": "bts:Stepbrother" - }, - { - "@id": "bts:Stepdaughter" - }, - { - "@id": "bts:Stepfather" - }, - { - "@id": "bts:Stepmother" - }, - { - "@id": "bts:Stepsister" - }, - { - "@id": "bts:Stepson" - }, - { - "@id": "bts:TwinSibling" - }, - { - "@id": "bts:Uncle" - }, - { - "@id": "bts:Unrelated" - }, - { - "@id": "bts:Ward" - }, - { - "@id": "bts:Wife" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Relationship Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GeneOntologyClass", - "@type": "rdfs:Class", - "rdfs:comment": "an ontology class that describes a functional aspect of a gene, gene prodoct or complex", - "rdfs:label": "GeneOntologyClass", - "rdfs:subClassOf": { - "@id": "bts:OntologyClass" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:OrganismTaxon", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "OrganismTaxon", - "rdfs:subClassOf": { - "@id": "bts:OntologyClass" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:OrganismalEntity", - "@type": "rdfs:Class", - "rdfs:comment": "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding molecular entities", - "rdfs:label": "OrganismalEntity", - "rdfs:subClassOf": { - "@id": "bts:BiologicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:IndividualOrganism", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "IndividualOrganism", - "rdfs:subClassOf": { - "@id": "bts:OrganismalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Case", - "@type": "rdfs:Class", - "rdfs:comment": "An individual organism that has a patient role in some clinical context.", - "rdfs:label": "Case", - "rdfs:subClassOf": { - "@id": "bts:IndividualOrganism" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:PopulationOfIndividualOrganisms", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "PopulationOfIndividualOrganisms", - "rdfs:subClassOf": { - "@id": "bts:OrganismalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Biosample", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "Biosample", - "rdfs:subClassOf": { - "@id": "bts:OrganismalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:DiseaseOrPhenotypicFeature", - "@type": "rdfs:Class", - "rdfs:comment": "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate.", - "rdfs:label": "DiseaseOrPhenotypicFeature", - "rdfs:subClassOf": { - "@id": "bts:BiologicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Disease", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "Disease", - "rdfs:subClassOf": { - "@id": "bts:DiseaseOrPhenotypicFeature" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:PhenotypicFeature", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "PhenotypicFeature", - "rdfs:subClassOf": { - "@id": "bts:DiseaseOrPhenotypicFeature" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Environment", - "@type": "rdfs:Class", - "rdfs:comment": "A feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes", - "rdfs:label": "Environment", - "rdfs:subClassOf": { - "@id": "bts:BiologicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:InformationContentEntity", - "@type": "rdfs:Class", - "rdfs:comment": "a piece of information that typically describes some piece of biology or is used as support.", - "rdfs:label": "InformationContentEntity", - "rdfs:subClassOf": { - "@id": "schema:Thing" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:ConfidenceLevel", - "@type": "rdfs:Class", - "rdfs:comment": "Level of confidence in a statement", - "rdfs:label": "ConfidenceLevel", - "rdfs:subClassOf": { - "@id": "bts:InformationContentEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:EvidenceType", - "@type": "rdfs:Class", - "rdfs:comment": "Class of evidence that supports an association", - "rdfs:label": "EvidenceType", - "rdfs:subClassOf": { - "@id": "bts:InformationContentEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Publication", - "@type": "rdfs:Class", - "rdfs:comment": "Any published piece of information. Can refer to a whole publication, or to a part of it (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web as well as journals.", - "rdfs:label": "Publication", - "rdfs:subClassOf": { - "@id": "bts:InformationContentEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:MolecularEntity", - "@type": "rdfs:Class", - "rdfs:comment": "A gene, gene product, small molecule or macromolecule (including protein complex)", - "rdfs:label": "MolecularEntity", - "rdfs:subClassOf": { - "@id": "bts:BiologicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:ChemicalSubstance", - "@type": "rdfs:Class", - "rdfs:comment": "May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part", - "rdfs:label": "ChemicalSubstance", - "rdfs:subClassOf": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Drug", - "@type": "rdfs:Class", - "rdfs:comment": "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease", - "rdfs:label": "Drug", - "rdfs:subClassOf": { - "@id": "bts:ChemicalSubstance" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Metabolite", - "@type": "rdfs:Class", - "rdfs:comment": "Any intermediate or product resulting from metabolism. Includes primary and secondary metabolites.", - "rdfs:label": "Metabolite", - "rdfs:subClassOf": { - "@id": "bts:ChemicalSubstance" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:AnatomicalEntity", - "@type": "rdfs:Class", - "rdfs:comment": "A subcellular location, cell type or gross anatomical part", - "rdfs:label": "AnatomicalEntity", - "rdfs:subClassOf": { - "@id": "bts:OrganismalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:LifeStage", - "@type": "rdfs:Class", - "rdfs:comment": "A stage of development or growth of an organism, including post-natal adult stages", - "rdfs:label": "LifeStage", - "rdfs:subClassOf": { - "@id": "bts:OrganismalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:PlanetaryEntity", - "@type": "rdfs:Class", - "rdfs:comment": "Any entity or process that exists at the level of the whole planet", - "rdfs:label": "PlanetaryEntity", - "rdfs:subClassOf": { - "@id": "schema:Thing" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:EnvironmentalProcess", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "EnvironmentalProcess", - "rdfs:subClassOf": { - "@id": "bts:PlanetaryEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:EnvironmentalFeature", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "EnvironmentalFeature", - "rdfs:subClassOf": { - "@id": "bts:PlanetaryEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:ClinicalEntity", - "@type": "rdfs:Class", - "rdfs:comment": "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities", - "rdfs:label": "ClinicalEntity", - "rdfs:subClassOf": { - "@id": "schema:Thing" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:ClinicalTrial", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "ClinicalTrial", - "rdfs:subClassOf": { - "@id": "bts:ClinicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:ClinicalIntervention", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "ClinicalIntervention", - "rdfs:subClassOf": { - "@id": "bts:ClinicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Device", - "@type": "rdfs:Class", - "rdfs:comment": "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment", - "rdfs:label": "Device", - "rdfs:subClassOf": { - "@id": "schema:Thing" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:GenomicEntity", - "@type": "rdfs:Class", - "rdfs:comment": "an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)", - "rdfs:label": "GenomicEntity", - "rdfs:subClassOf": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Genome", - "@type": "rdfs:Class", - "rdfs:comment": "A genome is the sum of genetic material within a cell or virion.", - "rdfs:label": "Genome", - "rdfs:subClassOf": { - "@id": "bts:GenomicEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Transcript", - "@type": "rdfs:Class", - "rdfs:comment": "An RNA synthesized on a DNA or RNA template by an RNA polymerase", - "rdfs:label": "Transcript", - "rdfs:subClassOf": { - "@id": "bts:GenomicEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Exon", - "@type": "rdfs:Class", - "rdfs:comment": "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing", - "rdfs:label": "Exon", - "rdfs:subClassOf": { - "@id": "bts:GenomicEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:CodingSequence", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "CodingSequence", - "rdfs:subClassOf": { - "@id": "bts:GenomicEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:MacromolecularMachine", - "@type": "rdfs:Class", - "rdfs:comment": "A union of gene, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this.", - "rdfs:label": "MacromolecularMachine", - "rdfs:subClassOf": { - "@id": "bts:GenomicEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:GeneOrGeneProduct", - "@type": "rdfs:Class", - "rdfs:comment": "a union of genes or gene products. Frequently an identifier for one will be used as proxy for another", - "rdfs:label": "GeneOrGeneProduct", - "rdfs:subClassOf": { - "@id": "bts:MacromolecularMachine" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Gene", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "Gene", - "rdfs:subClassOf": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:GeneProduct", - "@type": "rdfs:Class", - "rdfs:comment": "The functional molecular product of a single gene. 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"@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "schema:Text" - } - }, - { - "@id": "bts:hgnc", - "@type": "rdf:Property", - "rdfs:comment": "HGNC ID for gene", - "rdfs:label": "hgnc", - "schema:domainIncludes": { - "@id": "bts:Gene" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "schema:Integer" - } - }, - { - "@id": "bts:entrez", - "@type": "rdf:Property", - "rdfs:comment": "Entrez ID for gene", - "rdfs:label": "entrez", - "schema:domainIncludes": { - "@id": "bts:Gene" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "schema:Integer" - } - }, - { - "@id": "bts:refseq", - "@type": "rdf:Property", - "rdfs:comment": "Refseq ID for gene, protein or transcript", - "rdfs:label": "refseq", - "schema:domainIncludes": [ - { - "@id": "bts:Transcript" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "schema:Text" - } - }, - { - "@id": "bts:omim", - "@type": "rdf:Property", - "rdfs:comment": "Refseq ID for gene, protein or transcript", - "rdfs:label": "omim", - "schema:domainIncludes": [ - { - "@id": "bts:Disease" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "schema:Integer" - } - }, - { - "@id": "bts:umls", - "@type": "rdf:Property", - "rdfs:comment": "Refseq ID for gene, protein or transcript", - "rdfs:label": "umls", - "schema:domainIncludes": { - "@id": "bts:Disease" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "schema:Text" - } - }, - { - "@id": "bts:homologousTo", - "@type": "rdf:Property", - "rdfs:comment": "Shared ancestry between protein or gene", - "rdfs:label": "homologousTo", - "schema:domainIncludes": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneOrGeneProduct" - } - }, - { - "@id": "bts:molecularlyInteractsWith", - "@type": "rdf:Property", - "rdfs:comment": null, - "rdfs:label": "molecularlyInteractsWith", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:geneticallyInteractsWith", - "@type": "rdf:Property", - "rdfs:comment": "holds between two genes whose phenotypic effects are dependent on each other in some way - such that their combined phenotypic effects are the result of some interaction between the activity of their gene products. 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"@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesAbundanceOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the amount of the other within a system of interest", - "rdfs:label": "decreasesAbundanceOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsActivityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the activity of the other within a system of interest", - "rdfs:label": "affectsActivityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesActivityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the activity of the other within a system of interest", - "rdfs:label": "increasesActivityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesActivityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the activity of the other within a system of interest", - "rdfs:label": "decreasesActivityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsExpressionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the level of expression of the other within a system of interest", - "rdfs:label": "affectsExpressionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:increasesExpressionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the level of expression of the other within a system of interest", - "rdfs:label": "increasesExpressionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:decreasesExpressionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the level of expression of the other within a system of interest", - "rdfs:label": "decreasesExpressionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:affectsFoldingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the rate or quality of folding of the other ", - "rdfs:label": "affectsFoldingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesFoldingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate or quality of folding of the other ", - "rdfs:label": "increasesFoldingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesFoldingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate or quality of folding of the other ", - "rdfs:label": "decreasesFoldingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsLocalizationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the localization of the other within a system of interest", - "rdfs:label": "affectsLocalizationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesLocalizationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the proper localization of the other within a system of interest", - "rdfs:label": "increasesLocalizationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesLocalizationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the proper localization of the other within a system of interest", - "rdfs:label": "decreasesLocalizationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsMetabolicProcessingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the metabolic processing of the other within a system of interest", - "rdfs:label": "affectsMetabolicProcessingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesMetabolicProcessingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of metabolic processing of the other within a system of interest", - "rdfs:label": "increasesMetabolicProcessingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesMetabolicProcessingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of metabolic processing of the other within a system of interest", - "rdfs:label": "decreasesMetabolicProcessingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsMolecularModificationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one leads changes in the molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", - "rdfs:label": "affectsMolecularModificationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesMolecularModificationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one leads to increased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", - "rdfs:label": "increasesMolecularModificationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesMolecularModificationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one leads to decreased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", - "rdfs:label": "decreasesMolecularModificationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsSynthesisOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of chemical synthesis of the other", - "rdfs:label": "affectsSynthesisOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesSynthesisOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of chemical synthesis of the other", - "rdfs:label": "increasesSynthesisOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesSynthesisOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of chemical synthesis of the other", - "rdfs:label": "decreasesSynthesisOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsDegradationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of degradation of the other within a system of interest", - "rdfs:label": "affectsDegradationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesDegradationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of degradation of the other within a system of interest", - "rdfs:label": "increasesDegradationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesDegradationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of degradation of the other within a system of interest", - "rdfs:label": "decreasesDegradationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsMutationRateOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity impacts the rate of mutation of the genomic entity within a system of interest", - "rdfs:label": "affectsMutationRateOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:increasesMutationRateOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity increases the rate of mutation of the genomic entity within a system of interest", - "rdfs:label": "increasesMutationRateOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:decreasesMutationRateOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity decreases the rate of mutation of the genomic entity within a system of interest", - "rdfs:label": "decreasesMutationRateOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:affectsResponseTo", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other", - "rdfs:label": "affectsResponseTo", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesResponseTo", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other", - "rdfs:label": "increasesResponseTo", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesResponseTo", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other", - "rdfs:label": "decreasesResponseTo", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsSplicingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity impacts the splicing of the mRNA", - "rdfs:label": "affectsSplicingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Transcript" - } - }, - { - "@id": "bts:increasesSplicingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity increases the proper splicing of the mRNA", - "rdfs:label": "increasesSplicingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Transcript" - } - }, - { - "@id": "bts:decreasesSplicingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity decreases the proper splicing of the mRNA", - "rdfs:label": "decreasesSplicingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Transcript" - } - }, - { - "@id": "bts:affectsStabilityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the stability of the other within a system of interest", - "rdfs:label": "affectsStabilityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesStabilityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the stability of the other within a system of interest", - "rdfs:label": "increasesStabilityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesStabilityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the stability of the other within a system of interest", - "rdfs:label": "decreasesStabilityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsTransportOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of transport of the other across some boundary in a system of interest", - 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"@type": "rdfs:Class", - "rdfs:comment": "Microscope type (manufacturer, model, etc) used for this experiment", - "rdfs:label": "Microscope", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Microscope", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Objective", - "@type": "rdfs:Class", - "rdfs:comment": "Objective", - "rdfs:label": "Objective", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Objective", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NominalMagnification", - "@type": "rdfs:Class", - "rdfs:comment": "The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units)", - "rdfs:label": "NominalMagnification", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - 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Floating point value > 0.", - "rdfs:label": "LensNA", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "LensNA", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:WorkingDistance", - "@type": "rdfs:Class", - "rdfs:comment": "The working distance of the lens, expressed as a floating point number. Floating point > 0.", - "rdfs:label": "WorkingDistance", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "WorkingDistance", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:WorkingDistanceUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:WorkingDistanceUnit", - "@type": "rdfs:Class", - "rdfs:comment": "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "WorkingDistanceUnit", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "WorkingDistanceUnit", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Immersion", - "@type": "rdfs:Class", - "rdfs:comment": "Immersion medium", - "rdfs:label": "Immersion", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Air" - }, - { - "@id": "bts:Oil" - }, - { - "@id": "bts:Water" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "Immersion", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Pyramid", - "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain pyramid of images", - "rdfs:label": "Pyramid", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Pyramid", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Zstack", - "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a Z-stack of images", - "rdfs:label": "Zstack", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Zstack", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Tseries", - "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a time-series of images", - "rdfs:label": "Tseries", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Tseries", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PassedQC", - "@type": "rdfs:Class", - "rdfs:comment": "Did all channels pass QC (if not add free text Comment)", - "rdfs:label": "PassedQC", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No-ChannelsQC" - } - ], - "sms:displayName": "Passed QC", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:No-ChannelsQC", - "@type": "rdfs:Class", - "rdfs:comment": "Not all channels passed QC", - "rdfs:label": "No-ChannelsQC", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "No - Channels QC", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Comment" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:Comment", - "@type": "rdfs:Class", - "rdfs:comment": "Free text field (generally for QC comment)", - "rdfs:label": "Comment", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Comment", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FOVnumber", - "@type": "rdfs:Class", - "rdfs:comment": "Index of FOV (as it pertains to its sequence order). Integer >= 1", - "rdfs:label": "FOVnumber", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FOV number", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FOVX", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension. Floating point", - "rdfs:label": "FOVX", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FOVX", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:FOVXUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:FOVXUnit", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVXUnit", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "FOVXUnit", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FOVY", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension. Floating point value", - "rdfs:label": "FOVY", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FOVY", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:FOVYUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:FOVYUnit", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVYUnit", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "FOVYUnit", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FrameAveraging", - "@type": "rdfs:Class", - "rdfs:comment": "Number of frames averaged together (if no averaging, set to 1). Integer >= 1", - "rdfs:label": "FrameAveraging", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Frame Averaging", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImageID", - "@type": "rdfs:Class", - "rdfs:comment": "Unique internal image identifier. eg \"\"Image:0\"\". (To be extracted from OME-XML)", - "rdfs:label": "ImageID", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Image ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DimensionOrder", - "@type": "rdfs:Class", - "rdfs:comment": "The order in which the individual planes of data are interleaved.", - "rdfs:label": "DimensionOrder", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:XYZCT" - }, - { - "@id": "bts:XYZTC" - }, - { - "@id": "bts:XYCTZ" - }, - { - "@id": "bts:XYCZT" - }, - { - "@id": "bts:XYTZC" - }, - { - "@id": "bts:ZYX" - } - ], - "sms:displayName": "DimensionOrder", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PhysicalSizeX", - "@type": "rdfs:Class", - "rdfs:comment": "Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeX", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "PhysicalSizeX", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PhysicalSizeXUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:PhysicalSizeXUnit", - "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeXUnit", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeXUnit", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PhysicalSizeY", - "@type": "rdfs:Class", - "rdfs:comment": "Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeY", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "PhysicalSizeY", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PhysicalSizeYUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:PhysicalSizeYUnit", - "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeYUnit", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeYUnit", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PhysicalSizeZ", - "@type": "rdfs:Class", - "rdfs:comment": "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeZ", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "PhysicalSizeZ", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PhysicalSizeZUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:PhysicalSizeZUnit", - "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeZUnit", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeZUnit", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PixelsBigEndian", - "@type": "rdfs:Class", - "rdfs:comment": "Boolean (True/False)", - "rdfs:label": "PixelsBigEndian", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:True" - }, - { - "@id": "bts:False" - } - ], - "sms:displayName": "Pixels BigEndian", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PlaneCount", - "@type": "rdfs:Class", - "rdfs:comment": "Number of Z-planes (not to be confused with downsampled \"\"pyramid\"\"). Integer >=1", - "rdfs:label": "PlaneCount", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "PlaneCount", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SizeC", - "@type": "rdfs:Class", - "rdfs:comment": "Number of channels. Integer >= 1", - "rdfs:label": "SizeC", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SizeC", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SizeT", - "@type": "rdfs:Class", - "rdfs:comment": "Number of time points. Integer >= 1", - "rdfs:label": "SizeT", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SizeT", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SizeX", - "@type": "rdfs:Class", - "rdfs:comment": "Size of image: X dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeX", - "rdfs:subClassOf": [ - { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SizeX", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SizeY", - "@type": "rdfs:Class", - "rdfs:comment": "Size of image: Y dimension (in pixels). 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RNA / DNA / Protein Lysate) obtained from a specimen", - "rdfs:label": "AnalyteBiospecimenType", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Analyte Biospecimen Type", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:AnalyteType" - }, - { - "@id": "bts:FixationDuration" - }, - { - "@id": "bts:SlideChargeType" - }, - { - "@id": "bts:SectionThicknessValue" - }, - { - "@id": "bts:SectioningDaysfromIndex" - }, - { - "@id": "bts:ShippingConditionType" - }, - { - "@id": "bts:IschemicTime" - }, - { - "@id": "bts:IschemicTemperature" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:TissueBiospecimenType", - "@type": "rdfs:Class", - "rdfs:comment": "Tissue biospecimen", - "rdfs:label": "TissueBiospecimenType", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tissue Biospecimen Type", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:IschemicTime" - }, - { - "@id": "bts:IschemicTemperature" - }, - { - "@id": "bts:SiteofResectionorBiopsy" - }, - { - "@id": "bts:SpecimenLaterality" - }, - { - "@id": "bts:PortionWeight" - }, - { - "@id": "bts:TotalVolume" - }, - { - "@id": "bts:TumorTissueType" - }, - { - "@id": "bts:HistologicMorphologyCode" - }, - { - "@id": "bts:PreservationMethod" - }, - { - "@id": "bts:BiospecimenDimension1" - }, - { - "@id": "bts:BiospecimenDimension2" - }, - { - "@id": "bts:BiospecimenDimension3" - }, - { - "@id": "bts:SectionNumberinSequence" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:BoneMarrowBiospecimenType", - "@type": "rdfs:Class", - "rdfs:comment": "Bone Marrow biospecimen", - "rdfs:label": "BoneMarrowBiospecimenType", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Bone Marrow Biospecimen Type", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:IschemicTime" - }, - { - "@id": "bts:IschemicTemperature" - }, - { - "@id": "bts:SiteofResectionorBiopsy" - }, - { - "@id": "bts:SpecimenLaterality" - }, - { - "@id": "bts:PortionWeight" - }, - { - "@id": "bts:TotalVolume" - }, - { - "@id": "bts:TumorTissueType" - }, - { - "@id": "bts:HistologicMorphologyCode" - }, - { - "@id": "bts:PreservationMethod" - }, - { - "@id": "bts:BiospecimenDimension1" - }, - { - "@id": "bts:BiospecimenDimension2" - }, - { - "@id": "bts:BiospecimenDimension3" - }, - { - "@id": "bts:SectionNumberinSequence" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:UrineBiospecimenType", - "@type": "rdfs:Class", - "rdfs:comment": "Urine biospecimen", - "rdfs:label": "UrineBiospecimenType", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Urine Biospecimen Type", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:IschemicTime" - }, - { - "@id": "bts:IschemicTemperature" - }, - { - "@id": "bts:SiteofResectionorBiopsy" - }, - { - "@id": "bts:SpecimenLaterality" - }, - { - "@id": "bts:PortionWeight" - }, - { - "@id": "bts:TotalVolume" - }, - { - "@id": "bts:TumorTissueType" - }, - { - "@id": "bts:HistologicMorphologyCode" - }, - { - "@id": "bts:PreservationMethod" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:BloodBiospecimenType", - "@type": "rdfs:Class", - "rdfs:comment": "Blood biospecimen", - "rdfs:label": "BloodBiospecimenType", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Blood Biospecimen Type", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:ShippingConditionType" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:TimepointLabel", - "@type": "rdfs:Class", - "rdfs:comment": "Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.", - "rdfs:label": "TimepointLabel", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Timepoint Label", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CollectionDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was obtained.", - "rdfs:label": "CollectionDaysfromIndex", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Collection Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AdjacentSampleIDs", - "@type": "rdfs:Class", - "rdfs:comment": "List of Identifiers (separated by commas) of adjacent biospecimens cut from the same sample", - "rdfs:label": "AdjacentSampleIDs", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adjacent Sample IDs", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MountingMedium", - "@type": "rdfs:Class", - "rdfs:comment": "The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media", - "rdfs:label": "MountingMedium", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Aqueouswaterbased" - }, - { - "@id": "bts:Non-AqueousSolventbased" - }, - { - "@id": "bts:Xylene" - }, - { - "@id": "bts:Toluene" - }, - { - "@id": "bts:AntifadewithDAPI" - }, - { - "@id": "bts:AntifadewithoutDAPI" - }, - { - "@id": "bts:PBS" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Mounting Medium", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AnalyteType", - "@type": "rdfs:Class", - "rdfs:comment": "The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen", - "rdfs:label": "AnalyteType", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:CfDNAAnalyte" - }, - { - "@id": "bts:DNAAnalyte" - }, - { - "@id": "bts:RNAAnalyte" - }, - { - "@id": "bts:TotalRNAAnalyte" - }, - { - "@id": "bts:TissueBlockAnalyte" - }, - { - "@id": "bts:TissueSectionAnalyte" - }, - { - "@id": "bts:PBMCsorPlasmaorSerumAnalyte" - }, - { - "@id": "bts:CDNALibrariesAnalyte" - }, - { - "@id": "bts:PBMCs" - }, - { - "@id": "bts:Plasma" - }, - { - "@id": "bts:SerumAnalyte" - } - ], - "sms:displayName": "Analyte Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AcquisitionMethodType", - "@type": "rdfs:Class", - "rdfs:comment": "Records the method of acquisition or source for the specimen under consideration.", - "rdfs:label": "AcquisitionMethodType", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Autopsy" - }, - { - "@id": "bts:Biopsy" - }, - { - "@id": "bts:FineNeedleAspirate" - }, - { - "@id": "bts:SurgicalResection" - }, - { - "@id": "bts:PunchBiopsy" - }, - { - "@id": "bts:ShaveBiopsy" - }, - { - "@id": "bts:Excision" - }, - { - "@id": "bts:Re-excision" - }, - { - "@id": "bts:SentinelNodeBiopsy" - }, - { - "@id": "bts:Lymphadenectomy-RegionalNodes" - }, - { - "@id": "bts:OtherAcquisitionMethod" - }, - { - "@id": "bts:Noninducedsputum" - }, - { - "@id": "bts:Inducedsputum" - }, - { - "@id": "bts:BAL(bronchialalveolarlavage)" - }, - { - "@id": "bts:Cytobrush" - }, - { - "@id": "bts:Blooddraw" - }, - { - "@id": "bts:Fluidcollection" - }, - { - "@id": "bts:Forcepsbiopsy" - }, - { - "@id": "bts:Coreneedlebiopsy" - }, - { - "@id": "bts:Endoscopicbiopsy" - }, - { - "@id": "bts:Notspecified" - } - ], - "sms:displayName": "Acquisition Method Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:OtherAcquisitionMethod", - "@type": "rdfs:Class", - "rdfs:comment": "A custom acquisition method", - "rdfs:label": "OtherAcquisitionMethod", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Other Acquisition Method", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:AcquisitionMethodOtherSpecify" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:AcquisitionMethodOtherSpecify", - "@type": "rdfs:Class", - "rdfs:comment": "A custom acquisition method [Text - max length 100 characters]", - "rdfs:label": "AcquisitionMethodOtherSpecify", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Acquisition Method Other Specify", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PreservationMethod", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the method used to preserve the sample.", - "rdfs:label": "PreservationMethod", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Archival" - }, - { - "@id": "bts:Cryopreserved" - }, - { - "@id": "bts:Cryopreservationinliquidnitrogen-deadtissue" - }, - { - "@id": "bts:Cryopreservationindryice-deadtissue" - }, - { - "@id": "bts:Cryopreservationinliquidnitrogen-livecells" - }, - { - "@id": "bts:Formalinfixedparaffinembedded-FFPE" - }, - { - "@id": "bts:Formalinfixed-unbuffered" - }, - { - "@id": "bts:Formalinfixed-buffered" - }, - { - "@id": "bts:Fresh" - }, - { - "@id": "bts:FreshdissociatedandsinglecellsortedintoplatesinNP40buffer" - }, - { - "@id": "bts:OCT" - }, - { - "@id": "bts:SnapFrozen" - }, - { - "@id": "bts:Frozen" - }, - { - "@id": "bts:Negative80DegC" - }, - { - "@id": "bts:LiquidNitrogen" - }, - { - "@id": "bts:Freshdissociated" - }, - { - "@id": "bts:Freshdissociatedandsinglecellsorted" - }, - { - "@id": "bts:Freshdissociatedandsinglecellsortedintoplates" - }, - { - "@id": "bts:Methacarnfixedparaffinembedded-MFPE" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Preservation Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:FixativeType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the type of fixative used to preserve a tissue specimen", - "rdfs:label": "FixativeType", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Acetone" - }, - { - "@id": "bts:Alcohol" - }, - { - "@id": "bts:Formalin" - }, - { - "@id": "bts:Glutaraldehyde" - }, - { - "@id": "bts:OCTmedia" - }, - { - "@id": "bts:RNAlater" - }, - { - "@id": "bts:Saline" - }, - { - "@id": "bts:95%Ethanol" - }, - { - "@id": "bts:Dimidoester" - }, - { - "@id": "bts:Carbodiimide" - }, - { - "@id": "bts:Dimethylacetamide" - }, - { - "@id": "bts:Para-benzoquinone" - }, - { - "@id": "bts:PAXgenetissue" - }, - { - "@id": "bts:TCLlysisbuffer" - }, - { - "@id": "bts:NP40lysisbuffer" - }, - { - "@id": "bts:Methacarn" - }, - { - "@id": "bts:Cryo-store" - }, - { - "@id": "bts:Carnoy'sFixative" - }, - { - "@id": "bts:Polaxamer" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:None" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Fixative Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:FixationDuration", - "@type": "rdfs:Class", - "rdfs:comment": "The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)", - "rdfs:label": "FixationDuration", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fixation Duration", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:IschemicTime", - "@type": "rdfs:Class", - "rdfs:comment": "Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.", - "rdfs:label": "IschemicTime", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ischemic Time", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:IschemicTemperature", - "@type": "rdfs:Class", - "rdfs:comment": "Specify whether specimen experienced warm or cold ischemia.", - "rdfs:label": "IschemicTemperature", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:WarmIschemia" - }, - { - "@id": "bts:ColdIschemia" - }, - { - "@id": "bts:Ambientair" - }, - { - "@id": "bts:4Cwetice" - }, - { - "@id": "bts:Negative-20C" - }, - { - "@id": "bts:DryIce" - }, - { - "@id": "bts:LiquidNitrogen" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Ischemic Temperature", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CollectionMedia", - "@type": "rdfs:Class", - "rdfs:comment": "Material Specimen is collected into post procedure", - "rdfs:label": "CollectionMedia", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:DMEM" - }, - { - "@id": "bts:DMEM+Serum" - }, - { - "@id": "bts:RPMI" - }, - { - "@id": "bts:RPMI+Serum" - }, - { - "@id": "bts:PBS" - }, - { - "@id": "bts:PBS+Serum" - }, - { - "@id": "bts:None" - } - ], - "sms:displayName": "Collection Media", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SpecimenLaterality", - "@type": "rdfs:Class", - "rdfs:comment": "For samples in paired organs, designates the side from which obtained.", - "rdfs:label": "SpecimenLaterality", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Bilateral" - }, - { - "@id": "bts:Left" - }, - { - "@id": "bts:Right" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Specimen Laterality", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PortionWeight", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the sample portion weight, measured in milligrams.", - "rdfs:label": "PortionWeight", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Portion Weight", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TotalVolume", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value for the total amount of sample or specimen", - "rdfs:label": "TotalVolume", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Total Volume", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:TotalVolumeUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:TotalVolumeUnit", - "@type": "rdfs:Class", - "rdfs:comment": "Unit of measurement used for the total amount of sample or specimen", - "rdfs:label": "TotalVolumeUnit", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:ML" - }, - { - "@id": "bts:Mm^3" - }, - { - "@id": "bts:Cm^2" - } - ], - "sms:displayName": "Total Volume Unit", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorTissueType", - "@type": "rdfs:Class", - "rdfs:comment": "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)", - "rdfs:label": "TumorTissueType", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AdditionalPrimary" - }, - { - "@id": "bts:Localrecurrence" - }, - { - "@id": "bts:Metastatic" - }, - { - "@id": "bts:Premalignant" - }, - { - "@id": "bts:Primary" - }, - { - "@id": "bts:Recurrent" - }, - { - "@id": "bts:Normal" - }, - { - "@id": "bts:Normaladjacent" - }, - { - "@id": "bts:Normaldistant" - }, - { - "@id": "bts:Posttherapy" - }, - { - "@id": "bts:Posttherapyneoadjuvant" - }, - { - "@id": "bts:Posttherapyadjuvant" - }, - { - "@id": "bts:NotOtherwiseSpecified" - }, - { - "@id": "bts:Premalignant-insitu" - }, - { - "@id": "bts:Atypia-hyperplasia" - } - ], - "sms:displayName": "Tumor Tissue Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:HistologicMorphologyCode", - "@type": "rdfs:Class", - "rdfs:comment": "Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. 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"rdfs:label": "SectionThicknessValue", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Section Thickness Value", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SectioningDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was sectioned after collection", - "rdfs:label": "SectioningDaysfromIndex", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sectioning Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:StorageMethod", - "@type": "rdfs:Class", - "rdfs:comment": "The method by which a biomaterial was stored after preservation or before another protocol was used.", - "rdfs:label": "StorageMethod", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Ambienttemperature" - }, - { - "@id": "bts:Cutslide" - }, - { - "@id": "bts:Fresh" - }, - { - "@id": "bts:Frozenat-70C" - }, - { - "@id": "bts:Frozenat-80C" - }, - { - "@id": "bts:Frozenat-150C" - }, - { - "@id": "bts:Frozeninliquidnitrogen" - }, - { - "@id": "bts:Frozeninvaporphase" - }, - { - "@id": "bts:Paraffinblock" - }, - { - "@id": "bts:RNAlaterat4C" - }, - { - "@id": "bts:RNAlaterat25C" - }, - { - "@id": "bts:RNAlaterat-20C" - }, - { - "@id": "bts:Refrigeratedat4degrees" - }, - { - "@id": "bts:Refrigeratedvacuumchamber" - }, - { - "@id": "bts:4Cinvacuumchamber" - }, - { - "@id": "bts:Desiccantat4C" - }, - { - "@id": "bts:NotApplicable" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Storage Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ProcessingDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was processed", - "rdfs:label": "ProcessingDaysfromIndex", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Processing Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ShippingConditionType", - "@type": "rdfs:Class", - "rdfs:comment": "Text descriptor of the shipping environment of a biospecimen.", - "rdfs:label": "ShippingConditionType", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AmbientPack" - }, - { - "@id": "bts:ColdPack" - }, - { - "@id": "bts:DryIce" - }, - { - "@id": "bts:IcePack" - }, - { - "@id": "bts:LiquidNitrogen" - }, - { - "@id": "bts:SpecimenatRoomTemperature" - }, - { - "@id": "bts:OtherShippingEnvironment" - }, - { - "@id": "bts:NotShipped" - } - ], - "sms:displayName": "Shipping Condition Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SiteDataSource", - "@type": "rdfs:Class", - "rdfs:comment": "Text to identify the data source for the specimen/sample from within the center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.", - "rdfs:label": "SiteDataSource", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Site Data Source", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProcessingLocation", - "@type": "rdfs:Class", - "rdfs:comment": "Site with an center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.", - "rdfs:label": "ProcessingLocation", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Processing Location", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistologyAssessmentBy", - "@type": "rdfs:Class", - "rdfs:comment": "Text term describing who (in what role) made the histological assessments of the sample", - "rdfs:label": "HistologyAssessmentBy", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Pathologist" - }, - { - "@id": "bts:ResearchScientist" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Histology Assessment By", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistologyAssessmentMedium", - "@type": "rdfs:Class", - "rdfs:comment": "The method of assessment used to characterize histology", - "rdfs:label": "HistologyAssessmentMedium", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Digital" - }, - { - "@id": "bts:Microscopy" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Histology Assessment Medium", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorInfiltratingLymphocytes", - "@type": "rdfs:Class", - "rdfs:comment": "Measure of Tumor-Infiltrating Lymphocytes [Number]", - "rdfs:label": "TumorInfiltratingLymphocytes", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tumor Infiltrating Lymphocytes", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DegreeofDysplasia", - "@type": "rdfs:Class", - "rdfs:comment": "Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.", - "rdfs:label": "DegreeofDysplasia", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Normalorbasalcellhyperplasiaormetaplasia" - }, - { - "@id": "bts:Milddysplasia" - }, - { - "@id": "bts:Moderatedysplasia" - }, - { - "@id": "bts:Severedysplasia" - }, - { - "@id": "bts:CarcinomainSitu" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Degree of Dysplasia", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DysplasiaFraction", - "@type": "rdfs:Class", - "rdfs:comment": "Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5]", - "rdfs:label": "DysplasiaFraction", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Dysplasia Fraction", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NumberProliferatingCells", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).", - "rdfs:label": "NumberProliferatingCells", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Number Proliferating Cells", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentEosinophilInfiltration", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.", - "rdfs:label": "PercentEosinophilInfiltration", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Eosinophil Infiltration", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentGranulocyteInfiltration", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.", - "rdfs:label": "PercentGranulocyteInfiltration", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Granulocyte Infiltration", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentInflamInfiltration", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.", - "rdfs:label": "PercentInflamInfiltration", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Inflam Infiltration", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentLymphocyteInfiltration", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.", - "rdfs:label": "PercentLymphocyteInfiltration", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Lymphocyte Infiltration", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentMonocyteInfiltration", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.", - "rdfs:label": "PercentMonocyteInfiltration", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Monocyte Infiltration", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentNecrosis", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.", - "rdfs:label": "PercentNecrosis", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Necrosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentNeutrophilInfiltration", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.", - "rdfs:label": "PercentNeutrophilInfiltration", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Neutrophil Infiltration", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentNormalCells", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.", - "rdfs:label": "PercentNormalCells", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Normal Cells", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentStromalCells", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.", - "rdfs:label": "PercentStromalCells", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Stromal Cells", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentTumorCells", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the percentage of infiltration by tumor cells in a sample.", - "rdfs:label": "PercentTumorCells", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Tumor Cells", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentTumorNuclei", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.", - "rdfs:label": "PercentTumorNuclei", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Tumor Nuclei", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FiducialMarker", - "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.", - "rdfs:label": "FiducialMarker", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:NuclearStain-DAPI" - }, - { - "@id": "bts:FluorescentBeads" - }, - { - "@id": "bts:GridSlides-Hemocytometer" - }, - { - "@id": "bts:AdhesiveMarkers" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Fiducial Marker", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SlicingMethod", - "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: the method by which the tissue was sliced.", - "rdfs:label": "SlicingMethod", - "rdfs:subClassOf": [ - 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}, - { - "@id": "bts:PrecursorB-celllymphoblasticleukemia" - }, - { - "@id": "bts:PrecursorB-celllymphoblasticlymphoma" - }, - { - "@id": "bts:PrecursorcelllymphoblasticleukemiaNOS" - }, - { - "@id": "bts:PrecursorT-celllymphoblasticleukemia" - }, - { - "@id": "bts:PrecursorT-celllymphoblasticlymphoma" - }, - { - "@id": "bts:Preleukemia" - }, - { - "@id": "bts:Preleukemicsyndrome" - }, - { - "@id": "bts:Primaryamyloidosis" - }, - { - "@id": "bts:Pro-BALL" - }, - { - "@id": "bts:Pro-TALL" - }, - { - "@id": "bts:ProstaticintraepithelialneoplasiagradeIII" - }, - { - "@id": "bts:Pulmonaryadenomatosis" - }, - { - "@id": "bts:Pulmonaryarteryintimalsarcoma" - }, - { - "@id": "bts:Pulmonaryblastoma" - }, - { - "@id": "bts:Renalcarcinomacollectingducttype" - }, - { - "@id": "bts:Renalcelladenocarcinoma" - }, - { - "@id": "bts:Renalcellcarcinomachromophobetype" - }, - { - "@id": "bts:RenalcellcarcinomaNOS" - }, - { - "@id": "bts:Renalcellcarcinomasarcomatoid" - }, - { - "@id": "bts:Renalcellcarcinomaspindlecell" - }, - { - "@id": "bts:Renalcellcarcinomaunclassified" - }, - { - "@id": "bts:Renalmedullarycarcinoma" - }, - { - "@id": "bts:Rhabdoidmeningioma" - }, - { - "@id": "bts:Rhabdoidsarcoma" - }, - { - "@id": "bts:RhabdoidtumorNOS" - }, - { - "@id": "bts:RhabdomyomaNOS" - }, - { - "@id": "bts:Rhabdomyosarcomawithganglionicdifferentiation" - }, - { - "@id": "bts:RhabdomyosarcomaNOS" - }, - { - "@id": "bts:Rhabdosarcoma" - }, - { - "@id": "bts:Rodentulcer" - }, - { - "@id": "bts:SarcomaNOS" - }, - { - "@id": "bts:Sclerosinghemangioma" - }, - { - "@id": "bts:Sclerosinghepaticcarcinoma" - }, - { - "@id": "bts:Secondarycarcinoma" - }, - { - "@id": "bts:Secretorycarcinomaofbreast" - }, - { - "@id": "bts:SerouscystadenocarcinomaNOS" - }, - { - "@id": "bts:Seroussurfacepapillarycarcinoma" - }, - { - "@id": "bts:High-gradeserouscarcinoma" - }, - { - "@id": "bts:Skinappendagecarcinoma" - }, - { - "@id": "bts:SmallcellcarcinomaNOS" - }, - { - "@id": "bts:Smallcellneuroendocrinecarcinoma" - }, - { - "@id": "bts:Smallcellosteosarcoma" - }, - { - "@id": "bts:Smallcellsarcoma" - }, - { - "@id": "bts:Smallcongenitalnevus" - }, - { - "@id": "bts:SpindlecellcarcinomaNOS" - }, - { - "@id": "bts:SpindlecellmelanomaNOS" - }, - { - "@id": "bts:SplenicB-celllymphoma/leukemiaunclassifiable" - }, - { - "@id": "bts:SplenicdiffuseredpulpsmallB-celllymphoma" - }, - { - "@id": "bts:Spleniclymphomawithvillouslymphocytes" - }, - { - "@id": "bts:SplenicmarginalzoneB-celllymphoma" - }, - { - "@id": "bts:SplenicmarginalzonelymphomaNOS" - }, - { - "@id": "bts:SquamouscellcarcinomainsituNOS" - }, - { - "@id": "bts:Squamouscellcarcinomaadenoid" - }, - { - "@id": "bts:Squamouscellcarcinomaclearcelltype" - }, - { - "@id": "bts:SquamouscellcarcinomaNOS" - }, - { - "@id": "bts:Tlymphoblasticleukemia/lymphoma" - }, - { - "@id": "bts:T-celllargegranularlymphocyticleukemia" - }, - { - "@id": "bts:T-celllargegranularlymphocytosis" - }, - { - "@id": "bts:T-celllymphomaNOS" - }, - { - "@id": "bts:TeratomamalignantNOS" - }, - { - "@id": "bts:TeratomaNOS" - }, - { - "@id": "bts:Therapyrelatedmyeloidneoplasm" - }, - { - "@id": "bts:Transitionalcarcinoma" - }, - { - "@id": "bts:Transitionalcellcarcinoma" - }, - { - "@id": "bts:Transitionalcellcarcinomainsitu" - }, - { - "@id": "bts:Tubularadenocarcinoma" - }, - { - "@id": "bts:TubularadenomaNOS" - }, - { - "@id": "bts:Tubularandroblastomawithlipidstorage" - }, - { - "@id": "bts:TubularandroblastomaNOS" - }, - { - "@id": "bts:Tubularcarcinoid" - }, - { - "@id": "bts:Tubularcarcinoma" - }, - { - "@id": "bts:Tubulo-papillaryadenoma" - }, - { - "@id": "bts:Tubulocysticrenalcellcarcinoma" - }, - { - "@id": "bts:Tubulolobularcarcinoma" - }, - { - "@id": "bts:Tubulopapillaryadenocarcinoma" - }, - { - "@id": "bts:TubulovillousadenomaNOS" - }, - { - "@id": "bts:Tumorcellsbenign" - }, - { - "@id": "bts:Tumorcellsmalignant" - }, - { - "@id": "bts:TumorcellsNOS" - }, - { - "@id": "bts:Tumorcellsuncertainwhetherbenignormalignant" - }, - { - "@id": "bts:Tumorembolus" - }, - { - "@id": "bts:Tumorbenign" - 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}, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Primary Diagnosis", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PriorMalignancy", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.", - "rdfs:label": "PriorMalignancy", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:NotAllowedToCollect" - } - ], - "sms:displayName": "Prior Malignancy", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PriorTreatment", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.", - "rdfs:label": "PriorTreatment", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:NotAllowedToCollect" - } - ], - "sms:displayName": "Prior Treatment", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SiteofResectionorBiopsy", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "SiteofResectionorBiopsy", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AbdomenNOS" - }, - { - "@id": "bts:Abdominalesophagus" - }, - { - "@id": "bts:AccessorysinusNOS" - }, - { - "@id": "bts:Acousticnerve" - }, - { - "@id": "bts:AdrenalglandNOS" - }, - { - "@id": "bts:AmpullaofVater" - }, - { - "@id": "bts:Analcanal" - }, - { - "@id": "bts:Anterior2/3oftongueNOS" - }, - { - "@id": "bts:Anteriorfloorofmouth" - }, - { - "@id": "bts:Anteriormediastinum" - }, - { - "@id": "bts:Anteriorsurfaceofepiglottis" - }, - { - "@id": "bts:Anteriorwallofbladder" - }, - { - "@id": "bts:Anteriorwallofnasopharynx" - }, - { - "@id": "bts:AnusNOS" - }, - { - "@id": "bts:Aorticbodyandotherparaganglia" - }, - { - "@id": "bts:Appendix" - }, - { - "@id": "bts:Ascendingcolon" - }, - { - "@id": "bts:AutonomicnervoussystemNOS" - }, - { - "@id": "bts:Axillarytailofbreast" - }, - { - "@id": "bts:BaseoftongueNOS" - }, - { - "@id": "bts:Bladderneck" - }, - { - "@id": "bts:BladderNOS" - }, - { - "@id": "bts:Blood" - }, - { - "@id": "bts:Bodyofpancreas" - }, - { - "@id": "bts:Bodyofpenis" - }, - { - "@id": "bts:Bodyofstomach" - 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}, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" - }, - { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" - }, - { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" - }, - { - "@id": "bts:CorneaNOS" - }, - { - "@id": "bts:Corpusuteri" - }, - { - "@id": "bts:Cortexofadrenalgland" - }, - { - "@id": "bts:CranialnerveNOS" - }, - { - "@id": "bts:Craniopharyngealduct" - }, - { - "@id": "bts:Descendedtestis" - }, - { - "@id": "bts:Descendingcolon" - }, - { - "@id": "bts:Domeofbladder" - }, - { - "@id": "bts:DorsalsurfaceoftongueNOS" - }, - { - "@id": "bts:Duodenum" - }, - { - "@id": "bts:Endocervix" - }, - { - "@id": "bts:EndocrineglandNOS" - }, - { - "@id": "bts:Endometrium" - }, - { - "@id": "bts:Epididymis" - }, - { - "@id": "bts:EsophagusNOS" - }, - { - "@id": "bts:Ethmoidsinus" - }, - { - "@id": "bts:Exocervix" - }, - { - "@id": "bts:Externalear" - }, - { - "@id": "bts:ExternallipNOS" - }, - { - "@id": "bts:Externallowerlip" - }, - { - "@id": "bts:Externalupperlip" - }, - { - "@id": "bts:Extrahepaticbileduct" - }, - { - "@id": "bts:EyeNOS" - }, - { - "@id": "bts:Eyelid" - }, - { - "@id": "bts:Fallopiantube" - }, - { - "@id": "bts:FemalegenitaltractNOS" - }, - { - "@id": "bts:FloorofmouthNOS" - }, - { - "@id": "bts:Frontallobe" - }, - { - "@id": "bts:Frontalsinus" - }, - { - "@id": "bts:Fundusofstomach" - }, - { - "@id": "bts:Fundusuteri" - }, - { - "@id": "bts:Gallbladder" - }, - { - "@id": "bts:Gastricantrum" - }, - { - "@id": "bts:GastrointestinaltractNOS" - }, - { - "@id": "bts:Glanspenis" - }, - { - "@id": "bts:Glottis" - }, - { - "@id": "bts:GreatercurvatureofstomachNOS" - }, - { - "@id": "bts:GumNOS" - }, - { - "@id": "bts:Hardpalate" - }, - { - "@id": "bts:Headofpancreas" - }, - { - "@id": "bts:HeadfaceorneckNOS" - }, - { - "@id": "bts:Heart" - }, - { - "@id": "bts:HematopoieticsystemNOS" - }, - { - "@id": "bts:Hepaticflexureofcolon" - }, - { - "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" - }, - { - "@id": "bts:HypopharynxNOS" - }, - { - "@id": "bts:Ileum" - }, - { - "@id": "bts:Ill-definedsiteswithinrespiratorysystem" - }, - { - "@id": "bts:IntestinaltractNOS" - }, - { - "@id": "bts:Intra-abdominallymphnodes" - }, - { - "@id": "bts:Intrahepaticbileduct" - }, - { - "@id": "bts:Intrathoraciclymphnodes" - }, - { - "@id": "bts:IsletsofLangerhans" - }, - { - "@id": "bts:Isthmusuteri" - }, - { - "@id": "bts:Jejunum" - }, - { - "@id": "bts:KidneyNOS" - }, - { - "@id": "bts:Labiummajus" - }, - { - "@id": "bts:Labiumminus" - }, - { - "@id": "bts:Lacrimalgland" - }, - { - "@id": "bts:Laryngealcartilage" - }, - { - "@id": "bts:LarynxNOS" - }, - { - "@id": "bts:Lateralfloorofmouth" - }, - { - "@id": "bts:Lateralwallofbladder" - }, - { - "@id": "bts:Lateralwallofnasopharynx" - }, - { - "@id": "bts:Lateralwalloforopharynx" - }, - { - "@id": "bts:LessercurvatureofstomachNOS" - }, - { - "@id": "bts:Lingualtonsil" - }, - { - "@id": "bts:LipNOS" - }, - { - "@id": "bts:Liver" - }, - { - "@id": "bts:Longbonesoflowerlimbandassociatedjoints" - }, - { - "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" - }, - { - "@id": "bts:Lowergum" - }, - { - "@id": "bts:LowerlimbNOS" - }, - { - "@id": "bts:Lowerlobelung" - }, - { - "@id": "bts:Lowerthirdofesophagus" - }, - { - "@id": "bts:Lower-innerquadrantofbreast" - }, - { - "@id": "bts:Lower-outerquadrantofbreast" - }, - { - "@id": "bts:LungNOS" - }, - { - "@id": "bts:LymphnodeNOS" - }, - { - "@id": "bts:Lymphnodesofaxillaorarm" - }, - { - "@id": "bts:Lymphnodesofheadfaceandneck" - }, - { - "@id": "bts:Lymphnodesofinguinalregionorleg" - }, - { - "@id": "bts:Lymphnodesofmultipleregions" - }, - { - "@id": "bts:Mainbronchus" - }, - { - "@id": "bts:MajorsalivaryglandNOS" - }, - { - "@id": "bts:MalegenitalorgansNOS" - }, - { - "@id": "bts:Mandible" - }, - { - "@id": "bts:Maxillarysinus" - }, - { - "@id": "bts:Meckeldiverticulum" - }, - { - "@id": "bts:MediastinumNOS" - }, - { - "@id": "bts:Medullaofadrenalgland" - }, - { - "@id": "bts:MeningesNOS" - }, - { - "@id": "bts:Middleear" - }, - { - "@id": "bts:Middlelobelung" - }, - { - "@id": "bts:Middlethirdofesophagus" - }, - { - "@id": "bts:MouthNOS" - }, - { - "@id": "bts:MucosaoflipNOS" - }, - { - "@id": "bts:Mucosaoflowerlip" - }, - { - "@id": "bts:Mucosaofupperlip" - }, - { - "@id": "bts:Myometrium" - }, - { - "@id": "bts:Nasalcavity" - }, - { - "@id": "bts:NasopharynxNOS" - }, - { - "@id": "bts:NervoussystemNOS" - }, - { - "@id": "bts:Nipple" - }, - { - "@id": "bts:Occipitallobe" - }, - { - "@id": "bts:Olfactorynerve" - }, - { - "@id": "bts:Opticnerve" - }, - { - "@id": "bts:OrbitNOS" - }, - { - "@id": "bts:OropharynxNOS" - }, - { - "@id": "bts:Otherill-definedsites" - }, - { - "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" - }, - { - "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" - }, - { - "@id": "bts:Otherspecifiedpartsofpancreas" - }, - { - "@id": "bts:Ovary" - }, - { - "@id": "bts:Overlappinglesionofaccessorysinuses" - }, - { - "@id": "bts:Overlappinglesionofbladder" - }, - { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" - }, - { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" - }, - { - "@id": "bts:Overlappinglesionofbrain" - }, - { - "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" - }, - { - "@id": "bts:Overlappinglesionofbreast" - }, - { - "@id": "bts:Overlappinglesionofcervixuteri" - }, - { - "@id": "bts:Overlappinglesionofcolon" - }, - { - "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" - }, - { - "@id": "bts:Overlappinglesionofcorpusuteri" - }, - { - "@id": "bts:Overlappinglesionofdigestivesystem" - }, - { - "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" - }, - { - "@id": "bts:Overlappinglesionofesophagus" - }, - { - "@id": "bts:Overlappinglesionofeyeandadnexa" - }, - { - "@id": "bts:Overlappinglesionoffemalegenitalorgans" - }, - { - "@id": "bts:Overlappinglesionoffloorofmouth" - }, - { - "@id": "bts:Overlappinglesionofheartmediastinumandpleura" - }, - { - "@id": "bts:Overlappinglesionofhypopharynx" - }, - { - "@id": "bts:Overlappinglesionofill-definedsites" - }, - { - "@id": "bts:Overlappinglesionoflarynx" - }, - { - "@id": "bts:Overlappinglesionoflip" - }, - { - "@id": "bts:Overlappinglesionofliporalcavityandpharynx" - }, - { - "@id": "bts:Overlappinglesionoflung" - }, - { - "@id": "bts:Overlappinglesionofmajorsalivaryglands" - }, - { - "@id": "bts:Overlappinglesionofmalegenitalorgans" - }, - { - "@id": "bts:Overlappinglesionofnasopharynx" - }, - { - "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" - }, - { - "@id": "bts:Overlappinglesionofpalate" - }, - { - "@id": "bts:Overlappinglesionofpancreas" - }, - { - "@id": "bts:Overlappinglesionofpenis" - }, - { - "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" - }, - { - "@id": "bts:Overlappinglesionofrectumanusandanalcanal" - }, - { - "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" - }, - { - "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" - }, - { - "@id": "bts:Overlappinglesionofskin" - }, - { - "@id": "bts:Overlappinglesionofsmallintestine" - }, - { - "@id": "bts:Overlappinglesionofstomach" - }, - { - "@id": "bts:Overlappinglesionoftongue" - }, - { - "@id": "bts:Overlappinglesionoftonsil" - }, - { - "@id": "bts:Overlappinglesionofurinaryorgans" - }, - { - "@id": "bts:Overlappinglesionofvulva" - }, - { - "@id": "bts:Overlappinglesionsoforopharynx" - }, - { - "@id": "bts:PalateNOS" - }, - { - "@id": "bts:PancreasNOS" - }, - { - "@id": "bts:Pancreaticduct" - }, - { - "@id": "bts:Parametrium" - }, - { - "@id": "bts:Paraspinal" - }, - { - "@id": "bts:Parathyroidgland" - }, - { - "@id": "bts:Paraurethralgland" - }, - { - "@id": "bts:Parietallobe" - }, - { - "@id": "bts:Parotidgland" - }, - { - "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" - }, - { - "@id": "bts:Pelviclymphnodes" - }, - { - "@id": "bts:PelvisNOS" - }, - { - "@id": "bts:PenisNOS" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" - }, - { - "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" - }, - { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" - }, - { - "@id": "bts:PeritoneumNOS" - }, - { - "@id": "bts:PharynxNOS" - }, - { - "@id": "bts:Pinealgland" - }, - { - "@id": "bts:Pituitarygland" - }, - { - "@id": "bts:Placenta" - }, - { - "@id": "bts:PleuraNOS" - }, - { - "@id": "bts:Postcricoidregion" - }, - { - "@id": "bts:Posteriormediastinum" - }, - { - "@id": "bts:Posteriorwallofbladder" - }, - { - "@id": "bts:Posteriorwallofhypopharynx" - }, - { - "@id": "bts:Posteriorwallofnasopharynx" - }, - { - "@id": "bts:Posteriorwalloforopharynx" - }, - { - "@id": "bts:Prepuce" - }, - { - "@id": "bts:Prostategland" - }, - { - "@id": "bts:Pylorus" - }, - { - "@id": "bts:Pyriformsinus" - }, - { - "@id": "bts:Rectosigmoidjunction" - }, - { - "@id": "bts:RectumNOS" - }, - { - "@id": "bts:Renalpelvis" - }, - { - "@id": "bts:ReticuloendothelialsystemNOS" - }, - { - "@id": "bts:Retina" - }, - { - "@id": "bts:Retromolararea" - }, - { - "@id": "bts:Retroperitoneum" - }, - { - "@id": "bts:Ribsternumclavicleandassociatedjoints" - }, - { - "@id": "bts:Roundligament" - }, - { - "@id": "bts:ScrotumNOS" - }, - { - "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" - }, - { - "@id": "bts:Shortbonesofupperlimbandassociatedjoints" - }, - { - "@id": "bts:Sigmoidcolon" - }, - { - "@id": "bts:SkinoflipNOS" - }, - { - "@id": "bts:Skinoflowerlimbandhip" - }, - { - "@id": "bts:Skinofotherandunspecifiedpartsofface" - }, - { - "@id": "bts:Skinofscalpandneck" - }, - { - "@id": "bts:Skinoftrunk" - }, - { - "@id": "bts:Skinofupperlimbandshoulder" - }, - { - "@id": "bts:SkinNOS" - }, - { - "@id": "bts:SmallintestineNOS" - }, - { - "@id": "bts:SoftpalateNOS" - }, - { - "@id": "bts:Specifiedpartsofperitoneum" - }, - { - "@id": "bts:Spermaticcord" - }, - { - "@id": "bts:Sphenoidsinus" - }, - { - "@id": "bts:Spinalcord" - }, - { - "@id": "bts:Spinalmeninges" - }, - { - "@id": "bts:Spleen" - }, - { - "@id": "bts:Splenicflexureofcolon" - }, - { - "@id": "bts:StomachNOS" - }, - { - "@id": "bts:Subglottis" - }, - { - "@id": "bts:Sublingualgland" - }, - { - "@id": "bts:Submandibulargland" - }, - { - "@id": "bts:Superiorwallofnasopharynx" - }, - { - "@id": "bts:Supraglottis" - }, - { - "@id": "bts:Tailofpancreas" - }, - { - "@id": "bts:Temporallobe" - }, - { - "@id": "bts:TestisNOS" - }, - { - "@id": "bts:Thoracicesophagus" - }, - { - "@id": "bts:ThoraxNOS" - }, - { - "@id": "bts:Thymus" - }, - { - "@id": "bts:Thyroidgland" - }, - { - "@id": "bts:TongueNOS" - }, - { - "@id": "bts:TonsilNOS" - }, - { - "@id": "bts:Tonsillarfossa" - }, - { - "@id": "bts:Tonsillarpillar" - }, - { - "@id": "bts:Trachea" - }, - { - "@id": "bts:Transversecolon" - }, - { - "@id": "bts:Trigoneofbladder" - }, - { - "@id": "bts:Undescendedtestis" - }, - { - "@id": "bts:Unknownprimarysite" - }, - { - "@id": "bts:Uppergum" - }, - { - "@id": "bts:UpperlimbNOS" - }, - { - "@id": "bts:Upperlobelung" - }, - { - "@id": "bts:UpperrespiratorytractNOS" - }, - { - "@id": "bts:Upperthirdofesophagus" - }, - { - "@id": "bts:Upper-innerquadrantofbreast" - }, - { - "@id": "bts:Upper-outerquadrantofbreast" - }, - { - "@id": "bts:Urachus" - }, - { - "@id": "bts:Ureter" - }, - { - "@id": "bts:Uretericorifice" - }, - { - "@id": "bts:Urethra" - }, - { - "@id": "bts:UrinarysystemNOS" - }, - { - "@id": "bts:Uterineadnexa" - }, - { - "@id": "bts:UterusNOS" - }, - { - "@id": "bts:Uvula" - }, - { - "@id": "bts:VaginaNOS" - }, - { - "@id": "bts:Vallecula" - }, - { - "@id": "bts:VentralsurfaceoftongueNOS" - }, - { - "@id": "bts:VentricleNOS" - }, - { - "@id": "bts:Vertebralcolumn" - }, - { - "@id": "bts:Vestibuleofmouth" - }, - { - "@id": "bts:VulvaNOS" - }, - { - "@id": "bts:Waldeyerring" - }, - { - "@id": "bts:BiliarytractNOS" - }, - { - "@id": "bts:Cheekmucosa" - }, - { - "@id": "bts:Clitoris" - }, - { - "@id": "bts:Overlappinglesionofbiliarytract" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Site of Resection or Biopsy", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:TissueorOrganofOrigin", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "TissueorOrganofOrigin", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:AbdomenNOS" - }, - { - "@id": "bts:Abdominalesophagus" - }, - { - "@id": "bts:AccessorysinusNOS" - }, - { - "@id": "bts:Acousticnerve" - }, - { - "@id": "bts:AdrenalglandNOS" - }, - { - "@id": "bts:AmpullaofVater" - }, - { - "@id": "bts:Analcanal" - }, - { - "@id": "bts:Anterior2/3oftongueNOS" - }, - { - "@id": "bts:Anteriorfloorofmouth" - }, - { - "@id": "bts:Anteriormediastinum" - }, - { - "@id": "bts:Anteriorsurfaceofepiglottis" - }, - { - "@id": "bts:Anteriorwallofbladder" - }, - { - "@id": "bts:Anteriorwallofnasopharynx" - }, - { - "@id": "bts:AnusNOS" - }, - { - "@id": "bts:Aorticbodyandotherparaganglia" - }, - { - "@id": "bts:Appendix" - }, - { - "@id": "bts:Ascendingcolon" - }, - { - "@id": "bts:AutonomicnervoussystemNOS" - }, - { - "@id": "bts:Axillarytailofbreast" - }, - { - "@id": "bts:BaseoftongueNOS" - }, - { - "@id": "bts:Bladderneck" - }, - { - "@id": "bts:BladderNOS" - }, - { - "@id": "bts:Blood" - }, - { - "@id": "bts:Bodyofpancreas" - }, - { - "@id": "bts:Bodyofpenis" - }, - { - "@id": "bts:Bodyofstomach" - }, - { - "@id": "bts:Bonemarrow" - }, - { - "@id": "bts:BoneoflimbNOS" - }, - { - "@id": "bts:BoneNOS" - }, - { - "@id": "bts:Bonesofskullandfaceandassociatedjoints" - }, - { - "@id": "bts:Borderoftongue" - }, - { - "@id": "bts:Brainstem" - }, - { - "@id": "bts:BrainNOS" - }, - { - "@id": "bts:Branchialcleft" - }, - { - "@id": "bts:BreastNOS" - }, - { - "@id": "bts:Broadligament" - }, - { - "@id": "bts:CardiaNOS" - }, - { - "@id": "bts:Carotidbody" - }, - { - "@id": "bts:Caudaequina" - }, - { - "@id": "bts:Cecum" - }, - { - "@id": "bts:Centralportionofbreast" - }, - { - "@id": "bts:CerebellumNOS" - }, - { - "@id": "bts:Cerebralmeninges" - }, - { - "@id": "bts:Cerebrum" - }, - { - "@id": "bts:Cervicalesophagus" - }, - { - "@id": "bts:Cervixuteri" - }, - { - "@id": "bts:Choroid" - }, - { - "@id": "bts:Ciliarybody" - }, - { - "@id": "bts:Cloacogeniczone" - }, - { - "@id": "bts:ColonNOS" - }, - { - "@id": "bts:Commissureoflip" - }, - { - "@id": "bts:Conjunctiva" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" - }, - { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" - }, - { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" - }, - { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" - }, - { - "@id": "bts:CorneaNOS" - }, - { - "@id": "bts:Corpusuteri" - }, - { - "@id": "bts:Cortexofadrenalgland" - }, - { - "@id": "bts:CranialnerveNOS" - }, - { - "@id": "bts:Craniopharyngealduct" - }, - { - "@id": "bts:Descendedtestis" - }, - { - "@id": "bts:Descendingcolon" - }, - { - "@id": "bts:Domeofbladder" - 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Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.", - "rdfs:label": "MitoticCount", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mitotic Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentTumorInvasion", - "@type": "rdfs:Class", - "rdfs:comment": "The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.", - "rdfs:label": "PercentTumorInvasion", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Tumor Invasion", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PeritonealFluidCytologicalStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.", - "rdfs:label": "PeritonealFluidCytologicalStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Atypical" - }, - { - "@id": "bts:Malignant" - }, - { - "@id": "bts:Non-Malignant" - }, - { - "@id": "bts:Unsatisfactory" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Peritoneal Fluid Cytological Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerineuralInvasionPresent", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.", - "rdfs:label": "PerineuralInvasionPresent", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Perineural Invasion Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ResidualDisease", - "@type": "rdfs:Class", - "rdfs:comment": "Text terms to describe the status of a tissue margin following surgical resection.", - "rdfs:label": "ResidualDisease", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:R0" - }, - { - "@id": "bts:R1" - }, - { - "@id": "bts:R2" - }, - { - "@id": "bts:RX" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Residual Disease", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SynchronousMalignancy", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.", - "rdfs:label": "SynchronousMalignancy", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Synchronous Malignancy", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorConfinedtoOrganofOrigin", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.", - "rdfs:label": "TumorConfinedtoOrganofOrigin", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - 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}, - { - "@id": "bts:Yes-VascularInvasionPresent", - "@type": "rdfs:Class", - "rdfs:comment": "Indicates venous invasion was detected by surgery or presence in a tumor specimen", - "rdfs:label": "Yes-VascularInvasionPresent", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Yes - Vascular Invasion Present", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:VascularInvasionType" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:VascularInvasionType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the type of vascular tumor invasion.", - "rdfs:label": "VascularInvasionType", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Extramural" - }, - { - "@id": "bts:Intramural" - }, - { - "@id": "bts:Macro" - }, - { - 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}, - "sms:displayName": "Topography Code", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdditionalTopography", - "@type": "rdfs:Class", - "rdfs:comment": "Topography not included in the ICD-O-3 Topography codes.", - "rdfs:label": "AdditionalTopography", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Skinofscalp" - }, - { - "@id": "bts:Skinofeyelid" - }, - { - "@id": "bts:Skinofnose" - }, - { - "@id": "bts:Skinoflip" - }, - { - "@id": "bts:Skinofear" - }, - { - "@id": "bts:Skinofneck" - }, - { - "@id": "bts:Skinofotherpartsofface" - }, - { - "@id": "bts:Skinofchest" - }, - { - "@id": "bts:Skinofback" - }, - { - "@id": "bts:Skinofabdomen" - }, - { - "@id": "bts:Skinoftrunk" - }, - { - "@id": "bts:Skinofbreast" - }, - { - "@id": "bts:Skinofupperlimbandshoulder" - }, - { - "@id": "bts:Skinofpalm" - }, - { - "@id": "bts:Skinoflowerlimbandhip" - 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"rdfs:comment": "Individual has been exposed to smoke; requires additional metadata", - "rdfs:label": "Yes-SmokingExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Yes - Smoking Exposure", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:YearsSmoked" - }, - { - "@id": "bts:PackYearsSmoked" - }, - { - "@id": "bts:CigarettesperDay" - }, - { - "@id": "bts:SmokingFrequency" - }, - { - "@id": "bts:TypeofSmokeExposure" - }, - { - "@id": "bts:TimebetweenWakingandFirstSmoke" - }, - { - "@id": "bts:TobaccoSmokingOnsetYear" - }, - { - "@id": "bts:TobaccoSmokingQuitYear" - }, - { - "@id": "bts:TobaccoSmokingStatus" - }, - { - "@id": "bts:TypeofTobaccoUsed" - }, - { - "@id": "bts:SecondhandSmokeasChild" - }, - { - "@id": "bts:SmokeExposureDuration" - }, - { - "@id": "bts:TobaccoUseperDay" - }, - { - "@id": "bts:SmokelessTobaccoQuitAge" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:PackYearsSmoked", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.", - "rdfs:label": "PackYearsSmoked", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Pack Years Smoked", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:YearsSmoked", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value (or unknown) to represent the number of years a person has been smoking.", - "rdfs:label": "YearsSmoked", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Years Smoked", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SmokingFrequency", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to generally decribe how often the patient smokes.", - 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}, - { - "@id": "bts:TobaccoUseperDay", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the number of times the patient uses tobacco each day.", - "rdfs:label": "TobaccoUseperDay", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tobacco Use per Day", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TobaccoSmokingStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Category describing current smoking status and smoking history as self-reported by a patient", - "rdfs:label": "TobaccoSmokingStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:LifelongNon-Smoker" - }, - { - "@id": "bts:CurrentSmoker" - }, - { - "@id": "bts:CurrentReformedSmokerfor>15yrs" - }, - { - "@id": "bts:CurrentReformedSmokerfor15yrs", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "CurrentReformedSmokerfor>15yrs", - "rdfs:subClassOf": [ - { - "@id": "bts:TobaccoSmokingStatus" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Current Reformed Smoker for > 15 yrs", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CurrentReformedSmokerfor= 1", + "rdfs:label" : "SizeC", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SizeC", + "sms:required" : "sms:false" + }, { + "@id" : "bts:SpecializedMolecularTest", + "@type" : "rdfs:Class", + "rdfs:comment" : "Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "SpecializedMolecularTest", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SpecializedMolecularTest", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Locus", + "@type" : "rdfs:Class", + "rdfs:comment" : "Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.", + "rdfs:label" : "Locus", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Locus", + "sms:required" : "sms:false" + }, { + "@id" : "bts:PlaneCount", + "@type" : "rdfs:Class", + "rdfs:comment" : "Number of Z-planes (not to be confused with downsampled \"\"pyramid\"\"). Integer >=1", + "rdfs:label" : "PlaneCount", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PlaneCount", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:DissociationMethod", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:NotApplicable" + }, { + "@id" : "bts:gentleMACS" + }, { + "@id" : "bts:Dounce" + }, { + "@id" : "bts:EnzymaticDigestion" + } ], + "rdfs:label" : "DissociationMethod", + "rdfs:comment" : "The tissue dissociation method used for scRNASeq or scATAC-seq assays", + "@type" : "rdfs:Class", + "sms:displayName" : "DissociationMethod" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:PRStainingIntensity", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Other" + }, { + "@id" : 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"bts:Re-excision" + } ], + "rdfs:label" : "BreastCarcinomaSurgicalProcedureName", + "rdfs:comment" : "Text name of a surgical procedure performed for a person with a diagnosis of breast cancer", + "@type" : "rdfs:Class", + "sms:displayName" : "BreastCarcinomaSurgicalProcedureName" + }, { + "@id" : "bts:BreastCarcinomaERStatusPercentageValue", + "@type" : "rdfs:Class", + "rdfs:comment" : "A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer", + "rdfs:label" : "BreastCarcinomaERStatusPercentageValue", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BreastCarcinomaERStatusPercentageValue", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BreastCarcinomaPRStatusPercentageValue", + "@type" : "rdfs:Class", + "rdfs:comment" : "A numerical quantity measured or assigned or computed which captures the progesterone receptor level 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Integer value.", + "rdfs:label" : "IschemicTime", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "IschemicTime", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ProgressionorRecurrenceType", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ProgressionorRecurrenceType", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ProgressionorRecurrenceType", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:AlcoholType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Other" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:Beer" + }, { + "@id" : "bts:Liquor" + }, { + "@id" : "bts:Wine" + } ], + "rdfs:label" : "AlcoholType", + "rdfs:comment" : "Type of alcohol use", + "@type" : "rdfs:Class", + "sms:displayName" : "AlcoholType" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:MismatchRepairMutation", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "MismatchRepairMutation", + "rdfs:comment" : "The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "MismatchRepairMutation" + }, { + "@id" : "bts:Filename", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Filename", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Filename", + "sms:required" : "sms:false" + }, { + "@id" : "bts:CountryofBirth", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "CountryofBirth", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "CountryofBirth", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:LibraryConstructionMethod", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:10xV3" + }, { + "@id" : "bts:inDropsV2" + }, { + "@id" : "bts:10xV1.1" + 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result of Estrogen Receptor (ER) testing in a participant with breast cancer", + "@type" : "rdfs:Class", + "sms:displayName" : "ERReceptorStatus" + }, { + "@id" : "bts:Comment", + "@type" : "rdfs:Class", + "rdfs:comment" : "Free text field (generally for QC comment)", + "rdfs:label" : "Comment", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Comment", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:BreastQuadrantSite", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Datanotavailable" + }, { + "@id" : "bts:Upperouterquadrant" + }, { + "@id" : "bts:Lowerouterquadrant" + }, { + "@id" : "bts:Upperinnerquadrant" + }, { + "@id" : "bts:Lowerinnerquadrant" + }, { + "@id" : "bts:Central" + }, { + "@id" : "bts:Nipple" + } ], + "rdfs:label" : "BreastQuadrantSite", + "rdfs:comment" : "The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.", + "@type" : "rdfs:Class", + "sms:displayName" : "BreastQuadrantSite" + }, { + "@id" : "bts:LinkedDatasets", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "LinkedDatasets", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "LinkedDatasets", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BreastCarcinomaHER2Chromosome17Ratio", + "@type" : "rdfs:Class", + "rdfs:comment" : "HER2 chromosome 17 ratio in participants with breast cancer", + "rdfs:label" : "BreastCarcinomaHER2Chromosome17Ratio", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BreastCarcinomaHER2Chromosome17Ratio", + "sms:required" : "sms:false" + }, { + "@id" : "bts:PhysicalSizeY", + "@type" : "rdfs:Class", + "rdfs:comment" : "Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.", + "rdfs:label" : "PhysicalSizeY", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PhysicalSizeY", + "sms:required" : "sms:false" + }, { + "@id" : "bts:MetalIsotopeMass", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "MetalIsotopeMass", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "MetalIsotopeMass", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BiospecimenDimension2", + "@type" : "rdfs:Class", + "rdfs:comment" : "Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the \"\"dimensions_unit\"\" CDE", + "rdfs:label" : "BiospecimenDimension2", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BiospecimenDimension2", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : 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"DaystoProgressionFree", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "DaystoProgressionFree", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:MultifocalBreastCarcinomaPresentIndicator", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "MultifocalBreastCarcinomaPresentIndicator", + "rdfs:comment" : "A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from the same clone and usually located in the same quadrant of the breast.", + "@type" : "rdfs:Class", + "sms:displayName" : "MultifocalBreastCarcinomaPresentIndicator" + }, { + "@id" : "bts:BiospecimenID", + "@type" : "rdfs:Class", + "rdfs:comment" : " Alias for Sample ID", + "rdfs:label" : "BiospecimenID", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BiospecimenID", + "sms:required" : "sms:true" + }, { + "@id" : "bts:BloodTestNormalRangeLower", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.", + "rdfs:label" : "BloodTestNormalRangeLower", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BloodTestNormalRangeLower", + "sms:required" : "sms:false" + }, { + "@id" : "bts:RuralvsUrban", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "RuralvsUrban", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "RuralvsUrban", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:MulticentricBreastCarcinomaPresentIndicator", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "MulticentricBreastCarcinomaPresentIndicator", + "rdfs:comment" : "A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from different clones and usually located in different quadrants of the breast.", + "@type" : "rdfs:Class", + "sms:displayName" : "MulticentricBreastCarcinomaPresentIndicator" + }, { + "@id" : "bts:UMITag", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "UMITag", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "UMITag", + "sms:required" : "sms:false" + }, { + "@id" : "bts:CellBarcodeLength", + "@type" : "rdfs:Class", + "rdfs:comment" : "Length of cell barcode read (in bp): number", + "rdfs:label" : "CellBarcodeLength", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "CellBarcodeLength", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ClassBRCA1", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ClassBRCA1", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ClassBRCA1", + "sms:required" : "sms:false" + }, { + "@id" : "bts:SectionNumberinSequence", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)", + "rdfs:label" : "SectionNumberinSequence", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SectionNumberinSequence", + "sms:required" : "sms:false" + }, { + "@id" : "bts:SampleCollectionCenter", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "SampleCollectionCenter", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SampleCollectionCenter", + "sms:required" : "sms:false" + }, { + "@id" : "bts:CopyNumber", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "CopyNumber", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "CopyNumber", + "sms:required" : "sms:false" + }, { + "@id" : "bts:SectioningDaysfromIndex", + "@type" : "rdfs:Class", + "rdfs:comment" : "Number of days from the research participant's index date that the biospecimen was sectioned after collection", + "rdfs:label" : "SectioningDaysfromIndex", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SectioningDaysfromIndex", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Immersion", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Air" + }, { + "@id" : "bts:Oil" + }, { + "@id" : "bts:Water" + }, { + "@id" : "bts:Other" + } ], + "rdfs:label" : "Immersion", + "rdfs:comment" : "Immersion medium", + "@type" : "rdfs:Class", + "sms:displayName" : "Immersion" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Pyramid", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "Pyramid", + "rdfs:comment" : "Does data file contain pyramid of images", + "@type" : "rdfs:Class", + "sms:displayName" : "Pyramid" + }, { + "@id" : "bts:SampleSite", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "SampleSite", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SampleSite", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:MismatchRepairSystemStatus", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:MismatchrepairdeficiencyMMRD" + }, { + "@id" : "bts:MismatchrepairproficiencyMMPP" + }, { + "@id" : "bts:MicrosatelliteinstabilityhighMSIH" + }, { + "@id" : "bts:MicrosatellitestableMSS" + }, { + "@id" : "bts:unknownorother" + } ], + "rdfs:label" : "MismatchRepairSystemStatus", + "rdfs:comment" : "The text that best describes the condition or state of MMR (mismatch repair system) in the patient", + "@type" : "rdfs:Class", + "sms:displayName" : "MismatchRepairSystemStatus" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Tseries", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + } ], + "rdfs:label" : "Tseries", + "rdfs:comment" : "Does data file contain a time-series of images", + "@type" : "rdfs:Class", + "sms:displayName" : "Tseries" + }, { + "@id" : "bts:Component", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Component", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Component", + "sms:required" : "sms:false" + }, { + "@id" : "bts:RelativeswithCancerHistoryCount", + "@type" : "rdfs:Class", + "rdfs:comment" : "The number of relatives the patient has with a known history of cancer.", + "rdfs:label" : "RelativeswithCancerHistoryCount", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "RelativeswithCancerHistoryCount", + "sms:required" : "sms:false" + }, { + "@id" : "bts:AlcoholDrinksPerDay", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value used to describe the average number of alcoholic beverages a person consumes per day.", + "rdfs:label" : "AlcoholDrinksPerDay", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AlcoholDrinksPerDay", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:EndBias", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:3Prime" + }, { + "@id" : "bts:5Prime" + }, { + "@id" : "bts:FullLengthTranscript" + } ], + "rdfs:label" : "EndBias", + "rdfs:comment" : "The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript", + "@type" : "rdfs:Class", + "sms:displayName" : "EndBias" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:SatelliteMetastasisPresentIndicator", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "SatelliteMetastasisPresentIndicator", + "rdfs:comment" : "A yes/no indicator to ask if intransit metastases or satellite lesions are present.", + "@type" : "rdfs:Class", + "sms:displayName" : "SatelliteMetastasisPresentIndicator" + }, { + "@id" : "bts:ParentBiospecimenID", + "@type" : "rdfs:Class", + "rdfs:comment" : " Biospecimen identifier indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated", + "rdfs:label" : "ParentBiospecimenID", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ParentBiospecimenID", + "sms:required" : "sms:false" + }, { + "@id" : "bts:AlcoholUse", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AlcoholUse", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AlcoholUse", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:NucleusIdentifier", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "NucleusIdentifier", + "rdfs:comment" : "Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from", + "@type" : "rdfs:Class", + "sms:displayName" : "NucleusIdentifier" + }, { + "@id" : "bts:Title", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Title", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Title", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:ClinicalBiospecimenType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:ConnectiveTissue" + }, { + "@id" : "bts:PeritonealFluid" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:Saliva" + }, { + "@id" : "bts:TissueNOS" + }, { + "@id" : "bts:Skin" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Feces" + }, { + "@id" : "bts:UninvolvedTissueNOS" + }, { + "@id" : "bts:Plasma" + }, { + "@id" : "bts:Granulocyte" + }, { + "@id" : "bts:EmbryonicTissue" + }, { + "@id" : "bts:BuccalMucosa" + }, { + "@id" : "bts:Blood" + }, { + "@id" : "bts:MuscleTissue" + }, { + "@id" : "bts:CerebrospinalFluid" + }, { + "@id" : "bts:SoftTissue" + }, { + "@id" : "bts:Urine" + }, { + "@id" : "bts:PleuralFluid" + }, { + "@id" : "bts:BoneMarrow" + }, { + "@id" : "bts:Serum" + }, { + "@id" : "bts:EmbryonicFluid" + }, { + "@id" : "bts:NerveTissue" + }, { + "@id" : "bts:BuffyCoat" + } ], + "rdfs:label" : "ClinicalBiospecimenType", + "rdfs:comment" : "The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "ClinicalBiospecimenType" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Antigen", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:CA19-9" + }, { + "@id" : "bts:CD79A" + }, { + "@id" : "bts:CD5" + }, { + "@id" : "bts:CD30" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:CD20" + }, { + "@id" : "bts:CD14" + }, { + "@id" : "bts:CD19" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:CD34" + }, { + "@id" : "bts:CCND1" + }, { + "@id" : "bts:CD25" + }, { + "@id" : "bts:HLA-DR" + }, { + "@id" : "bts:Mesothelin" + }, { + "@id" : "bts:CD10" + }, { + "@id" : "bts:CD56" + }, { + "@id" : "bts:CD3" + }, { + "@id" : "bts:NSE" + }, { + "@id" : "bts:CA-125" + }, { + "@id" : "bts:CD22" + }, { + "@id" : "bts:CD23" + }, { + "@id" : "bts:SquamousCellCarcinomaAntigen" + }, { + "@id" : "bts:CEA" + }, { + "@id" : "bts:CD33" + }, { + "@id" : "bts:CD138" + }, { + "@id" : "bts:BCL6" + }, { + "@id" : "bts:CD7" + }, { + "@id" : "bts:CD117" + }, { + "@id" : "bts:CD15" + }, { + "@id" : "bts:CD45" + } ], + "rdfs:label" : "Antigen", + "rdfs:comment" : "The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "Antigen" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:OncotypeRiskGroup", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Datanotavailable" + }, { + "@id" : "bts:Highrisk" + }, { + "@id" : "bts:Intermediaterisk" + }, { + "@id" : "bts:Lowrisk" + } ], + "rdfs:label" : "OncotypeRiskGroup", + "rdfs:comment" : "Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.", + "@type" : "rdfs:Class", + "sms:displayName" : "OncotypeRiskGroup" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:ModeofCancerDetection", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Datanotavailable" + }, { + "@id" : "bts:StandardofCareScreening" + }, { + "@id" : "bts:ClinicalExaminationofunrelatedcancersymptoms" + }, { + "@id" : "bts:Incidentaloma" + }, { + "@id" : "bts:IntervalCancer" + } ], + "rdfs:label" : "ModeofCancerDetection", + "rdfs:comment" : "Text term used to describe the mode of cancer detection, like standard of care screening or random detection", + "@type" : "rdfs:Class", + "sms:displayName" : "ModeofCancerDetection" + }, { + "@id" : "bts:RelationshipType", + "@type" : "rdfs:Class", + "rdfs:comment" : "The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.", + "rdfs:label" : "RelationshipType", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "RelationshipType", + "sms:required" : "sms:false" + }, { + "@id" : "bts:FeatureReferenceId", + "@type" : "rdfs:Class", + "rdfs:comment" : "Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]", + "rdfs:label" : "FeatureReferenceId", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "FeatureReferenceId", + "sms:required" : "sms:false" + }, { + "@id" : "bts:RelationshipAgeatDiagnosis", + "@type" : "rdfs:Class", + "rdfs:comment" : "The age (in years) when the patient's relative was first diagnosed.", + "rdfs:label" : "RelationshipAgeatDiagnosis", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "RelationshipAgeatDiagnosis", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:SmokingExposure", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes-SmokingExposure" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:No-SmokingExposure" + } ], + "rdfs:label" : "SmokingExposure", + "rdfs:comment" : "Indicate if individual has smoking exposure", + "@type" : "rdfs:Class", + "sms:displayName" : "SmokingExposure" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:TestResult", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Normal" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:TestValueReported" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Overexpressed" + }, { + "@id" : "bts:Intermediate" + }, { + "@id" : "bts:NotApplicable" + }, { + "@id" : "bts:LossofExpression" + }, { + "@id" : "bts:Low" + }, { + "@id" : "bts:High" + }, { + "@id" : "bts:Equivocal" + }, { + "@id" : "bts:CopyNumberReported" + }, { + "@id" : "bts:Positive" + }, { + "@id" : "bts:Negative" + }, { + "@id" : "bts:AbnormalNOS" + } ], + "rdfs:label" : "TestResult", + "rdfs:comment" : "The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "TestResult" + }, { + "@id" : "bts:MedianFractionofReadsinAnnotatedcisDNAElements", + "@type" : "rdfs:Class", + "rdfs:comment" : "Median fraction of reads in annotated cis-DNA elements (FRIADE)", + "rdfs:label" : "MedianFractionofReadsinAnnotatedcisDNAElements", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "MedianFractionofReadsinAnnotatedcisDNAElements", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Zygosity", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:Heterozygous" + }, { + "@id" : "bts:Hemizygous" + }, { + "@id" : "bts:Homozygous" + }, { + "@id" : "bts:Nullizygous" + } ], + "rdfs:label" : "Zygosity", + "rdfs:comment" : "The text term used to describe the zygosity of a specific genetic variant.", + "@type" : "rdfs:Class", + "sms:displayName" : "Zygosity" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:BreastImagingPerformedType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Datanotavailable" + }, { + "@id" : "bts:Mammogram" + }, { + "@id" : "bts:Ultrasound" + }, { + "@id" : "bts:MRI" + }, { + "@id" : "bts:PET/CT" + }, { + "@id" : "bts:CT" + }, { + "@id" : "bts:Multipleimagingmodalities" + } ], + "rdfs:label" : "BreastImagingPerformedType", + "rdfs:comment" : "The kind of technology or method performed for screening, diagnosis, surgical procedures or therapy that aids in the visualization of the breast(s).", + "@type" : "rdfs:Class", + "sms:displayName" : "BreastImagingPerformedType" + }, { + "@id" : "bts:PackYearsSmoked", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.", + "rdfs:label" : "PackYearsSmoked", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PackYearsSmoked", + "sms:required" : "sms:false" + }, { + "@id" : "bts:TobaccoUseperDay", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value that represents the number of times the patient uses tobacco each day.", + "rdfs:label" : "TobaccoUseperDay", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TobaccoUseperDay", + "sms:required" : "sms:false" + }, { + "@id" : "bts:TechnicalReplicateGroup", + "@type" : "rdfs:Class", + "rdfs:comment" : "A common term for all files belonging to the same cell or library. 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"bts:Frontallobe" + } ], + "rdfs:label" : "SiteofResectionorBiopsy", + "rdfs:comment" : "The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "@type" : "rdfs:Class", + "sms:displayName" : "SiteofResectionorBiopsy" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Clonality", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Clonal" + }, { + "@id" : "bts:Non-clonal" + } ], + "rdfs:label" : "Clonality", + "rdfs:comment" : "The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "Clonality" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Sex", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:female" + }, { + "@id" : "bts:male" + }, { + "@id" : "bts:unspecified" + } ], + "rdfs:label" : "Sex", + "rdfs:comment" : "Sex of individual", + "@type" : "rdfs:Class", + "sms:displayName" : "Sex" + }, { + "@id" : "bts:YearOfBirth", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value to represent the calendar year in which an individual was born.", + "rdfs:label" : "YearOfBirth", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "YearOfBirth", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:FOVXUnit", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:cm" + }, { + "@id" : "bts:mm" + }, { + "@id" : "bts:µm" + }, { + "@id" : "bts:nm" + }, { + "@id" : "bts:Å" + } ], + "rdfs:label" : "FOVXUnit", + "rdfs:comment" : "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "@type" : "rdfs:Class", + "sms:displayName" : "FOVXUnit" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Pathogenicity", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Benign" + }, { + "@id" : "bts:LikelyBenign" + }, { + "@id" : "bts:LikelyPathogenic" + }, { + "@id" : "bts:Pathogenic" + }, { + "@id" : "bts:UncertainSignificance" + } ], + "rdfs:label" : "Pathogenicity", + "rdfs:comment" : "The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).", + "@type" : "rdfs:Class", + "sms:displayName" : "Pathogenicity" + }, { + "@id" : "bts:SmokelessTobaccoQuitAge", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "SmokelessTobaccoQuitAge", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SmokelessTobaccoQuitAge", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:PixelsBigEndian", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "PixelsBigEndian", + "rdfs:comment" : "Boolean (True/False)", + "@type" : "rdfs:Class", + "sms:displayName" : "PixelsBigEndian" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:BreastCarcinomaDetectionMethodType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Other" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:ClinicalExam" + }, { + "@id" : "bts:Datanotavailable" + }, { + "@id" : "bts:NippleDischarge" + }, { + "@id" : "bts:ScreeningMammography" + }, { + "@id" : "bts:ScreeningMRI" + }, { + "@id" : "bts:Selfexam" + } ], + "rdfs:label" : "BreastCarcinomaDetectionMethodType", + "rdfs:comment" : "The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.", + "@type" : "rdfs:Class", + "sms:displayName" : "BreastCarcinomaDetectionMethodType" + }, { + "@id" : "bts:SizeZ", + "@type" : "rdfs:Class", + "rdfs:comment" : "Size of image: Z dimension (in pixels). Integer >= 1", + "rdfs:label" : "SizeZ", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SizeZ", + "sms:required" : "sms:false" + }, { + "@id" : "bts:COVID19AntibodyTesting", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "COVID19AntibodyTesting", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "COVID19AntibodyTesting", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BMI", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BMI", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BMI", + "sms:required" : "sms:false" + }, { + "@id" : "bts:EmptyWellBarcode", + "@type" : "rdfs:Class", + "rdfs:comment" : "Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.", + "rdfs:label" : "EmptyWellBarcode", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "EmptyWellBarcode", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BreastCarcinomaHER2RatioDiagnosis", + "@type" : "rdfs:Class", + "rdfs:comment" : "HER2 ratio of the participant at diagnosis", + "rdfs:label" : "BreastCarcinomaHER2RatioDiagnosis", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BreastCarcinomaHER2RatioDiagnosis", + "sms:required" : "sms:false" + }, { + "@id" : "bts:TimebetweenWakingandFirstSmoke", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TimebetweenWakingandFirstSmoke", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TimebetweenWakingandFirstSmoke", + "sms:required" : "sms:false" + }, { + "@id" : "bts:MedianPercentageofMitochondrialReadsperNucleus", + "@type" : "rdfs:Class", + "rdfs:comment" : "Contamination from mitochondrial sequences", + "rdfs:label" : "MedianPercentageofMitochondrialReadsperNucleus", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "MedianPercentageofMitochondrialReadsperNucleus", + "sms:required" : "sms:false" + }, { + "@id" : "bts:PhysicalSizeZ", + "@type" : "rdfs:Class", + "rdfs:comment" : "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", + "rdfs:label" : "PhysicalSizeZ", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PhysicalSizeZ", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:CountryofResidence", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:TrinidadandTobago" + }, { + "@id" : "bts:Botswana" + }, { + "@id" : "bts:Malaysia" + }, { + "@id" : "bts:Suriname" + }, { + "@id" : "bts:Uruguay" + }, { + "@id" : "bts:Gibraltar" + }, { + "@id" : "bts:Andorra" + }, { + "@id" : "bts:CaymanIslands" + }, { + "@id" : "bts:Mozambique" + }, { + "@id" : "bts:Dominica" + }, { + "@id" : "bts:Tajikistan" + }, { + "@id" : "bts:Barbados" + }, { + "@id" : "bts:Seychelles" + }, { + "@id" : "bts:Curacao" + }, { + "@id" : "bts:Coted'Ivoire" + }, { + "@id" : "bts:Albania" + }, { + "@id" : "bts:China" + }, { + "@id" : "bts:Oman" + }, { + "@id" : "bts:Congo" + }, { + "@id" : "bts:Burundi" + }, { + "@id" : "bts:FalklandIslands(Malvinas)" + }, { + "@id" : "bts:Kazakhstan" + }, { + "@id" : "bts:Australia" + }, { + "@id" : "bts:France" + }, { + "@id" : "bts:Bahrain" + }, { + "@id" : "bts:SolomonIslands" + }, { + "@id" : "bts:Tanzania" + }, { + "@id" : "bts:FrenchGuiana" + }, { + "@id" : "bts:FederatedStatesofMicronesia" + }, { + "@id" : "bts:AntiguaandBarbuda" + }, { + "@id" : "bts:Colombia" + }, { + "@id" : "bts:Fiji" + }, { + "@id" : "bts:SaoTomeandPrincipe" + }, { + "@id" : "bts:Brazil" + }, { + "@id" : "bts:Guam" + }, { + "@id" : "bts:SouthAfrica" + }, { + "@id" : "bts:Denmark" + }, { + "@id" : "bts:Kyrgyzstan" + }, { + "@id" : "bts:Tunisia" + }, { + "@id" : "bts:Mexico" + }, { + "@id" : "bts:Martinique" + }, { + "@id" : "bts:BurkinaFaso" + }, { + "@id" : "bts:India" + }, { + "@id" : "bts:Myanmar" + }, { + "@id" : "bts:Malawi" + }, { + "@id" : "bts:Sweden" + }, { + "@id" : "bts:Macau" + }, { + "@id" : "bts:Cambodia" + }, { + "@id" : "bts:EquatorialGuinea" + }, { + "@id" : "bts:Senegal" + }, { + "@id" : "bts:Guernsey" + }, { + "@id" : "bts:Azerbaijan" + }, { + "@id" : "bts:Angola" + }, { + "@id" : "bts:Kuwait" + }, { + "@id" : "bts:PapuaNewGuinea" + }, { + "@id" : "bts:CentralAfricanRepublic" + }, { + "@id" : "bts:Bhutan" + }, { + "@id" : "bts:Uzbekistan" + }, { + "@id" : "bts:Portugal" + }, { + "@id" : "bts:IsleofMan" + }, { + "@id" : "bts:Guatemala" + }, { + "@id" : "bts:SaintHelenaAscensionandTristandaCunha" + }, { + "@id" : "bts:Kiribati" + }, { + "@id" : "bts:Peru" + }, { + "@id" : "bts:SouthSudan" + }, { + "@id" : "bts:NorthMacedonia" + }, { + "@id" : "bts:DemocraticRepublicoftheCongo" + }, { + "@id" : "bts:Belarus" + }, { + "@id" : "bts:Madagascar" + }, { + "@id" : "bts:Singapore" + }, { + "@id" : "bts:Togo" + }, { + "@id" : "bts:Gambia" + }, { + "@id" : "bts:Georgia" + }, { + "@id" : "bts:Italy" + }, { + "@id" : "bts:Tuvalu" + }, { + "@id" : "bts:Eswatini" + }, { + "@id" : "bts:Nepal" + }, { + "@id" : "bts:Kenya" + }, { + "@id" : "bts:Niger" + }, { + "@id" : "bts:Israel" + }, { + "@id" : "bts:Iran" + }, { + "@id" : "bts:Liberia" + }, { + "@id" : "bts:Mali" + }, { + "@id" : "bts:Belize" + }, { + "@id" : "bts:Hungary" + }, { + "@id" : "bts:HolySee" + }, { + "@id" : "bts:Serbia" + }, { + "@id" : "bts:Belgium" + }, { + "@id" : "bts:Bermuda" + }, { + "@id" : "bts:Anguilla" + }, { + "@id" : "bts:Jamaica" + }, { + "@id" : "bts:Lebanon" + }, { + "@id" : "bts:Svalbard&JanMayenIslands" + }, { + "@id" : "bts:Cyprus" + }, { + "@id" : "bts:Norway" + }, { + "@id" : "bts:Somalia" + }, { + "@id" : "bts:Japan" + }, { + "@id" : "bts:Guyana" + }, { + "@id" : "bts:Paraguay" + }, { + "@id" : "bts:NewZealand" + }, { + "@id" : "bts:Palau" + }, { + "@id" : "bts:Laos" + }, { + "@id" : "bts:Latvia" + }, { + "@id" : "bts:Ethiopia" + }, { + "@id" : "bts:Cuba" + }, { + "@id" : "bts:FrenchPolynesia" + }, { + "@id" : "bts:Slovenia" + }, { + "@id" : "bts:Philippines" + }, { + "@id" : "bts:Mongolia" + }, { + "@id" : "bts:Switzerland" + }, { + "@id" : "bts:Bahamas" + }, { + "@id" : "bts:Samoa" + }, { + "@id" : "bts:ElSalvador" + }, { + "@id" : "bts:Chad" + }, { + "@id" : "bts:Honduras" + }, { + "@id" : "bts:Bangladesh" + }, { + "@id" : "bts:Tonga" + }, { + "@id" : "bts:Croatia" + }, { + "@id" : "bts:BosniaandHerzegovina" + }, { + "@id" : "bts:Eritrea" + }, { + "@id" : "bts:SaintKittsandNevis" + }, { + "@id" : "bts:Vietnam" + }, { + "@id" : "bts:NorthernMarianaIslands" + }, { + "@id" : "bts:CapeVerde" + }, { + "@id" : "bts:CookIslands" + }, { + "@id" : "bts:Turkmenistan" + }, { + "@id" : "bts:WesternSahara" + }, { + "@id" : "bts:Jordan" + }, { + "@id" : "bts:Romania" + }, { + "@id" : "bts:Uganda" + }, { + "@id" : "bts:Aruba" + }, { + "@id" : "bts:HongKong" + }, { + "@id" : "bts:Syria" + }, { + "@id" : "bts:Germany" + }, { + "@id" : "bts:Chile" + }, { + "@id" : "bts:Austria" + }, { + "@id" : "bts:Gabon" + }, { + "@id" : "bts:Kosovo" + }, { + "@id" : "bts:Qatar" + }, { + "@id" : "bts:Comoros" + }, { + "@id" : "bts:Mayotte" + }, { + "@id" : "bts:Spain" + }, { + "@id" : "bts:Libya" + }, { + "@id" : "bts:CostaRica" + }, { + "@id" : "bts:Bolivia" + }, { + "@id" : "bts:Taiwan" + }, { + "@id" : "bts:Iraq" + }, { + "@id" : "bts:Finland" + }, { + "@id" : "bts:Netherlands" + }, { + "@id" : "bts:Venezuela" + }, { + "@id" : "bts:Malta" + }, { + "@id" : "bts:Niue" + }, { + "@id" : "bts:Algeria" + }, { + "@id" : "bts:Guinea" + }, { + "@id" : "bts:Ireland" + }, { + "@id" : "bts:Montenegro" + }, { + "@id" : "bts:UnitedArabEmirates" + }, { + "@id" : "bts:Maldives" + }, { + "@id" : "bts:Zambia" + }, { + "@id" : "bts:Slovakia" + }, { + "@id" : "bts:Lesotho" + }, { + "@id" : "bts:DominicanRepublic" + }, { + "@id" : "bts:SaintPierreandMiquelon" + }, { + "@id" : "bts:Moldova" + }, { + "@id" : "bts:SanMarino" + }, { + "@id" : "bts:Nauru" + }, { + "@id" : "bts:Luxembourg" + }, { + "@id" : "bts:Monaco" + }, { + "@id" : "bts:Zimbabwe" + }, { + "@id" : "bts:SaudiArabia" + }, { + "@id" : "bts:Mauritania" + }, { + "@id" : "bts:Panama" + }, { + "@id" : "bts:UnitedStates" + }, { + "@id" : "bts:Montserrat" + }, { + "@id" : "bts:Nicaragua" + }, { + "@id" : "bts:FaroeIslands" + }, { + "@id" : "bts:UnitedKingdom" + }, { + "@id" : "bts:Canada" + }, { + "@id" : "bts:Ghana" + }, { + "@id" : "bts:Armenia" + }, { + "@id" : "bts:Bulgaria" + }, { + "@id" : "bts:Egypt" + }, { + "@id" : "bts:Reunion" + }, { + "@id" : "bts:Cameroon" + }, { + "@id" : "bts:Rwanda" + }, { + "@id" : "bts:Timor-Leste" + }, { + "@id" : "bts:Yemen" + }, { + "@id" : "bts:SaintLucia" + }, { + "@id" : "bts:Poland" + }, { + "@id" : "bts:Namibia" + }, { + "@id" : "bts:Guinea-Bissau" + }, { + "@id" : "bts:Thailand" + }, { + "@id" : "bts:Argentina" + }, { + "@id" : "bts:Turkey" + }, { + "@id" : "bts:Djibouti" + }, { + "@id" : "bts:Greece" + }, { + "@id" : "bts:Jersey" + }, { + "@id" : "bts:Mauritius" + }, { + "@id" : "bts:WallisandFutuna" + }, { + "@id" : "bts:Pakistan" + }, { + 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"bts:Secretorycarcinomaofbreast" + }, { + "@id" : "bts:Lobularcarcinomanoninfiltrating" + }, { + "@id" : "bts:Mixedadenocarcinomaandsquamouscellcarcinoma" + }, { + "@id" : "bts:Melanoticneurofibroma" + }, { + "@id" : "bts:ChronicgranulocyticleukemiaPhiladelphiachromosome(Ph1)positive" + }, { + "@id" : "bts:Hepatocellularadenoma" + }, { + "@id" : "bts:BurkittlymphomaNOS(Includesallvariants)" + }, { + "@id" : "bts:ParagangliomaNOS" + }, { + "@id" : "bts:DiffuselargeB-celllymphomaNOS" + }, { + "@id" : "bts:NevusNOS" + }, { + "@id" : "bts:Hepatoidcarcinoma" + }, { + "@id" : "bts:MixedtumormalignantNOS" + }, { + "@id" : "bts:Rhabdoidsarcoma" + }, { + "@id" : "bts:Tubulolobularcarcinoma" + }, { + "@id" : "bts:Papillomatosisglandular" + }, { + "@id" : "bts:Bronchialadenomacarcinoid" + }, { + "@id" : "bts:Tumorembolus" + }, { + "@id" : "bts:DuctcarcinomaNOS" + }, { + "@id" : "bts:RhabdomyosarcomaNOS" + }, { + "@id" : "bts:LobularcarcinomaNOS" + }, { + "@id" : "bts:Bronchialadenomacylindroid" + }, { + "@id" : "bts:EpidermoidcarcinomaNOS" + }, { + "@id" : "bts:Papillaryglioneuronaltumor" + }, { + "@id" : "bts:DuctalcarcinomainsituNOS" + }, { + "@id" : "bts:Unclassifiedtumormalignantuncertainwhetherprimaryormetastatic" + }, { + "@id" : "bts:Glioblastoma" + }, { + "@id" : "bts:Papillaryandfollicularcarcinoma" + }, { + "@id" : "bts:DuctalcarcinomaNOS" + }, { + "@id" : "bts:Tumorbenign" + }, { + "@id" : "bts:Pagetdiseasemammary" + }, { + "@id" : "bts:Diffuseastrocytomalowgrade" + }, { + "@id" : "bts:Ductcellcarcinoma" + }, { + "@id" : "bts:Preleukemicsyndrome" + }, { + "@id" : "bts:Carcinomadiffusetype" + }, { + "@id" : "bts:Neurosarcoma" + }, { + "@id" : "bts:PapillomatosisNOS" + }, { + "@id" : "bts:Therapyrelatedmyeloidneoplasm" + }, { + "@id" : "bts:Renalcarcinomacollectingducttype" + }, { + "@id" : "bts:NeurofibromaNOS" + }, { + "@id" : "bts:Meningiomaanaplastic" + }, { + "@id" : "bts:CementomaNOS" + }, { + "@id" : "bts:DermatofibromaNOS" + }, { + "@id" : "bts:AstrocytomaNOS" + }, { + "@id" : "bts:Livercelladenoma" + }, { + "@id" : "bts:TubulovillousadenomaNOS" + }, { + "@id" : "bts:MelanomaNOS" + }, { + "@id" : "bts:PapillomaNOS" + }, { + "@id" : "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)highgrade" + }, { + "@id" : "bts:Tumorcellsmalignant" + }, { + "@id" : "bts:MalignantlymphomadiffuseNOS" + }, { + "@id" : "bts:Renalcellcarcinomachromophobetype" + }, { + "@id" : "bts:Tubularcarcinoid" + }, { + "@id" : "bts:Nonpigmentednevus" + }, { + "@id" : "bts:Rodentulcer" + }, { + "@id" : "bts:HodgkindiseaseNOS" + }, { + "@id" : "bts:Acinarcellcarcinoma" + }, { + "@id" : "bts:Papillaryadenofibroma" + }, { + "@id" : "bts:Oatcellcarcinoma" + }, { + "@id" : "bts:Adenocarcinomainadenomatouspolyp" + }, { + "@id" : "bts:SpindlecellcarcinomaNOS" + }, { + "@id" : "bts:Adenocarcinomainpolypoidadenoma" + }, { + "@id" : "bts:Papillaryserousadenocarcinoma" + }, { + "@id" : "bts:SplenicdiffuseredpulpsmallB-celllymphoma" + }, { + "@id" : "bts:ChondromaNOS" + }, { + "@id" : "bts:Bileductadenoma" + }, { + "@id" : "bts:Adenocarcinomainvillousadenoma" + }, { + "@id" : "bts:SpindlecellmelanomaNOS" + }, { + "@id" : "bts:ClassicalHodgkinlymphomamixedcellularityNOS" + }, { + "@id" : "bts:Combinedsmallcell-largecarcinoma" + }, { + "@id" : "bts:Eosinophilcarcinoma" + }, { + "@id" : "bts:PancreaticendocrinetumorNOS" + }, { + "@id" : "bts:AdenocarcinomaNOS" + }, { + "@id" : "bts:SarcomaNOS" + }, { + "@id" : "bts:ChronicmyelocyticleukemiaNOS" + }, { + "@id" : "bts:Adenocarcinomainsitunon-mucinous" + }, { + "@id" : "bts:ChronicleukemiaNOS" + }, { + "@id" : "bts:Pro-TALL" + }, { + "@id" : "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)lowgrade" + }, { + "@id" : "bts:Lymphoblastoma" + }, { + "@id" : "bts:Mixedmedullary-papillarycarcinoma" + }, { + "@id" : "bts:ClassicalHodgkinlymphomanodularsclerosisNOS" + }, { + "@id" : "bts:OsteoblastomaNOS" + }, { + "@id" : "bts:CerebellarsarcomaNOS" + }, { + "@id" : "bts:Paragangliomabenign" + }, { + "@id" : "bts:Intraductaltubular-papillaryneoplasmlowgrade" + }, { + "@id" : "bts:Familialadenomatouspolyposis" + }, { + "@id" : "bts:Mixedsquamouscellandglandularpapilloma" + }, { + "@id" : "bts:IntraductalcarcinomaNOS" + }, { + "@id" : "bts:Transitionalcarcinoma" + }, { + "@id" : "bts:Gastrinomamalignant" + }, { + "@id" : "bts:Melanocytomaeyeball" + }, { + "@id" : "bts:Mixedmedullary-follicularcarcinoma" + }, { + "@id" : "bts:ChronicmyelogenousleukemiaBCR-ABLpositive" + }, { + "@id" : "bts:Basophilcarcinoma" + }, { + "@id" : "bts:NeuroepitheliomaNOS" + }, { + "@id" : "bts:Adenocarcinomapancreatobiliarytype" + }, { + "@id" : "bts:PrecancerousmelanosisNOS" + }, { + "@id" : "bts:Undifferentiatedroundcellsarcoma" + }, { + "@id" : "bts:MalignantlymphomalargecellNOS" + }, { + "@id" : "bts:Tubulo-papillaryadenoma" + }, { + "@id" : "bts:ClassicalHodgkinlymphomalymphocytedepletiondiffusefibrosis" + }, { + "@id" : "bts:Cerebellarliponeurocytoma" + }, { + "@id" : "bts:Pulmonaryblastoma" + }, { + "@id" : "bts:Burkitt-likelymphoma" + }, { + "@id" : "bts:GangliogliomaNOS" + }, { + "@id" : "bts:T-celllymphomaNOS" + }, { + "@id" : "bts:Papillarytumorofthepinealregion" + }, { + "@id" : "bts:IntraductalpapillaryadenocarcinomaNOS" + }, { + "@id" : "bts:MalignantlymphomaNOS" + }, { + "@id" : "bts:Hepatoidadenocarcinoma" + }, { + "@id" : "bts:PapillaryadenomaNOS" + }, { + "@id" : "bts:Carcinomainsituinadenomatouspolyp" + }, { + "@id" : "bts:Eosinophilicgranuloma" + }, { + "@id" : "bts:Medullaryadenocarcinoma" + }, { + "@id" : "bts:Malignantlymphomamixedcelltypenodular" + }, { + "@id" : "bts:IntraductalcarcinomanoninfiltratingNOS" + }, { + "@id" : "bts:Interstitialcelltumormalignant" + }, { + "@id" : "bts:LymphomaNOS" + }, { + "@id" : "bts:Unclassifiedtumorborderlinemalignancy" + }, { + "@id" : "bts:Adenocarcinomaintubularadenoma" + }, { + "@id" : "bts:Intraductalpapillarycarcinoma" + }, { + "@id" : "bts:MyelocyticleukemiaNOS" + }, { + "@id" : "bts:TumorcellsNOS" + }, { + "@id" : "bts:LiposarcomaNOS" + }, { + "@id" : "bts:Interstitialcelltumorbenign" + }, { + "@id" : "bts:Neoplasmmetastatic" + }, { + "@id" : "bts:Chronicneutrophilicleukemia" + }, { + "@id" : "bts:Bronchiolo-alveolarcarcinomagobletcelltype" + }, { + "@id" : "bts:Papillaryadenocarcinomafollicularvariant" + }, { + "@id" : "bts:Hepatocarcinoma" + }, { + "@id" : "bts:Undifferentiateduterinesarcoma" + }, { + "@id" : "bts:Renalcellcarcinomaunclassified" + }, { + "@id" : "bts:Papillaryepidermoidcarcinoma" + }, { + "@id" : "bts:PigmentednevusNOS" + }, { + "@id" : "bts:MyeloidleukemiaNOS" + }, { + "@id" : "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)highgrade" + }, { + "@id" : "bts:MalignantlymphomalargeB-cellNOS" + }, { + "@id" : "bts:Non-lymphocyticleukemiaNOS" + }, { + "@id" : "bts:Basalcelladenocarcinoma" + }, { + "@id" : "bts:AdultT-celllymphoma/leukemia" + }, { + "@id" : "bts:Mixedpancreaticendocrineandexocrinetumormalignant" + }, { + "@id" : "bts:EpendymomaNOS" + }, { + "@id" : "bts:PeripheralT-celllymphomaNOS" + }, { + "@id" : "bts:Pulmonaryadenomatosis" + }, { + "@id" : "bts:Pleomorphiclobularcarcinoma" + }, { + "@id" : "bts:Pagetdiseaseofbreast" + }, { + "@id" : "bts:HodgkinparagranulomaNOS" + }, { + "@id" : "bts:MalignantmelanomaNOS" + }, { + "@id" : "bts:Papillarytransitionalcellcarcinoma" + }, { + "@id" : "bts:Acutelymphocyticleukemia" + }, { + "@id" : "bts:Seroussurfacepapillarycarcinoma" + }, { + "@id" : "bts:Basalcelltumor" + }, { + "@id" : "bts:ChronicmyelomonocyticleukemiaNOS" + }, { + "@id" : "bts:LymphaticleukemicNOS" + }, { + "@id" : "bts:TeratomaNOS" + }, { + "@id" : "bts:Malignantlymphomamixedcelltypefollicular" + }, { + "@id" : "bts:Bronchiolaradenocarcinoma" + }, { + "@id" : "bts:Basophiladenocarcinoma" + }, { + "@id" : "bts:Non-HodgkinlymphomaNOS" + }, { + "@id" : "bts:Haemangioblastoma" + }, { + "@id" : "bts:Intraductaltubular-papillaryneoplasmhighgrade" + }, { + "@id" : "bts:ChronicmyeloproliferativediseaseNOS" + }, { + "@id" : "bts:Rhabdoidmeningioma" + }, { + "@id" : "bts:RhabdoidtumorNOS" + }, { + "@id" : "bts:Carcinomaintestinaltype" + }, { + "@id" : "bts:ClassicalHodgkinlymphomalymphocytedepletionNOS" + }, { + "@id" : "bts:ChronicmyeloidleukemiaNOS" + }, { + "@id" : "bts:Melanoticmedulloblastoma" + }, { + "@id" : "bts:Melanoticneuroectodermaltumor" + }, { + "@id" : "bts:LobularcarcinomainsituNOS" + }, { + "@id" : "bts:Mixedsmallcellcarcinoma" + }, { + "@id" : "bts:Intradermalnevus" + }, { + "@id" : "bts:Bronchiolo-alveolarcarcinomaClaracell" + }, { + "@id" : "bts:Papillarysquamouscellcarcinomainsitu" + }, { + "@id" : "bts:Smallcellneuroendocrinecarcinoma" + }, { + "@id" : "bts:Malignantmelanomainprecancerousmelanosis" + }, { + "@id" : "bts:CarcinomaanaplasticNOS" + }, { + "@id" : "bts:Dysplasticnevus" + }, { + "@id" : "bts:Liposarcomadifferentiated" + }, { + "@id" : "bts:Combinedsmallcell-squamouscellcarcinoma" + }, { + "@id" : "bts:Acutelymphaticleukemia" + }, { + "@id" : "bts:Gliomamalignant" + }, { + "@id" : "bts:AdenocarcinomainsituNOS" + }, { + "@id" : "bts:Mucosal-associatedlymphoidtissuelymphoma" + }, { + "@id" : "bts:Spleniclymphomawithvillouslymphocytes" + }, { + "@id" : "bts:LargecellcarcinomaNOS" + }, { + "@id" : "bts:MicropapillarycarcinomaNOS" + }, { + "@id" : "bts:Undifferentiatedspindlecellsarcoma" + }, { + "@id" : "bts:IntraepidermalsquamouscellcarcinomaBowentype" + }, { + "@id" : "bts:EndometrioidadenofibromaNOS" + }, { + "@id" : "bts:MedullarycarcinomaNOS" + }, { + "@id" : "bts:T-celllargegranularlymphocytosis" + }, { + "@id" : "bts:IntraductaladenocarcinomanoninfiltratingNOS" + }, { + "@id" : "bts:OsteosarcomaNOS" + }, { + "@id" : "bts:Pancreatobiliary-typecarcinoma" + }, { + "@id" : "bts:Adenocarcinoidtumor" + }, { + "@id" : "bts:DiffuseastrocytomaIDH-mutant" + }, { + "@id" : "bts:Medullaryosteosarcoma" + }, { + "@id" : "bts:Adenocarcinomaintestinaltype" + }, { + "@id" : "bts:CarcinomainsituinapolypNOS" + }, { + "@id" : "bts:CarcinosarcomaNOS" + }, { + "@id" : "bts:Basalcelladenoma" + }, { + "@id" : "bts:AdultT-celllymphoma" + }, { + "@id" : "bts:Lobularadenocarcinoma" + }, { + "@id" : "bts:Melanocyticnevus" + }, { + "@id" : "bts:AdenocarcinomametastaticNOS" + }, { + "@id" : "bts:Pigmentedbasalcellcarcinoma" + }, { + "@id" : "bts:Astrocytomaanaplastic" + }, { + "@id" : "bts:Melanomamalignantofsoftparts" + }, { + "@id" : "bts:Smallcellosteosarcoma" + }, { + "@id" : "bts:Unclassifiedtumoruncertainwhetherbenignormalignant" + }, { + "@id" : "bts:Transitionalcellcarcinoma" + }, { + "@id" : "bts:Intraductalcarcinomaandlobularcarcinomainsitu" + }, { + "@id" : "bts:RhabdomyomaNOS" + }, { + "@id" : "bts:B-celllymphocyticleukemia/smalllymphocyticlymphoma" + }, { + "@id" : "bts:Capillaryhemangioma" + }, { + "@id" : "bts:PrecursorB-celllymphoblasticleukemia" + }, { + "@id" : "bts:Bronchiolo-alveolarcarcinomaClaracellandgobletcelltype" + }, { + "@id" : "bts:Eosinophiladenoma" + }, { + "@id" : "bts:SplenicB-celllymphoma/leukemiaunclassifiable" + }, { + "@id" : "bts:CompositeHodgkinandnon-Hodgkinlymphoma" + }, { + "@id" : "bts:Pagetdiseaseandinfiltratingductcarcinomaofbreast" + }, { + "@id" : "bts:NeurofibromatosisNOS" + }, { + "@id" : "bts:HodgkinlymphomaNOS" + }, { + "@id" : "bts:Melanomainsitu" + }, { + "@id" : "bts:SerouscystadenocarcinomaNOS" + }, { + "@id" : "bts:MalignantlymphomaHodgkin" + }, { + "@id" : "bts:Acutelymphoblasticleukemia-lymphomaNOS" + }, { + "@id" : "bts:Unclassifiedtumormalignant" + }, { + "@id" : "bts:Adultrhabdomyoma" + }, { + "@id" : "bts:Neoplasmuncertainwhetherbenignormalignant" + }, { + "@id" : "bts:ChronicmyelomonocyticleukemiaType1" + }, { + "@id" : "bts:DuctadenomaNOS" + }, { + "@id" : "bts:Neoplasmbenign" + }, { + "@id" : "bts:CarcinomaundifferentiatedNOS" + }, { + "@id" : "bts:Malignancy" + }, { + "@id" : "bts:Adenocarcinomainsitumucinous" + }, { + "@id" : "bts:Papillarysquamouscellcarcinoma" + }, { + "@id" : "bts:Blymphoblasticleukemia/lymphomawithhyperdiploidy" + }, { + "@id" : "bts:PrecursorT-celllymphoblasticleukemia" + }, { + "@id" : "bts:Tumorsecondary" + }, { + "@id" : "bts:Pancreatobiliaryneoplasmnon-invasive" + }, { + "@id" : "bts:Malignantmelanomaingiantpigmentednevus" + }, { + "@id" : "bts:Squamouscellcarcinomaadenoid" + }, { + "@id" : "bts:Acutemyelomonocyticleukemia" + }, { + "@id" : "bts:Bileductcystadenocarcinoma" + }, { + "@id" : "bts:Pancreaticendocrinetumornonfunctioning" + }, { + "@id" : "bts:Pleomorphicadenoma" + }, { + "@id" : "bts:Blymphoblasticleukemia/lymphomawithhypodiploidy(HypodiploidALL)" + }, { + "@id" : "bts:Renalcellcarcinomasarcomatoid" + }, { + "@id" : "bts:SplenicmarginalzoneB-celllymphoma" + }, { + "@id" : "bts:MalignantlymphomalargeB-celldiffuseNOS" + }, { + "@id" : "bts:Infiltratingductandcolloidcarcinoma" + }, { + "@id" : "bts:ChronicmyelomonocyticleukemiaTypeII" + }, { + "@id" : "bts:DuctadenocarcinomaNOS" + }, { + "@id" : "bts:Combined/mixedcarcinoidandadenocarcinoma" + }, { + "@id" : "bts:Haemangiosarcoma" + }, { + "@id" : "bts:Acutelymphoidleukemia" + }, { + "@id" : "bts:DiffuseastrocytomaIDH-wildtype" + }, { + "@id" : "bts:Intraductaltubulopapillaryneoplasm" + }, { + "@id" : "bts:Acutebasophilicleukaemia" + }, { + "@id" : "bts:Unclassifiedtumorbenign" + }, { + "@id" : "bts:Intraductalmicropapillarycarcinoma" + }, { + "@id" : "bts:Hodgkingranuloma" + }, { + "@id" : "bts:ChroniclymphocyticleukemiaB-celltype(includesallvariantsofBCLL)" + }, { + "@id" : "bts:Pancreatoblastoma" + }, { + "@id" : "bts:Bileductadenocarcinoma" + }, { + "@id" : "bts:Meningealmelanocytoma" + }, { + "@id" : "bts:HodgkinlymphomamixedcellularityNOS" + }, { + "@id" : "bts:InfiltratingductcarcinomaNOS" + }, { + "@id" : "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)lowgrade" + }, { + "@id" : "bts:SmallcellcarcinomaNOS" + }, { + "@id" : "bts:Inflammatorycarcinoma" + }, { + "@id" : "bts:Papillaryurothelialcarcinoma" + }, { + "@id" : "bts:Melanoticprogonoma" + }, { + "@id" : "bts:Centralneuroblastoma" + }, { + "@id" : "bts:MalignantlymphomalymphocyticNOS" + }, { + "@id" : "bts:MyelomaNOS" + }, { + "@id" : "bts:Adenocarcinomaendocervicaltype" + }, { + "@id" : "bts:AdenocarcinomainsituinapolypNOS" + }, { + "@id" : "bts:Neoplasmmalignantuncertainwhetherprimaryormetastatic" + }, { + "@id" : "bts:Pulmonaryarteryintimalsarcoma" + }, { + "@id" : "bts:IntraepidermalcarcinomaNOS" + }, { + "@id" : "bts:PapillaryserouscystadenomaNOS" + }, { + "@id" : "bts:CarcinomainsituNOS" + }, { + "@id" : "bts:TubularadenomaNOS" + }, { + "@id" : "bts:Tubulopapillaryadenocarcinoma" + }, { + "@id" : "bts:Pancreaticmicroadenoma" + }, { + "@id" : "bts:AcutelymphoblasticleukemiamatureB-celltype" + }, { + "@id" : "bts:c-ALL" + }, { + "@id" : "bts:AcuteleukemiaBurkitttype" + }, { + "@id" : "bts:Cervicalintraepithelialneoplasialowgrade" + }, { + "@id" : "bts:MixedtumorNOS" + }, { + "@id" : "bts:Bronchiolo-alveolaradenocarcinomaNOS" + }, { + "@id" : "bts:Myoepithelioma" + }, { + "@id" : "bts:Pancreaticendocrinetumormalignant" + }, { + "@id" : "bts:EndometrioidadenocarcinomaNOS" + }, { + "@id" : "bts:InfiltratingbasalcellcarcinomaNOS" + }, { + "@id" : "bts:PrecursorB-celllymphoblasticlymphoma" + }, { + "@id" : "bts:Pleomorphiclobularcarcinomainsitu" + }, { + "@id" : "bts:Mucousadenocarcinoma" + }, { + "@id" : "bts:Meningealmelanoma" + }, { + "@id" : "bts:Acutemyeloidleukemiaminimaldifferentiation" + }, { + "@id" : "bts:LymphoblasticleukemiaNOS" + }, { + "@id" : "bts:MelanoticMPNST" + }, { + "@id" : "bts:Astrocytomalowgrade" + }, { + "@id" : "bts:Multiplemyeloma" + }, { + "@id" : "bts:Papillaryrenalcellcarcinoma" + }, { + "@id" : "bts:MedulloblastomaNOS" + }, { + "@id" : "bts:AdenocarcinomainapolypNOS" + }, { + "@id" : "bts:Combinedsmallcellcarcinoma" + }, { + "@id" : "bts:Bileductcarcinoma" + }, { + "@id" : "bts:ChronicgranulocyticleukemiaNOS" + }, { + "@id" : "bts:Juvenilemyelomonocyticleukemia" + }, { + "@id" : "bts:NeoplasmNOS" + }, { + "@id" : "bts:Capillarylymphangioma" + }, { + "@id" : "bts:Malignantlymphomamixedcelltypediffuse" + }, { + "@id" : "bts:Neoplasmmalignant" + }, { + "@id" : "bts:Papillarymeningioma" + }, { + "@id" : "bts:Bileductcystadenoma" + }, { + "@id" : "bts:Malignantmelanomaincongenitalmelanocyticnevus" + }, { + "@id" : "bts:Adenocarcinomadiffusetype" + }, { + "@id" : "bts:Pancreaticendocrinetumorbenign" + }, { + "@id" : "bts:SquamouscellcarcinomaNOS" + }, { + "@id" : "bts:Chronicmyelomonocyticleukemiaintransformation" + }, { + "@id" : "bts:T-celllargegranularlymphocyticleukemia" + }, { + "@id" : "bts:Basophiladenoma" + }, { + "@id" : "bts:Bronchiolarcarcinoma" + }, { + "@id" : "bts:Tubularcarcinoma" + }, { + "@id" : "bts:Neurofibrosarcoma" + }, { + "@id" : "bts:Adenocarcinomainsituinadenomatouspolyp" + }, { + "@id" : "bts:IntravascularB-celllymphoma" + }, { + "@id" : "bts:Pleomorphicliposarcoma" + }, { + "@id" : "bts:Tumormetastatic" + } ], + "rdfs:label" : "PrimaryDiagnosis", + "rdfs:comment" : "Text term used to describe the patient's histologic 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Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. 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Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "TestAnalyteType" + }, { + "@id" : "bts:DataCategory", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "DataCategory", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "DataCategory", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Ethnicity", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:hispanicorlatino" + }, { + "@id" : "bts:nothispanicorlatino" + }, { + "@id" : "bts:notallowedtocollect" + } ], + "rdfs:label" : "Ethnicity", + "rdfs:comment" : "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.", + "@type" : "rdfs:Class", + "sms:displayName" : "Ethnicity" + }, { + "@id" : "bts:WorkingDistance", + "@type" : "rdfs:Class", + "rdfs:comment" : "The working distance of the lens, expressed as a floating point number. 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"@id" : "bts:UrineBiospecimenType" + }, { + "@id" : "bts:StoolBiospecimenType" + } ], + "rdfs:label" : "BiospecimenType", + "rdfs:comment" : "Biospecimen Type", + "@type" : "rdfs:Class", + "sms:displayName" : "BiospecimenType" + }, { + "@id" : "bts:SmokeExposureDuration", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "SmokeExposureDuration", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SmokeExposureDuration", + "sms:required" : "sms:false" + }, { + "@id" : "bts:MenstrualCyclePhase", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "MenstrualCyclePhase", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "MenstrualCyclePhase", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ThresholdforMinimumPassingReads", + "@type" : "rdfs:Class", + "rdfs:comment" : "Threshold for calling cells", + "rdfs:label" : "ThresholdforMinimumPassingReads", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ThresholdforMinimumPassingReads", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:ShippingConditionType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:LiquidNitrogen" + }, { + "@id" : "bts:DryIce" + }, { + "@id" : "bts:AmbientPack" + }, { + "@id" : "bts:ColdPack" + }, { + "@id" : "bts:IcePack" + }, { + "@id" : "bts:SpecimenatRoomTemperature" + }, { + "@id" : "bts:OtherShippingEnvironment" + }, { + "@id" : "bts:NotShipped" + } ], + "rdfs:label" : "ShippingConditionType", + "rdfs:comment" : "Text descriptor of the shipping environment of a biospecimen.", + "@type" : "rdfs:Class", + "sms:displayName" : "ShippingConditionType" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:AntibioticUse", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:No" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Yes-withinlastmonthh" + }, { + "@id" : "bts:Yes-withinlast1-6months" + }, { + "@id" : "bts:Yes-over6monthsago" + } ], + "rdfs:label" : "AntibioticUse", + "rdfs:comment" : "Antibiotic use", + "@type" : "rdfs:Class", + "sms:displayName" : "AntibioticUse" + }, { + "@id" : "bts:ERStatus", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ERStatus", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ERStatus", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:MolecularConsequence", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:TFBindingSiteVariant" + }, { + "@id" : "bts:TranscriptAmplification" + }, { + "@id" : "bts:SpliceRegionVariant" + }, { + "@id" : "bts:DownstreamGeneVariant" + }, { + "@id" : "bts:5PrimeUTRVariant" + }, { + "@id" : "bts:SpliceDonorVariant" + }, { + "@id" : "bts:SpliceAcceptorVariant" + }, { + "@id" : "bts:StopGain" + }, { + "@id" : "bts:StopRetainedVariant" + }, { + "@id" : "bts:TFBSAmplification" + }, { + "@id" : "bts:3PrimeUTRVariant" + }, { + "@id" : "bts:UpstreamGeneVariant" + }, { + "@id" : "bts:IntergenicVariant" + }, { + "@id" : "bts:RegulatoryRegionAblation" + }, { + "@id" : "bts:NMDTranscriptVariant" + }, { + "@id" : "bts:TranscriptAblation" + }, { + "@id" : "bts:Non-codingTranscriptExonVariant" + }, { + "@id" : "bts:SynonymousVariant" + }, { + "@id" : "bts:RegulatoryRegionVariant" + }, { + "@id" : "bts:StopLost" + }, { + "@id" : "bts:MaturemiRNAVariant" + }, { + "@id" : "bts:InframeInsertion" + }, { + "@id" : "bts:InframeDeletion" + }, { + "@id" : "bts:ProteinAlteringVariant" + }, { + "@id" : "bts:IncompleteTerminalCodonVariant" + }, { + "@id" : "bts:TFBSAblation" + }, { + "@id" : "bts:IntronVariant" + }, { + "@id" : "bts:CodingSequenceVariant" + }, { + "@id" : "bts:MissenseVariant" + }, { + "@id" : "bts:FrameshiftVariant" + }, { + "@id" : "bts:Non-codingTranscriptVariant" + }, { + "@id" : "bts:FeatureTruncation" + }, { + "@id" : "bts:RegulatoryRegionAmplification" + }, { + "@id" : "bts:StartLost" + }, { + "@id" : "bts:FeatureElongation" + } ], + "rdfs:label" : "MolecularConsequence", + "rdfs:comment" : "The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "MolecularConsequence" + }, { + "@id" : "bts:SampleCollectionYear", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "SampleCollectionYear", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SampleCollectionYear", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:WorkingDistanceUnit", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:cm" + }, { + "@id" : "bts:mm" + }, { + "@id" : "bts:µm" + }, { + "@id" : "bts:nm" + }, { + "@id" : "bts:Å" + } ], + "rdfs:label" : "WorkingDistanceUnit", + "rdfs:comment" : "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "@type" : "rdfs:Class", + "sms:displayName" : "WorkingDistanceUnit" + }, { + "@id" : "bts:PriorSitesofRadiation", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "PriorSitesofRadiation", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PriorSitesofRadiation", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:AlcoholHistory", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotReported" + } ], + "rdfs:label" : "AlcoholHistory", + "rdfs:comment" : "A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.", + "@type" : "rdfs:Class", + "sms:displayName" : "AlcoholHistory" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:AgeIsObfuscated", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:True" + }, { + "@id" : "bts:False" + } ], + "rdfs:label" : "AgeIsObfuscated", + "rdfs:comment" : "The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.", + "@type" : "rdfs:Class", + "sms:displayName" : "AgeIsObfuscated" + }, { + "@id" : "bts:TargetName", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TargetName", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TargetName", + "sms:required" : "sms:false" + }, { + "@id" : "bts:SecondExon", + "@type" : "rdfs:Class", + "rdfs:comment" : "The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.", + "rdfs:label" : "SecondExon", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SecondExon", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:HistoneFamily", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:H1" + }, { + "@id" : "bts:H2A" + }, { + "@id" : "bts:H2B" + }, { + "@id" : "bts:H3" + }, { + "@id" : "bts:H4" + } ], + "rdfs:label" : "HistoneFamily", + "rdfs:comment" : "The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.", + "@type" : "rdfs:Class", + "sms:displayName" : "HistoneFamily" + }, { + "@id" : "bts:BloodTestNormalRangeUpper", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.", + "rdfs:label" : "BloodTestNormalRangeUpper", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BloodTestNormalRangeUpper", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:ScATACseqLibraryLayout", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "ScATACseqLibraryLayout", + "rdfs:comment" : "Sequencing read type", + "@type" : "rdfs:Class", + "sms:displayName" : "ScATACseqLibraryLayout" + }, { + "@id" : "bts:Immunosuppression", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Immunosuppression", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Immunosuppression", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Authors", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Authors", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Authors", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:OvarianCancerPlatinumStatus", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Datanotavailable" + }, { + "@id" : "bts:Platinum-refractory" + }, { + "@id" : "bts:Platinum-sensitive" + }, { + "@id" : "bts:Platinum-resistant" + } ], + "rdfs:label" : "OvarianCancerPlatinumStatus", + "rdfs:comment" : "Text term to indicate the status of treatment with platinum in participant with ovarian cancer", + "@type" : "rdfs:Class", + "sms:displayName" : "OvarianCancerPlatinumStatus" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:AlcoholIntensity", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:Drinker" + }, { + "@id" : "bts:HeavyDrinker" + }, { + "@id" : "bts:LifelongNon-Drinker" + }, { + "@id" : "bts:Non-Drinker" + }, { + "@id" : "bts:OccasionalDrinker" + } ], + "rdfs:label" : "AlcoholIntensity", + "rdfs:comment" : "Category to describe the patient's current level of alcohol use as self-reported by the patient.", + "@type" : "rdfs:Class", + "sms:displayName" : "AlcoholIntensity" + }, { + "@id" : "bts:Transcript", + "@type" : "rdfs:Class", + "rdfs:comment" : "Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "Transcript", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Transcript", + "sms:required" : "sms:false" + }, { + "@id" : "bts:EducationLevel", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "EducationLevel", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "EducationLevel", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:DimensionOrder", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:XYZCT" + }, { + "@id" : "bts:XYZTC" + }, { + "@id" : "bts:XYCTZ" + }, { + "@id" : "bts:XYCZT" + }, { + "@id" : "bts:XYTZC" + }, { + "@id" : "bts:ZYX" + } ], + "rdfs:label" : "DimensionOrder", + "rdfs:comment" : "The order in which the individual planes of data are interleaved.", + "@type" : "rdfs:Class", + "sms:displayName" : "DimensionOrder" + }, { + "@id" : "bts:Parity", + "@type" : "rdfs:Class", + "rdfs:comment" : "Number of pregnancies carried over the threshold of viability", + "rdfs:label" : "Parity", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Parity", + "sms:required" : "sms:false" + }, { + "@id" : "bts:AlcoholDaysPerWeek", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.", + "rdfs:label" : "AlcoholDaysPerWeek", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AlcoholDaysPerWeek", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:AnalyteType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:TissueSectionAnalyte" + }, { + "@id" : "bts:SerumAnalyte" + }, { + "@id" : "bts:PBMCsorPlasmaorSerumAnalyte" + }, { + "@id" : "bts:Plasma" + }, { + "@id" : "bts:TissueBlockAnalyte" + }, { + "@id" : "bts:cfDNAAnalyte" + }, { + "@id" : "bts:DNAAnalyte" + }, { + "@id" : "bts:RNAAnalyte" + }, { + "@id" : "bts:cDNALibrariesAnalyte" + }, { + "@id" : "bts:PBMCs" + }, { + "@id" : "bts:TotalRNAAnalyte" + } ], + "rdfs:label" : "AnalyteType", + "rdfs:comment" : "The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen", + "@type" : "rdfs:Class", + "sms:displayName" : "AnalyteType" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:FOVYUnit", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:cm" + }, { + "@id" : "bts:mm" + }, { + "@id" : "bts:µm" + }, { + "@id" : "bts:nm" + }, { + "@id" : "bts:Å" + } ], + "rdfs:label" : "FOVYUnit", + "rdfs:comment" : "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "@type" : "rdfs:Class", + "sms:displayName" : "FOVYUnit" + }, { + "@id" : "bts:AgeatDiagnosis", + "@type" : "rdfs:Class", + "rdfs:comment" : "Age at the time of diagnosis expressed in number of days since birth.", + "rdfs:label" : "AgeatDiagnosis", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AgeatDiagnosis", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Cytoband", + "@type" : "rdfs:Class", + "rdfs:comment" : "Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "Cytoband", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Cytoband", + "sms:required" : "sms:false" + }, { + "@id" : "bts:PeaksCallingSoftware", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "PeaksCallingSoftware", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PeaksCallingSoftware", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:SecondhandSmokeasChild", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotReported" + } ], + "rdfs:label" : "SecondhandSmokeasChild", + "rdfs:comment" : "The text term used to indicate whether the patient was exposed to secondhand smoke as a child.", + "@type" : "rdfs:Class", + "sms:displayName" : "SecondhandSmokeasChild" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:PhysicalSizeXUnit", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:cm" + }, { + "@id" : "bts:mm" + }, { + "@id" : "bts:µm" + }, { + "@id" : "bts:nm" + }, { + "@id" : "bts:Å" + } ], + "rdfs:label" : "PhysicalSizeXUnit", + "rdfs:comment" : "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "@type" : "rdfs:Class", + "sms:displayName" : "PhysicalSizeXUnit" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:CancerAssociatedGeneMutations", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:PMS2mutation" + }, { + "@id" : "bts:POT1mutation" + }, { + "@id" : "bts:TP53mutation" + }, { + "@id" : "bts:H3K27Mmutation" + }, { + "@id" : "bts:SMARCA4mutation" + }, { + "@id" : "bts:SDHDmutation" + }, { + "@id" : "bts:BRCA1mutation" + }, { + "@id" : "bts:CHKmutation" + }, { + "@id" : "bts:RB1mutation" + }, { + "@id" : "bts:H3G34R/Vmutation" + }, { + "@id" : "bts:SDHCmutation" + }, { + "@id" : "bts:SDHBmutation" + }, { + "@id" : "bts:TSC2mutation" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:HOXB13mutation" + }, { + "@id" : "bts:NF1mutation" + }, { + "@id" : "bts:VHLmutation" + }, { + "@id" : "bts:BAP1mutation" + }, { + "@id" : "bts:SETD2mutation" + }, { + "@id" : "bts:BRCA1and2mutation" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:PTENmutation" + }, { + "@id" : "bts:NotApplicable" + }, { + "@id" : "bts:STK11mutation" + }, { + "@id" : "bts:PAX5mutation" + }, { + "@id" : "bts:RETmutation" + }, { + "@id" : "bts:NF2mutation" + }, { + "@id" : "bts:ETV6mutation" + }, { + "@id" : "bts:PolDmutation" + }, { + "@id" : "bts:IKZF1mutation" + }, { + "@id" : "bts:PALB2mutation" + }, { + "@id" : "bts:SDHAF2mutation" + }, { + "@id" : "bts:EGFRmutation" + }, { + "@id" : "bts:PDGFRAmutation" + }, { + "@id" : "bts:ARFmutation" + }, { + "@id" : "bts:PTCHmutation" + }, { + "@id" : "bts:PRKAR1Amutation" + }, { + "@id" : "bts:MUTYHmutation" + }, { + "@id" : "bts:MSH6mutation" + }, { + "@id" : "bts:CDKN2Aandp14ARFmutation" + }, { + "@id" : "bts:GREM1mutation" + }, { + "@id" : "bts:MAXmutation" + }, { + "@id" : "bts:FHmutation" + }, { + "@id" : "bts:PHOX2Bmutation" + }, { + "@id" : "bts:CDH1mutation" + }, { + "@id" : "bts:MSH2mutation" + }, { + "@id" : "bts:MLH1mutation" + }, { + "@id" : "bts:METmutation" + }, { + "@id" : "bts:ATRXmutation" + }, { + "@id" : "bts:KRASmutation" + }, { + "@id" : "bts:KITmutation" + }, { + "@id" : "bts:PolEmutation" + }, { + "@id" : "bts:TSC1mutation" + }, { + "@id" : "bts:BLMmutation" + }, { + "@id" : "bts:ATMmutation" + }, { + "@id" : "bts:ACVR1mutation" + }, { + "@id" : "bts:FLCNmutation" + }, { + "@id" : "bts:MEN1mutation" + }, { + "@id" : "bts:TMEM127mutation" + }, { + "@id" : "bts:BRAFmutation" + }, { + "@id" : "bts:ROS1mutation" + }, { + "@id" : "bts:SMAD4mutation" + }, { + "@id" : "bts:ALKmutation" + }, { + "@id" : "bts:BMPR1Amutation" + }, { + "@id" : "bts:APCmutation" + }, { + "@id" : "bts:BRCA2mutation" + }, { + "@id" : "bts:SMARCB1mutation" + }, { + "@id" : "bts:CDKN2Amutation" + }, { + "@id" : "bts:RAD51Cmutation" + }, { + "@id" : "bts:p14ARFmutation" + } ], + "rdfs:label" : "CancerAssociatedGeneMutations", + "rdfs:comment" : "Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history", + "@type" : "rdfs:Class", + "sms:displayName" : "CancerAssociatedGeneMutations" + }, { + "@id" : "bts:FOVnumber", + "@type" : "rdfs:Class", + "rdfs:comment" : "Index of FOV (as it pertains to its sequence order). 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Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "AAChange", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AAChange", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:NucleicAcidSource", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:SingleCell" + }, { + "@id" : "bts:BulkWholeCell" + }, { + "@id" : "bts:SingleNucleus" + }, { + "@id" : "bts:BulkNuclei" + } ], + "rdfs:label" : "NucleicAcidSource", + "rdfs:comment" : "The source of the input nucleic molecule", + "@type" : "rdfs:Class", + "sms:displayName" : "NucleicAcidSource" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:ExtentofTumorResection", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Minor" + }, { + "@id" : "bts:OpenBiopsy" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:GrossTotalResection" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotApplicable" + }, { + "@id" : "bts:Segmental" + }, { + "@id" : "bts:NTR" + }, { + "@id" : "bts:Suboptimaldebulking" + }, { + "@id" : "bts:SubtotalResection" + }, { + "@id" : "bts:Other" + }, { + "@id" : "bts:Partialdebulking" + }, { + "@id" : "bts:Suboptimal" + }, { + "@id" : "bts:Optimaldebulking" + }, { + "@id" : "bts:ExtensiveSubtotal" + } ], + "rdfs:label" : "ExtentofTumorResection", + "rdfs:comment" : "The degree to which the lesion has been cut out, or resected.", + "@type" : "rdfs:Class", + "sms:displayName" : "ExtentofTumorResection" + }, { + "@id" : "bts:TimepointLabel", + "@type" : "rdfs:Class", + "rdfs:comment" : "Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.", + "rdfs:label" : "TimepointLabel", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TimepointLabel", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Ploidy", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:Aneuploid" + }, { + "@id" : "bts:Diploid" + }, { + "@id" : "bts:Hyperdiploid" + }, { + "@id" : "bts:Hypodiploid" + }, { + "@id" : "bts:NearDiploid" + }, { + "@id" : "bts:Tetraploid" + } ], + "rdfs:label" : "Ploidy", + "rdfs:comment" : "Text term used to describe the number of sets of homologous chromosomes.", + "@type" : "rdfs:Class", + "sms:displayName" : "Ploidy" + }, { + "@id" : "bts:PortionWeight", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value that represents the sample portion weight, measured in milligrams.", + "rdfs:label" : "PortionWeight", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PortionWeight", + "sms:required" : "sms:false" + }, { + "@id" : "bts:DaystoProgression", + "@type" : "rdfs:Class", + "rdfs:comment" : "Number of days between the date used for index and the date the patient's disease progressed.", + "rdfs:label" : "DaystoProgression", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "DaystoProgression", + "sms:required" : "sms:false" + }, { + "@id" : "bts:RRIDidentifier", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "RRIDidentifier", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "RRIDidentifier", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ClassBRCA2", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ClassBRCA2", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ClassBRCA2", + "sms:required" : "sms:false" + }, { + "@id" : "bts:WhitelistCellBarcodeFileLink", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "WhitelistCellBarcodeFileLink", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "WhitelistCellBarcodeFileLink", + "sms:required" : "sms:false" + }, { + "@id" : "bts:StartDaysfromIndex", + "@type" : "rdfs:Class", + "rdfs:comment" : "Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'", + "rdfs:label" : "StartDaysfromIndex", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "StartDaysfromIndex", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Ecigvapetimesperday", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Ecigvapetimesperday", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Ecigvapetimesperday", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:FamilyMemberVitalStatusIndicator", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "FamilyMemberVitalStatusIndicator", + "rdfs:comment" : "The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1)", + "@type" : "rdfs:Class", + "sms:displayName" : "FamilyMemberVitalStatusIndicator" + }, { + "@id" : "bts:SectionThicknessValue", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).", + "rdfs:label" : "SectionThicknessValue", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SectionThicknessValue", + "sms:required" : "sms:false" + }, { + "@id" : "bts:SoftwareandVersion", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "SoftwareandVersion", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SoftwareandVersion", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:KnownGeneticPredispositionMutation", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "KnownGeneticPredispositionMutation", + "rdfs:comment" : "A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.", + "@type" : "rdfs:Class", + "sms:displayName" : "KnownGeneticPredispositionMutation" + }, { + "@id" : "bts:BiospecimenDimension1", + "@type" : "rdfs:Class", + "rdfs:comment" : "First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the \"\"dimensions_unit\"\" CDE", + "rdfs:label" : "BiospecimenDimension1", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BiospecimenDimension1", + "sms:required" : "sms:false" + }, { + "@id" : "bts:NucleiBarcodeLength", + "@type" : "rdfs:Class", + "rdfs:comment" : "Nuclei Barcode Length", + "rdfs:label" : "NucleiBarcodeLength", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "NucleiBarcodeLength", + "sms:required" : "sms:false" + }, { + "@id" : "bts:HER2BreastCarcinomaCopyNumberTotal", + "@type" : "rdfs:Class", + "rdfs:comment" : "Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values.", + "rdfs:label" : "HER2BreastCarcinomaCopyNumberTotal", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "HER2BreastCarcinomaCopyNumberTotal", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:MammaprintRiskGroup", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Datanotavailable" + }, { + "@id" : "bts:Highrisk" + }, { + "@id" : "bts:Intermediaterisk" + }, { + "@id" : "bts:Lowrisk" + } ], + "rdfs:label" : "MammaprintRiskGroup", + "rdfs:comment" : "Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.", + "@type" : "rdfs:Class", + "sms:displayName" : "MammaprintRiskGroup" + }, { + "@id" : "bts:Height", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Height", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Height", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Race", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:americanindianoralaskanative" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:white" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:blackorafricanamerican" + }, { + "@id" : "bts:notallowedtocollect" + }, { + "@id" : "bts:asian" + }, { + "@id" : "bts:Other" + }, { + "@id" : "bts:nativehawaiianorotherpacificislander" + } ], + "rdfs:label" : "Race", + "rdfs:comment" : "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", + "@type" : "rdfs:Class", + "sms:displayName" : "Race" + }, { + "@id" : "bts:BiospecimenDimension3", + "@type" : "rdfs:Class", + "rdfs:comment" : "Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the \"\"dimensions_unit\"\" CDE", + "rdfs:label" : "BiospecimenDimension3", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BiospecimenDimension3", + "sms:required" : "sms:false" + }, { + "@id" : "bts:OncotypeScore", + "@type" : "rdfs:Class", + "rdfs:comment" : "OncotypeDX recurrence score", + "rdfs:label" : "OncotypeScore", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "OncotypeScore", + "sms:required" : "sms:false" + }, { + "@id" : "bts:InputCellsandNuclei", + "@type" : "rdfs:Class", + "rdfs:comment" : "Number of cells and number of nuclei input; entry format: number, number", + "rdfs:label" : "InputCellsandNuclei", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "InputCellsandNuclei", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:PRReceptorStatus", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Borderline" + }, { + "@id" : "bts:Equivocal" + }, { + "@id" : "bts:Indeterminate" + }, { + "@id" : "bts:Negative" + }, { + "@id" : "bts:NotPerformed" + }, { + "@id" : "bts:PerformedbutNotAvailable" + }, { + "@id" : "bts:Positive" + } ], + "rdfs:label" : "PRReceptorStatus", + "rdfs:comment" : "Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer", + "@type" : "rdfs:Class", + "sms:displayName" : "PRReceptorStatus" + }, { + "@id" : "bts:Fluorophore", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Fluorophore", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Fluorophore", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Typeofsmokeexposurecumulativeyears", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Typeofsmokeexposurecumulativeyears", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Typeofsmokeexposurecumulativeyears", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Clone", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Clone", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Clone", + "sms:required" : "sms:false" + }, { + "@id" : "bts:DiagnosisStatusType", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "DiagnosisStatusType", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "DiagnosisStatusType", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Age", + "@type" : "rdfs:Class", + "rdfs:comment" : "Age of individual", + "rdfs:label" : "Age", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Age", + "sms:required" : "sms:true" + }, { + "@id" : "bts:TobaccoUse", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TobaccoUse", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TobaccoUse", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Zstack", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "Zstack", + "rdfs:comment" : "Does data file contain a Z-stack of images", + "@type" : "rdfs:Class", + "sms:displayName" : "Zstack" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Chromosome", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:chr7" + }, { + "@id" : "bts:chr15" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:chr3" + }, { + "@id" : "bts:chr1" + }, { + "@id" : "bts:chr18" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:chrY" + }, { + "@id" : "bts:chr22" + }, { + "@id" : "bts:chr14" + }, { + "@id" : "bts:chr12" + }, { + "@id" : "bts:chr11" + }, { + "@id" : "bts:chr17" + }, { + "@id" : "bts:chrM" + }, { + "@id" : "bts:chr4" + }, { + "@id" : "bts:chr21" + }, { + "@id" : "bts:chr6" + }, { + "@id" : "bts:chr10" + }, { + "@id" : "bts:chr16" + }, { + "@id" : "bts:chrX" + }, { + "@id" : "bts:chr23" + }, { + "@id" : "bts:chr8" + }, { + "@id" : "bts:chr2" + }, { + "@id" : "bts:chr13" + }, { + "@id" : "bts:chr19" + }, { + "@id" : "bts:chr20" + }, { + "@id" : "bts:chr5" + }, { + "@id" : "bts:chr9" + } ], + "rdfs:label" : "Chromosome", + "rdfs:comment" : "The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "Chromosome" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:MutationalSignatures", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Signature19" + }, { + "@id" : "bts:Signature1A" + }, { + "@id" : "bts:Iggenehypermutation" + }, { + "@id" : "bts:alteredactivityoftheerror-pronepolymerasePOLε(POLE)" + }, { + "@id" : "bts:Signature3" + }, { + "@id" : "bts:Signature20" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:Signature17" + }, { + "@id" : "bts:Signature4" + }, { + "@id" : "bts:Datanotavailable" + }, { + "@id" : "bts:Signature5" + }, { + "@id" : "bts:Signature9" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Signature14" + }, { + "@id" : "bts:Signature13" + }, { + "@id" : "bts:NotApplicable" + }, { + "@id" : "bts:Signature12" + }, { + "@id" : "bts:Signature8" + }, { + "@id" : "bts:ActivationInducedDeaminases(AID)associatedmutations" + }, { + "@id" : "bts:Signature7" + }, { + "@id" : "bts:microsatelliteinstability(additionsanddeletions)" + }, { + "@id" : "bts:AlkylatingAgents(Temozolomide)inducedmutations" + }, { + "@id" : "bts:localizedsubstitutionhypermutation(kataegis)" + }, { + "@id" : "bts:Signature16" + }, { + "@id" : "bts:Signature6" + }, { + "@id" : "bts:Other" + }, { + "@id" : "bts:Signature21" + }, { + "@id" : "bts:DNAMMRDeficiency" + }, { + "@id" : "bts:APOBECenzymesassociatedmutations" + }, { + "@id" : "bts:Tobaccouseassociatedmutations" + }, { + "@id" : "bts:transcriptionalstrandbias" + }, { + "@id" : "bts:Signature1B" + }, { + "@id" : "bts:Signature10" + }, { + "@id" : "bts:UVlightinducedmutations" + }, { + "@id" : "bts:Signature18" + }, { + "@id" : "bts:Signature11" + }, { + "@id" : "bts:Signature2" + }, { + "@id" : "bts:methylatedCpGsequencesmutagenesis(deaminationof5-methyl-cytosine)" + }, { + "@id" : "bts:Signature15" + }, { + "@id" : "bts:ageofcancerdiagnosis" + } ], + "rdfs:label" : "MutationalSignatures", + "rdfs:comment" : "Mutational signatures identified in the patient, includes signatures linked to selected exogenous carcinogens, endogenous and enzymatic modification of DNA or defective DNA repair. Note: Include only outputs of tests that were completed clinically for the participant and only include data from a diagnostic array that was completed prior to research sequencing was done. 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"http://schema.biothings.io/" + }, + "sms:displayName" : "Not sampled or dissected", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Melanocyticnevus", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Melanocyticnevus", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Melanocytic nevus", + "sms:required" : "sms:false" + }, { + "@id" : "bts:WGS", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "WGS", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "WGS", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Bonemarrow", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Bonemarrow", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Bone marrow", + "sms:required" : "sms:false" + }, { + "@id" : "bts:FosterSister", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "FosterSister", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Foster Sister", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Bronchiolo-alveolarcarcinomaClaracellandgobletcelltype", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Bronchiolo-alveolarcarcinomaClaracellandgobletcelltype", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Bronchiolo-alveolar carcinoma Clara cell and goblet cell type", + "sms:required" : "sms:false" + }, { + "@id" : "bts:CD14", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "CD14", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "CD14", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Promyelocytes", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Promyelocytes", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Promyelocytes", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Tlymphoblasticleukemia/lymphoma", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Tlymphoblasticleukemia/lymphoma", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "T lymphoblastic leukemia/lymphoma", + "sms:required" : "sms:false" + }, { + "@id" : "bts:vonHippel-LindauSyndrome", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "vonHippel-LindauSyndrome", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "von Hippel-Lindau Syndrome", + "sms:required" : "sms:false" + }, { + "@id" : "bts:mpg", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "mpg", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "mpg", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Albumin", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Albumin", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Albumin", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Creatinine", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Creatinine", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Creatinine", + "sms:required" : "sms:false" + }, { + "@id" : "bts:GreatGrandchild", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "GreatGrandchild", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Great Grandchild", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BladderNOS", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BladderNOS", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Bladder NOS", + "sms:required" : "sms:false" + }, { + "@id" : "bts:VitalStatusAlive", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "VitalStatusAlive", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Vital Status Alive", + "sms:required" : "sms:false" + }, { + "@id" : "bts:HalfSister", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "HalfSister", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Half Sister", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Blymphoblasticleukemia/lymphomawithhyperdiploidy", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Blymphoblasticleukemia/lymphomawithhyperdiploidy", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "B lymphoblastic leukemia/lymphoma with hyperdiploidy", + "sms:required" : "sms:false" + }, { + "@id" : "bts:chr12", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "chr12", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "chr12", + "sms:required" : "sms:false" + }, { + "@id" : "bts:GrandNiece", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "GrandNiece", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Grand Niece", + "sms:required" : "sms:false" + }, { + "@id" : "bts:DownstreamGeneVariant", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "DownstreamGeneVariant", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Downstream Gene Variant", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Paragangliomabenign", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Paragangliomabenign", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Paraganglioma benign", + "sms:required" : "sms:false" + }, { + "@id" : "bts:EpidermoidcarcinomainsituNOS", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "EpidermoidcarcinomainsituNOS", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Epidermoid carcinoma in situ NOS", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Overlappinglesionofrespiratorysystemandintrathoracicorgans", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Overlapping lesion of respiratory system and intrathoracic organs", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Undifferentiatedsarcoma", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Undifferentiatedsarcoma", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Undifferentiated sarcoma", + "sms:required" : "sms:false" + }, { + "@id" : "bts:miRNA", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "miRNA", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "miRNA", + "sms:required" : "sms:false" + }, { + "@id" : "bts:LowerlimbNOS", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "LowerlimbNOS", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Lower limb NOS", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BladderCancer", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BladderCancer", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Bladder Cancer", + "sms:required" : "sms:false" + }, { + "@id" : "bts:MalegenitalorgansNOS", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "MalegenitalorgansNOS", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Male genital organs NOS", + "sms:required" : "sms:false" + }, { + "@id" : "bts:MalignantlymphomalargecellNOS", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "MalignantlymphomalargecellNOS", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Malignant lymphoma large cell NOS", + "sms:required" : "sms:false" + }, { + "@id" : "bts:InframeInsertion", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "InframeInsertion", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Inframe Insertion", + "sms:required" : "sms:false" + }, { + "@id" : "bts:EsophagealCancer", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "EsophagealCancer", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Esophageal Cancer", + "sms:required" : "sms:false" + }, { + "@id" : "bts:AcuteleukemiaBurkitttype", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AcuteleukemiaBurkitttype", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Acute leukemia Burkitt type", + "sms:required" : "sms:false" + }, { + "@id" : "bts:MaternalGreatUncle", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "MaternalGreatUncle", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Maternal Great Uncle", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Wine", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Wine", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Wine", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Thyroidgland", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Thyroidgland", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Thyroid gland", + "sms:required" : "sms:false" + }, { + "@id" : "bts:maf", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "maf", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "maf", + "sms:required" : "sms:false" + }, { + "@id" : "bts:RNASequencing", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "RNASequencing", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "RNA Sequencing", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Cryopreservationinliquidnitrogen-livecells", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Cryopreservationinliquidnitrogen-livecells", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Cryopreservation in liquid nitrogen - live cells", + "sms:required" : "sms:false" + }, { + "@id" : "bts:RT-PCR", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "RT-PCR", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "RT-PCR", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Hereditaryretinoblastoma", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Hereditaryretinoblastoma", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Hereditary retinoblastoma", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Labiumminus", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Labiumminus", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Labium minus", + "sms:required" : "sms:false" + }, { + "@id" : "bts:mL", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "mL", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "mL", + "sms:required" : "sms:false" + } ] } \ No newline at end of file diff --git a/Makefile b/Makefile index 7fa0391..12368ee 100644 --- a/Makefile +++ b/Makefile @@ -1,14 +1,8 @@ -SHELL:=/bin/bash -O globstar -CSV := GF.csv +all: convert -all: collate convert - -collate: - @echo "Collating module components..." - ls modules/**/*.csv - head -1 modules/schema.csv > ${CSV} - tail -n +2 -q modules/**/*.csv >> ${CSV} +# TODO Implement analysis on data model changes +analyze: + @echo "Analyzing data model..." convert: - schematic schema convert ${CSV} - + bb ./retold/retold as-jsonld --dir modules --out GF.jsonld diff --git a/modules/Assay/Assay.csv b/modules/Assay/Assay.csv deleted file mode 100644 index 4a0d731..0000000 --- a/modules/Assay/Assay.csv +++ /dev/null @@ -1,4 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Protocol Link,"URL to a free/open protocol resource describing 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 sample was obtained or generated.",,,,TRUE,Information Content Entity,,, -File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","HEIC, hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn",,,TRUE,,,, -Checksum,MD5 checksum of the BAM file,,,,TRUE,Information Content Entity,,, diff --git a/modules/Assay/Imaging/Imaging_Level_2.csv b/modules/Assay/Imaging/Imaging_Level_2.csv deleted file mode 100644 index 3b93304..0000000 --- a/modules/Assay/Imaging/Imaging_Level_2.csv +++ /dev/null @@ -1,41 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Imaging Level 2,Raw and pre-processed image data,"","Component, Filename, File Format, Lab ID, Channel Metadata Filename, Imaging Assay Type, Protocol Link, Software and Version, Microscope, Objective, NominalMagnification, LensNA, WorkingDistance, WorkingDistanceUnit, Immersion, Pyramid, Zstack, Tseries, Passed QC, Comment, FOV number, FOVX, FOVXUnit, FOVY, FOVYUnit, Frame Averaging, Image ID, DimensionOrder, PhysicalSizeX, PhysicalSizeXUnit, PhysicalSizeY, PhysicalSizeYUnit, PhysicalSizeZ, PhysicalSizeZUnit, Pixels BigEndian, PlaneCount, SizeC, SizeT, SizeX, SizeY, SizeZ, PixelType","",FALSE,Assay,"Biospecimen, Imaging Level 2 Channels","","" -Imaging Level 2 Channels,Channel-level Metadata Attributes,"","Channel ID, Channel Name, Channel Passed QC, Cycle Number, Sub Cycle Number, Target Name, Antibody Name, RRID identifier, Fluorophore, Clone, Lot, Vendor, Catalog Number, Excitation Wavelength, Emission Wavelength, Excitation Bandwidth, Emission Bandwidth, Metal Isotope Element, Metal Isotope Mass, Oligo Barcode Upper Strand, Oligo Barcode Lower Strand, Dilution, Concentration","",FALSE,Imaging Level 2,"","","" -Imaging Assay Type,Type of imaging assay,"H&E, CyCIF, t-CyCIF, IHC, mIHC, MxIF, SABER, IMC, CODEX, GeoMX-DSP, MIBI, MERFISH, ExSeq, Not Applicable","","",TRUE,Imaging Level 2,"","","" -Channel Metadata Filename,Full path of uploaded companion CSV file containing channel-level metadata details,"","","",TRUE,Imaging Level 2,"","","" -Image Acquisition Date,Date of image acquisition,"","","",FALSE,Imaging Level 2,"","","" -Microscope,"Microscope type (manufacturer, model, etc) used for this experiment","","","",TRUE,Imaging Level 2,"",http://purl.obolibrary.org/obo/OBI_0400169,"" -Objective,Objective,"","","",FALSE,Imaging Level 2,"","","" -NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),"","","",TRUE,Imaging Level 2,"","","" -LensNA,The numerical aperture of the lens. Floating point value > 0.,"","","",FALSE,Imaging Level 2,"","","" -WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.","",WorkingDistanceUnit,"",FALSE,Imaging Level 2,"","","" -WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å","","",FALSE,Imaging Level 2,"","","" -Immersion,Immersion medium,"Air, Oil, Water, Other","","",FALSE,Imaging Level 2,"","","" -Pyramid,Does data file contain pyramid of images,"Yes, No","","",TRUE,Imaging Level 2,"","","" -Zstack,Does data file contain a Z-stack of images,"Yes, No","","",TRUE,Imaging Level 2,"","","" -Tseries,Does data file contain a time-series of images,"Yes, No","","",TRUE,Imaging Level 2,"","","" -Passed QC,Did all channels pass QC (if not add free text Comment),"Yes, No - Channels QC","","",TRUE,Imaging Level 2,"","","" -No - Channels QC,Not all channels passed QC,"",Comment,"",FALSE,Imaging Level 2,"","","" -Comment,Free text field (generally for QC comment),"","","",FALSE,Imaging Level 2,"","","" -FOV number,Index of FOV (as it pertains to its sequence order). Integer >= 1,"","","",FALSE,Imaging Level 2,"","","" -FOVX,Field of view X dimension. Floating point,"",FOVXUnit,"",FALSE,Imaging Level 2,"","","" -FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å","","",FALSE,Imaging Level 2,"","","" -FOVY,Field of view Y dimension. Floating point value,"",FOVYUnit,"",FALSE,Imaging Level 2,"","","" -FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å","","",FALSE,Imaging Level 2,"","","" -Frame Averaging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1","","","",FALSE,Imaging Level 2,"","","" -Image ID,"Unique internal image identifier. eg """"Image:0"""". (To be extracted from OME-XML)","","","",TRUE,Imaging Level 2,"","","" -DimensionOrder,The order in which the individual planes of data are interleaved.,"XYZCT, XYZTC, XYCTZ, XYCZT, XYTZC, ZYX","","",TRUE,Imaging Level 2,"","","" -PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,"",PhysicalSizeXUnit,"",TRUE,Imaging Level 2,"","","" -PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å","","",TRUE,Imaging Level 2,"","","" -PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,"",PhysicalSizeYUnit,"",TRUE,Imaging Level 2,"","","" -PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å","","",TRUE,Imaging Level 2,"","","" -PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,"",PhysicalSizeZUnit,"",TRUE,Imaging Level 2,"","","" -PhysicalSizeZUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),"cm, mm, µm, nm, Å","","",TRUE,Imaging Level 2,"","","" -Pixels BigEndian,Boolean (True/False),"True, False","","",TRUE,Imaging Level 2,"","","" -PlaneCount,"Number of Z-planes (not to be confused with downsampled """"pyramid""""). Integer >=1","","","",TRUE,Imaging Level 2,"","","" -SizeC,Number of channels. Integer >= 1,"","","",TRUE,Imaging Level 2,"","","" -SizeT,Number of time points. Integer >= 1,"","","",TRUE,Imaging Level 2,"","","" -SizeX,Size of image: X dimension (in pixels). Integer >= 1,"","","",TRUE,Imaging Level 2,"","","" -SizeY,Size of image: Y dimension (in pixels). Integer >= 1,"","","",TRUE,Imaging Level 2,"","","" -SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,"","","",TRUE,Imaging Level 2,"","","" -PixelType,"Data type for each pixel value. E.g. """"uint16""""","int8, int16, int32, uint8, uint16, uint32, float, double, bit","","",TRUE,Imaging Level 2,"","","" diff --git a/modules/Assay/Sequencing/Sequencing.csv b/modules/Assay/Sequencing/Sequencing.csv deleted file mode 100644 index 621f93f..0000000 --- a/modules/Assay/Sequencing/Sequencing.csv +++ /dev/null @@ -1,10 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Sequencing,Module for next generation sequencing assays,"","","",FALSE,Assay,"",http://example.org/htan/Sequencing,"" -Sequencing Platform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,"Illumina Next Seq 500, Illumina Next Seq 550, Illumina Next Seq 2500, Illumina NovaSeq 6000, Illumina MiSeq, 454 GS FLX Titanium, AB SOLiD 4 AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, NovaSeq 6000, NovaSeqS4, Ultima Genomics UG100, Oxford Nanopore minION, GridION, PromethION, PacBio Sequel2, Revio, Other, unknown, Not Reported",,,TRUE,Device,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group, -Library Construction Method,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],"Smart-seq2, Smart-SeqV4, 10xV1.0, 10xV1.1, 10xV2, 10xV3,10xV3.1, CEL-seq2, Drop-seq, inDropsV2, inDropsV3, TruDrop, sci-ATAC-seq",,,TRUE,Sequencing,,http://purl.obolibrary.org/obo/OBI_0000711, -Nucleic Acid Source,The source of the input nucleic molecule,"Single Cell, Bulk Whole Cell, Single Nucleus, Bulk Nuclei",,,TRUE,Sequencing,,http://example.org/htan/NucleicAcidSource, -Read1,Read 1 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert, DNA Insert, Sample Index, Cell Barcode","","",TRUE,Sequencing,"","","" -Read2,Read 2 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert, DNA Insert, Sample Index, Cell Barcode","","",TRUE,Sequencing,"","","" -Technical Replicate Group,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),,,,FALSE,Sequencing,,, -Sequencing Batch ID,Links samples to a specific local sequencer run. Can be string or 'null',,,,TRUE,Sequencing,,, -Total Reads,Total number of reads per sample. Integer,,,,FALSE,Sequencing,,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group_qc, diff --git a/modules/Assay/Sequencing/Single_Cell_Sequencing/Single_Cell_Sequencing.csv b/modules/Assay/Sequencing/Single_Cell_Sequencing/Single_Cell_Sequencing.csv deleted file mode 100644 index a3c7fc8..0000000 --- a/modules/Assay/Sequencing/Single_Cell_Sequencing/Single_Cell_Sequencing.csv +++ /dev/null @@ -1,6 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Dissociation Method,The tissue dissociation method used for scRNASeq or scATAC-seq assays,"gentleMACS, Dounce, Enzymatic Digestion, Not Applicable",,,TRUE,Single_Cell_Sequencing,,, -Cryopreserved Cells in Sample,Indicate if library preparation was based on revived frozen cells.,"Yes, No",,,TRUE,Single_Cell_Sequencing,,, -Single Cell Isolation Method,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)","Microfluidics Chip, Droplets, FACS, Plates, 10x, Nuclei Isolation",,,TRUE,Single_Cell_Sequencing,,, -Total Number of Input Cells,Number of cells loaded/placed on plates,,,,TRUE,Single_Cell_Sequencing,,, -Input Cells and Nuclei,"Number of cells and number of nuclei input; entry format: number, number",,,,TRUE,Single_Cell_Sequencing,,, diff --git a/modules/Assay/Sequencing/Single_Cell_Sequencing/scATAC-seq/scATAC-seq_Level_1.csv b/modules/Assay/Sequencing/Single_Cell_Sequencing/scATAC-seq/scATAC-seq_Level_1.csv deleted file mode 100644 index 8219149..0000000 --- a/modules/Assay/Sequencing/Single_Cell_Sequencing/scATAC-seq/scATAC-seq_Level_1.csv +++ /dev/null @@ -1,18 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -scATAC-seq Level 1,"scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files",,"Component, Filename, File Format, Participant ID, Sample ID, Detailed Sample ID,Nucleic Acid Source, Dissociation Method, Single Nucleus Buffer, Single Cell Isolation Method, Transposition Reaction, scATACseq Library Layout, Nucleus Identifier, Nuclei Barcode Length, Nuclei Barcode Read, scATACseq Read1, scATACseq Read2, scATACseq Read3, Library Construction Method, Sequencing Platform, Threshold for Minimum Passing Reads, Total Number of Passing Nuclei, Median Fraction of Reads in Peaks, Median Fraction of Reads in Annotated cis DNA Elements, Median Passing Read Percentage, Median Percentage of Mitochondrial Reads per Nucleus,Technical Replicate Group, Total Reads, Protocol Link",,FALSE,Single_Cell_Sequencing,,, -Transposition Reaction,"Name of the transposase, transposon sequences","Tn5, EZ-Tn5, Tn5-059, Nextera Tn5, Diagenode-unloaded Apex-Bio, Diagenode-loaded Apex-Bio, In-House",,,TRUE,scATAC-seq Level 1,,, -Single Nucleus Buffer,Nuclei isolation buffer,"NIB, 10x, Omni",,,TRUE,scATAC-seq Level 1,,, -scATACseq Library Layout,Sequencing read type,scATACseq Paired End,,,TRUE,scATAC-seq Level 1,,, -Nucleus Identifier,Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from,Nuclei Barcode,,,TRUE,scATAC-seq Level 1,,, -Nuclei Barcode Read,Nuclei Barcode Read,,,,TRUE,scATAC-seq Level 1,,, -Nuclei Barcode Length,Nuclei Barcode Length,,,,TRUE,scATAC-seq Level 1,,, -scATACseq Paired End,A library layout type,"scATACseq Read1, scATACseq Read2",,,FALSE,scATAC-seq Level 1,,, -scATACseq Read1,Read 1 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert, DNA Insert, Sample Index, Cell Barcode",,,TRUE,scATAC-seq Level 1,,, -scATACseq Read2,Read 2 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert, DNA Insert, Sample Index, Cell Barcode",,,TRUE,scATAC-seq Level 1,,, -scATACseq Read3,Read 3 content description,"Cell Barcode and DNA Insert, Sample Index and DNA Insert, DNA Insert, Sample Index, Cell Barcode",,,FALSE,scATAC-seq Level 1,,, -Threshold for Minimum Passing Reads,Threshold for calling cells,,,,TRUE,scATAC-seq Level 1,,, -Total Number of Passing Nuclei,Number of nuclei sequenced,,,,TRUE,scATAC-seq Level 1,,, -Median Fraction of Reads in Peaks,Median fraction of reads in peaks (FRIP),,Peaks Calling Software,,TRUE,scATAC-seq Level 1,,, -Median Fraction of Reads in Annotated cis DNA Elements,Median fraction of reads in annotated cis-DNA elements (FRIADE),,Peaks Calling Software,,TRUE,scATAC-seq Level 1,,, -Median Passing Read Percentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,,,,TRUE,scATAC-seq Level 1,,, -Median Percentage of Mitochondrial Reads per Nucleus,Contamination from mitochondrial sequences,,,,TRUE,scATAC-seq Level 1,,, diff --git a/modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_1.csv b/modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_1.csv deleted file mode 100644 index d7ded56..0000000 --- a/modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_1.csv +++ /dev/null @@ -1,19 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -scRNA-seq Level 1,Single-cell RNA-seq [EFO_0008913],,"Component, Filename, File Format, Participant ID, Sample ID, Detailed Sample ID, Cryopreserved Cells in Sample, Single Cell Isolation Method, Dissociation Method, Library Construction Method, Read Indicator, Read1, Read2, End Bias, Reverse Transcription Primer, Spike In, Sequencing Platform, Total Number of Input Cells, Input Cells and Nuclei,Protocol Link, Technical Replicate Group",,FALSE,Single_Cell_Sequencing,Biospecimen,http://www.ebi.ac.uk/efo/EFO_0008913, -Cell Barcode and UMI,Cell and transcript identifiers,"","UMI Barcode Offset, UMI Barcode Length, Median UMIs per Cell Number, Cell Barcode Offset, Cell Barcode Length, Valid Barcodes Cell Number","",FALSE,scRNA-seq Level 1,"","","" -Cell Barcode Offset,Offset in sequence for cell barcode read (in bp): number,"","","",TRUE,scRNA-seq Level 1,"","","" -Cell Barcode Length,Length of cell barcode read (in bp): number,"","","",TRUE,scRNA-seq Level 1,"","","" -Valid Barcodes Cell Number,Number,"","","",TRUE,scRNA-seq Level 1,"","","" -UMI Barcode Offset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read","","","",TRUE,scRNA-seq Level 1,"",https://www.ebi.ac.uk/arrayexpress/help/single-cell_submission_guide.html,"" -UMI Barcode Length,Length of UMI barcode read (in bp): number,"","","",TRUE,scRNA-seq Level 1,"","","" -Median UMIs per Cell Number,Number,"","","",TRUE,scRNA-seq Level 1,"","","" -Input Cells and Nuclei,"Number of cells and number of nuclei input; entry format: number, number","","","",TRUE,scRNA-seq Level 1,"","","" -CEL-seq2,Highly-multiplexed plate-based single-cell RNA-Seq assay,"","Empty Well Barcode, Well Index","",FALSE,scRNA-seq Level 1,"","","" -Empty Well Barcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,"","","",TRUE,scRNA-seq Level 1,"","","" -Well Index,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,"Yes, No","","",FALSE,scRNA-seq Level 1,"","","" -Single Cell Dissociation Days from Index,Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number],"","","",TRUE,scRNA-seq Level 1,"","","" -End Bias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript","3 Prime, 5 Prime, Full Length Transcript","","",TRUE,scRNA-seq Level 1,"","","" -Reverse Transcription Primer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA","Oligo-dT, Poly-dT, Feature barcoding, Random","","",TRUE,scRNA-seq Level 1,"",http://www.sequenceontology.org/so_wiki/index.php/Category:SO:0000112_!_primer,"" -Feature barcoding,A method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc],"",Feature Reference Id,"",FALSE,scRNA-seq Level 1,"",https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc,"" -Feature Reference Id,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]","","","",TRUE,scRNA-seq Level 1,"","","" -Spike In,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,"ERCC, Other Spike In, No Spike In, PhiX","","",TRUE,scRNA-seq Level 1,"","","" diff --git a/modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_2.csv b/modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_2.csv deleted file mode 100644 index f6d183e..0000000 --- a/modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_2.csv +++ /dev/null @@ -1,2 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -scRNA-seq Level 2,Alignment workflows downstream of scRNA-seq Level 1,,"Component, Filename, File Format, Participant ID, Sample ID, Detailed Sample ID, scRNAseq Workflow Type, Workflow Version, scRNAseq Workflow Parameters Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Whitelist Cell Barcode File Link, Cell Barcode Tag, UMI Tag, Applied Hard Trimming",,FALSE,Single_Cell_Sequencing,scRNA-seq Level 1,, diff --git a/modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_3.csv b/modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_3.csv deleted file mode 100644 index d2ff461..0000000 --- a/modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_3.csv +++ /dev/null @@ -1,5 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -scRNA-seq Level 3,Gene and Isoform expression files,,"Component, Filename, File Format, Participant ID, Sample ID, Detailed Sample ID, Data Category, Matrix Type, Linked Matrices, Cell Median Number Reads, Cell Median Number Genes, Cell Total, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Link, Workflow Version",,FALSE,Single_Cell_Sequencing,,, -Cell Median Number Reads,Median number of reads per cell. Number,"","","",TRUE,scRNA-seq Level 3,"","","" -Cell Median Number Genes,Median number of genes detected per cell. Number,"","","",TRUE,scRNA-seq Level 3,"","","" -Cell Total,Number of sequenced cells. Applies to raw counts matrix only.,"","","",TRUE,scRNA-seq Level 3,"","","" diff --git a/modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_4.csv b/modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_4.csv deleted file mode 100644 index c03dff4..0000000 --- a/modules/Assay/Sequencing/Single_Cell_Sequencing/scRNA-seq/scRNA-seq_Level_4.csv +++ /dev/null @@ -1,2 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -scRNA-seq Level 4,"Gene and Isoform expression files",,"Component, Filename, File Format, Participant ID, Sample ID, Detailed Sample ID,Data Category, Matrix Type, Linked Matrices, Cell Median Number Reads, Cell Median Number Genes, Cell Total, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Link, Workflow Version",,FALSE,Single_Cell_Sequencing,,, diff --git a/modules/Biospecimen/Biospecimen.csv b/modules/Biospecimen/Biospecimen.csv deleted file mode 100644 index 5b5d0d8..0000000 --- a/modules/Biospecimen/Biospecimen.csv +++ /dev/null @@ -1,71 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Biospecimen,"Biological entity; this can be tissue, blood, analyte and subsamples of those","","Biospecimen ID, Parent ID, Parent Biospecimen ID, Adjacent Biospecimen IDs,Biospecimen Type,Timepoint Label,Specimen Laterality","",FALSE,Patient,"","","" -Sample ID, ID associated with a biosample,"","","",TRUE,Biospecimen,"",,"" -Biospecimen ID, Alias for Sample ID,"","","",TRUE,Biospecimen,"",,"" -Detailed Sample ID, Additional alternative ID associated with a biosample,"","","",TRUE,Biospecimen,"",,"" -Parent ID, ID of parent biospecimen,"","","",TRUE,Biospecimen,"",https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,"" -Parent Biospecimen ID, Biospecimen identifier indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,"","","",TRUE,Biospecimen,"",https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,"" -Biospecimen Type,Biospecimen Type,"Tissue Biospecimen Type, Blood Biospecimen Type, Analyte Biospecimen Type, Mouth Rinse Biospecimen Type, Stool Biospecimen Type, Urine Biospecimen Type, Ascites Biospecimen Type, Sputum Biospecimen Type, Fluids Biospecimen Type, Bone Marrow Biospecimen Type, Cells Biospecimen Type","","",TRUE,Biospecimen,"","","" -Analyte Biospecimen Type,A molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,"","Analyte Type, Fixation Duration, Slide Charge Type, Section Thickness Value, Sectioning Days from Index, Shipping Condition Type, Ischemic Time, Ischemic Temperature","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2513915&version=2.0,"" -Tissue Biospecimen Type,Tissue biospecimen,"","Ischemic Time, Ischemic Temperature, Site of Resection or Biopsy, Specimen Laterality, Portion Weight, Total Volume, Tumor Tissue Type, Histologic Morphology Code, Preservation Method, Biospecimen Dimension 1, Biospecimen Dimension 2, Biospecimen Dimension 3, Section Number in Sequence","",FALSE,Biospecimen,"","","" -Bone Marrow Biospecimen Type,Bone Marrow biospecimen,"","Ischemic Time, Ischemic Temperature, Site of Resection or Biopsy, Specimen Laterality, Portion Weight, Total Volume, Tumor Tissue Type, Histologic Morphology Code, Preservation Method, Biospecimen Dimension 1, Biospecimen Dimension 2, Biospecimen Dimension 3, Section Number in Sequence","",FALSE,Biospecimen,"","","" -Urine Biospecimen Type,Urine biospecimen,"","Ischemic Time, Ischemic Temperature, Site of Resection or Biopsy, Specimen Laterality, Portion Weight, Total Volume, Tumor Tissue Type, Histologic Morphology Code, Preservation Method","",FALSE,Biospecimen,"","","" -Blood Biospecimen Type,Blood biospecimen,"",Shipping Condition Type,"",FALSE,Biospecimen,"","","" -Timepoint Label,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.","","","",TRUE,Biospecimen,"","","" -Collection Days from Index,Number of days from the research participant's index date that the biospecimen was obtained.,"","","",TRUE,Biospecimen,"","","" -Adjacent Sample IDs,"List of Identifiers (separated by commas) of adjacent biospecimens cut from the same sample","","","",FALSE,Biospecimen,"","","" -Mounting Medium,"The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media","Aqueous water based, Non-Aqueous Solvent based, Xylene,Toluene,Antifade with DAPI,Antifade without DAPI,PBS,unknown,Not Reported","","",FALSE,Biospecimen,"","","" -Analyte Type,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,"cfDNA Analyte, DNA Analyte, RNA Analyte, Total RNA Analyte, Tissue Block Analyte, Tissue Section Analyte, PBMCs or Plasma or Serum Analyte, cDNA Libraries Analyte, PBMCs, Plasma, Serum Analyte","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2513915&version=2.0,"" -Acquisition Method Type,Records the method of acquisition or source for the specimen under consideration.,"Autopsy, Biopsy, Fine Needle Aspirate, Surgical Resection, Punch Biopsy, Shave Biopsy, Excision, Re-excision, Sentinel Node Biopsy, Lymphadenectomy - Regional Nodes, Other Acquisition Method, Non induced sputum, Induced sputum, BAL (bronchial alveolar lavage), Cytobrush, Blood draw, Fluid collection, Forceps biopsy, Core needle biopsy, Endoscopic biopsy, Not specified","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6626651&version=1.0,"" -Other Acquisition Method,A custom acquisition method,"",Acquisition Method Other Specify,"",FALSE,Biospecimen,"","","" -Acquisition Method Other Specify,A custom acquisition method [Text - max length 100 characters],"","","",TRUE,Biospecimen,"","","" -Preservation Method,Text term that represents the method used to preserve the sample.,"Archival,Cryopreserved, Cryopreservation in liquid nitrogen - dead tissue, Cryopreservation in dry ice - dead tissue, Cryopreservation in liquid nitrogen - live cells, Formalin fixed paraffin embedded - FFPE, Formalin fixed-unbuffered, Formalin fixed-buffered, Fresh, Fresh dissociated and single cell sorted into plates in NP40 buffer, OCT, Snap Frozen, Frozen, Negative 80 Deg C, Liquid Nitrogen, Fresh dissociated, Fresh dissociated and single cell sorted, Fresh dissociated and single cell sorted into plates, Methacarn fixed paraffin embedded - MFPE, unknown, Not Reported","","",TRUE,Biospecimen,"","","" -Fixative Type,Text term to identify the type of fixative used to preserve a tissue specimen,"Acetone, Alcohol, Formalin, Glutaraldehyde, OCT media, RNAlater, Saline, 95% Ethanol, Dimidoester, Carbodiimide, Dimethylacetamide, Para-benzoquinone, PAXgene tissue, TCL lysis buffer, NP40 lysis buffer, Methacarn, Cryo-store, Carnoy's Fixative, Polaxamer, Other, None, unknown","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=65078&version=3.0,"" -Fixation Duration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)","","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5230144&version=1.0,"" -Ischemic Time,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.","","","",FALSE,Biospecimen,"",https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-state_of_specimen-gross_description,"" -Ischemic Temperature,Specify whether specimen experienced warm or cold ischemia.,"Warm Ischemia, Cold Ischemia, Ambient air, 4C wet ice, Negative -20C, Dry Ice, Liquid Nitrogen, unknown","","",FALSE,Biospecimen,"",https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-state_of_specimen-gross_description,"" -Collection Media,Material Specimen is collected into post procedure,"DMEM, DMEM+Serum, RPMI, RPMI+Serum, PBS, PBS+Serum, None","","",FALSE,Biospecimen,"","","" -Specimen Laterality,"For samples in paired organs, designates the side from which obtained.","Bilateral, Left, Right, unknown, Not Reported, Not Applicable","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2007875&version=1.0,"" -Portion Weight,"Numeric value that represents the sample portion weight, measured in milligrams.","","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5432593&version=1.0,"" -Total Volume,Numeric value for the total amount of sample or specimen,"",Total Volume Unit,"",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3005019&version=1.0,"" -Total Volume Unit,Unit of measurement used for the total amount of sample or specimen,"mL, mm^3, cm^2","","",FALSE,Biospecimen,"","","" -Tumor Tissue Type,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),"Additional Primary, Local recurrence, Metastatic, Premalignant, Primary, Recurrent, Normal, Normal adjacent, Normal distant, Post therapy, Post therapy neoadjuvant, Post therapy adjuvant, Not Otherwise Specified, Premalignant - in situ, Atypia - hyperplasia","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3288124&version=1.0,"" -Histologic Morphology Code,"Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510","","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3226275&version=1.0,"" -Preinvasive Morphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the ","Melanocytic hyperplasia, Atypical melanocytic proliferation, Melanoma in situ - superficial spreading, Melanoma in situ - lentigo maligna type, Melanoma in situ - acral-lentiginous, Melanoma in situ - arising in a giant congenital nevus, Persistent melanoma in situ, Melanoma in situ - not otherwise classified, Scar - no residual melanoma, Invasive melanoma - superficial spreading, Invasive melanoma - nodular type, Invasive melanoma - lentigo maligna, Invasive melanoma - acral lentiginous, Invasive melanoma - desmoplastic, Invasive melanoma - nevoid, Invasive melanoma - other, Normal WDA, Reserve cell hyperplasia, Squamous metaplasia - mature, Squamous metaplasia - immature, Mild dysplasia, Moderate dysplasia, Severe dysplasia, Squamous Carcinoma in situ, Atypical adenomatous hyperplasia, Adenocarcinoma in situ - non mucinous, Adenocarcinoma in situ - mucinous, Benign tumor NOS, Hamartoma, Carcinoma NOS, No diagnosis possible","","",FALSE,Biospecimen,"","","" -Slide Charge Type,A description of the charge on the glass slide.,"Uncharged, Charged, Coverslip, Not applicable, Other","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5227611&version=1.0,"" -Section Thickness Value,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).","","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3024951&version=1.0,"" -Sectioning Days from Index,Number of days from the research participant's index date that the biospecimen was sectioned after collection,"","","",TRUE,Biospecimen,"","","" -Storage Method,The method by which a biomaterial was stored after preservation or before another protocol was used.,"Ambient temperature, Cut slide, Fresh, Frozen at -70C, Frozen at -80C, Frozen at -150C, Frozen in liquid nitrogen, Frozen in vapor phase, Paraffin block, RNAlater at 4C, RNAlater at 25C, RNAlater at -20C, Refrigerated at 4 degrees, Refrigerated vacuum chamber, 4C in vacuum chamber, Desiccant at 4C, Not Applicable, unknown","","",TRUE,Biospecimen,"",https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-preservation_storage-storage_method,"" -Processing Days from Index,Number of days from the research participant's index date that the biospecimen was processed,"","","",TRUE,Biospecimen,"","","" -Shipping Condition Type,Text descriptor of the shipping environment of a biospecimen.,"Ambient Pack, Cold Pack, Dry Ice, Ice Pack, Liquid Nitrogen, Specimen at Room Temperature, Other Shipping Environment, Not Shipped","","",TRUE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5495533&version=1.0,"" -Site Data Source,"Text to identify the data source for the specimen/sample from within the center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.","","","",FALSE,Biospecimen,"","","" -Processing Location,"Site with an center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.","","","",FALSE,Biospecimen,"","","" -Histology Assessment By,Text term describing who (in what role) made the histological assessments of the sample,"Pathologist, Research Scientist, Other, unknown","","",FALSE,Biospecimen,"","","" -Histology Assessment Medium,The method of assessment used to characterize histology,"Digital, Microscopy, Other, unknown","","",FALSE,Biospecimen,"","","" -Tumor Infiltrating Lymphocytes,Measure of Tumor-Infiltrating Lymphocytes [Number],"","","",FALSE,Biospecimen,"","","" -Degree of Dysplasia,Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.,"Normal or basal cell hyperplasia or metaplasia, Mild dysplasia, Moderate dysplasia, Severe dysplasia, Carcinoma in Situ, unknown","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5543188&version=1.0,"" -Dysplasia Fraction,Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5],"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2390593&version=1.0,"" -Number Proliferating Cells,Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5432636&version=1.0,"" -Percent Eosinophil Infiltration,Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897700&version=2.0,"" -Percent Granulocyte Infiltration,Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897705&version=2.0,"" -Percent Inflam Infiltration,"Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.","","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897695&version=1.0,"" -Percent Lymphocyte Infiltration,Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897710&version=2.0,"" -Percent Monocyte Infiltration,Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5455535&version=1.0,"" -Percent Necrosis,Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841237&version=1.0,"" -Percent Neutrophil Infiltration,Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841233&version=1.0,"" -Percent Normal Cells,Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841233&version=1.0,"" -Percent Stromal Cells,"Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.","","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841241&version=1.0,"" -Percent Tumor Cells,Numeric value that represents the percentage of infiltration by tumor cells in a sample.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5432686&version=1.0,"" -Percent Tumor Nuclei,Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.,"","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2841225&version=1.0,"" -Fiducial Marker,Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.,"Nuclear Stain - DAPI, Fluorescent Beads, Grid Slides - Hemocytometer, Adhesive Markers, Other, unknown, Not Reported","","",FALSE,Biospecimen,"",https://data.humancellatlas.org/metadata/dictionary/protocol/imaging/imaging_preparation_protocol#imaging_preparation_protocol-protocol_core-protocols_io_doi,"" -Slicing Method,Imaging specific: the method by which the tissue was sliced.,"Vibratome, Cryosectioning, Tissue molds, Sliding microtome, Sectioning, Other, unknown, Not Reported","","",FALSE,Biospecimen,"",https://data.humancellatlas.org/metadata/dictionary/protocol/imaging/imaging_preparation_protocol#imaging_preparation_protocol-protocol_core-protocols_io_doi,"" -Antigen Retrieval,"Imaging specific: information on antigen retrieval when it is used for a pathology specimen. E.g. pH 6 (Citric Acid), pH 8 (tris), or pH 10. [Text - max length 100] ","","","",FALSE,Biospecimen,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64676&version=3.0,"" -Biospecimen Slide Location,Imaging specific: text term to capture the relative position and orientation of the core location within a piece of tissue on the slide relative to the region of interest slide coordinates. use https://docs.openmicroscopy.org/ome-model/6.0.1/developers/roi.html#shape-concrete-implementations if applciable,"","","",FALSE,Biospecimen,"","","" -Staining Markers,Imaging specific: text to identify proteins/ antibodies selected for staining,"","","",FALSE,Biospecimen,"","","" -Lysis Buffer,scRNA-seq specific: Type of lysis buffer used,"","","",FALSE,Biospecimen,"","","" -Method of Nucleic Acid Isolation,"Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]","","","",FALSE,Biospecimen,"","","" -Biospecimen Dimension 1,"First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the """"dimensions_unit"""" CDE","",Dimensions Unit,"",FALSE,Biospecimen,"","","" -Biospecimen Dimension 2,"Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the """"dimensions_unit"""" CDE","","","",FALSE,Biospecimen,"","","" -Biospecimen Dimension 3,"Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the """"dimensions_unit"""" CDE","","","",FALSE,Biospecimen,"","","" -Dimensions Unit,"Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)","mm, cm","","",FALSE,Biospecimen,"","","" -Section Number in Sequence,"Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)","","","",FALSE,Biospecimen,"","","" diff --git a/modules/Biospecimen/Characteristics.csv b/modules/Biospecimen/Characteristics.csv deleted file mode 100644 index c77ba62..0000000 --- a/modules/Biospecimen/Characteristics.csv +++ /dev/null @@ -1,8 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Sample Core Template,Minimal required set of sample-level clinical data,"","Participant ID, Sample ID, Detailed Sample ID, Adjacent Sample IDs, Sample Site, ER Status, PR Status, HER2 Status",,FALSE,Sample,Sample,"","" -Morphology,"The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.","","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3226275&version=1.0,"" -Gross Tumor Weight,"Numeric value used to describe the gross pathologic tumor weight, measured in grams.","","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6133606&version=1.0,"" -Classification of Tumor,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.,"Primary, Metastasis, Recurrence, Other, unknown, Not Reported, Not Allowed To Collect","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3288124&version=1.0,"" -Breslow Thickness,"The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.","","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64809&version=3.0,"" -Tumor Depth,"Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).","","","",FALSE,Diagnosis,"","","" -Tumor Grade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.","G1, G2, G3, G4, GX, GB, High Grade, Intermediate Grade, Low Grade, unknown, Not Reported","","",FALSE,Diagnosis,"","","" diff --git a/modules/Other/Publication.csv b/modules/Other/Publication.csv deleted file mode 100644 index b0bcba8..0000000 --- a/modules/Other/Publication.csv +++ /dev/null @@ -1,2 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Publication Template,Publication entity.,,"Publication DOI, Title, Authors, Linked Project, Linked Datasets",,FALSE,Publication,Publication,, diff --git a/modules/Patient/Breast_Cancer_Tier_3.csv b/modules/Patient/Breast_Cancer_Tier_3.csv deleted file mode 100644 index 01aeaeb..0000000 --- a/modules/Patient/Breast_Cancer_Tier_3.csv +++ /dev/null @@ -1,33 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Breast Carcinoma Detection Method Type,"The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.","Clinical Exam, Data not available, Nipple Discharge, Other, Screening Mammography, Screening MRI, Self exam, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma Histology Category,Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.,"Infiltrating ductal carcinoma, Infiltrating lobular carcinoma, Invasive mammary carcinoma NOS, Invasive mixed ductal and lobular carcinoma, Other","","",FALSE,Breast Cancer Tier 3,"","","" -Invasive Lobular Breast Carcinoma Histologic Category,The histologic subtype for an infiltrating lobular carcinoma of the breast.,"Alveolar type, Classical type, Data not available, Pleomorphic type, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Invasive Ductal Breast Carcinoma Histologic Category,The histologic subtype for the most common type of invasive breast carcinoma.,"Classical type, Invasive carcinoma-type cannot be determined, Invasive cribriform carcinoma, Invasive micropapillary carcinoma, Invasive papillary carcinoma, Invasive tubular carcinoma, Medullary carcinoma, Mucinous carcinoma, Tubulolobular carcinoma, Other, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Biopsy Procedure Finding Type,Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease.,"Atypical hyperplasia, DCIS, LCIS, Cancer, No cancer, Other","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Quadrant Site,The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.,"Upper outer quadrant, Lower outer quadrant, Upper inner quadrant, Lower inner quadrant, Central, Nipple, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Cancer Assessment Tests,Text term to identify assessment tests done in participants during diagnosis,"Estrogen receptor IHC, Progesterone receptor IHC, HER2 IHC, HER2 FISH-CISH, HER2 FISH, Other, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Cancer Genomic Test Performed,Text term that represents the name of the genomic test performed for breast cancer.,"Oncotype, MammaPrint, Other, Data not available, unknown, Not performed","","",FALSE,Breast Cancer Tier 3,"","","" -Mammaprint Risk Group,Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.,"High risk, Intermediate risk, Low risk, Data not available, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Oncotype Risk Group,Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.,"High risk, Intermediate risk, Low risk, Data not available, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma Estrogen Receptor Status,Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer,"Borderline, Equivocal, Indeterminate, Negative, Not Performed, Performed but Not Available, Positive, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma Progesteroner Receptor Status,Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer,"Borderline, Equivocal, Indeterminate, Negative, Not Performed, Performed but Not Available, Positive, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Cancer Allred Estrogen Receptor Score,"The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.","0, 1, 2, 3, 4, 5, 6, 7, 8, 10, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Prior Invasive Breast Disease,Text term to indicate prior invasive breast condition in the participant,"DCIS, LCIS, Invasive breast cancer (unrelated to the current cancer), Other, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma ER Status Percentage Value,A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer,"","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma PR Status Percentage Value,A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer,"","","",FALSE,Breast Cancer Tier 3,"","","" -HER2 Breast Carcinoma Copy Number Total,"Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values.","","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma Centromere 17 Copy Number,"Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.","","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma HER2 Centromere17 Copynumber Total,Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer,"","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma HER2 Chromosome17 Ratio,HER2 chromosome 17 ratio in participants with breast cancer,"","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma Surgical Procedure Name,Text name of a surgical procedure performed for a person with a diagnosis of breast cancer,"Lumpectomy, Radical mastectomy, Modified radical mastectomy, Other, Partial mastectomy, Re-excision, Simple mastectomy, Surgery not performed, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma HER2 Ratio Diagnosis,HER2 ratio of the participant at diagnosis,"","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma HER2 Status,Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 in a participant with breast cancer,"Positive, Negative, Amplified, Non-amplified, Equivocal, Indeterminate, Not Performed, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Hormone Therapy Breast Cancer Prevention Indicator,Did the patient receive hormonal therapy for prevention of breast cancer?,"Yes, No, unknown, Not Applicable","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma ER Staining Intensity,Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer,"Strong, Moderate, Weak, Weak-Moderate, Moderate-Strong, Weak-Strong, Other, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Carcinoma PR Staining Intensity,Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer,"Strong, Moderate, Weak, Weak-Moderate, Moderate-Strong, Weak-Strong, Other, unknown","","",FALSE,Breast Cancer Tier 3,"","","" -Oncotype Score,OncotypeDX recurrence score,"","","",FALSE,Breast Cancer Tier 3,"","","" -Breast Imaging Performed Type,"The kind of technology or method performed for screening, diagnosis, surgical procedures or therapy that aids in the visualization of the breast(s).","Mammogram, Ultrasound, MRI, PET/CT, CT, Multiple imaging modalities, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -Multifocal Breast Carcinoma Present Indicator,A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from the same clone and usually located in the same quadrant of the breast.,"Yes, No, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -Multicentric Breast Carcinoma Present Indicator,A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from different clones and usually located in different quadrants of the breast.,"Yes, No, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -BIRADS Mammography Breast Density Category,The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines.,"Predominantly fatty, Scattered fibroglandular densities, Heterogeneously dense, Extremely dense, unknown, Data not available","","",FALSE,Breast Cancer Tier 3,"","","" -BIRADS Score,Score within the BI-RADS system to characterize abnormal findings,"0,1,2,3,4,4A,4B,4C,5,6","","",FALSE,Breast Cancer Tier 3,"","","" diff --git a/modules/Patient/Core.csv b/modules/Patient/Core.csv deleted file mode 100644 index 0479b2c..0000000 --- a/modules/Patient/Core.csv +++ /dev/null @@ -1,2 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Cohort Core Template,Set of individual-level clinical data across different cohort collections,"","Participant ID,Age,Sex,BMI,Race,Ethnicity,Vital Status,Height,Weight,Gravidity,Parity,Age At Menarche,Menstrual Cycle Phase,Menopause Status,Primary Diagnosis,Age at Diagnosis,Diagnosis Status Type,Class BRCA1,Class BRCA2,Tobacco Use,Pack Years Smoked,Alcohol Use,Number of Drinks Per Week,Antibiotic Use,Sample Collection Center,Sample Collection Year,ER Status, PR Status, HER2 Status","",FALSE,Patient,,"","" diff --git a/modules/Patient/Demographics.csv b/modules/Patient/Demographics.csv deleted file mode 100644 index bfb2c7e..0000000 --- a/modules/Patient/Demographics.csv +++ /dev/null @@ -1,27 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Ethnicity,"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.","hispanic or latino, not hispanic or latino, unknown, Not Reported, not allowed to collect","","",TRUE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2192217&version=2.0,"" -Gender,"Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]","female, male, unknown, unspecified, Not Reported","","",TRUE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2200604&version=3.0,"" -Race,"An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.","white, american indian or alaska native, black or african american, asian, native hawaiian or other pacific islander, other, unknown, Not Reported, not allowed to collect","","",TRUE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2192199&version=1.0,"" -Vital Status,The survival state of the person registered on the protocol.,"Alive, Dead, unknown, Not Reported","","",TRUE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5&version=5.0,"" -Dead,This indicates the participant is dead and defines further required metadata,"","Year of Death, Cause of Death, Cause of Death Source, Days to Death","",FALSE,Demographics,"","","" -Days to Birth,Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days.,"","","",FALSE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154723&version=1.0,"" -Year of Death,Numeric value to represent the year of the death of an individual.,"","","",TRUE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2897030&version=1.0,"" -Country of Residence,Country of Residence at enrollment,"Afghanistan,Albania,Algeria,Andorra,Angola,Anguilla,Antigua and Barbuda,Argentina,Armenia,Aruba,Australia,Austria,Azerbaijan,Bahamas,Bahrain,Bangladesh,Barbados,Belarus,Belgium,Belize,Benin,Bermuda,Bhutan,Bolivia,Bosnia and Herzegovina,Botswana,Brazil,Brunei,Bulgaria,Burkina Faso,Burundi,Cambodia,Cameroon,Canada,Cape Verde,Cayman Islands,Central African Republic,Chad,Chile,China,Colombia,Comoros,Congo,Cook Islands,Costa Rica,Cote d'Ivoire,Croatia,Cuba,Curacao,Cyprus,Czech Republic (Czechia),Democratic Republic of the Congo,Denmark,Djibouti,Dominica,Dominican Republic,Ecuador,Egypt,El Salvador,Equatorial Guinea,Eritrea,Estonia,Eswatini,Ethiopia,Falkland Islands (Malvinas),Faroe Islands,Federated States of Micronesia,Fiji,Finland,France,French Guiana,French Polynesia,Gabon,Gambia,Georgia,Germany,Ghana,Gibraltar,Greece,Greenland,Grenada,Guadeloupe,Guam,Guatemala,Guernsey,Guinea,Guinea-Bissau,Guyana,Haiti,Holy See,Honduras,Hong Kong,Hungary,Iceland,India,Indonesia,Iran,Iraq,Ireland,Isle of Man,Israel,Italy,Jamaica,Japan,Jersey,Jordan,Kazakhstan,Kenya,Kiribati,Kosovo,Kuwait,Kyrgyzstan,Laos,Latvia,Lebanon,Lesotho,Liberia,Libya,Liechtenstein,Lithuania,Luxembourg,Macau,Madagascar,Malawi,Malaysia,Maldives,Mali,Malta,Marshall Islands,Martinique,Mauritania,Mauritius,Mayotte,Mexico,Moldova,Monaco,Mongolia,Montenegro,Montserrat,Morocco,Mozambique,Myanmar,Namibia,Nauru,Nepal,Netherlands,New Caledonia,New Zealand,Nicaragua,Niger,Nigeria,Niue,North Korea,North Macedonia,Northern Mariana Islands,Norway,Oman,Pakistan,Palau,Panama,Papua New Guinea,Paraguay,Peru,Philippines,Poland,Portugal,Puerto Rico,Qatar,Reunion,Romania,Russia,Rwanda,Saint Helena Ascension and Tristan da Cunha,Saint Kitts and Nevis,Saint Lucia,Saint Pierre and Miquelon,Saint Vincent and the Grenadines,Samoa,San Marino,Sao Tome and Principe,Saudi Arabia,Senegal,Serbia,Seychelles,Sierra Leone,Singapore,Slovakia,Slovenia,Solomon Islands,Somalia,South Africa,South Korea,South Sudan,Spain,Sri Lanka,State of Palestine,Sudan,Suriname,Svalbard & Jan Mayen Islands,Sweden,Switzerland,Syria,Taiwan,Tajikistan,Tanzania,Thailand,Timor-Leste,Togo,Tokelau,Tonga,Trinidad and Tobago,Tunisia,Turkey,Turkmenistan,Tuvalu,Uganda,Ukraine,United Arab Emirates,United Kingdom,United States,Uruguay,Uzbekistan,Vanuatu,Venezuela,Vietnam,Virgin Islands British,Virgin Islands U.S.,Wallis and Futuna,Western Sahara,Yemen,Zambia,Zimbabwe","","",FALSE,Demographics,"","","" -Age at Index,For GDC submission only - this is going to be always 0 since 's index is the date of birth,"","","",FALSE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6028530&version=1.0,"" -Age Is Obfuscated,The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.,"true, false","","",FALSE,Demographics,"","","" -Year Of Birth,Numeric value to represent the calendar year in which an individual was born.,"","","",FALSE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2896954&version=1.0,"" -Cause of Death,The cause of death,"Cancer Related, Cardiovascular Disorder NOS, End-stage Renal Disease, Infection, Not Cancer Related, Renal Disorder NOS, Spinal Muscular Atrophy, Surgical Complications, Toxicity, Not Reported, unknown, Not Applicable","","",TRUE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2554674&version=3.0,"" -Days to Death,Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days.,"","","",FALSE,Demographics,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154724&version=1.0,"" -Sex,Sex of individual,"female, male, unknown, unspecified, Not Reported",,,FALSE,Demographics Extended,,, -Age,Age of individual,,,,FALSE,Demographics Extended,,, -Age at Menarche,Age at first period,,,,FALSE,Demographics Extended,,, -Age at Menopause,Age at menopause,,,,FALSE,Demographics Extended,,, -Menopause Cause,Causal history of menopause,"Natural, Surgically induced, unknown",,,FALSE,Demographics Extended,,, -Obstetric History,Obstetric history notation such as “G1 P1”,,,,FALSE,Demographics Extended,,, -Parity,Number of pregnancies carried over the threshold of viability,,,,FALSE,Demographics Extended,,, -Gravidity,Total number of pregnancies regardless of outcome,,,,FALSE,Demographics Extended,,, -Age at First Birth,Age when individual gave first birth,,,,FALSE,Demographics Extended,,, -Yes - Given Birth,Has given birth,"Yes, No, unknown",,,FALSE,Demographics Extended,,, -Number of Live Births,Number of live births,,,,FALSE,Demographics Extended,,, -Yes - Issues With Pregnancy,Whether there was an issue with any pregnancy,,,,FALSE,Demographics Extended,,, -Years of Contraceptive Use,Years of contraceptive use,,,,FALSE,Demographics Extended,,, diff --git a/modules/Patient/Diagnosis.csv b/modules/Patient/Diagnosis.csv deleted file mode 100644 index f953afb..0000000 --- a/modules/Patient/Diagnosis.csv +++ /dev/null @@ -1,92 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Days to Progression,Number of days between the date used for index and the date the patient's disease progressed.,"","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154730&version=1.0,"" -Days to Progression Free,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free.,"","","",FALSE,Diagnosis,"","","" -Progression or Recurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,"Yes - Progression or Recurrence, No, unknown, Not Reported","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3121376&version=1.0,"" -Yes - Progression or Recurrence,The patient has had a new tumor event after initial treatment,"","Progression or Recurrence Type, Days to Progression, Days to Progression Free, Days to Recurrence, Days to Recurrence, Progression or Recurrence Anatomic Site","",FALSE,Diagnosis,"","","" -Sentinel Lymph Node Count,Numeric count of sentinel lymph nodes.,"","","",FALSE,Diagnosis,"","","" -Sentinel Node Positive Assessment Count,The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.,"","","",FALSE,Diagnosis,"","","" -Tumor Extranodal Extension Indicator,The indicator to determine extranodal involvement or extent of the disease.,"Absent,Indeterminate,NO, YES, No source documentation,Not applicable,Not sampled or dissected,Present,Present - extensive,Present - minimal,UNKNOWN,Unspecified","","",FALSE,Diagnosis,"","","" -Satellite Metastasis Present Indicator,A yes/no indicator to ask if intransit metastases or satellite lesions are present.,"Yes, No, unknown","","",FALSE,Diagnosis,"","","" -Other Biopsy Resection Site,A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under Clinical Data Tier 1),"","","",FALSE,Diagnosis,"","","" -Extent of Tumor Resection,"The degree to which the lesion has been cut out, or resected.","Gross Total Resection, Open Biopsy, Subtotal Resection, Extensive Subtotal, Minor, Optimal debulking, Other, Partial debulking, Segmental, Suboptimal, Suboptimal debulking, NTR, unknown, Not Reported, Not Applicable ","","",FALSE,Diagnosis,"","","" -Precancerous Condition Type,The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).,"Ductal Carcinoma In Situ,Pancreatic Intraductal Papillary-Mucinous Neoplasm,Atypical Adenomatous Lung Hyperplasia,Other,Pancreatic Intraepithelial Neoplasia,Prostatic Intraepithelial Neoplasia,Melanocytic hyperplasia,Atypical melanocytic proliferation,Melanoma in situ,Superficial spreading,Melanoma in situ,Lentigo maligna type,Melanoma in situ,Acral-lentiginous,Melanoma in situ arising in a giant congenital nevus,Persistent melanoma in situ,Melanoma in situ not otherwise classified,Scar - no residual melanoma,Invasive melanoma - superficial spreading,Invasive melanoma - nodular type,Invasive melanoma - lentigo maligna,Invasive melanoma - acral lentiginous,Invasive melanoma - desmoplastic,Invasive melanoma - nevoid,Invasive melanoma,Normal WDA,Reserve cell hyperplasia,Squamous metaplasia - mature,Squamous metaplasia - immature,Mild dysplasia,Moderate dysplasia,Severe dysplasia,Atypical adenomatous hyperplasia,Adenocarcinoma in situ - non mucinous,Adenocarcinoma in situ - mucinous,Benign tumor NOS,Hamartoma,Carcinoma NOS,No diagnosis possible","","",FALSE,Diagnosis,"","","" -Mode of Cancer Detection,"Text term used to describe the mode of cancer detection, like standard of care screening or random detection","Standard of Care Screening, Clinical Examination of unrelated cancer symptoms, Incidentaloma, Interval Cancer, Data not available","","",FALSE,Diagnosis,"","","" -Gleason Grade Group,"The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.","Group 1, Group 2, Group 3, Group 4, Group 5","","",FALSE,Diagnosis,"","","" -Gleason Grade Tertiary,The text term used to describe the tertiary pattern as described by the Gleason Grading System.,"Pattern 4, Pattern 5","","",FALSE,Diagnosis,"","","" -Gleason Patterns Percent,"Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.","","","",FALSE,Diagnosis,"","","" -Greatest Tumor Dimension,Numeric value that represents the measurement of the widest portion of the tumor in centimeters.,"","","",FALSE,Diagnosis,"","","" -Lymph Node Involved Site,The text term used to describe the anatomic site of lymph node involvement.,"Axillary,Cervical,Epitrochlear,Femoral,Hilar,Iliac-common,Iliac-external,Iliac, NOS,Inguinal,Mediastinal,Mesenteric,None,Occipital,Paraaortic,Parotid,Popliteal,Retroperitoneal,Splenic,Submandibular,Supraclavicular,unknown,Not Reported","","",FALSE,Diagnosis,"","","" -Margin Distance,Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.,"","","",FALSE,Diagnosis,"","","" -Margins Involved edulloblastoma Molecular ClassificationSite,The text term used to describe the anatomic sites that were involved in the survival margins.,"Gerota Fascia, Parenchyma, Perinephric Fat, Renal, Renal Capsule, Renal Sinus, Renal Vein, Ureter","","",FALSE,Diagnosis,"","","" -M,The text term used to describe the classification of medulloblastoma tumors based on molecular features.,"Not Determined, Non-WNT/non-SHH Activated, SHH-Activated, WNT-Activated, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Micropapillary Features,The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.,"Absent, Present, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Non Nodal Regional Disease,The text term used to describe whether the patient had non-nodal regional disease.,"Absent, Indeterminate, Present, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Non Nodal Tumor Deposits,The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.,"Yes, No, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Ovarian Specimen Status,The text term used to describe the physical condition of the involved ovary.,"Ovarian Capsule Intact, Ovarian Capsule Ruptured, Ovarian Capsule Fragmented, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Ovarian Surface Involvement,The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.,"Absent, Present, Indeterminate, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Pregnant at Diagnosis,The text term used to indicate whether the patient was pregnant at the time they were diagnosed.,"Yes, No, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Primary Gleason Grade,"The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.","Pattern 1, Pattern 2, Pattern 3, Pattern 4, Pattern 5","","",FALSE,Diagnosis,"","","" -Secondary Gleason Grade,"The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.","Pattern 1, Pattern 2, Pattern 3, Pattern 4, Pattern 5","","",FALSE,Diagnosis,"","","" -WHO CNS Grade,WHO CNS Grade,"Grade I, Grade II, Grade III, Grade IV, Grade Not Assigned, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -WHO NTE Grade,WHO NTE Grade,"G1, G2, G3, GX, unknown, Not Reported","","",FALSE,Diagnosis,"","","" -Age at Diagnosis,Age at the time of diagnosis expressed in number of days since birth.,"","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3225640&version=2.0,"" -Days to Last Follow up,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.","","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3008273&version=1.0,"" -Days to Last Known Disease Status,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.","","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3008273&version=1.0,"" -Last Known Disease Status,Text term that describes the last known state or condition of an individual's neoplasm.,"Distant met recurrence/progression, Loco-regional recurrence/progression, Biochemical evidence of disease without structural correlate, Tumor free, unknown tumor status, With tumor, Not Reported, Not Allowed To Collect, Not Applicable","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2759550&version=1.0,"" -Primary Diagnosis,"Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).","Acinar cell carcinoma,Acute basophilic leukaemia,Acute leukemia Burkitt type,Acute leukemia NOS,Acute lymphatic leukemia,Acute lymphoblastic leukemia-lymphoma NOS,Acute lymphoblastic leukemia mature B-cell type,Acute lymphoblastic leukemia NOS,Acute lymphoblastic leukemia precursor cell type,Acute lymphocytic leukemia,Acute lymphoid leukemia,Acute myeloid leukemia minimal differentiation,Acute myeloid leukemia MLL,Acute myeloid leukemia NOS,Acute myelomonocytic leukemia,Acute promyelocytic leukemia NOS,Adenocarcinoid tumor,Adenocarcinoma combined with other types of carcinoma,Adenocarcinoma in a polyp NOS,Adenocarcinoma in adenomatous polyp,Adenocarcinoma in polypoid adenoma,Adenocarcinoma in situ in a polyp NOS,Adenocarcinoma in situ in adenomatous polyp,Adenocarcinoma in situ in tubular adenoma,Adenocarcinoma in situ mucinous,Adenocarcinoma in situ non-mucinous,Adenocarcinoma in situ NOS,Adenocarcinoma in tubular adenoma,Adenocarcinoma in villous adenoma,Adenocarcinoma of anal ducts,Adenocarcinoma of anal glands,Adenocarcinoma diffuse type,Adenocarcinoma endocervical type,Adenocarcinoma intestinal type,Adenocarcinoma metastatic NOS,Adenocarcinoma NOS,Adenocarcinoma pancreatobiliary type,Adult rhabdomyoma,Adult T-cell lymphoma,Adult T-cell lymphoma/leukemia,Astrocytoma anaplastic,Astrocytoma low grade,Astrocytoma NOS,B cell lymphoma NOS,B lymphoblastic leukemia/lymphoma with hyperdiploidy,B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL),B lymphoblastic leukemia/lymphoma NOS,B-ALL,B-cell lymphocytic leukemia/small lymphocytic lymphoma,Basal cell adenocarcinoma,Basal cell adenoma,Basal cell carcinoma NOS,Basal cell epithelioma,Basal cell tumor,Basophil adenocarcinoma,Basophil adenoma,Basophil carcinoma,Bile duct adenocarcinoma,Bile duct adenoma,Bile duct carcinoma,Bile duct cystadenocarcinoma,Bile duct cystadenoma,Bronchial adenoma carcinoid,Bronchial adenoma cylindroid,Bronchial adenoma NOS,Bronchial-associated lymphoid tissue lymphoma,Bronchio-alveolar carcinoma mixed mucinous and non-mucinous,Bronchio-alveolar carcinoma mucinous,Bronchiolar adenocarcinoma,Bronchiolar carcinoma,Bronchiolo-alveolar adenocarcinoma NOS,Bronchiolo-alveolar carcinoma Clara cell,Bronchiolo-alveolar carcinoma Clara cell and goblet cell type,Bronchiolo-alveolar carcinoma goblet cell type,Bronchiolo-alveolar carcinoma indeterminate type,Bronchiolo-alveolar carcinoma non-mucinous,Bronchiolo-alveolar carcinoma NOS,Burkitt cell leukemia,Burkitt lymphoma NOS (Includes all variants),Burkitt tumor,Burkitt-like lymphoma,c-ALL,Cancer,Capillary hemangioma,Capillary lymphangioma,Carcinoma in a polyp NOS,Carcinoma in adenomatous polyp,Carcinoma in pleomorphic adenoma,Carcinoma in situ in a polyp NOS,Carcinoma in situ in adenomatous polyp,Carcinoma in situ NOS,Carcinoma anaplastic NOS,Carcinoma diffuse type,Carcinoma intestinal type,Carcinoma metastatic NOS,Carcinoma NOS,Carcinosarcoma NOS,Carcinoma undifferentiated NOS,Cementoma NOS,Central neuroblastoma,Central neurocytoma,Cerebellar liponeurocytoma,Cerebellar sarcoma NOS,Cervical intraepithelial neoplasia grade III,Cervical intraepithelial neoplasia low grade,Chondroma NOS,Chondrosarcoma grade 2/3,Chronic granulocytic leukemia BCR/ABL,Chronic granulocytic leukemia NOS,Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive,Chronic leukemia NOS,Chronic lymphatic leukemia,Chronic lymphocytic leukemia,Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL),Chronic lymphoid leukemia,Chronic monocytic leukemia,Chronic myelocytic leukemia NOS,Chronic myelogenous leukemia BCR-ABL positive,Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive,Chronic myeloid leukemia NOS,Chronic myelomonocytic leukemia in transformation,Chronic myelomonocytic leukemia NOS,Chronic myelomonocytic leukemia Type 1,Chronic myelomonocytic leukemia Type II,Chronic myeloproliferative disease NOS,Chronic myeloproliferative disorder,Chronic neutrophilic leukemia,Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis,Classical Hodgkin lymphoma lymphocyte depletion NOS,Classical Hodgkin lymphoma lymphocyte depletion reticular,Classical Hodgkin lymphoma lymphocyte-rich,Classical Hodgkin lymphoma mixed cellularity NOS,Classical Hodgkin lymphoma nodular sclerosis cellular phase,Classical Hodgkin lymphoma nodular sclerosis grade 1,Classical Hodgkin lymphoma nodular sclerosis grade 2,Classical Hodgkin lymphoma nodular sclerosis NOS,Combined hepatocellular carcinoma and cholangiocarcinoma,Combined large cell neuroendocrine carcinoma,Combined small cell carcinoma,Combined small cell-adenocarcinoma,Combined small cell-large carcinoma,Combined small cell-squamous cell carcinoma,Combined/mixed carcinoid and adenocarcinoma,Composite Hodgkin and non-Hodgkin lymphoma,Dermal nevus,Dermatofibroma NOS,Diffuse astrocytoma IDH-mutant,Diffuse astrocytoma IDH-wildtype,Diffuse astrocytoma low grade,Diffuse large B-cell lymphoma NOS,Diffuse melanocytosis,Duct adenocarcinoma NOS,Duct adenoma NOS,Duct carcinoma desmoplastic type,Duct carcinoma NOS,Duct cell carcinoma,Ductal carcinoma in situ NOS,Ductal carcinoma NOS,Dysplastic nevus,Endometrial sarcoma NOS,Endometrioid adenocarcinoma NOS,Endometrioid adenofibroma NOS,Endometrioid adenoma NOS,Endometrioid carcinoma NOS,Eosinophil adenocarcinoma,Eosinophil adenoma,Eosinophil carcinoma,Eosinophilic granuloma,Eosinophilic leukemia,Ependymoma NOS,Epidermoid carcinoma in situ NOS,Epidermoid carcinoma NOS,Epithelial tumor benign,Epithelial tumor malignant,Esophageal glandular dysplasia (intraepithelial neoplasia) high grade,Esophageal glandular dysplasia (intraepithelial neoplasia) low grade,Esophageal intraepithelial neoplasia high grade,Esophageal squamous intraepithelial neoplasia (dysplasia) high grade,Esophageal squamous intraepithelial neoplasia (dysplasia) low grade,Ewing sarcoma,Ganglioglioma NOS,Familial adenomatous polyposis,Gastrin cell tumor,Gastrin cell tumor malignant,Gastrinoma malignant,Gastrinoma NOS,Gastrointestinal stromal tumor malignant,Glioblastoma,Glioma malignant,Glioma NOS,Haemangioblastoma,Haemangiosarcoma,Hepatocarcinoma,Hepatocellular adenoma,Hepatocellular carcinoma NOS,Hepatocholangiocarcinoma,Hepatoid adenocarcinoma,Hepatoid carcinoma,Hodgkin disease NOS,Hodgkin granuloma,Hodgkin lymphoma mixed cellularity NOS,Hodgkin lymphoma nodular sclerosis NOS,Hodgkin lymphoma NOS,Hodgkin paragranuloma NOS,Hodgkin sarcoma,Infiltrating basal cell carcinoma NOS, Infiltrating duct carcinoma NOS, Infiltrating duct and colloid carcinoma,Infiltrating duct and cribriform carcinoma,Inflammatory adenocarcinoma,Inflammatory carcinoma,Interstitial cell tumor benign,Interstitial cell tumor malignant,Interstitial cell tumor NOS,Intracystic papilloma,Intradermal nevus,Intraductal adenocarcinoma noninfiltrating NOS,Intraductal and lobular carcinoma,Intraductal carcinoma and lobular carcinoma in situ,Intraductal carcinoma clinging,Intraductal carcinoma noninfiltrating NOS,Intraductal carcinoma NOS,Intraductal carcinoma solid type,Intraductal micropapillary carcinoma,Intraductal papillary adenocarcinoma with invasion,Intraductal papillary adenocarcinoma NOS,Intraductal papillary carcinoma,Intraductal tubular-papillary neoplasm high grade,Intraductal tubular-papillary neoplasm low grade,Intraductal tubulopapillary neoplasm,Intraepidermal carcinoma NOS,Intraepidermal squamous cell carcinoma Bowen type,Intravascular B-cell lymphoma,Juvenile myelomonocytic leukemia,Kaposi sarcoma,Large cell carcinoma NOS,Liposarcoma differentiated,Liposarcoma NOS,Liposarcoma well differentiated,Liver cell adenoma,Liver cell carcinoma,Lobular adenocarcinoma,Lobular and ductal carcinoma,Lobular carcinoma in situ NOS,Lobular carcinoma noninfiltrating,Lobular carcinoma NOS,Lymphatic leukemic NOS,Lymphoblastic leukemia NOS,Lymphoblastoma,Lymphocytic leukemia NOS,Lymphoma NOS,Malignancy,Malignant lymphoma diffuse NOS,Malignant lymphoma Hodgkin,Malignant lymphoma immunoblastic NOS,Malignant lymphoma large B-cell diffuse NOS,Malignant lymphoma large B-cell NOS,Malignant lymphoma large cell NOS,Malignant lymphoma lymphoblastic NOS,Malignant lymphoma lymphocytic diffuse NOS,Malignant lymphoma lymphocytic nodular NOS,Malignant lymphoma lymphocytic NOS,Malignant lymphoma mixed cell type diffuse,Malignant lymphoma mixed cell type follicular,Malignant lymphoma mixed cell type nodular,Malignant lymphoma nodular NOS,Malignant lymphoma non-Hodgkin NOS,Malignant lymphoma NOS,Malignant lymphoma small B lymphocytic NOS,Malignant melanoma in congenital melanocytic nevus,Malignant melanoma in giant pigmented nevus,Malignant melanoma in Hutchinson melanotic freckle,Malignant melanoma in junctional nevus,Malignant melanoma in precancerous melanosis,Malignant melanoma NOS,Malignant melanoma regressing,Mammary carcinoma in situ,Medullary adenocarcinoma,Medullary carcinoma NOS,Medullary osteosarcoma,Medulloblastoma NOS,Melanoameloblastoma,Melanocytic nevus,Melanocytoma eyeball,Melanocytoma NOS,Melanoma in situ,Melanoma malignant of soft parts,Melanoma NOS,Melanotic medulloblastoma,Melanotic MPNST,Melanotic neuroectodermal tumor,Melanotic neurofibroma,Melanotic progonoma,Melanotic psammomatous MPNST,Melanotic schwannoma,Meningeal melanocytoma,Meningeal melanoma,Meningioma anaplastic,Meningioma malignant,Meningioma NOS,Micropapillary carcinoma NOS,Mixed adenocarcinoma and epidermoid carcinoma,Mixed adenocarcinoma and squamous cell carcinoma,Mixed medullary-follicular carcinoma,Mixed medullary-papillary carcinoma,Mixed pancreatic endocrine and exocrine tumor malignant,Mixed pineal tumor,Mixed small cell carcinoma,Mixed squamous cell and glandular papilloma,Mixed tumor malignant NOS,Mixed tumor NOS,Monocytic leukemia NOS,Mucosal-associated lymphoid tissue lymphoma,Mucous adenocarcinoma,Multiple myeloma,Myelocytic leukemia NOS,Myeloid leukemia NOS,Myeloma NOS,Myoepithelioma,Neoplasm benign,Neoplasm malignant,Neoplasm malignant uncertain whether primary or metastatic,Neoplasm metastatic,Neoplasm NOS,Neoplasm secondary,Neoplasm uncertain whether benign or malignant,Nephroblastoma NOS,Neuroblastoma NOS,Neuroendocrine carcinoma NOS,Neuroepithelioma NOS,Neurofibroma NOS,Neurofibromatosis NOS,Neurofibrosarcoma,Neurosarcoma,Nevus NOS,Non-Hodgkin lymphoma NOS,Non-invasive low grade serous carcinoma,Non-lymphocytic leukemia NOS,Non-small cell carcinoma,Nonpigmented nevus,Not Reported,Oat cell carcinoma,Osteoblastoma malignant,Osteoblastoma NOS,Osteosarcoma NOS,Paget disease and infiltrating duct carcinoma of breast,Paget disease and intraductal carcinoma of breast,Paget disease of breast,Paget disease extramammary,Paget disease mammary,Pagetoid reticulosis,Pancreatic endocrine tumor benign,Pancreatic endocrine tumor malignant,Pancreatic endocrine tumor nonfunctioning,Pancreatic endocrine tumor NOS,Pancreatic microadenoma,Pancreatobiliary neoplasm non-invasive,Pancreatobiliary-type carcinoma,Pancreatoblastoma,Papillary adenocarcinoma follicular variant,Papillary adenocarcinoma NOS,Papillary adenofibroma,Papillary adenoma NOS,Papillary and follicular carcinoma,Papillary carcinoma in situ,Papillary carcinoma NOS,Papillary cystadenoma NOS,Papillary epidermoid carcinoma,Papillary glioneuronal tumor,Papillary meningioma,Papillary microcarcinoma,Papillary renal cell carcinoma,Papillary serous adenocarcinoma,Papillary serous cystadenocarcinoma,Papillary serous cystadenoma NOS,Papillary squamous cell carcinoma,Papillary squamous cell carcinoma in situ,Papillary transitional cell carcinoma,Papillary tumor of the pineal region,Papillary urothelial carcinoma,Papilloma of bladder,Papilloma NOS,Papillomatosis glandular,Papillomatosis NOS,Papillotubular adenocarcinoma,Papillotubular adenoma,Paraganglioma benign,Paraganglioma malignant,Paraganglioma NOS,Peripheral T-cell lymphoma large cell,Peripheral T-cell lymphoma NOS,Pigmented adenoma,Pigmented basal cell carcinoma,Pigmented nevus NOS,Pituitary adenoma NOS,Pituitary carcinoma NOS,Pleomorphic adenoma,Pleomorphic carcinoma,Pleomorphic lipoma,Pleomorphic liposarcoma,Pleomorphic lobular carcinoma,Pleomorphic lobular carcinoma in situ,Precancerous melanosis NOS,Precursor B-cell lymphoblastic leukemia,Precursor B-cell lymphoblastic lymphoma,Precursor cell lymphoblastic leukemia NOS,Precursor T-cell lymphoblastic leukemia,Precursor T-cell lymphoblastic lymphoma,Preleukemia,Preleukemic syndrome,Primary amyloidosis,Pro-B ALL,Pro-T ALL,Prostatic intraepithelial neoplasia grade III,Pulmonary adenomatosis,Pulmonary artery intimal sarcoma,Pulmonary blastoma,Renal carcinoma collecting duct type,Renal cell adenocarcinoma,Renal cell carcinoma chromophobe type,Renal cell carcinoma NOS,Renal cell carcinoma sarcomatoid,Renal cell carcinoma spindle cell,Renal cell carcinoma unclassified,Renal medullary carcinoma,Rhabdoid meningioma,Rhabdoid sarcoma,Rhabdoid tumor NOS,Rhabdomyoma NOS,Rhabdomyosarcoma with ganglionic differentiation,Rhabdomyosarcoma NOS,Rhabdosarcoma,Rodent ulcer,Sarcoma NOS,Sclerosing hemangioma,Sclerosing hepatic carcinoma,Secondary carcinoma,Secretory carcinoma of breast,Serous cystadenocarcinoma NOS,Serous surface papillary carcinoma,High-grade serous carcinoma,Skin appendage carcinoma,Small cell carcinoma NOS,Small cell neuroendocrine carcinoma,Small cell osteosarcoma,Small cell sarcoma,Small congenital nevus,Spindle cell carcinoma NOS,Spindle cell melanoma NOS,Splenic B-cell lymphoma/leukemia unclassifiable,Splenic diffuse red pulp small B-cell lymphoma,Splenic lymphoma with villous lymphocytes,Splenic marginal zone B-cell lymphoma,Splenic marginal zone lymphoma NOS,Squamous cell carcinoma in situ NOS,Squamous cell carcinoma adenoid,Squamous cell carcinoma clear cell type,Squamous cell carcinoma NOS,T lymphoblastic leukemia/lymphoma,T-cell large granular lymphocytic leukemia,T-cell large granular lymphocytosis,T-cell lymphoma NOS,Teratoma malignant NOS,Teratoma NOS,Therapy related myeloid neoplasm,Transitional carcinoma,Transitional cell carcinoma,Transitional cell carcinoma in situ,Tubular adenocarcinoma,Tubular adenoma NOS,Tubular androblastoma with lipid storage,Tubular androblastoma NOS,Tubular carcinoid,Tubular carcinoma,Tubulo-papillary adenoma,Tubulocystic renal cell carcinoma,Tubulolobular carcinoma,Tubulopapillary adenocarcinoma,Tubulovillous adenoma NOS,Tumor cells benign,Tumor cells malignant,Tumor cells NOS,Tumor cells uncertain whether benign or malignant,Tumor embolus,Tumor benign,Tumor malignant NOS,Tumor metastatic,Tumor NOS,Tumor secondary,Tumorlet benign,Typical carcinoid,Unclassified tumor benign,Unclassified tumor borderline malignancy,Unclassified tumor malignant,Unclassified tumor malignant uncertain whether primary or metastatic,Unclassified tumor uncertain whether benign or malignant,Undifferentiated epithelioid sarcoma,Undifferentiated high-grade pleomorphic sarcoma,Undifferentiated leukaemia,Undifferentiated pleomorphic sarcoma,Undifferentiated round cell sarcoma,Undifferentiated sarcoma,Undifferentiated spindle cell sarcoma,Undifferentiated uterine sarcoma,unknown","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161032&version=1.0,"" -Prior Malignancy,The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.,"Yes, No, unknown, Not Reported, Not Allowed To Collect","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3382736&version=2.0,"" -Prior Treatment,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.,"Yes, No, unknown, Not Reported, Not Allowed To Collect","","",FALSE,Diagnosis,"","","" -Site of Resection or Biopsy,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).","Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Paraspinal,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,unknown,Not Reported","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161034&version=1.0,"" -Tissue or Organ of Origin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).","Abdomen NOS,Abdominal esophagus,Accessory sinus NOS,Acoustic nerve,Adrenal gland NOS,Ampulla of Vater,Anal canal,Anterior 2/3 of tongue NOS,Anterior floor of mouth,Anterior mediastinum,Anterior surface of epiglottis,Anterior wall of bladder,Anterior wall of nasopharynx,Anus NOS,Aortic body and other paraganglia,Appendix,Ascending colon,Autonomic nervous system NOS,Axillary tail of breast,Base of tongue NOS,Bladder neck,Bladder NOS,Blood,Body of pancreas,Body of penis,Body of stomach,Bone marrow,Bone of limb NOS,Bone NOS,Bones of skull and face and associated joints,Border of tongue,Brain stem,Brain NOS,Branchial cleft,Breast NOS,Broad ligament,Cardia NOS,Carotid body,Cauda equina,Cecum,Central portion of breast,Cerebellum NOS,Cerebral meninges,Cerebrum,Cervical esophagus,Cervix uteri,Choroid,Ciliary body,Cloacogenic zone,Colon NOS,Commissure of lip,Conjunctiva,Connective subcutaneous and other soft tissues of abdomen,Connective subcutaneous and other soft tissues of head face and neck,Connective subcutaneous and other soft tissues of lower limb and hip,Connective subcutaneous and other soft tissues of pelvis,Connective subcutaneous and other soft tissues of thorax,Connective subcutaneous and other soft tissues of trunk NOS,Connective subcutaneous and other soft tissues of upper limb and shoulder,Connective subcutaneous and other soft tissues NOS,Cornea NOS,Corpus uteri,Cortex of adrenal gland,Cranial nerve NOS,Craniopharyngeal duct,Descended testis,Descending colon,Dome of bladder,Dorsal surface of tongue NOS,Duodenum,Endocervix,Endocrine gland NOS,Endometrium,Epididymis,Esophagus NOS,Ethmoid sinus,Exocervix,External ear,External lip NOS,External lower lip,External upper lip,Extrahepatic bile duct,Eye NOS,Eyelid,Fallopian tube,Female genital tract NOS,Floor of mouth NOS,Frontal lobe,Frontal sinus,Fundus of stomach,Fundus uteri,Gallbladder,Gastric antrum,Gastrointestinal tract NOS,Glans penis,Glottis,Greater curvature of stomach NOS,Gum NOS,Hard palate,Head of pancreas,Head face or neck NOS,Heart,Hematopoietic system NOS,Hepatic flexure of colon,Hypopharyngeal aspect of aryepiglottic fold,Hypopharynx NOS,Ileum,Ill-defined sites within respiratory system,Intestinal tract NOS,Intra-abdominal lymph nodes,Intrahepatic bile duct,Intrathoracic lymph nodes,Islets of Langerhans,Isthmus uteri,Jejunum,Kidney NOS,Labium majus,Labium minus,Lacrimal gland,Laryngeal cartilage,Larynx NOS,Lateral floor of mouth,Lateral wall of bladder,Lateral wall of nasopharynx,Lateral wall of oropharynx,Lesser curvature of stomach NOS,Lingual tonsil,Lip NOS,Liver,Long bones of lower limb and associated joints,Long bones of upper limb scapula and associated joints,Lower gum,Lower limb NOS,Lower lobe lung,Lower third of esophagus,Lower-inner quadrant of breast,Lower-outer quadrant of breast,Lung NOS,Lymph node NOS,Lymph nodes of axilla or arm,Lymph nodes of head face and neck,Lymph nodes of inguinal region or leg,Lymph nodes of multiple regions,Main bronchus,Major salivary gland NOS,Male genital organs NOS,Mandible,Maxillary sinus,Meckel diverticulum,Mediastinum NOS,Medulla of adrenal gland,Meninges NOS,Middle ear,Middle lobe lung,Middle third of esophagus,Mouth NOS,Mucosa of lip NOS,Mucosa of lower lip,Mucosa of upper lip,Myometrium,Nasal cavity,Nasopharynx NOS,Nervous system NOS,Nipple,Occipital lobe,Olfactory nerve,Optic nerve,Orbit NOS,Oropharynx NOS,Other ill-defined sites,Other specified parts of female genital organs,Other specified parts of male genital organs,Other specified parts of pancreas,Ovary,Overlapping lesion of accessory sinuses,Overlapping lesion of bladder,Overlapping lesion of bones joints and articular cartilage,Overlapping lesion of bones joints and articular cartilage of limbs,Overlapping lesion of brain,Overlapping lesion of brain and central nervous system,Overlapping lesion of breast,Overlapping lesion of cervix uteri,Overlapping lesion of colon,Overlapping lesion of connective subcutaneous and other soft tissues,Overlapping lesion of corpus uteri,Overlapping lesion of digestive system,Overlapping lesion of endocrine glands and related structures,Overlapping lesion of esophagus,Overlapping lesion of eye and adnexa,Overlapping lesion of female genital organs,Overlapping lesion of floor of mouth,Overlapping lesion of heart mediastinum and pleura,Overlapping lesion of hypopharynx,Overlapping lesion of ill-defined sites,Overlapping lesion of larynx,Overlapping lesion of lip,Overlapping lesion of lip oral cavity and pharynx,Overlapping lesion of lung,Overlapping lesion of major salivary glands,Overlapping lesion of male genital organs,Overlapping lesion of nasopharynx,Overlapping lesion of other and unspecified parts of mouth,Overlapping lesion of palate,Overlapping lesion of pancreas,Overlapping lesion of penis,Overlapping lesion of peripheral nerves and autonomic nervous system,Overlapping lesion of rectum anus and anal canal,Overlapping lesion of respiratory system and intrathoracic organs,Overlapping lesion of retroperitoneum and peritoneum,Overlapping lesion of skin,Overlapping lesion of small intestine,Overlapping lesion of stomach,Overlapping lesion of tongue,Overlapping lesion of tonsil,Overlapping lesion of urinary organs,Overlapping lesion of vulva,Overlapping lesions of oropharynx,Palate NOS,Pancreas NOS,Pancreatic duct,Parametrium,Paraspinal,Parathyroid gland,Paraurethral gland,Parietal lobe,Parotid gland,Pelvic bones sacrum coccyx and associated joints,Pelvic lymph nodes,Pelvis NOS,Penis NOS,Peripheral nerves and autonomic nervous system of abdomen,Peripheral nerves and autonomic nervous system of head face and neck,Peripheral nerves and autonomic nervous system of lower limb and hip,Peripheral nerves and autonomic nervous system of pelvis,Peripheral nerves and autonomic nervous system of thorax,Peripheral nerves and autonomic nervous system of trunk NOS,Peripheral nerves and autonomic nervous system of upper limb and shoulder,Peritoneum NOS,Pharynx NOS,Pineal gland,Pituitary gland,Placenta,Pleura NOS,Postcricoid region,Posterior mediastinum,Posterior wall of bladder,Posterior wall of hypopharynx,Posterior wall of nasopharynx,Posterior wall of oropharynx,Prepuce,Prostate gland,Pylorus,Pyriform sinus,Rectosigmoid junction,Rectum NOS,Renal pelvis,Reticuloendothelial system NOS,Retina,Retromolar area,Retroperitoneum,Rib sternum clavicle and associated joints,Round ligament,Scrotum NOS,Short bones of lower limb and associated joints,Short bones of upper limb and associated joints,Sigmoid colon,Skin of lip NOS,Skin of lower limb and hip,Skin of other and unspecified parts of face,Skin of scalp and neck,Skin of trunk,Skin of upper limb and shoulder,Skin NOS,Small intestine NOS,Soft palate NOS,Specified parts of peritoneum,Spermatic cord,Sphenoid sinus,Spinal cord,Spinal meninges,Spleen,Splenic flexure of colon,Stomach NOS,Subglottis,Sublingual gland,Submandibular gland,Superior wall of nasopharynx,Supraglottis,Tail of pancreas,Temporal lobe,Testis NOS,Thoracic esophagus,Thorax NOS,Thymus,Thyroid gland,Tongue NOS,Tonsil NOS,Tonsillar fossa,Tonsillar pillar,Trachea,Transverse colon,Trigone of bladder,Undescended testis,unknown primary site,Upper gum,Upper limb NOS,Upper lobe lung,Upper respiratory tract NOS,Upper third of esophagus,Upper-inner quadrant of breast,Upper-outer quadrant of breast,Urachus,Ureter,Ureteric orifice,Urethra,Urinary system NOS,Uterine adnexa,Uterus NOS,Uvula,Vagina NOS,Vallecula,Ventral surface of tongue NOS,Ventricle NOS,Vertebral column,Vestibule of mouth,Vulva NOS,Waldeyer ring,Biliary tract NOS,Cheek mucosa,Clitoris,Overlapping lesion of biliary tract,unknown,Not Reported","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161035&version=1.0,"" -Tumor Grade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.","G1, G2, G3, G4, GX, GB, High Grade, Low Grade, unknown, Not Reported, Not Applicable","","",TRUE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2785839&version=2.0,"" -AJCC Clinical M,"Extent of the distant metastasis for the cancer based on evidence obtained from clinical - assessment parameters determined prior to treatment.","M0, M1, M1a, M1b, M1c, MX, cM0 (i+), unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440331&version=1.0,"" -AJCC Clinical N,"Extent of the regional lymph node involvement for the cancer based on evidence obtained from - clinical assessment parameters determined prior to treatment.","N0, N0 (i+), N0 (i-), N0 (mol+), N0 (mol-), N1, N1a, N1b, N1bI, N1bII, N1bIII, N1bIV, N1c, N1mi, N2, N2a, N2b, N2c, N3, N3a, N3b, N3c, N4, NX, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440330&version=1.0,"" -AJCC Clinical Stage,"Stage group determined from clinical information on the tumor (T), regional node (N) and - metastases (M) and by grouping cases with similar prognosis for cancer.","Stage 0, Stage 0a, Stage 0is, Stage I, Stage IA, Stage IA1, Stage IA2, Stage IB, Stage IB1, Stage IB2, Stage IC, Stage II, Stage IIA, Stage IIA1, Stage IIA2, Stage IIB, Stage IIC, Stage IIC1, Stage III, Stage IIIA, Stage IIIB, Stage IIIC, Stage IIIC1, Stage IIIC2, Stage IS, Stage IV, Stage IVA, Stage IVB, Stage IVC, Stage Tis, Stage X, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440332&version=1.0,"" -AJCC Clinical T,"Extent of the primary cancer based on evidence obtained from clinical assessment parameters - determined prior to treatment.","T0, T1, T1a, T1a1, T1a2, T1b, T1b1, T1b2, T1c, T1mi, T2, T2a, T2a1, T2a2, T2b, T2c, T2d, T3, T3a, T3b, T3c, T3d, T4, T4a, T4b, T4c, T4d, T4e, TX, Ta, Tis, Tis (DCIS), Tis (LCIS), Tis (Paget's), unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3440328&version=1.0,"" -AJCC Pathologic M,"Code to represent the defined absence or presence of distant spread or metastases (M) to - locations via vascular channels or lymphatics beyond the regional lymph nodes, using - criteria established by the American Joint Committee on Cancer (AJCC).","M0, M1, M1a, M1b, M1c, MX, cM0 (i+), unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3045439&version=1.0,"" -AJCC Pathologic N,"The codes that represent the stage of cancer based on the nodes present (N stage) according - to criteria based on multiple editions of the AJCC's Cancer Staging Manual.","N0, N0 (i+), N0 (i-), N0 (mol+), N0 (mol-), N1, N1a, N1b, N1bI, N1bII, N1bIII, N1bIV, N1c, N1mi, N2, N2a, N2b, N2c, N3, N3a, N3b, N3c, N4, NX, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3203106&version=1.0,"" -AJCC Pathologic Stage,"The extent of a cancer, especially whether the disease has spread from the original site to - other parts of the body based on AJCC staging criteria.","Stage 0, Stage 0a, Stage 0is, Stage I, Stage IA, Stage IA1, Stage IA2, Stage IB, Stage IB1, Stage IB2, Stage IC, Stage II, Stage IIA, Stage IIA1, Stage IIA2, Stage IIB, Stage IIC, Stage IIC1, Stage III, Stage IIIA, Stage IIIB, Stage IIIC, Stage IIIC1, Stage IIIC2, Stage IS, Stage IV, Stage IVA, Stage IVB, Stage IVC, Stage Tis, Stage X, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3203222&version=1.0,"" -AJCC Pathologic T,"Code of pathological T (primary tumor) to define the size or contiguous extension of the - primary tumor (T), using staging criteria from the American Joint Committee on Cancer - (AJCC).","T0, T1, T1a, T1a1, T1a2, T1b, T1b1, T1b2, T1c, T1mi, T2, T2a, T2a1, T2a2, T2b, T2c, T2d, T3, T3a, T3b, T3c, T3d, T4, T4a, T4b, T4c, T4d, T4e, TX, Ta, Tis, Tis (DCIS), Tis (LCIS), Tis (Paget's), unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3045435&version=1.0,"" -AJCC Staging System Edition,"The text term used to describe the version or edition of the American Joint Committee on Cancer - Staging Handbooks, a publication by the group formed for the purpose of developing a system of - staging for cancer that is acceptable to the American medical profession and is compatible with - other accepted classifications.","1st, 2nd, 3rd, 4th, 5th, 6th, 7th, 8th, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2722309&version=1.0,"" -Anaplasia Present,"Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.","Yes - Anaplasia Present, No, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6059599&version=1.0,"" -Yes - Anaplasia Present,Indicates anaplasia is present,"",Anaplasia Present Type,"",FALSE,Diagnosis,"","","" -Anaplasia Present Type,"The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.","Absent, Diffuse, Equivocal, Focal, Present, Sclerosis, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4925534&version=1.0,"" -Best Overall Response,The best improvement achieved throughout the entire course of protocol treatment.,"AJ-Adjuvant Therapy, CPD-Clinical Progression, CR-Complete Response, CRU-Complete Response Unconfirmed, DU-Disease Unchanged, IMR-Immunoresponse, IPD-Immunoprogression, MR-Minimal/Marginal Response, MX-Mixed Response, Non-CR/Non-PD-Non-CR/Non-PD, NPB-No Palliative Benefit, NR-No Response, PA-Palliative Therapy, PB-Palliative Benefit, PD-Progressive Disease, PPD-Pseudoprogression, PR-Partial Response, PSR-Pseudoresponse, RD-Responsive Disease, RP-Response, RPD-Radiographic Progressive Disease, sCR-Stringent Complete Response, SD-Stable Disease, SPD-Surgical Progression, TE-Too Early, VGPR-Very Good Partial Response","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2003324&version=4.0,"" -Days to Diagnosis,Number of days between the date used for index and the date the patient was diagnosed with the malignant disease.,"","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6154733&version=1.0,"" -Pathology from Left Breast,"Pathology description for left breast.","","","",FALSE,Diagnosis,"",,"" -Pathology from Right Breast,"Pathology description for right breast.","","","",FALSE,Diagnosis,"",,"" -Laterality,"For paired organs, designates the side on which the cancer originates.","Bilateral, Left, Midline, Right, Unilateral, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=827&version=3.0,"" -Lymph Nodes Positive,The number of lymph nodes involved with disease as determined by pathologic examination.,"","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=89&version=3.0,"" -Lymph Nodes Tested,The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.,"","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3&version=3.0,"" -Lymphatic Invasion Present,"A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement","Yes, No, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64171&version=3.0,"" -Metastasis at Diagnosis,The text term used to describe the extent of metastatic disease present at diagnosis.,"Distant Metastasis, Metastasis NOS, No Metastasis, Regional Metastasis, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6133614&version=1.0,"" -Metastasis at Diagnosis Site,Text term to identify an anatomic site in which metastatic disease involvement is found.,"Abdomen, Adrenal Gland, Ascites, Bone, Bone Marrow, Brain, Cerebrospinal Fluid, Central Nervous System, Colon, Distant Nodes, Distant Organ, Groin, Kidney, Liver, Lung, Lymph Node, Axillary, Lymph Node, Inguinal, Lymph Node NOS, Mediastinum, Omentum, Ovary, Pelvis, Peritoneal Cavity, Peritoneum, Pleura, Scalp, Skin, Small Intestine, Soft Tissue, Spinal Cord, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3029815&version=1.0,"" -Method of Diagnosis,Text term used to describe the method used to confirm the patients malignant diagnosis.,"Autopsy,Biopsy,Blood Draw,Bone Marrow Aspirate,Core Biopsy,Cytology,Cystoscopy,Debulking,Diagnostic Imaging,Dilation and Curettage Procedure,Enucleation,Excisional Biopsy,Fine Needle Aspiration,Imaging,Incisional Biopsy,Laparoscopy,Laparotomy,Other,Pap Smear,Physical Exam,Pathologic Review,Surgical Resection,Thoracentesis,Ultrasound Guided Biopsy,unknown,Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161031&version=1.0,"" -Mitotic Count,"The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.","","","",FALSE,Diagnosis,"","","" -Percent Tumor Invasion,The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.,"","","",FALSE,Diagnosis,"","","" -Peritoneal Fluid Cytological Status,The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.,"Atypical, Malignant, Non-Malignant, Unsatisfactory, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6690681&version=1.0,"" -Perineural Invasion Present,A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.,"Yes, No, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64181&version=3.0,"" -Residual Disease,Text terms to describe the status of a tissue margin following surgical resection.,"R0, R1, R2, RX, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2608702&version=1.0,"" -Synchronous Malignancy,"A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.","Yes, No, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6142390&version=1.0,"" -Tumor Confined to Organ of Origin,The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.,"Yes, No, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=4925494&version=1.0,"" -Tumor Focality,The text term used to describe whether the patient's disease originated in a single location or multiple locations.,"Multifocal, Unifocal, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3174022&version=1.0,"" -Tumor Largest Dimension Diameter,"Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.","","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64215&version=3.0,"" -Vascular Invasion Present,The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.,"Yes - Vascular Invasion Present, No, unknown, Not Reported, Not Allowed To Collect","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=64358&version=3.0,"" -Yes - Vascular Invasion Present,Indicates venous invasion was detected by surgery or presence in a tumor specimen,"",Vascular Invasion Type,"",FALSE,Diagnosis,"","","" -Vascular Invasion Type,Text term that represents the type of vascular tumor invasion.,"Extramural, Intramural, Macro, Micro, No Vascular Invasion, unknown, Not Reported","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3168001&version=1.0,"" -Year of Diagnosis,Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.,"","","",FALSE,Diagnosis,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2896960&version=1.0,"" -Topography Code,"Topography Code, indicating site within the body, based on ICD-O-3.","","","",FALSE,Diagnosis,"","","" -Additional Topography,Topography not included in the ICD-O-3 Topography codes.,"Skin of scalp, Skin of eye lid, Skin of nose, Skin of lip, Skin of ear, Skin of neck, Skin of other parts of face, Skin of chest, Skin of back, Skin of abdomen, Skin of trunk, Skin of breast, Skin of upper limb and shoulder, Skin of palm, Skin of lower limb and hip, Skin of sole, Skin of penis, Skin of scrotum, Skin of vulva, Skin NOS, Hilar Airway, Peri-tumoral Airway, Not Reported","","",FALSE,Diagnosis,"","","" diff --git a/modules/Patient/Exposure.csv b/modules/Patient/Exposure.csv deleted file mode 100644 index bcb6828..0000000 --- a/modules/Patient/Exposure.csv +++ /dev/null @@ -1,19 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Smoking Exposure,Indicate if individual has smoking exposure,"Yes - Smoking Exposure, No - Smoking Exposure, Not Reported","","",TRUE,Exposure,"","","" -Yes - Smoking Exposure,Individual has been exposed to smoke; requires additional metadata,"","Years Smoked, Pack Years Smoked, Cigarettes per Day, Smoking Frequency, Type of Smoke Exposure, Time between Waking and First Smoke, Tobacco Smoking Onset Year, Tobacco Smoking Quit Year, Tobacco Smoking Status, Type of Tobacco Used, Secondhand Smoke as Child, Smoke Exposure Duration, Tobacco Use per Day, Smokeless Tobacco Quit Age","",FALSE,Exposure,"","","" -Pack Years Smoked,Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.,"","","",TRUE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2955385&version=1.0,"" -Years Smoked,Numeric value (or unknown) to represent the number of years a person has been smoking.,"","","",TRUE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3137957&version=1.0,"" -Smoking Frequency,The text term used to generally decribe how often the patient smokes.,"Every day, Some days, unknown","","",FALSE,Exposure,"","","" -Secondhand Smoke as Child,The text term used to indicate whether the patient was exposed to secondhand smoke as a child.,"Yes, No, unknown, Not Reported","","",FALSE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6841888&version=1.0,"" -Tobacco Use per Day,Numeric value that represents the number of times the patient uses tobacco each day.,"","","",FALSE,Exposure,"","","" -Tobacco Smoking Status,Category describing current smoking status and smoking history as self-reported by a patient,"Lifelong Non-Smoker, Current Smoker, Current Reformed Smoker for > 15 yrs, Current Reformed Smoker for < or = 15 yrs, Current Reformed Smoker, Duration Not Specified, Smoking history not documented, unknown, Not Reported","","",FALSE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2181650&version=1.0,"" -Alcohol Exposure,Indicate if individual has alcohol exposure,"Yes - Alcohol Exposure, No - Alcohol Exposure, Not Reported","","",TRUE,Exposure,"","","" -Yes - Alcohol Exposure,"","","Alcohol Days Per Week, Alcohol Drinks Per Day, Alcohol History, Alcohol Intensity, Alcohol Type","",FALSE,Exposure,"","","" -Alcohol Days Per Week,Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.,"","","",FALSE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3114013&version=1.0,"" -Alcohol Drinks Per Day,Numeric value used to describe the average number of alcoholic beverages a person consumes per day.,"","","",FALSE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3124961&version=1.0,"" -Alcohol History,A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.,"Yes, No, unknown, Not Reported","","",FALSE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2201918&version=1.0,"" -Alcohol Intensity,Category to describe the patient's current level of alcohol use as self-reported by the patient.,"Drinker, Heavy Drinker, Lifelong Non-Drinker, Non-Drinker, Occasional Drinker, unknown, Not Reported","","",FALSE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=3457767&version=1.0,"" -Alcohol Type,Type of alcohol use,"Beer, Liquor, Other, Wine, unknown, Not Reported","","",FALSE,Exposure,"","","" -Cigarettes per Day,The average number of cigarettes smoked per day.,"","","",FALSE,Exposure,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2001716&version=4.0,"" -Environmental Tobacco Smoke Exposure,"The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.","Yes, No, unknown","","",FALSE,Exposure,"","","" -Antibiotic Use,"Antibiotic use","No, Yes - within last monthh, Yes - within last 1-6 months, Yes - over 6 months ago,unknown","","",FALSE,Exposure,"","","" diff --git a/modules/Patient/Family_History.csv b/modules/Patient/Family_History.csv deleted file mode 100644 index 3f1d50e..0000000 --- a/modules/Patient/Family_History.csv +++ /dev/null @@ -1,16 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Relationship Gender,The text term used to describe the gender of the patient's relative with a history of cancer.,"Female, Male, unknown, unspecified, Not Reported","","",FALSE,Family History,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161021&version=1.0,"" -Relationship Age at Diagnosis,The age (in years) when the patient's relative was first diagnosed.,"","","",FALSE,Family History,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=5300571&version=1.0,"" -Relationship Primary Diagnosis,The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.,"Adrenal Gland Cancer, Basal Cell Cancer, Bile Duct Cancer, Bladder Cancer, Blood Cancer, Bone Cancer, Brain Cancer, Breast Cancer, Cancer, Cervical Cancer, Chondrosarcoma, CNS Cancer, Colorectal Cancer, Esophageal Cancer, Ewing Sarcoma, Gallbladder Cancer, Gastric Cancer, Glioblastoma, Gynecologic Cancer, Head and Neck Cancer, Hematologic Cancer, Kaposi Sarcoma, Kidney Cancer, Laryngeal Cancer, Leukemia, Liver Cancer, Lung Cancer, Lymph Node Cancer, Lymphoma, Melanoma, Mesothelioma, Multiple Myeloma, Neuroblastoma, Osteosarcoma, Ovarian Cancer, Pancreas Cancer, Prostate Cancer, Rectal Cancer, Rhabdomyosarcoma, Sarcoma, Skin Cancer, Spleen Cancer, Testicular Cancer, Throat Cancer, Thyroid Cancer, Tongue Cancer, Tonsillar Cancer, Uterine Cancer, Wilms Tumor, unknown, Not Reported","","",FALSE,Family History,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161022&version=1.0,"" -Relationship Type,The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.,"Adopted Daughter, Adopted Son, Adoptive Brother, Adoptive Father, Adoptive Mother, Adoptive Sister, Aunt, Brother, Brother-in-law, Child, Cousin, Daughter, Daughter-in-law, Domestic Partner, Father, Father-in-law, Female Cousin, First Cousin, First Cousin Once Removed, Foster Brother, Foster Daughter, Foster Father, Foster Mother, Foster Sister, Foster Son, Fraternal Twin Brother, Fraternal Twin Sibling, Fraternal Twin Sister, Full Brother, Full Sister, Grand Nephew, Grand Niece, Grandchild, Granddaughter, Grandfather, Grandmother, Grandparent, Grandson, Great Grandchild, Half Brother, Half Sibling, Half Sister, Husband, Identical Twin Brother, Identical Twin Sibling, Identical Twin Sister, Legal Guardian, Male Cousin, Maternal Aunt, Maternal First Cousin, Maternal First Cousin Once Removed, Maternal Grandfather, Maternal Grandmother, Maternal Grandparent, Maternal Great Aunt, Maternal Great Grandparent, Maternal Great Uncle, Maternal Half Brother, Maternal Half Sibling, Maternal Half Sister, Maternal Uncle, Mother, Mother-in-law, Natural Brother, Natural Child, Natural Daughter, Natural Father, Natural Grandchild, Natural Grandfather, Natural Grandmother, Natural Grandparent, Natural Mother, Natural Parent, Natural Sibling, Natural Sister, Natural Son, Nephew, Niece, Niece Second Degree Relative, Other, Parent, Paternal Aunt, Paternal First Cousin, Paternal First Cousin Once Removed, Paternal Grandfather, Paternal Grandmother, Paternal Grandparent, Paternal Great Aunt, Paternal Great Grandparent, Paternal Great Uncle, Paternal Half Brother, Paternal Half Sibling, Paternal Half Sister, Paternal Uncle, Refused, Sibling, Sister, Sister-in-law, Son, Son-in-law, Spouse, Step Child, Step Sibling, Stepbrother, Stepdaughter, Stepfather, Stepmother, Stepsister, Stepson, Twin Sibling, Uncle, Unrelated, Ward, Wife, unknown, Not Reported","","",FALSE,Family History,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=2690165&version=2.0,"" -Relative with Cancer History,The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.,"Yes - Cancer History Relative, None, unknown, Not Reported","","",FALSE,Family History,"",https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161023&version=1.0,"" -First or Second Degree Relatives with Breast Cancer History Count,The number of close relatives the patient has with a known history of breast cancer.,"","","",FALSE,Family History,"","","" -Third Degree Relatives with Breast Cancer History Count,The number of 3rd degree relatives the patient has with a known history of breast cancer.,"","","",FALSE,Family History,"","","" -First or Second Degree Relatives with Ovarian Cancer History Count,The number of close relatives the patient has with a known history of ovarian cancer.,"","","",FALSE,Family History,"","","" -Third Degree Relatives with Ovarian Cancer History Count,The number of 3rd degree relatives the patient has with a known history of ovarian cancer.,"","","",FALSE,Family History,"","","" -Relatives with Cancer History Count,The number of relatives the patient has with a known history of cancer.,"","","",FALSE,Family History,"","","" -Yes - Cancer History Relative,Individual has a relative with cancer history,"","Relatives with Cancer History Count, Relationship Type, Relationship Primary Diagnosis, Relationship Gender,Relationship Age at Diagnosis","",FALSE,Family History,"","","" -Family Member Vital Status Indicator,The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1),"Vital Status Alive, Vital Status Dead, unknown, Not Reported","","",FALSE,Family History,"","","" -Known Genetic Predisposition Mutation,A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.,"Yes, No, unknown","","",FALSE,Family History,"","","" -Hereditary Cancer Predisposition Syndrome,History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.,"Alpha-1 antitrypsin,Attenuated familial adenomatous polyposis,BAP1 mutant disease,Beckwith-Wiedemann,Biliary disorder,Birt-Hogg-Dube syndrome,Carney complex,Cirrhosis unknown etiology,Constitutional mismatch repair deficiency,Familial adenomatous polyposis,Familial gastrointestinal stromal tumor,Familial pancreatic cancer,Familial prostate cancer,Familial renal cancer,Fanconi anemia,Glycogen Storage Disease,Gorlin syndrome,Hereditary breast–ovarian cancer syndrome,Hereditary diffuse gastric cancer ,Hereditary leiomyoma-renal cell carcinoma,Hereditary melanoma,Hereditary mixed polyposis syndrome,Hereditary papillary RCC ,Hereditary papillary renal cell carcinoma,Hereditary paraganglioma–pheochromocytoma syndrome,Hereditary renal oncocytoma,Hereditary retinoblastoma ,Juvenile polyposis syndrome,Li-Fraumeni syndrome,Lynch syndrome,Melanoma–astrocytoma syndrome,Multiple endocrine neoplasia type I,Multiple endocrine neoplasia type II,MUTYH-associated polyposis,Nevoid basal cell carcinoma syndrome ,Not Applicable ,Not Reported,Peutz–Jeghers syndrome,Cowden syndrome,Rhabdoid tumor predisposition syndrome type I,Rhabdoid tumor predisposition syndrome type II,Rubinstein-Taybi syndrome,SDH associated renal cancer,Serrated polyposis syndrome,Tuberous sclerosis complex ,Turcot syndrome,Tyrosinemia,unknown,von Hippel-Lindau Syndrome","","",FALSE,Family History,"","","" -Cancer Associated Gene Mutations,Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history,"APC mutation,ALK mutation,ARF mutation,ATM mutation,ATRX mutation,ACVR1 mutation,BAP1 mutation,BMPR1A mutation,BLM mutation,BRCA1 mutation,BRCA1 and 2 mutation,BRCA2 mutation,BRAF mutation,CDH1 mutation,CDKN2A mutation,CDKN2A and p14ARF mutation,CHK mutation,ETV6 mutation, EGFR mutation, FH mutation,FLCN mutation,GREM1 mutation,HOXB13 mutation,H3K27M mutation,H3G34R/V mutation,IKZF1 mutation,KIT mutation, KRAS mutation, MAX mutation,MEN1 mutation,MET mutation,MLH1 mutation,MSH2 mutation,MSH6 mutation,MUTYH mutation,NF1 mutation,NF2 mutation,Not Applicable,Not Reported,p14ARF mutation,PALB2 mutation,PAX5 mutation,PDGFRA mutation,PHOX2B mutation,PMS2 mutation,PolD mutation,PolE mutation,POT1 mutation,PRKAR1A mutation,PTCH mutation,PTEN mutation,RAD51C mutation,ROS1 mutation,RB1 mutation,RET mutation,SDHAF2 mutation,SDHB mutation,SDHC mutation,SDHD mutation,SETD2 mutation,SMAD4 mutation,SMARCA4 mutation,SMARCB1 mutation,STK11 mutation,TMEM127 mutation,TP53 mutation,TSC1 mutation,TSC2 mutation,unknown,VHL mutation","","",FALSE,Family History,"","","" diff --git a/modules/Patient/Molecular_Test.csv b/modules/Patient/Molecular_Test.csv deleted file mode 100644 index 3d0fdcf..0000000 --- a/modules/Patient/Molecular_Test.csv +++ /dev/null @@ -1,39 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Mutational Signatures,"Mutational signatures identified in the patient, includes signatures linked to selected exogenous carcinogens, endogenous and enzymatic modification of DNA or defective DNA repair. Note: Include only outputs of tests that were completed clinically for the participant and only include data from a diagnostic array that was completed prior to research sequencing was done. ","UV light induced mutations,Alkylating Agents (Temozolomide) induced mutations,Tobacco use associated mutations,age of cancer diagnosis,transcriptional strand bias,microsatellite instability (additions and deletions),methylated CpG sequences mutagenesis(deamination of 5-methyl-cytosine) ,Activation Induced Deaminases (AID) associated mutations,APOBEC enzymes associated mutations,altered activity of the error-prone polymerase POLε (POLE) ,localized substitution hypermutation (kataegis),DNA MMR Deficiency,Ig gene hypermutation,Signature 1A,Signature 1B,Signature 2,Signature 3,Signature 4,Signature 5,Signature 6,Signature 7,Signature 8,Signature 9,Signature 10,Signature 11,Signature 12,Signature 13,Signature 14,Signature 15,Signature 16,Signature 17,Signature 18,Signature 19,Signature 20,Signature 21,Other,Data not available,Not Applicable,Not Reported,unknown","","",FALSE,Molecular Test,"","","" -Mismatch Repair System Status,The text that best describes the condition or state of MMR (mismatch repair system) in the patient,"Mismatch repair deficiency MMRD, Mismatch repair proficiency MMPP, Microsatellite instability high MSIH, Microsatellite stable MSS, unknown or other","","",FALSE,Molecular Test,"","","" -Lab Tests for MMR Status,Laboratory tests used to evaluate the status of mismatch repair pathways,"IHC staining for mismatch repair proteins, PCR to evaluate microsatellite instability, MLH1 promoter methylation analysis, BRAF sequencing, Other, Not Applicable, unknown","","",FALSE,Molecular Test,"","","" -Gene Symbol,"The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","","","",TRUE,Molecular Test,"","","" -Molecular Analysis Method,The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"Comparative Genomic Hybridization,Cytogenetics NOS,FISH,Flow Cytometry,IHC,ISH,Karyotype,Microarray,Microsatellite Analysis,Nuclear Staining,Other,RNA Sequencing,RT-PCR,Sequencing NOS,Southern Blotting,Targeted Sequencing,WGS,WXS,unknown,Not Reported,Not Applicable","","",TRUE,Molecular Test,"","","" -Test Result,The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"Abnormal NOS,Copy Number Reported,Equivocal,High,Intermediate,Loss of Expression,Low,Negative,Normal,Overexpressed,Positive,Test Value Reported,unknown,Not Reported,Not Applicable","","",TRUE,Molecular Test,"","","" -AA Change,Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"","","",FALSE,Molecular Test,"","","" -Antigen,The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"BCL6, CA-125, CA19-9, CCND1, CD10, CD117, CD138, CD14, CD15, CD19, CD20, CD22, CD23, CD25, CD3, CD30, CD33, CD34, CD45, CD5, CD56, CD7, CD79A, CEA, HLA-DR, Mesothelin, NSE, Squamous Cell Carcinoma Antigen, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Clinical Biospecimen Type,"The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","Blood, Bone Marrow, Buccal Mucosa, Buffy Coat, Cerebrospinal Fluid, Connective Tissue, Embryonic Fluid, Embryonic Tissue, Feces, Granulocyte, Muscle Tissue, Nerve Tissue, Peritoneal Fluid, Plasma, Pleural Fluid, Saliva, Serum, Skin, Soft Tissue, Tissue NOS, Uninvolved Tissue NOS, Urine, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Blood Test Normal Range Upper,Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.,"","","",FALSE,Molecular Test,"","","" -Blood Test Normal Range Lower,Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.,"","","",FALSE,Molecular Test,"","","" -Cell Count,Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"","","",FALSE,Molecular Test,"","","" -Chromosome,"The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr23,chrM,chrX,chrY,unknown,Not Reported","","",FALSE,Molecular Test,"","","" -Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"Clonal, Non-clonal","","",FALSE,Molecular Test,"","","" -Copy Number,"Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","","","",FALSE,Molecular Test,"","","" -Cytoband,"Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","","","",FALSE,Molecular Test,"","","" -Exon,"Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","","","",FALSE,Molecular Test,"","","" -Histone Family,"The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.","H1, H2A, H2B, H3, H4, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Histone Variant,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.","CENP-A, H2A-Bbd, H2A.X, H2A.Z,H2A.Z.1, H2A.Z.2, H2A.Z.2.2, H3.1, H3.2, H3.3, H3.5, H3.X, H3.Y, H3t (H3.4), mH2A, mH2A.1, mH2A.2, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Intron,"Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.","","","",FALSE,Molecular Test,"","","" -Laboratory Test,"The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.","Absolute Neutrophil,Albumin,Alpha Fetoprotein,B-cell genotyping,Basophil,Beta 2 Microglobulin,Blood Urea Nitrogen,C-Reactive Protein,Calcium,Cellularity,Circulating Tumor Cells,Creatinine,Eosinophil,Epstein-Barr Virus,Glucose,Hematocrit,Hemoglobin,HPV-E6/E7,Human Chorionic Gonadotropin,Human Papillomavirus,Immunoglobulin A,Immunoglobulin G,Immunoglobulin M,Lactate Dehydrogenase,Leukocytes,Luteinizing Hormone,Lymphoblasts,Lymphocytes,M Protein,Metamyelocytes,Myeloblasts,Myelocytes,Neutrophil Bands,Platelets,Prolymphocytes,Promonocytes,Promyelocytes,Segmented Neutrophil,Serum Free Immunoglobulin Light Chain, Kappa,Serum Free Immunoglobulin Light Chain, Lambda,Serum Free Immunoglobulin Light Chain, NOS,Testosterone,Total Bilirubin,Total Protein,unknown,Not Reported","","",FALSE,Molecular Test,"","","" -Loci Abnormal Count,Numeric value used to describe the number of loci determined to be abnormal.,"","","",FALSE,Molecular Test,"","","" -Loci Count,Numeric value used to describe the number of loci tested.,"","","",FALSE,Molecular Test,"","","" -Locus,Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.,"","","",FALSE,Molecular Test,"","","" -Mismatch Repair Mutation,The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"Yes, No, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Molecular Consequence,The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"3 Prime UTR Variant, 5 Prime UTR Variant, Coding Sequence Variant, Downstream Gene Variant, Feature Elongation, Feature Truncation, Frameshift Variant, Incomplete Terminal Codon Variant, Inframe Deletion, Inframe Insertion, Intergenic Variant, Intron Variant, Mature miRNA Variant, Missense Variant, NMD Transcript Variant, Non-coding Transcript Exon Variant, Non-coding Transcript Variant, Protein Altering Variant, Regulatory Region Ablation, Regulatory Region Amplification, Regulatory Region Variant, Splice Acceptor Variant, Splice Donor Variant, Splice Region Variant, Start Lost, Stop Gain, Stop Lost, Stop Retained Variant, Synonymous Variant, TF Binding Site Variant, TFBS Ablation, TFBS Amplification, Transcript Ablation, Transcript Amplification, Upstream Gene Variant","","",FALSE,Molecular Test,"","","" -Pathogenicity,The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).,"Benign, Likely Benign, Likely Pathogenic, Pathogenic, Uncertain Significance","","",FALSE,Molecular Test,"","","" -Ploidy,Text term used to describe the number of sets of homologous chromosomes.,"Aneuploid, Diploid, Hyperdiploid, Hypodiploid, Near Diploid, Tetraploid, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Second Exon,"The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.","","","",FALSE,Molecular Test,"","","" -Second Gene Symbol,"The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.","","","",FALSE,Molecular Test,"","","" -Specialized Molecular Test,Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"","","",FALSE,Molecular Test,"","","" -Test Analyte Type,The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"DNA, mRNA, miRNA, Protein Analyte, Total RNA, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Test Units,The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"","","",FALSE,Molecular Test,"","","" -Test Value,The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here,"","","",FALSE,Molecular Test,"","","" -Transcript,Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"","","",FALSE,Molecular Test,"","","" -Variant Origin,The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,"Germline, Somatic, unknown","","",FALSE,Molecular Test,"","","" -Variant Type,The text term used to describe the type of genetic variation.,"Alleles, Amplification, Chrimerism, Conversion, Deletion, Deletion-Insertion, Duplication, Extension, Gain, Hypermethylation, Insertion, Inversion, Loss, Methylation, Mosaicism, Other, Partial Methylation, Rearrangement, Repeated Sequences, Splice, Substitution, Translocation, unknown, Not Reported","","",FALSE,Molecular Test,"","","" -Zygosity,The text term used to describe the zygosity of a specific genetic variant.,"Heterozygous, Hemizygous, Homozygous, Nullizygous, unknown, Not Reported","","",FALSE,Molecular Test,"","","" diff --git a/modules/Patient/Ovarian_Cancer_Tier_3.csv b/modules/Patient/Ovarian_Cancer_Tier_3.csv deleted file mode 100644 index 1e427b7..0000000 --- a/modules/Patient/Ovarian_Cancer_Tier_3.csv +++ /dev/null @@ -1,4 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Ovarian Cancer Histologic Subtype,Text term to describe the histological subtype of ovarian cancer in the participant,"High-grade serous, Low-grade serous, High-grade endometrioid, Low-grade endometrioid, Clear cell, Mucinous, Sex-cord stromal, Germ cell, Other, unknown, Data not available","","",FALSE,Ovarian Cancer Tier 3,"","","" -Ovarian Cancer Surgical Outcome,Text term that describes the kind of surgical treatment administered.,"R0 resection,Optimal cytoreduction, Sub-optimal cytoreduction, Other, unknown, Data not available","","",FALSE,Ovarian Cancer Tier 3,"","","" -Ovarian Cancer Platinum Status,Text term to indicate the status of treatment with platinum in participant with ovarian cancer,"Platinum-refractory, Platinum-sensitive, Platinum-resistant, Data not available, unknown","","",FALSE,Ovarian Cancer Tier 3,"","","" diff --git a/modules/Patient/Patient.csv b/modules/Patient/Patient.csv deleted file mode 100644 index 642cf0e..0000000 --- a/modules/Patient/Patient.csv +++ /dev/null @@ -1,11 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules -Participant ID, ID associated with a patient,"","","",TRUE,Patient,"",,"" -Clinical Data Tier 2,Cancer related clinical data,"","Component, Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Sentinel Lymph Node Count, Sentinel Node Positive Assessment Count, Tumor Extranodal Extension Indicator, Satellite Metastasis Present Indicator, Other Biopsy Resection Site, Extent of Tumor Resection, Precancerous Condition Type, Prior Sites of Radiation, Immunosuppression, Concomitant Medication Received Type, Family Member Vital Status Indicator, COVID19 Occurrence Indicator, COVID19 Current Status, COVID19 Positive Lab Test Indicator, COVID19 Antibody Testing, COVID19 Complications Severity, COVID19 Cancer Treatment Followup, Ecig vape use, Ecig vape 30 day use num, Ecig vape times per day, Type of smoke exposure cumulative years, Chewing tobacco daily use count, Second hand smoke exposure years, Known Genetic Predisposition Mutation, Hereditary Cancer Predisposition Syndrome, Cancer Associated Gene Mutations, Mutational Signatures, Mismatch Repair System Status, Lab Tests for MMR Status, Mode of Cancer Detection, Education Level, Country of Birth, Medically Underserved Area, Rural vs Urban, Cancer Incidence, Cancer Incidence Location","",FALSE,Patient,Patient,"","" -Breast Cancer Tier 3,Breast cancer specific attributes in Clinical Data Tier 3,"","Component, Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Breast Carcinoma Detection Method Type, Breast Carcinoma Histology Category, Invasive Lobular Breast Carcinoma Histologic Category, Invasive Ductal Breast Carcinoma Histologic Category, Breast Biopsy Procedure Finding Type, Breast Quadrant Site, Breast Cancer Assessment Tests, Breast Cancer Genomic Test Performed, Mammaprint Risk Group, Oncotype Risk Group, Breast Carcinoma Estrogen Receptor Status, Breast Carcinoma Progesteroner Receptor Status, Breast Cancer Allred Estrogen Receptor Score, Prior Invasive Breast Disease, Breast Carcinoma ER Status Percentage Value, Breast Carcinoma PR Status Percentage Value, HER2 Breast Carcinoma Copy Number Total, Breast Carcinoma Centromere 17 Copy Number, Breast Carcinoma HER2 Centromere17 Copynumber Total, Breast Carcinoma HER2 Chromosome17 Ratio, Breast Carcinoma Surgical Procedure Name, Breast Carcinoma HER2 Ratio Diagnosis, Breast Carcinoma HER2 Status, Hormone Therapy Breast Cancer Prevention Indicator, Breast Carcinoma ER Staining Intensity, Breast Carcinoma PR Staining Intensity, Oncotype Score, Breast Imaging Performed Type, Multifocal Breast Carcinoma Present Indicator, Multicentric Breast Carcinoma Present Indicator, BIRADS Mammography Breast Density Category","",FALSE,Patient,Patient,"","" -Ovarian Cancer Tier 3,Ovarian cancer specific attributes in Clinical Data Tier 3,"","Component, Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Ovarian Cancer Histologic Subtype, Ovarian Cancer Surgical Outcome, Ovarian Cancer Platinum Status","",FALSE,Patient,Patient,"","" -Demographics,Individual biomedical demographics attributes,"","Component, Participant ID, Ethnicity, Gender, Race, Vital Status, Days to Birth, Country of Residence, Age Is Obfuscated, Year Of Birth","",FALSE,Patient,"","","" -Family History,Individual's family cancer history,"","Component, Participant ID, Relative with Cancer History","",FALSE,Patient,"","","" -Exposure,Individual's exposure to carcenogens,"","Component, Participant ID, Start Days from Index, Smoking Exposure, Alcohol Exposure, Environmental Tobacco Smoke Exposure","",FALSE,Patient,"","","" -Molecular Test,Individual's clinical molecular test data,"","Component, Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Gene Symbol, Molecular Analysis Method, Test Result, AA Change, Antigen, Clinical Biospecimen Type, Blood Test Normal Range Upper, Blood Test Normal Range Lower, Cell Count, Chromosome, Clonality, Copy Number, Cytoband, Exon, Histone Family, Histone Variant, Intron, Laboratory Test, Loci Abnormal Count, Loci Count, Locus, Mismatch Repair Mutation, Molecular Consequence, Pathogenicity, Ploidy, Second Exon, Second Gene Symbol, Specialized Molecular Test, Test Analyte Type, Test Units, Test Value, Transcript, Variant Origin, Variant Type, Zygosity","",FALSE,Patient,"","","" -Start Days from Index,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'","","","",TRUE,Patient,"","","" -Stop Days from Index,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'","","","",FALSE,Patient,"","","" diff --git a/modules/classes/imaging.yaml b/modules/classes/imaging.yaml new file mode 100644 index 0000000..bd5d7bf --- /dev/null +++ b/modules/classes/imaging.yaml @@ -0,0 +1,82 @@ +classes: + + ImagingLevel2: + is_a: Assay + annotations: + requiresComponent: '' + required: false + slots: + - Component + - Filename + - FileFormat + - LabID + - ChannelMetadataFilename + - ImagingAssayType + - ProtocolLink + - SoftwareandVersion + - Microscope + - Objective + - NominalMagnification + - LensNA + - WorkingDistance + - WorkingDistanceUnit + - Immersion + - Pyramid + - Zstack + - Tseries + - PassedQC + - Comment + - FOVnumber + - FOVX + - FOVXUnit + - FOVY + - FOVYUnit + - FrameAveraging + - ImageID + - DimensionOrder + - PhysicalSizeX + - PhysicalSizeXUnit + - PhysicalSizeY + - PhysicalSizeYUnit + - PhysicalSizeZ + - PhysicalSizeZUnit + - PixelsBigEndian + - PlaneCount + - SizeC + - SizeT + - SizeX + - SizeY + - SizeZ + - PixelType + + ImagingLevel2Channels: + is_a: ImagingLevel2 + annotations: + requiresComponent: '' + required: false + slots: + - ChannelID + - ChannelName + - ChannelPassedQC + - CycleNumber + - SubCycleNumber + - TargetName + - AntibodyName + - RRIDidentifier + - Fluorophore + - Clone + - Lot + - Vendor + - CatalogNumber + - ExcitationWavelength + - EmissionWavelength + - ExcitationBandwidth + - EmissionBandwidth + - MetalIsotopeElement + - MetalIsotopeMass + - OligoBarcodeUpperStrand + - OligoBarcodeLowerStrand + - Dilution + - Concentration + + \ No newline at end of file diff --git a/modules/classes/other_assets.yaml b/modules/classes/other_assets.yaml new file mode 100644 index 0000000..265ebf7 --- /dev/null +++ b/modules/classes/other_assets.yaml @@ -0,0 +1,13 @@ +classes: + + PublicationTemplate: + is_a: Publication + annotations: + requiresComponent: '' + required: false + slots: + - PublicationDOI + - Title + - Authors + - LinkedProject + - LinkedDatasets diff --git a/modules/classes/patient_and_specimen.yaml b/modules/classes/patient_and_specimen.yaml new file mode 100644 index 0000000..3d7ff49 --- /dev/null +++ b/modules/classes/patient_and_specimen.yaml @@ -0,0 +1,424 @@ +classes: + + CohortCoreTemplate: + is_a: Patient + annotations: + requiresComponent: '' + required: false + slots: + - ParticipantID + - Age + - Sex + - BMI + - Race + - Ethnicity + - VitalStatus + - Height + - Weight + - Gravidity + - Parity + - AgeAtMenarche + - MenstrualCyclePhase + - MenopauseStatus + - PrimaryDiagnosis + - AgeatDiagnosis + - DiagnosisStatusType + - ClassBRCA1 + - ClassBRCA2 + - TobaccoUse + - PackYearsSmoked + - AlcoholUse + - NumberofDrinksPerWeek + - AntibioticUse + - SampleCollectionCenter + - SampleCollectionYear + - ERStatus + - PRStatus + - HER2Status + + Patient: + annotations: + requiresComponent: '' + required: false + slots: + - Component + - ParticipantID + - TimepointLabel + + PatientExtended: + is_a: Patient + annotations: + requiresComponent: '' + required: false + slots: + - StartDaysfromIndex + - StopDaysfromIndex + - SentinelLymphNodeCount + - SentinelNodePositiveAssessmentCount + - TumorExtranodalExtensionIndicator + - SatelliteMetastasisPresentIndicator + - OtherBiopsyResectionSite + - ExtentofTumorResection + - PrecancerousConditionType + - PriorSitesofRadiation + - Immunosuppression + - ConcomitantMedicationReceivedType + - FamilyMemberVitalStatusIndicator + - COVID19OccurrenceIndicator + - COVID19CurrentStatus + - COVID19PositiveLabTestIndicator + - COVID19AntibodyTesting + - COVID19ComplicationsSeverity + - COVID19CancerTreatmentFollowup + - Ecigvapeuse + - Ecigvape30dayusenum + - Ecigvapetimesperday + - Typeofsmokeexposurecumulativeyears + - Chewingtobaccodailyusecount + - Secondhandsmokeexposureyears + - KnownGeneticPredispositionMutation + - HereditaryCancerPredispositionSyndrome + - CancerAssociatedGeneMutations + - MutationalSignatures + - MismatchRepairSystemStatus + - LabTestsforMMRStatus + - ModeofCancerDetection + - EducationLevel + - CountryofBirth + - MedicallyUnderservedArea + - RuralvsUrban + - CancerIncidence + - CancerIncidenceLocation + + BreastCancerPatient: + is_a: Patient + annotations: + requiresComponent: '' + required: false + slots: + - BreastCarcinomaDetectionMethodType + - BreastCarcinomaHistologyCategory + - InvasiveLobularBreastCarcinomaHistologicCategory + - InvasiveDuctalBreastCarcinomaHistologicCategory + - BreastBiopsyProcedureFindingType + - BreastQuadrantSite + - BreastCancerAssessmentTests + - BreastCancerGenomicTestPerformed + - MammaprintRiskGroup + - OncotypeRiskGroup + - ERReceptorStatus + - PRReceptorStatus + - BreastCancerAllredEstrogenReceptorScore + - PriorInvasiveBreastDisease + - BreastCarcinomaERStatusPercentageValue + - BreastCarcinomaPRStatusPercentageValue + - HER2BreastCarcinomaCopyNumberTotal + - BreastCarcinomaCentromere17CopyNumber + - BreastCarcinomaHER2Centromere17CopynumberTotal + - BreastCarcinomaHER2Chromosome17Ratio + - BreastCarcinomaSurgicalProcedureName + - BreastCarcinomaHER2RatioDiagnosis + - BreastCarcinomaHER2Status + - HormoneTherapyBreastCancerPreventionIndicator + - ERStainingIntensity + - PRStainingIntensity + - OncotypeScore + - BreastImagingPerformedType + - MultifocalBreastCarcinomaPresentIndicator + - MulticentricBreastCarcinomaPresentIndicator + - BIRADSMammographyBreastDensityCategory + + OvarianCancerPatient: + is_a: Patient + annotations: + requiresComponent: '' + required: false + slots: + - OvarianCancerHistologicSubtype + - OvarianCancerSurgicalOutcome + - OvarianCancerPlatinumStatus + + Exposure: + is_a: Patient + annotations: + requiresComponent: '' + required: false + slots: + - Component + - ParticipantID + - StartDaysfromIndex + - SmokingExposure + - AlcoholExposure + - EnvironmentalTobaccoSmokeExposure + + Yes-SmokingExposure: + is_a: Exposure + annotations: + requiresComponent: '' + required: false + slots: + - YearsSmoked + - PackYearsSmoked + - CigarettesperDay + - SmokingFrequency + - TypeofSmokeExposure + - TimebetweenWakingandFirstSmoke + - TobaccoSmokingOnsetYear + - TobaccoSmokingQuitYear + - TobaccoSmokingStatus + - TypeofTobaccoUsed + - SecondhandSmokeasChild + - SmokeExposureDuration + - TobaccoUseperDay + - SmokelessTobaccoQuitAge + + MolecularTest: + annotations: + requiresComponent: '' + required: false + slots: + - Component + - ParticipantID + - TimepointLabel + - StartDaysfromIndex + - StopDaysfromIndex + - GeneSymbol + - MolecularAnalysisMethod + - TestResult + - AAChange + - Antigen + - ClinicalBiospecimenType + - BloodTestNormalRangeUpper + - BloodTestNormalRangeLower + - CellCount + - Chromosome + - Clonality + - CopyNumber + - Cytoband + - Exon + - HistoneFamily + - HistoneVariant + - Intron + - LaboratoryTest + - LociAbnormalCount + - LociCount + - Locus + - MismatchRepairMutation + - MolecularConsequence + - Pathogenicity + - Ploidy + - SecondExon + - SecondGeneSymbol + - SpecializedMolecularTest + - TestAnalyteType + - TestUnits + - TestValue + - Transcript + - VariantOrigin + - VariantType + - Zygosity + + Yes-CancerHistoryRelative: + is_a: FamilyHistory + annotations: + requiresComponent: '' + required: false + slots: + - RelativeswithCancerHistoryCount + - RelationshipType + - RelationshipPrimaryDiagnosis + - RelationshipGender + - RelationshipAgeatDiagnosis + + Yes-AlcoholExposure: + is_a: Exposure + annotations: + requiresComponent: '' + required: false + slots: + - AlcoholDaysPerWeek + - AlcoholDrinksPerDay + - AlcoholHistory + - AlcoholIntensity + - AlcoholType + + Yes-VascularInvasionPresent: + is_a: Diagnosis + annotations: + requiresComponent: '' + required: false + slots: + - VascularInvasionType + + TotalVolume: + is_a: Biospecimen + annotations: + requiresComponent: '' + required: false + slots: + - TotalVolumeUnit + + Yes-ProgressionorRecurrence: + is_a: Diagnosis + annotations: + requiresComponent: '' + required: false + slots: + - ProgressionorRecurrenceType + - DaystoProgression + - DaystoProgressionFree + - DaystoRecurrence + - DaystoRecurrence + - ProgressionorRecurrenceAnatomicSite + + Dead: + is_a: Demographics + annotations: + requiresComponent: '' + required: false + slots: + - YearofDeath + - CauseofDeath + - CauseofDeathSource + - DaystoDeath + +################## +# Biospecimen +################# + + SampleCoreTemplate: + annotations: + requiresComponent: '' + required: false + slots: + - ParticipantID + - SampleID + - DetailedSampleID + - AdjacentSampleIDs + - SampleSite + - ERStatus + - PRStatus + - HER2Status + - Laterality + + Biospecimen: + annotations: + requiresComponent: '' + required: false + slots: + - BiospecimenID + - ParentID + - ParentBiospecimenID + - AdjacentBiospecimenIDs + - BiospecimenType + - TimepointLabel + - SpecimenLaterality + + TissueBiospecimenType: + annotations: + requiresComponent: '' + required: false + is_a: Biospecimen + slots: + - IschemicTime + - IschemicTemperature + - SiteofResectionorBiopsy + - PortionWeight + - TotalVolume + - TumorTissueType + - HistologicMorphologyCode + - PreservationMethod + - BiospecimenDimension1 + - BiospecimenDimension2 + - BiospecimenDimension3 + - SectionNumberinSequence + + FamilyHistory: + is_a: Patient + annotations: + requiresComponent: '' + required: false + slots: + - RelativewithCancerHistory + + Demographics: + is_a: Patient + annotations: + requiresComponent: '' + required: false + slots: + - Ethnicity + - Gender + - Race + - VitalStatus + - DaystoBirth + - CountryofResidence + - AgeIsObfuscated + - YearOfBirth + + BiospecimenDimension1: + is_a: Biospecimen + annotations: + requiresComponent: '' + required: false + slots: + - DimensionsUnit + + BloodBiospecimenType: + is_a: Biospecimen + annotations: + requiresComponent: '' + required: false + slots: + - ShippingConditionType + + UrineBiospecimenType: + is_a: Biospecimen + annotations: + requiresComponent: '' + required: false + slots: + - IschemicTime + - IschemicTemperature + - SiteofResectionorBiopsy + - SpecimenLaterality + - PortionWeight + - TotalVolume + - TumorTissueType + - HistologicMorphologyCode + - PreservationMethod + + BoneMarrowBiospecimenType: + is_a: Biospecimen + annotations: + requiresComponent: '' + required: false + slots: + - IschemicTime + - IschemicTemperature + - SiteofResectionorBiopsy + - SpecimenLaterality + - PortionWeight + - TotalVolume + - TumorTissueType + - HistologicMorphologyCode + - PreservationMethod + - BiospecimenDimension1 + - BiospecimenDimension2 + - BiospecimenDimension3 + - SectionNumberinSequence + + AnalyteBiospecimenType: + is_a: Biospecimen + annotations: + requiresComponent: '' + required: false + slots: + - AnalyteType + - FixationDuration + - SlideChargeType + - SectionThicknessValue + - SectioningDaysfromIndex + - ShippingConditionType + - IschemicTime + - IschemicTemperature diff --git a/modules/classes/sequencing.yaml b/modules/classes/sequencing.yaml new file mode 100644 index 0000000..24a28c6 --- /dev/null +++ b/modules/classes/sequencing.yaml @@ -0,0 +1,156 @@ +classes: + + Sequencing: + annotations: + requiresComponent: '' + required: false + slots: + - Component + - Filename + - FileFormat + - ParticipantID + - SampleID + - DetailedSampleID + - SequencingPlatform + - NucleicAcidSource + - LibraryConstructionMethod + - ReadIndicator + - Read1 + - Read2 + - TechnicalReplicateGroup + + SingleCellSequencing: + is_a: Sequencing + annotations: + requiresComponent: '' + required: false + slots: + - DissociationMethod + - CryopreservedCellsinSample + - SingleCellIsolationMethod + - TotalNumberofInputCells + - InputCellsandNuclei + - ReverseTranscriptionPrimer + - SpikeIn + - EndBias + + ScRNA-seqLevel1: + is_a: SingleCellSequencing + annotations: + requiresComponent: '' + required: false + slots: + - UMIBarcodeOffset + - UMIBarcodeLength + - MedianUMIsperCellNumber + - CellBarcodeOffset + - CellBarcodeLength + - ValidBarcodesCellNumber + + ScRNA-seqLevel2: + is_a: SingleCellSequencing + annotations: + requiresComponent: '' + required: false + slots: + - ScRNAseqWorkflowType + - WorkflowVersion + - ScRNAseqWorkflowParametersDescription + - WorkflowLink + - GenomicReference + - GenomicReferenceURL + - GenomeAnnotationURL + - WhitelistCellBarcodeFileLink + - CellBarcodeTag + - UMITag + - AppliedHardTrimming + + ScRNA-seqLevel3: + is_a: SingleCellSequencing + annotations: + requiresComponent: '' + required: false + slots: + - DataCategory + - MatrixType + - LinkedMatrices + - CellMedianNumberReads + - CellMedianNumberGenes + - CellTotal + - ScRNAseqWorkflowType + - ScRNAseqWorkflowParametersDescription + - WorkflowLink + - WorkflowVersion + + ScRNA-seqLevel4: + is_a: SingleCellSequencing + annotations: + requiresComponent: '' + required: false + slots: + - DataCategory + - MatrixType + - LinkedMatrices + - CellMedianNumberReads + - CellMedianNumberGenes + - CellTotal + - ScRNAseqWorkflowType + - ScRNAseqWorkflowParametersDescription + - WorkflowLink + - WorkflowVersion + + ScATAC-seqLevel1: + is_a: SingleCellSequencing + annotations: + requiresComponent: '' + required: false + slots: + - SingleNucleusBuffer + - TranspositionReaction + - ScATACseqLibraryLayout + - NucleusIdentifier + - NucleiBarcodeLength + - NucleiBarcodeRead + - Read3 + - ThresholdforMinimumPassingReads + - TotalNumberofPassingNuclei + - MedianFractionofReadsinPeaks + - MedianFractionofReadsinAnnotatedcisDNAElements + - MedianPassingReadPercentage + - MedianPercentageofMitochondrialReadsperNucleus + - TotalReads + + BulkMethylation-seqLevel1: + is_a: Sequencing + annotations: + requiresComponent: '' + required: false + slots: + - GenomicCoverageType + + + CEL-seq2: + is_a: ScRNA-seqLevel1 + annotations: + requiresComponent: '' + required: false + slots: + - EmptyWellBarcode + - WellIndex + + MedianFractionofReadsinPeaks: + is_a: ScATAC-seqLevel1 + annotations: + requiresComponent: '' + required: false + slots: + - PeaksCallingSoftware + + MedianFractionofReadsinAnnotatedcisDNAElements: + is_a: ScATAC-seqLevel1 + annotations: + requiresComponent: '' + required: false + slots: + - PeaksCallingSoftware + \ No newline at end of file diff --git a/modules/enums/Biospecimen.yaml b/modules/enums/Biospecimen.yaml new file mode 100644 index 0000000..a3182c6 --- /dev/null +++ b/modules/enums/Biospecimen.yaml @@ -0,0 +1,111 @@ +enums: + TotalVolumeUnitEnum: + permissible_values: + mL: null + mm^3: null + cm^2: null + IschemicTemperatureEnum: + permissible_values: + unknown: null + Liquid Nitrogen: null + Warm Ischemia: null + Cold Ischemia: null + Ambient air: null + 4C wet ice: null + Negative -20C: null + Dry Ice: null + AnalyteTypeEnum: + permissible_values: + Tissue Section Analyte: null + Serum Analyte: null + PBMCs or Plasma or Serum Analyte: null + Plasma: null + Tissue Block Analyte: null + cfDNA Analyte: null + DNA Analyte: null + RNA Analyte: null + cDNA Libraries Analyte: null + PBMCs: null + Total RNA Analyte: null + DimensionsUnitEnum: + permissible_values: + cm: null + mm: null + BiospecimenTypeEnum: + permissible_values: + Fluids Biospecimen Type: null + Sputum Biospecimen Type: null + Tissue Biospecimen Type: null + Mouth Rinse Biospecimen Type: null + Ascites Biospecimen Type: null + Cells Biospecimen Type: null + Blood Biospecimen Type: null + Analyte Biospecimen Type: null + Bone Marrow Biospecimen Type: null + Urine Biospecimen Type: null + Stool Biospecimen Type: null + PreservationMethodEnum: + permissible_values: + Negative 80 Deg C: null + Not Reported: null + Cryopreservation in dry ice - dead tissue: null + unknown: null + Fresh: null + Cryopreservation in liquid nitrogen - dead tissue: null + Formalin fixed paraffin embedded - FFPE: null + Archival: null + Formalin fixed-buffered: null + Formalin fixed-unbuffered: null + Cryopreserved: null + Frozen: null + Fresh dissociated and single cell sorted: null + Fresh dissociated and single cell sorted into plates in NP40 buffer: null + Methacarn fixed paraffin embedded - MFPE: null + Fresh dissociated: null + Fresh dissociated and single cell sorted into plates: null + Cryopreservation in liquid nitrogen - live cells: null + OCT: null + Snap Frozen: null + Liquid Nitrogen: null + TumorTissueTypeEnum: + permissible_values: + Normal: null + Normal adjacent: null + Recurrent: null + Post therapy neoadjuvant: null + Normal distant: null + Post therapy adjuvant: null + Post therapy: null + Atypia - hyperplasia: null + Not Otherwise Specified: null + Metastatic: null + Local recurrence: null + Premalignant - in situ: null + Additional Primary: null + Premalignant: null + Primary: null + SpecimenLateralityEnum: + permissible_values: + Not Applicable: null + unknown: null + Not Reported: null + Bilateral: null + Left: null + Right: null + SlideChargeTypeEnum: + permissible_values: + Other: null + Uncharged: null + Charged: null + Coverslip: null + Not applicable: null + ShippingConditionTypeEnum: + permissible_values: + Liquid Nitrogen: null + Dry Ice: null + Ambient Pack: null + Cold Pack: null + Ice Pack: null + Specimen at Room Temperature: null + Other Shipping Environment: null + Not Shipped: null diff --git a/modules/enums/BreastCancerTier3.yaml b/modules/enums/BreastCancerTier3.yaml new file mode 100644 index 0000000..3f1faf5 --- /dev/null +++ b/modules/enums/BreastCancerTier3.yaml @@ -0,0 +1,168 @@ +enums: + BreastCancerAssessmentTestsEnum: + permissible_values: + Other: null + unknown: null + Data not available: null + Estrogen receptor IHC: null + Progesterone receptor IHC: null + HER2 IHC: null + HER2 FISH-CISH: null + HER2 FISH: null + BreastCarcinomaDetectionMethodTypeEnum: + permissible_values: + Other: null + unknown: null + Clinical Exam: null + Data not available: null + Nipple Discharge: null + Screening Mammography: null + Screening MRI: null + Self exam: null + BreastCancerGenomicTestPerformedEnum: + permissible_values: + Other: null + unknown: null + Data not available: null + Oncotype: null + MammaPrint: null + Not performed: null + OncotypeRiskGroupEnum: + permissible_values: + unknown: null + Data not available: null + High risk: null + Intermediate risk: null + Low risk: null + InvasiveDuctalBreastCarcinomaHistologicCategoryEnum: + permissible_values: + Invasive carcinoma-type cannot be determined: null + Medullary carcinoma: null + Invasive papillary carcinoma: null + Invasive tubular carcinoma: null + Data not available: null + unknown: null + Invasive cribriform carcinoma: null + Invasive micropapillary carcinoma: null + Tubulolobular carcinoma: null + Other: null + Classical type: null + Mucinous carcinoma: null + PriorInvasiveBreastDiseaseEnum: + permissible_values: + Other: null + unknown: null + Data not available: null + DCIS: null + LCIS: null + Invasive breast cancer (unrelated to the current cancer): null + BreastBiopsyProcedureFindingTypeEnum: + permissible_values: + Other: null + Atypical hyperplasia: null + DCIS: null + LCIS: null + Cancer: null + No cancer: null + InvasiveLobularBreastCarcinomaHistologicCategoryEnum: + permissible_values: + unknown: null + Data not available: null + Alveolar type: null + Classical type: null + Pleomorphic type: null + BreastCarcinomaSurgicalProcedureNameEnum: + permissible_values: + Radical mastectomy: null + unknown: null + Simple mastectomy: null + Modified radical mastectomy: null + Partial mastectomy: null + Surgery not performed: null + Other: null + Lumpectomy: null + Re-excision: null + StainingIntensityEnum: + permissible_values: + Other: null + unknown: null + Strong: null + Moderate: null + Weak: null + Weak-Moderate: null + Moderate-Strong: null + Weak-Strong: null + BreastCarcinomaHER2StatusEnum: + permissible_values: + unknown: null + Equivocal: null + Indeterminate: null + Negative: null + Not Performed: null + Positive: null + Amplified: null + Non-amplified: null + BIRADSMammographyBreastDensityCategoryEnum: + permissible_values: + unknown: null + Data not available: null + Predominantly fatty: null + Scattered fibroglandular densities: null + Heterogeneously dense: null + Extremely dense: null + HormoneTherapyBreastCancerPreventionIndicatorEnum: + permissible_values: + Not Applicable: null + 'Yes': null + 'No': null + unknown: null + ReceptorStatusEnum: + permissible_values: + unknown: null + Borderline: null + Equivocal: null + Indeterminate: null + Negative: null + Not Performed: null + Performed but Not Available: null + Positive: null + BreastCancerAllredEstrogenReceptorScoreEnum: + permissible_values: + unknown: null + '10': null + '0': null + '4': null + '7': null + '1': null + '8': null + '2': null + '5': null + '3': null + '6': null + BreastQuadrantSiteEnum: + permissible_values: + unknown: null + Data not available: null + Upper outer quadrant: null + Lower outer quadrant: null + Upper inner quadrant: null + Lower inner quadrant: null + Central: null + Nipple: null + BreastCarcinomaHistologyCategoryEnum: + permissible_values: + Other: null + Infiltrating ductal carcinoma: null + Infiltrating lobular carcinoma: null + Invasive mammary carcinoma NOS: null + Invasive mixed ductal and lobular carcinoma: null + BreastImagingPerformedTypeEnum: + permissible_values: + unknown: null + Data not available: null + Mammogram: null + Ultrasound: null + MRI: null + PET/CT: null + CT: null + Multiple imaging modalities: null diff --git a/modules/enums/Demographics.yaml b/modules/enums/Demographics.yaml new file mode 100644 index 0000000..28aa45a --- /dev/null +++ b/modules/enums/Demographics.yaml @@ -0,0 +1,284 @@ +enums: + SexEnum: + permissible_values: + unknown: null + Not Reported: null + female: null + male: null + unspecified: null + CauseofDeathEnum: + permissible_values: + Not Reported: null + Renal Disorder NOS: null + Toxicity: null + Cardiovascular Disorder NOS: null + unknown: null + Not Applicable: null + Infection: null + Spinal Muscular Atrophy: null + Cancer Related: null + End-stage Renal Disease: null + Surgical Complications: null + Not Cancer Related: null + EthnicityEnum: + permissible_values: + unknown: null + Not Reported: null + hispanic or latino: null + not hispanic or latino: null + not allowed to collect: null + RaceEnum: + permissible_values: + american indian or alaska native: null + Not Reported: null + white: null + unknown: null + black or african american: null + not allowed to collect: null + asian: null + Other: null + native hawaiian or other pacific islander: null + AgeIsObfuscatedEnum: + permissible_values: + 'True': null + 'False': null + CountryofResidenceEnum: + permissible_values: + Trinidad and Tobago: null + Botswana: null + Malaysia: null + Suriname: null + Uruguay: null + Gibraltar: null + Andorra: null + Cayman Islands: null + Mozambique: null + Dominica: null + Tajikistan: null + Barbados: null + Seychelles: null + Curacao: null + Cote d'Ivoire: null + Albania: null + China: null + Oman: null + Congo: null + Burundi: null + Falkland Islands (Malvinas): null + Kazakhstan: null + Australia: null + France: null + Bahrain: null + Solomon Islands: null + Tanzania: null + French Guiana: null + Federated States of Micronesia: null + Antigua and Barbuda: null + Colombia: null + Fiji: null + Sao Tome and Principe: null + Brazil: null + Guam: null + South Africa: null + Denmark: null + Kyrgyzstan: null + Tunisia: null + Mexico: null + Martinique: null + Burkina Faso: null + India: null + Myanmar: null + Malawi: null + Sweden: null + Macau: null + Cambodia: null + Equatorial Guinea: null + Senegal: null + Guernsey: null + Azerbaijan: null + Angola: null + Kuwait: null + Papua New Guinea: null + Central African Republic: null + Bhutan: null + Uzbekistan: null + Portugal: null + Isle of Man: null + Guatemala: null + Saint Helena Ascension and Tristan da Cunha: null + Kiribati: null + Peru: null + South Sudan: null + North Macedonia: null + Democratic Republic of the Congo: null + Belarus: null + Madagascar: null + Singapore: null + Togo: null + Gambia: null + Georgia: null + Italy: null + Tuvalu: null + Eswatini: null + Nepal: null + Kenya: null + Niger: null + Israel: null + Iran: null + Liberia: null + Mali: null + Belize: null + Hungary: null + Holy See: null + Serbia: null + Belgium: null + Bermuda: null + Anguilla: null + Jamaica: null + Lebanon: null + Svalbard & Jan Mayen Islands: null + Cyprus: null + Norway: null + Somalia: null + Japan: null + Guyana: null + Paraguay: null + New Zealand: null + Palau: null + Laos: null + Latvia: null + Ethiopia: null + Cuba: null + French Polynesia: null + Slovenia: null + Philippines: null + Mongolia: null + Switzerland: null + Bahamas: null + Samoa: null + El Salvador: null + Chad: null + Honduras: null + Bangladesh: null + Tonga: null + Croatia: null + Bosnia and Herzegovina: null + Eritrea: null + Saint Kitts and Nevis: null + Vietnam: null + Northern Mariana Islands: null + Cape Verde: null + Cook Islands: null + Turkmenistan: null + Western Sahara: null + Jordan: null + Romania: null + Uganda: null + Aruba: null + Hong Kong: null + Syria: null + Germany: null + Chile: null + Austria: null + Gabon: null + Kosovo: null + Qatar: null + Comoros: null + Mayotte: null + Spain: null + Libya: null + Costa Rica: null + Bolivia: null + Taiwan: null + Iraq: null + Finland: null + Netherlands: null + Venezuela: null + Malta: null + Niue: null + Algeria: null + Guinea: null + Ireland: null + Montenegro: null + United Arab Emirates: null + Maldives: null + Zambia: null + Slovakia: null + Lesotho: null + Dominican Republic: null + Saint Pierre and Miquelon: null + Moldova: null + San Marino: null + Nauru: null + Luxembourg: null + Monaco: null + Zimbabwe: null + Saudi Arabia: null + Mauritania: null + Panama: null + United States: null + Montserrat: null + Nicaragua: null + Faroe Islands: null + United Kingdom: null + Canada: null + Ghana: null + Armenia: null + Bulgaria: null + Egypt: null + Reunion: null + Cameroon: null + Rwanda: null + Timor-Leste: null + Yemen: null + Saint Lucia: null + Poland: null + Namibia: null + Guinea-Bissau: null + Thailand: null + Argentina: null + Turkey: null + Djibouti: null + Greece: null + Jersey: null + Mauritius: null + Wallis and Futuna: null + Pakistan: null + Ukraine: null + State of Palestine: null + Ecuador: null + South Korea: null + Russia: null + Greenland: null + Liechtenstein: null + Nigeria: null + Benin: null + Vanuatu: null + Sri Lanka: null + Tokelau: null + Czech Republic (Czechia): null + Marshall Islands: null + Estonia: null + Saint Vincent and the Grenadines: null + Puerto Rico: null + Grenada: null + Guadeloupe: null + Sierra Leone: null + Afghanistan: null + Haiti: null + Lithuania: null + Indonesia: null + Virgin Islands British: null + Virgin Islands U.S.: null + Sudan: null + Morocco: null + Iceland: null + North Korea: null + New Caledonia: null + Brunei: null + VitalStatusEnum: + permissible_values: + Dead: null + unknown: null + Not Reported: null + Alive: null diff --git a/modules/enums/Device.yaml b/modules/enums/Device.yaml new file mode 100644 index 0000000..a5fa95c --- /dev/null +++ b/modules/enums/Device.yaml @@ -0,0 +1,35 @@ +enums: + SequencingPlatformEnum: + permissible_values: + PromethION: null + Illumina NovaSeq 6000: null + PacBio RS: null + Not Reported: null + Illumina Next Seq 500: null + NovaSeq 6000: null + Illumina Next Seq 2500: null + Illumina HiSeq 4000: null + unknown: null + Complete Genomics: null + Ultima Genomics UG100: null + Illumina MiSeq: null + Illumina HiSeq X Ten: null + Illumina Genome Analyzer IIx: null + Ion Torrent Proton: null + AB SOLiD 4 AB SOLiD 2: null + Illumina Genome Analyzer II: null + NovaSeqS4: null + Revio: null + Illumina HiSeq 2500: null + 454 GS FLX Titanium: null + Illumina Next Seq 550: null + GridION: null + Other: null + Illumina HiSeq 2000: null + Illumina HiSeq X Five: null + Illumina NextSeq: null + Ion Torrent S5: null + Ion Torrent PGM: null + Oxford Nanopore minION: null + AB SOLiD 3: null + PacBio Sequel2: null diff --git a/modules/enums/Diagnosis.yaml b/modules/enums/Diagnosis.yaml new file mode 100644 index 0000000..23d6d1c --- /dev/null +++ b/modules/enums/Diagnosis.yaml @@ -0,0 +1,944 @@ +enums: + ExtentofTumorResectionEnum: + permissible_values: + Minor: null + Open Biopsy: null + Not Reported: null + Gross Total Resection: null + unknown: null + Not Applicable: null + Segmental: null + NTR: null + Suboptimal debulking: null + Subtotal Resection: null + Other: null + Partial debulking: null + Suboptimal: null + Optimal debulking: null + Extensive Subtotal: null + SiteofResectionorBiopsyEnum: + permissible_values: + Tonsillar fossa: null + Overlapping lesion of lung: null + Overlapping lesion of other and unspecified parts of mouth: null + Endometrium: null + Bone of limb NOS: null + Posterior wall of nasopharynx: null + Small intestine NOS: null + Anterior wall of nasopharynx: null + Thoracic esophagus: null + Parietal lobe: null + Head face or neck NOS: null + Endocervix: null + Supraglottis: null + Ethmoid sinus: null + Ileum: null + Overlapping lesion of heart mediastinum and pleura: null + Exocervix: null + Pancreas NOS: null + Epididymis: null + Kidney NOS: null + Anus NOS: null + Cerebrum: null + Overlapping lesion of breast: null + Overlapping lesion of peripheral nerves and autonomic nervous system: null + Fundus of stomach: null + Oropharynx NOS: null + Urachus: null + Labium majus: null + Parametrium: null + Vestibule of mouth: null + Lower third of esophagus: null + Overlapping lesion of digestive system: null + Bones of skull and face and associated joints: null + Lymph nodes of axilla or arm: null + Soft palate NOS: null + Hepatic flexure of colon: null + Subglottis: null + Overlapping lesion of lip: null + Extrahepatic bile duct: null + Vallecula: null + Tongue NOS: null + Liver: null + Overlapping lesion of bones joints and articular cartilage: null + Not Reported: null + Peripheral nerves and autonomic nervous system of upper limb and shoulder: null + Lymph nodes of multiple regions: null + Duodenum: null + Maxillary sinus: null + Intrahepatic bile duct: null + Lateral wall of bladder: null + Overlapping lesion of hypopharynx: null + Overlapping lesion of rectum anus and anal canal: null + Middle third of esophagus: null + Lateral floor of mouth: null + Anterior mediastinum: null + Anterior floor of mouth: null + Nervous system NOS: null + Waldeyer ring: null + Rib sternum clavicle and associated joints: null + Long bones of lower limb and associated joints: null + Frontal sinus: null + Uterine adnexa: null + Trachea: null + Rectum NOS: null + Adrenal gland NOS: null + Pleura NOS: null + Lower limb NOS: null + Transverse colon: null + Lymph nodes of head face and neck: null + Greater curvature of stomach NOS: null + Upper respiratory tract NOS: null + Overlapping lesion of pancreas: null + Cerebellum NOS: null + Overlapping lesions of oropharynx: null + Axillary tail of breast: null + unknown: null + Vulva NOS: null + Floor of mouth NOS: null + Overlapping lesion of male genital organs: null + Uterus NOS: null + Body of stomach: null + Urethra: null + Middle lobe lung: null + Tail of pancreas: null + Pineal gland: null + Spermatic cord: null + Carotid body: null + Reticuloendothelial system NOS: null + Other specified parts of pancreas: null + External ear: null + Meckel diverticulum: null + Penis NOS: null + Lower-inner quadrant of breast: null + Superior wall of nasopharynx: null + Retina: null + Border of tongue: null + Intra-abdominal lymph nodes: null + Peripheral nerves and autonomic nervous system of thorax: null + Cauda equina: null + Overlapping lesion of palate: null + Nasopharynx NOS: null + Placenta: null + External lip NOS: null + Bone NOS: null + Ciliary body: null + Hematopoietic system NOS: null + Prepuce: null + Pelvic lymph nodes: null + Postcricoid region: null + External upper lip: null + Peripheral nerves and autonomic nervous system of pelvis: null + Pelvis NOS: null + Connective subcutaneous and other soft tissues of abdomen: null + Vertebral column: null + Body of pancreas: null + Trigone of bladder: null + Commissure of lip: null + Peripheral nerves and autonomic nervous system of abdomen: null + Upper-inner quadrant of breast: null + Palate NOS: null + Hypopharyngeal aspect of aryepiglottic fold: null + Upper gum: null + Thorax NOS: null + Spinal cord: null + Brain NOS: null + Mouth NOS: null + Connective subcutaneous and other soft tissues of upper limb and shoulder: null + Retroperitoneum: null + Long bones of upper limb scapula and associated joints: null + Hard palate: null + Gallbladder: null + Endocrine gland NOS: null + Brain stem: null + Cornea NOS: null + Overlapping lesion of nasopharynx: null + Dorsal surface of tongue NOS: null + Major salivary gland NOS: null + Abdominal esophagus: null + Olfactory nerve: null + Short bones of upper limb and associated joints: null + Overlapping lesion of tonsil: null + Autonomic nervous system NOS: null + Ill-defined sites within respiratory system: null + Lymph nodes of inguinal region or leg: null + Overlapping lesion of major salivary glands: null + Peripheral nerves and autonomic nervous system of trunk NOS: null + Fundus uteri: null + Testis NOS: null + Parotid gland: null + Ampulla of Vater: null + Cardia NOS: null + Skin of lip NOS: null + Overlapping lesion of stomach: null + Rectosigmoid junction: null + Gastric antrum: null + Cortex of adrenal gland: null + Renal pelvis: null + Middle ear: null + Overlapping lesion of female genital organs: null + Gastrointestinal tract NOS: null + Connective subcutaneous and other soft tissues of thorax: null + Skin NOS: null + Parathyroid gland: null + Pituitary gland: null + Overlapping lesion of tongue: null + Lung NOS: null + Cervix uteri: null + Skin of other and unspecified parts of face: null + Submandibular gland: null + Clitoris: null + Central portion of breast: null + Ovary: null + Lateral wall of oropharynx: null + Stomach NOS: null + Ventral surface of tongue NOS: null + Overlapping lesion of urinary organs: null + Sigmoid colon: null + Overlapping lesion of brain: null + Overlapping lesion of colon: null + Glans penis: null + Mediastinum NOS: null + Vagina NOS: null + Lower-outer quadrant of breast: null + Pharynx NOS: null + Intestinal tract NOS: null + Peripheral nerves and autonomic nervous system of head face and neck: null + Overlapping lesion of bladder: null + Pyriform sinus: null + Conjunctiva: null + Connective subcutaneous and other soft tissues NOS: null + Acoustic nerve: null + Lesser curvature of stomach NOS: null + Mucosa of lower lip: null + Bladder NOS: null + Intrathoracic lymph nodes: null + Pylorus: null + Blood: null + Biliary tract NOS: null + Accessory sinus NOS: null + Mandible: null + Overlapping lesion of retroperitoneum and peritoneum: null + Urinary system NOS: null + Sublingual gland: null + Tonsil NOS: null + Anterior surface of epiglottis: null + Branchial cleft: null + Peritoneum NOS: null + Lacrimal gland: null + Spleen: null + Optic nerve: null + Cervical esophagus: null + Fallopian tube: null + Base of tongue NOS: null + Skin of upper limb and shoulder: null + Craniopharyngeal duct: null + Specified parts of peritoneum: null + Pancreatic duct: null + External lower lip: null + Overlapping lesion of cervix uteri: null + Anterior wall of bladder: null + Uvula: null + Upper-outer quadrant of breast: null + Overlapping lesion of esophagus: null + Short bones of lower limb and associated joints: null + Ascending colon: null + Mucosa of upper lip: null + Connective subcutaneous and other soft tissues of head face and neck: null + Anal canal: null + Hypopharynx NOS: null + Aortic body and other paraganglia: null + Overlapping lesion of endocrine glands and related structures: null + Larynx NOS: null + Ureter: null + Eye NOS: null + Medulla of adrenal gland: null + Colon NOS: null + Lower lobe lung: null + Eyelid: null + Overlapping lesion of respiratory system and intrathoracic organs: null + Overlapping lesion of connective subcutaneous and other soft tissues: null + Esophagus NOS: null + Overlapping lesion of brain and central nervous system: null + Choroid: null + Bladder neck: null + Overlapping lesion of skin: null + Thyroid gland: null + Sphenoid sinus: null + Round ligament: null + Breast NOS: null + Upper lobe lung: null + Splenic flexure of colon: null + Cranial nerve NOS: null + Paraurethral gland: null + Posterior wall of oropharynx: null + Other specified parts of male genital organs: null + Undescended testis: null + Nasal cavity: null + Cerebral meninges: null + Overlapping lesion of floor of mouth: null + Overlapping lesion of corpus uteri: null + Lip NOS: null + Cheek mucosa: null + Upper limb NOS: null + Dome of bladder: null + Connective subcutaneous and other soft tissues of pelvis: null + unknown primary site: null + Posterior mediastinum: null + Ureteric orifice: null + Other ill-defined sites: null + Bone marrow: null + Peripheral nerves and autonomic nervous system of lower limb and hip: null + Lymph node NOS: null + Skin of scalp and neck: null + Retromolar area: null + Overlapping lesion of lip oral cavity and pharynx: null + Overlapping lesion of accessory sinuses: null + Overlapping lesion of penis: null + Overlapping lesion of vulva: null + Overlapping lesion of ill-defined sites: null + Occipital lobe: null + Overlapping lesion of eye and adnexa: null + Lingual tonsil: null + Gum NOS: null + Thymus: null + Male genital organs NOS: null + Islets of Langerhans: null + Isthmus uteri: null + Spinal meninges: null + Myometrium: null + Pelvic bones sacrum coccyx and associated joints: null + Connective subcutaneous and other soft tissues of lower limb and hip: null + Anterior 2/3 of tongue NOS: null + Upper third of esophagus: null + Meninges NOS: null + Prostate gland: null + Overlapping lesion of small intestine: null + Lower gum: null + Paraspinal: null + Appendix: null + Scrotum NOS: null + Overlapping lesion of larynx: null + Main bronchus: null + Descended testis: null + Cloacogenic zone: null + Connective subcutaneous and other soft tissues of trunk NOS: null + Heart: null + Mucosa of lip NOS: null + Broad ligament: null + Head of pancreas: null + Overlapping lesion of bones joints and articular cartilage of limbs: null + Temporal lobe: null + Body of penis: null + Overlapping lesion of biliary tract: null + Labium minus: null + Descending colon: null + Lateral wall of nasopharynx: null + Posterior wall of hypopharynx: null + Nipple: null + Jejunum: null + Posterior wall of bladder: null + Laryngeal cartilage: null + Cecum: null + Skin of lower limb and hip: null + Corpus uteri: null + Female genital tract NOS: null + Abdomen NOS: null + Tonsillar pillar: null + Other specified parts of female genital organs: null + Glottis: null + Orbit NOS: null + Skin of trunk: null + Ventricle NOS: null + Frontal lobe: null + VascularInvasionTypeEnum: + permissible_values: + unknown: null + Not Reported: null + Extramural: null + Intramural: null + Macro: null + Micro: null + No Vascular Invasion: null + ModeofCancerDetectionEnum: + permissible_values: + Data not available: null + Standard of Care Screening: null + Clinical Examination of unrelated cancer symptoms: null + Incidentaloma: null + Interval Cancer: null + PrimaryDiagnosisEnum: + permissible_values: + Paget disease and intraductal carcinoma of breast: null + Papillary microcarcinoma: null + Kaposi sarcoma: null + Carcinoma NOS: null + Acute myeloid leukemia NOS: null + Tumor NOS: null + Renal cell adenocarcinoma: null + Malignant lymphoma lymphoblastic NOS: null + Mammary carcinoma in situ: null + Adenocarcinoma in situ in tubular adenoma: null + Malignant lymphoma small B lymphocytic NOS: null + Eosinophilic leukemia: null + Acute lymphoblastic leukemia NOS: null + Malignant lymphoma lymphocytic nodular NOS: null + Basal cell epithelioma: null + Intracystic papilloma: null + Lobular and ductal carcinoma: null + Cancer: null + T lymphoblastic leukemia/lymphoma: null + Classical Hodgkin lymphoma lymphocyte-rich: null + Esophageal intraepithelial neoplasia high grade: null + Burkitt cell leukemia: null + Monocytic leukemia NOS: null + Acute leukemia NOS: null + Renal medullary carcinoma: null + Diffuse melanocytosis: null + Intraductal and lobular carcinoma: null + Melanotic psammomatous MPNST: null + Malignant melanoma in Hutchinson melanotic freckle: null + Pigmented adenoma: null + Chronic granulocytic leukemia BCR/ABL: null + Cervical intraepithelial neoplasia grade III: null + High-grade serous carcinoma: null + Classical Hodgkin lymphoma nodular sclerosis grade 1: null + Meningioma malignant: null + Interstitial cell tumor NOS: null + Bronchial adenoma NOS: null + Precursor T-cell lymphoblastic lymphoma: null + Tubular androblastoma with lipid storage: null + Combined large cell neuroendocrine carcinoma: null + Nephroblastoma NOS: null + Tumor cells benign: null + Tumorlet benign: null + Pleomorphic lipoma: null + Adenocarcinoma of anal ducts: null + Gastrointestinal stromal tumor malignant: null + Malignant melanoma in junctional nevus: null + Rhabdosarcoma: null + Endometrioid adenoma NOS: null + Hodgkin sarcoma: null + Malignant lymphoma immunoblastic NOS: null + Small congenital nevus: null + Tumor malignant NOS: null + Undifferentiated epithelioid sarcoma: null + Neuroendocrine carcinoma NOS: null + Acute lymphoblastic leukemia precursor cell type: null + Inflammatory adenocarcinoma: null + Tubular adenocarcinoma: null + Combined small cell-adenocarcinoma: null + Classical Hodgkin lymphoma nodular sclerosis cellular phase: null + Mixed adenocarcinoma and epidermoid carcinoma: null + Epidermoid carcinoma in situ NOS: null + Undifferentiated high-grade pleomorphic sarcoma: null + Sclerosing hepatic carcinoma: null + Pagetoid reticulosis: null + Central neurocytoma: null + Bronchiolo-alveolar carcinoma NOS: null + Chronic lymphoid leukemia: null + Paraganglioma malignant: null + Classical Hodgkin lymphoma nodular sclerosis grade 2: null + B-ALL: null + Skin appendage carcinoma: null + Epithelial tumor benign: null + B lymphoblastic leukemia/lymphoma NOS: null + Hodgkin lymphoma nodular sclerosis NOS: null + Malignant lymphoma lymphocytic diffuse NOS: null + Pro-B ALL: null + Gastrinoma NOS: null + Intraductal carcinoma clinging: null + Non-invasive low grade serous carcinoma: null + Acute promyelocytic leukemia NOS: null + Malignant lymphoma non-Hodgkin NOS: null + Not Reported: null + Melanotic schwannoma: null + Splenic marginal zone lymphoma NOS: null + Transitional cell carcinoma in situ: null + Chronic monocytic leukemia: null + Gastrin cell tumor: null + Papillary serous cystadenocarcinoma: null + Teratoma malignant NOS: null + Classical Hodgkin lymphoma lymphocyte depletion reticular: null + Tumor cells uncertain whether benign or malignant: null + Epithelial tumor malignant: null + Tubular androblastoma NOS: null + Papillary carcinoma in situ: null + Pituitary carcinoma NOS: null + Typical carcinoid: null + Non-small cell carcinoma: null + Meningioma NOS: null + Endometrial sarcoma NOS: null + Neuroblastoma NOS: null + B cell lymphoma NOS: null + Peripheral T-cell lymphoma large cell: null + Renal cell carcinoma NOS: null + Renal cell carcinoma spindle cell: null + Hepatocholangiocarcinoma: null + Malignant lymphoma nodular NOS: null + Bronchiolo-alveolar carcinoma non-mucinous: null + unknown: null + Bronchiolo-alveolar carcinoma indeterminate type: null + Pleomorphic carcinoma: null + Papillary cystadenoma NOS: null + Burkitt tumor: null + Basal cell carcinoma NOS: null + Hepatocellular carcinoma NOS: null + Undifferentiated leukaemia: null + Gastrin cell tumor malignant: null + Melanoameloblastoma: null + Prostatic intraepithelial neoplasia grade III: null + Mixed pineal tumor: null + Small cell sarcoma: null + Carcinoma in adenomatous polyp: null + Paget disease extramammary: null + Intraductal carcinoma solid type: null + Liver cell carcinoma: null + Undifferentiated sarcoma: null + Squamous cell carcinoma clear cell type: null + Pituitary adenoma NOS: null + Endometrioid carcinoma NOS: null + Papillary adenocarcinoma NOS: null + Duct carcinoma desmoplastic type: null + Chronic lymphatic leukemia: null + Squamous cell carcinoma in situ NOS: null + Intraductal papillary adenocarcinoma with invasion: null + Adenocarcinoma combined with other types of carcinoma: null + Combined hepatocellular carcinoma and cholangiocarcinoma: null + Primary amyloidosis: null + Preleukemia: null + Adenocarcinoma of anal glands: null + Secondary carcinoma: null + Dermal nevus: null + Infiltrating duct and cribriform carcinoma: null + Eosinophil adenocarcinoma: null + Chronic myeloproliferative disorder: null + Malignant melanoma regressing: null + Osteoblastoma malignant: null + Papillotubular adenocarcinoma: null + Carcinoma metastatic NOS: null + Sclerosing hemangioma: null + Lymphocytic leukemia NOS: null + Precursor cell lymphoblastic leukemia NOS: null + Papillary carcinoma NOS: null + Bronchio-alveolar carcinoma mucinous: null + Carcinoma in a polyp NOS: null + Acute myeloid leukemia MLL: null + Tubulocystic renal cell carcinoma: null + Melanocytoma NOS: null + Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive: null + Ewing sarcoma: null + Glioma NOS: null + Bronchial-associated lymphoid tissue lymphoma: null + Papillotubular adenoma: null + Papilloma of bladder: null + Bronchio-alveolar carcinoma mixed mucinous and non-mucinous: null + Carcinoma in pleomorphic adenoma: null + Chondrosarcoma grade 2/3: null + Neoplasm secondary: null + Rhabdomyosarcoma with ganglionic differentiation: null + Chronic lymphocytic leukemia: null + Liposarcoma well differentiated: null + Undifferentiated pleomorphic sarcoma: null + Secretory carcinoma of breast: null + Lobular carcinoma noninfiltrating: null + Mixed adenocarcinoma and squamous cell carcinoma: null + Melanotic neurofibroma: null + Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive: null + Hepatocellular adenoma: null + Burkitt lymphoma NOS (Includes all variants): null + Paraganglioma NOS: null + Diffuse large B-cell lymphoma NOS: null + Nevus NOS: null + Hepatoid carcinoma: null + Mixed tumor malignant NOS: null + Rhabdoid sarcoma: null + Tubulolobular carcinoma: null + Papillomatosis glandular: null + Bronchial adenoma carcinoid: null + Tumor embolus: null + Duct carcinoma NOS: null + Rhabdomyosarcoma NOS: null + Lobular carcinoma NOS: null + Bronchial adenoma cylindroid: null + Epidermoid carcinoma NOS: null + Papillary glioneuronal tumor: null + Ductal carcinoma in situ NOS: null + Unclassified tumor malignant uncertain whether primary or metastatic: null + Glioblastoma: null + Papillary and follicular carcinoma: null + Ductal carcinoma NOS: null + Tumor benign: null + Paget disease mammary: null + Diffuse astrocytoma low grade: null + Duct cell carcinoma: null + Preleukemic syndrome: null + Carcinoma diffuse type: null + Neurosarcoma: null + Papillomatosis NOS: null + Therapy related myeloid neoplasm: null + Renal carcinoma collecting duct type: null + Neurofibroma NOS: null + Meningioma anaplastic: null + Cementoma NOS: null + Dermatofibroma NOS: null + Astrocytoma NOS: null + Liver cell adenoma: null + Tubulovillous adenoma NOS: null + Melanoma NOS: null + Papilloma NOS: null + Esophageal glandular dysplasia (intraepithelial neoplasia) high grade: null + Tumor cells malignant: null + Malignant lymphoma diffuse NOS: null + Renal cell carcinoma chromophobe type: null + Tubular carcinoid: null + Nonpigmented nevus: null + Rodent ulcer: null + Hodgkin disease NOS: null + Acinar cell carcinoma: null + Papillary adenofibroma: null + Oat cell carcinoma: null + Adenocarcinoma in adenomatous polyp: null + Spindle cell carcinoma NOS: null + Adenocarcinoma in polypoid adenoma: null + Papillary serous adenocarcinoma: null + Splenic diffuse red pulp small B-cell lymphoma: null + Chondroma NOS: null + Bile duct adenoma: null + Adenocarcinoma in villous adenoma: null + Spindle cell melanoma NOS: null + Classical Hodgkin lymphoma mixed cellularity NOS: null + Combined small cell-large carcinoma: null + Eosinophil carcinoma: null + Pancreatic endocrine tumor NOS: null + Adenocarcinoma NOS: null + Sarcoma NOS: null + Chronic myelocytic leukemia NOS: null + Adenocarcinoma in situ non-mucinous: null + Chronic leukemia NOS: null + Pro-T ALL: null + Esophageal glandular dysplasia (intraepithelial neoplasia) low grade: null + Lymphoblastoma: null + Mixed medullary-papillary carcinoma: null + Classical Hodgkin lymphoma nodular sclerosis NOS: null + Osteoblastoma NOS: null + Cerebellar sarcoma NOS: null + Paraganglioma benign: null + Intraductal tubular-papillary neoplasm low grade: null + Familial adenomatous polyposis: null + Mixed squamous cell and glandular papilloma: null + Intraductal carcinoma NOS: null + Transitional carcinoma: null + Gastrinoma malignant: null + Melanocytoma eyeball: null + Mixed medullary-follicular carcinoma: null + Chronic myelogenous leukemia BCR-ABL positive: null + Basophil carcinoma: null + Neuroepithelioma NOS: null + Adenocarcinoma pancreatobiliary type: null + Precancerous melanosis NOS: null + Undifferentiated round cell sarcoma: null + Malignant lymphoma large cell NOS: null + Tubulo-papillary adenoma: null + Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis: null + Cerebellar liponeurocytoma: null + Pulmonary blastoma: null + Burkitt-like lymphoma: null + Ganglioglioma NOS: null + T-cell lymphoma NOS: null + Papillary tumor of the pineal region: null + Intraductal papillary adenocarcinoma NOS: null + Malignant lymphoma NOS: null + Hepatoid adenocarcinoma: null + Papillary adenoma NOS: null + Carcinoma in situ in adenomatous polyp: null + Eosinophilic granuloma: null + Medullary adenocarcinoma: null + Malignant lymphoma mixed cell type nodular: null + Intraductal carcinoma noninfiltrating NOS: null + Interstitial cell tumor malignant: null + Lymphoma NOS: null + Unclassified tumor borderline malignancy: null + Adenocarcinoma in tubular adenoma: null + Intraductal papillary carcinoma: null + Myelocytic leukemia NOS: null + Tumor cells NOS: null + Liposarcoma NOS: null + Interstitial cell tumor benign: null + Neoplasm metastatic: null + Chronic neutrophilic leukemia: null + Bronchiolo-alveolar carcinoma goblet cell type: null + Papillary adenocarcinoma follicular variant: null + Hepatocarcinoma: null + Undifferentiated uterine sarcoma: null + Renal cell carcinoma unclassified: null + Papillary epidermoid carcinoma: null + Pigmented nevus NOS: null + Myeloid leukemia NOS: null + Esophageal squamous intraepithelial neoplasia (dysplasia) high grade: null + Malignant lymphoma large B-cell NOS: null + Non-lymphocytic leukemia NOS: null + Basal cell adenocarcinoma: null + Adult T-cell lymphoma/leukemia: null + Mixed pancreatic endocrine and exocrine tumor malignant: null + Ependymoma NOS: null + Peripheral T-cell lymphoma NOS: null + Pulmonary adenomatosis: null + Pleomorphic lobular carcinoma: null + Paget disease of breast: null + Hodgkin paragranuloma NOS: null + Malignant melanoma NOS: null + Papillary transitional cell carcinoma: null + Acute lymphocytic leukemia: null + Serous surface papillary carcinoma: null + Basal cell tumor: null + Chronic myelomonocytic leukemia NOS: null + Lymphatic leukemic NOS: null + Teratoma NOS: null + Malignant lymphoma mixed cell type follicular: null + Bronchiolar adenocarcinoma: null + Basophil adenocarcinoma: null + Non-Hodgkin lymphoma NOS: null + Haemangioblastoma: null + Intraductal tubular-papillary neoplasm high grade: null + Chronic myeloproliferative disease NOS: null + Rhabdoid meningioma: null + Rhabdoid tumor NOS: null + Carcinoma intestinal type: null + Classical Hodgkin lymphoma lymphocyte depletion NOS: null + Chronic myeloid leukemia NOS: null + Melanotic medulloblastoma: null + Melanotic neuroectodermal tumor: null + Lobular carcinoma in situ NOS: null + Mixed small cell carcinoma: null + Intradermal nevus: null + Bronchiolo-alveolar carcinoma Clara cell: null + Papillary squamous cell carcinoma in situ: null + Small cell neuroendocrine carcinoma: null + Malignant melanoma in precancerous melanosis: null + Carcinoma anaplastic NOS: null + Dysplastic nevus: null + Liposarcoma differentiated: null + Combined small cell-squamous cell carcinoma: null + Acute lymphatic leukemia: null + Glioma malignant: null + Adenocarcinoma in situ NOS: null + Mucosal-associated lymphoid tissue lymphoma: null + Splenic lymphoma with villous lymphocytes: null + Large cell carcinoma NOS: null + Micropapillary carcinoma NOS: null + Undifferentiated spindle cell sarcoma: null + Intraepidermal squamous cell carcinoma Bowen type: null + Endometrioid adenofibroma NOS: null + Medullary carcinoma NOS: null + T-cell large granular lymphocytosis: null + Intraductal adenocarcinoma noninfiltrating NOS: null + Osteosarcoma NOS: null + Pancreatobiliary-type carcinoma: null + Adenocarcinoid tumor: null + Diffuse astrocytoma IDH-mutant: null + Medullary osteosarcoma: null + Adenocarcinoma intestinal type: null + Carcinoma in situ in a polyp NOS: null + Carcinosarcoma NOS: null + Basal cell adenoma: null + Adult T-cell lymphoma: null + Lobular adenocarcinoma: null + Melanocytic nevus: null + Adenocarcinoma metastatic NOS: null + Pigmented basal cell carcinoma: null + Astrocytoma anaplastic: null + Melanoma malignant of soft parts: null + Small cell osteosarcoma: null + Unclassified tumor uncertain whether benign or malignant: null + Transitional cell carcinoma: null + Intraductal carcinoma and lobular carcinoma in situ: null + Rhabdomyoma NOS: null + B-cell lymphocytic leukemia/small lymphocytic lymphoma: null + Capillary hemangioma: null + Precursor B-cell lymphoblastic leukemia: null + Bronchiolo-alveolar carcinoma Clara cell and goblet cell type: null + Eosinophil adenoma: null + Splenic B-cell lymphoma/leukemia unclassifiable: null + Composite Hodgkin and non-Hodgkin lymphoma: null + Paget disease and infiltrating duct carcinoma of breast: null + Neurofibromatosis NOS: null + Hodgkin lymphoma NOS: null + Melanoma in situ: null + Serous cystadenocarcinoma NOS: null + Malignant lymphoma Hodgkin: null + Acute lymphoblastic leukemia-lymphoma NOS: null + Unclassified tumor malignant: null + Adult rhabdomyoma: null + Neoplasm uncertain whether benign or malignant: null + Chronic myelomonocytic leukemia Type 1: null + Duct adenoma NOS: null + Neoplasm benign: null + Carcinoma undifferentiated NOS: null + Malignancy: null + Adenocarcinoma in situ mucinous: null + Papillary squamous cell carcinoma: null + B lymphoblastic leukemia/lymphoma with hyperdiploidy: null + Precursor T-cell lymphoblastic leukemia: null + Tumor secondary: null + Pancreatobiliary neoplasm non-invasive: null + Malignant melanoma in giant pigmented nevus: null + Squamous cell carcinoma adenoid: null + Acute myelomonocytic leukemia: null + Bile duct cystadenocarcinoma: null + Pancreatic endocrine tumor nonfunctioning: null + Pleomorphic adenoma: null + B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL): null + Renal cell carcinoma sarcomatoid: null + Splenic marginal zone B-cell lymphoma: null + Malignant lymphoma large B-cell diffuse NOS: null + Infiltrating duct and colloid carcinoma: null + Chronic myelomonocytic leukemia Type II: null + Duct adenocarcinoma NOS: null + Combined/mixed carcinoid and adenocarcinoma: null + Haemangiosarcoma: null + Acute lymphoid leukemia: null + Diffuse astrocytoma IDH-wildtype: null + Intraductal tubulopapillary neoplasm: null + Acute basophilic leukaemia: null + Unclassified tumor benign: null + Intraductal micropapillary carcinoma: null + Hodgkin granuloma: null + Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL): null + Pancreatoblastoma: null + Bile duct adenocarcinoma: null + Meningeal melanocytoma: null + Hodgkin lymphoma mixed cellularity NOS: null + Infiltrating duct carcinoma NOS: null + Esophageal squamous intraepithelial neoplasia (dysplasia) low grade: null + Small cell carcinoma NOS: null + Inflammatory carcinoma: null + Papillary urothelial carcinoma: null + Melanotic progonoma: null + Central neuroblastoma: null + Malignant lymphoma lymphocytic NOS: null + Myeloma NOS: null + Adenocarcinoma endocervical type: null + Adenocarcinoma in situ in a polyp NOS: null + Neoplasm malignant uncertain whether primary or metastatic: null + Pulmonary artery intimal sarcoma: null + Intraepidermal carcinoma NOS: null + Papillary serous cystadenoma NOS: null + Carcinoma in situ NOS: null + Tubular adenoma NOS: null + Tubulopapillary adenocarcinoma: null + Pancreatic microadenoma: null + Acute lymphoblastic leukemia mature B-cell type: null + c-ALL: null + Acute leukemia Burkitt type: null + Cervical intraepithelial neoplasia low grade: null + Mixed tumor NOS: null + Bronchiolo-alveolar adenocarcinoma NOS: null + Myoepithelioma: null + Pancreatic endocrine tumor malignant: null + Endometrioid adenocarcinoma NOS: null + Infiltrating basal cell carcinoma NOS: null + Precursor B-cell lymphoblastic lymphoma: null + Pleomorphic lobular carcinoma in situ: null + Mucous adenocarcinoma: null + Meningeal melanoma: null + Acute myeloid leukemia minimal differentiation: null + Lymphoblastic leukemia NOS: null + Melanotic MPNST: null + Astrocytoma low grade: null + Multiple myeloma: null + Papillary renal cell carcinoma: null + Medulloblastoma NOS: null + Adenocarcinoma in a polyp NOS: null + Combined small cell carcinoma: null + Bile duct carcinoma: null + Chronic granulocytic leukemia NOS: null + Juvenile myelomonocytic leukemia: null + Neoplasm NOS: null + Capillary lymphangioma: null + Malignant lymphoma mixed cell type diffuse: null + Neoplasm malignant: null + Papillary meningioma: null + Bile duct cystadenoma: null + Malignant melanoma in congenital melanocytic nevus: null + Adenocarcinoma diffuse type: null + Pancreatic endocrine tumor benign: null + Squamous cell carcinoma NOS: null + Chronic myelomonocytic leukemia in transformation: null + T-cell large granular lymphocytic leukemia: null + Basophil adenoma: null + Bronchiolar carcinoma: null + Tubular carcinoma: null + Neurofibrosarcoma: null + Adenocarcinoma in situ in adenomatous polyp: null + Intravascular B-cell lymphoma: null + Pleomorphic liposarcoma: null + Tumor metastatic: null + TumorExtranodalExtensionIndicatorEnum: + permissible_values: + Absent: null + Not applicable: null + 'YES': null + unspecified: null + No source documentation: null + UNKNOWN: null + Present: null + Present - extensive: null + Not sampled or dissected: null + Present - minimal: null + 'NO': null + Indeterminate: null + PrecancerousConditionTypeEnum: + permissible_values: + Carcinoma NOS: null + Atypical melanocytic proliferation: null + Superficial spreading: null + Melanoma in situ arising in a giant congenital nevus: null + Invasive melanoma: null + Invasive melanoma - acral lentiginous: null + Melanoma in situ not otherwise classified: null + Mild dysplasia: null + Adenocarcinoma in situ - non mucinous: null + Reserve cell hyperplasia: null + Invasive melanoma - nevoid: null + No diagnosis possible: null + Hamartoma: null + Adenocarcinoma in situ - mucinous: null + Squamous metaplasia - immature: null + Severe dysplasia: null + Invasive melanoma - lentigo maligna: null + Squamous metaplasia - mature: null + Acral-lentiginous: null + Invasive melanoma - superficial spreading: null + Atypical adenomatous hyperplasia: null + Moderate dysplasia: null + Atypical Adenomatous Lung Hyperplasia: null + Normal WDA: null + Other: null + Persistent melanoma in situ: null + Pancreatic Intraepithelial Neoplasia: null + Ductal Carcinoma In Situ: null + Pancreatic Intraductal Papillary-Mucinous Neoplasm: null + Melanocytic hyperplasia: null + Melanoma in situ: null + Invasive melanoma - desmoplastic: null + Benign tumor NOS: null + Lentigo maligna type: null + Scar - no residual melanoma: null + Invasive melanoma - nodular type: null + Prostatic Intraepithelial Neoplasia: null + IndicatorEnum: + permissible_values: + 'Yes': null + 'No': null + unknown: null + AnaplasiaPresentTypeEnum: + permissible_values: + unknown: null + Not Reported: null + Equivocal: null + Absent: null + Present: null + Diffuse: null + Focal: null + Sclerosis: null diff --git a/modules/enums/Exposure.yaml b/modules/enums/Exposure.yaml new file mode 100644 index 0000000..38b9aa1 --- /dev/null +++ b/modules/enums/Exposure.yaml @@ -0,0 +1,57 @@ +enums: + AlcoholTypeEnum: + permissible_values: + Other: + unknown: + Not Reported: + Beer: + Liquor: + Wine: + TobaccoSmokingStatusEnum: + permissible_values: + Not Reported: + unknown: + Current Reformed Smoker: + Current Smoker: + Current Reformed Smoker for > 15 yrs: + Duration Not Specified: + Smoking history not documented: + Lifelong Non-Smoker: + Current Reformed Smoker for < or = 15 yrs: + SmokingFrequencyEnum: + permissible_values: + unknown: + Every day: + Some days: + AlcoholExposureEnum: + permissible_values: + Yes - Alcohol Exposure: + Not Reported: + No - Alcohol Exposure: + HistoryEnum: + permissible_values: + 'Yes': + 'No': + unknown: + Not Reported: + AlcoholIntensityEnum: + permissible_values: + unknown: + Not Reported: + Drinker: + Heavy Drinker: + Lifelong Non-Drinker: + Non-Drinker: + Occasional Drinker: + AntibioticUseEnum: + permissible_values: + 'No': + unknown: + Yes - within last monthh: + Yes - within last 1-6 months: + Yes - over 6 months ago: + SmokingExposureEnum: + permissible_values: + Yes - Smoking Exposure: + Not Reported: + No - Smoking Exposure: diff --git a/modules/enums/FamilyHistory.yaml b/modules/enums/FamilyHistory.yaml new file mode 100644 index 0000000..c18e995 --- /dev/null +++ b/modules/enums/FamilyHistory.yaml @@ -0,0 +1,307 @@ +enums: + FamilyMemberVitalStatusIndicatorEnum: + permissible_values: + unknown: null + Not Reported: null + Vital Status Alive: null + Vital Status Dead: null + RelationshipPrimaryDiagnosisEnum: + permissible_values: + Prostate Cancer: null + Testicular Cancer: null + Cancer: null + Kaposi Sarcoma: null + Bone Cancer: null + Liver Cancer: null + CNS Cancer: null + Uterine Cancer: null + Not Reported: null + Lymph Node Cancer: null + Rectal Cancer: null + Wilms Tumor: null + unknown: null + Osteosarcoma: null + Chondrosarcoma: null + Mesothelioma: null + Gastric Cancer: null + Cervical Cancer: null + Ewing Sarcoma: null + Glioblastoma: null + Skin Cancer: null + Tonsillar Cancer: null + Bile Duct Cancer: null + Tongue Cancer: null + Laryngeal Cancer: null + Melanoma: null + Hematologic Cancer: null + Throat Cancer: null + Colorectal Cancer: null + Kidney Cancer: null + Spleen Cancer: null + Breast Cancer: null + Leukemia: null + Sarcoma: null + Blood Cancer: null + Neuroblastoma: null + Gynecologic Cancer: null + Rhabdomyosarcoma: null + Pancreas Cancer: null + Adrenal Gland Cancer: null + Thyroid Cancer: null + Multiple Myeloma: null + Lung Cancer: null + Basal Cell Cancer: null + Brain Cancer: null + Esophageal Cancer: null + Lymphoma: null + Ovarian Cancer: null + Gallbladder Cancer: null + Head and Neck Cancer: null + Bladder Cancer: null + RelationshipTypeEnum: + permissible_values: + Grand Niece: null + Foster Brother: null + Grand Nephew: null + Stepfather: null + Grandparent: null + Uncle: null + Natural Mother: null + Step Child: null + Daughter-in-law: null + Maternal Grandfather: null + Full Brother: null + Grandchild: null + Half Sibling: null + Grandfather: null + Not Reported: null + Father-in-law: null + Natural Brother: null + Maternal Half Brother: null + Paternal Half Sister: null + Fraternal Twin Sibling: null + Natural Sister: null + Legal Guardian: null + unknown: null + Foster Father: null + Paternal Grandmother: null + Husband: null + Brother-in-law: null + Twin Sibling: null + Mother: null + Natural Sibling: null + Brother: null + Wife: null + Paternal Grandfather: null + Great Grandchild: null + Mother-in-law: null + Granddaughter: null + Domestic Partner: null + Natural Grandparent: null + Fraternal Twin Brother: null + Cousin: null + Maternal Half Sister: null + Stepsister: null + Full Sister: null + Nephew: null + Niece Second Degree Relative: null + Paternal Uncle: null + Maternal Great Grandparent: null + Stepmother: null + Half Sister: null + Natural Grandfather: null + Paternal Great Uncle: null + Foster Sister: null + Natural Daughter: null + Foster Daughter: null + Step Sibling: null + First Cousin Once Removed: null + Adoptive Father: null + Paternal First Cousin Once Removed: null + Paternal Half Sibling: null + Spouse: null + Maternal Great Aunt: null + Female Cousin: null + Sister-in-law: null + Half Brother: null + Sibling: null + Maternal First Cousin Once Removed: null + Sister: null + Other: null + Natural Father: null + Stepdaughter: null + Natural Son: null + Natural Grandchild: null + Adoptive Brother: null + Stepson: null + Son: null + Refused: null + Child: null + Grandson: null + Ward: null + Aunt: null + Adopted Daughter: null + Maternal Great Uncle: null + Parent: null + Paternal Aunt: null + Adoptive Mother: null + First Cousin: null + Identical Twin Brother: null + Identical Twin Sister: null + Male Cousin: null + Son-in-law: null + Paternal First Cousin: null + Natural Grandmother: null + Maternal Grandparent: null + Foster Mother: null + Niece: null + Maternal Grandmother: null + Unrelated: null + Identical Twin Sibling: null + Paternal Great Grandparent: null + Fraternal Twin Sister: null + Adoptive Sister: null + Natural Child: null + Maternal Aunt: null + Grandmother: null + Foster Son: null + Maternal Uncle: null + Paternal Great Aunt: null + Paternal Half Brother: null + Daughter: null + Father: null + Paternal Grandparent: null + Natural Parent: null + Maternal Half Sibling: null + Adopted Son: null + Maternal First Cousin: null + Stepbrother: null + HereditaryCancerPredispositionSyndromeEnum: + permissible_values: + SDH associated renal cancer: null + Constitutional mismatch repair deficiency: null + Cirrhosis unknown etiology: null + Beckwith-Wiedemann: null + Hereditary melanoma: null + Not Reported: null + Gorlin syndrome: null + von Hippel-Lindau Syndrome: null + Tuberous sclerosis complex: null + Rhabdoid tumor predisposition syndrome type I: null + unknown: null + Tyrosinemia: null + Familial gastrointestinal stromal tumor: null + Not Applicable: null + Li-Fraumeni syndrome: null + Fanconi anemia: null + Turcot syndrome: null + Attenuated familial adenomatous polyposis: null + BAP1 mutant disease: null + Lynch syndrome: null + Hereditary paraganglioma–pheochromocytoma syndrome: null + Nevoid basal cell carcinoma syndrome: null + Multiple endocrine neoplasia type II: null + Rubinstein-Taybi syndrome: null + Cowden syndrome: null + Hereditary renal oncocytoma: null + Hereditary papillary RCC: null + Peutz–Jeghers syndrome: null + Familial adenomatous polyposis: null + Biliary disorder: null + MUTYH-associated polyposis: null + Rhabdoid tumor predisposition syndrome type II: null + Hereditary retinoblastoma: null + Glycogen Storage Disease: null + Carney complex: null + Hereditary diffuse gastric cancer: null + Juvenile polyposis syndrome: null + Hereditary mixed polyposis syndrome: null + Serrated polyposis syndrome: null + Familial renal cancer: null + Hereditary papillary renal cell carcinoma: null + Hereditary leiomyoma-renal cell carcinoma: null + Multiple endocrine neoplasia type I: null + Birt-Hogg-Dube syndrome: null + Familial pancreatic cancer: null + Hereditary breast–ovarian cancer syndrome: null + Familial prostate cancer: null + Melanoma–astrocytoma syndrome: null + Alpha-1 antitrypsin: null + RelativewithCancerHistoryEnum: + permissible_values: + Yes - Cancer History Relative: null + unknown: null + Not Reported: null + None: null + CancerAssociatedGeneMutationsEnum: + permissible_values: + PMS2 mutation: null + POT1 mutation: null + TP53 mutation: null + H3K27M mutation: null + SMARCA4 mutation: null + SDHD mutation: null + BRCA1 mutation: null + CHK mutation: null + RB1 mutation: null + H3G34R/V mutation: null + SDHC mutation: null + SDHB mutation: null + TSC2 mutation: null + Not Reported: null + HOXB13 mutation: null + NF1 mutation: null + VHL mutation: null + BAP1 mutation: null + SETD2 mutation: null + BRCA1 and 2 mutation: null + unknown: null + PTEN mutation: null + Not Applicable: null + STK11 mutation: null + PAX5 mutation: null + RET mutation: null + NF2 mutation: null + ETV6 mutation: null + PolD mutation: null + IKZF1 mutation: null + PALB2 mutation: null + SDHAF2 mutation: null + EGFR mutation: null + PDGFRA mutation: null + ARF mutation: null + PTCH mutation: null + PRKAR1A mutation: null + MUTYH mutation: null + MSH6 mutation: null + CDKN2A and p14ARF mutation: null + GREM1 mutation: null + MAX mutation: null + FH mutation: null + PHOX2B mutation: null + CDH1 mutation: null + MSH2 mutation: null + MLH1 mutation: null + MET mutation: null + ATRX mutation: null + KRAS mutation: null + KIT mutation: null + PolE mutation: null + TSC1 mutation: null + BLM mutation: null + ATM mutation: null + ACVR1 mutation: null + FLCN mutation: null + MEN1 mutation: null + TMEM127 mutation: null + BRAF mutation: null + ROS1 mutation: null + SMAD4 mutation: null + ALK mutation: null + BMPR1A mutation: null + APC mutation: null + BRCA2 mutation: null + SMARCB1 mutation: null + CDKN2A mutation: null + RAD51C mutation: null + p14ARF mutation: null diff --git a/modules/enums/ImagingLevel2.yaml b/modules/enums/ImagingLevel2.yaml new file mode 100644 index 0000000..01e21df --- /dev/null +++ b/modules/enums/ImagingLevel2.yaml @@ -0,0 +1,57 @@ +enums: + DimensionOrderEnum: + permissible_values: + XYZCT: null + XYZTC: null + XYCTZ: null + XYCZT: null + XYTZC: null + ZYX: null + ImagingAssayTypeEnum: + permissible_values: + MIBI: null + MxIF: null + IMC: null + Not Applicable: null + mIHC: null + H&E: null + IHC: null + CODEX: null + SABER: null + MERFISH: null + CyCIF: null + t-CyCIF: null + GeoMX-DSP: null + ExSeq: null + PixelTypeEnum: + permissible_values: + int32: null + int16: null + double: null + float: null + uint16: null + int8: null + uint32: null + bit: null + uint8: null + MicroscopyUnitEnum: + permissible_values: + cm: null + mm: null + µm: null + nm: null + Å: null + TseriesEnum: + permissible_values: + 'Yes': null + 'No': null + ImmersionEnum: + permissible_values: + Air: null + Oil: null + Water: null + Other: null + PassedQCEnum: + permissible_values: + No - Channels QC: null + 'Yes': null diff --git a/modules/enums/MolecularTest.yaml b/modules/enums/MolecularTest.yaml new file mode 100644 index 0000000..fd3d4bd --- /dev/null +++ b/modules/enums/MolecularTest.yaml @@ -0,0 +1,372 @@ +enums: + PathogenicityEnum: + permissible_values: + Benign: null + Likely Benign: null + Likely Pathogenic: null + Pathogenic: null + Uncertain Significance: null + LabTestsforMMRStatusEnum: + permissible_values: + Not Applicable: null + Other: null + unknown: null + IHC staining for mismatch repair proteins: null + PCR to evaluate microsatellite instability: null + MLH1 promoter methylation analysis: null + BRAF sequencing: null + MolecularAnalysisMethodEnum: + permissible_values: + WXS: null + WGS: null + ISH: null + Not Reported: null + Microsatellite Analysis: null + unknown: null + Not Applicable: null + Targeted Sequencing: null + Nuclear Staining: null + FISH: null + IHC: null + Karyotype: null + Flow Cytometry: null + Other: null + RNA Sequencing: null + Sequencing NOS: null + Southern Blotting: null + Microarray: null + Comparative Genomic Hybridization: null + Cytogenetics NOS: null + RT-PCR: null + ClonalityEnum: + permissible_values: + Clonal: null + Non-clonal: null + LaboratoryTestEnum: + permissible_values: + Absolute Neutrophil: null + Myeloblasts: null + Total Protein: null + Not Reported: null + Hemoglobin: null + NOS: null + Basophil: null + C-Reactive Protein: null + M Protein: null + Lambda: null + unknown: null + Circulating Tumor Cells: null + Epstein-Barr Virus: null + Promonocytes: null + Lactate Dehydrogenase: null + Cellularity: null + Human Chorionic Gonadotropin: null + Alpha Fetoprotein: null + Hematocrit: null + Promyelocytes: null + Testosterone: null + Lymphoblasts: null + Immunoglobulin M: null + Lymphocytes: null + Leukocytes: null + HPV-E6/E7: null + Luteinizing Hormone: null + Segmented Neutrophil: null + Immunoglobulin G: null + Beta 2 Microglobulin: null + Creatinine: null + Glucose: null + Serum Free Immunoglobulin Light Chain: null + Calcium: null + Metamyelocytes: null + Kappa: null + Prolymphocytes: null + Human Papillomavirus: null + Platelets: null + Neutrophil Bands: null + Myelocytes: null + Albumin: null + Blood Urea Nitrogen: null + Total Bilirubin: null + Eosinophil: null + Immunoglobulin A: null + B-cell genotyping: null + MutationalSignaturesEnum: + permissible_values: + Signature 19: null + Signature 1A: null + Ig gene hypermutation: null + altered activity of the error-prone polymerase POLε (POLE): null + Signature 3: null + Signature 20: null + Not Reported: null + Signature 17: null + Signature 4: null + Data not available: null + Signature 5: null + Signature 9: null + unknown: null + Signature 14: null + Signature 13: null + Not Applicable: null + Signature 12: null + Signature 8: null + Activation Induced Deaminases (AID) associated mutations: null + Signature 7: null + microsatellite instability (additions and deletions): null + Alkylating Agents (Temozolomide) induced mutations: null + localized substitution hypermutation (kataegis): null + Signature 16: null + Signature 6: null + Other: null + Signature 21: null + DNA MMR Deficiency: null + APOBEC enzymes associated mutations: null + Tobacco use associated mutations: null + transcriptional strand bias: null + Signature 1B: null + Signature 10: null + UV light induced mutations: null + Signature 18: null + Signature 11: null + Signature 2: null + methylated CpG sequences mutagenesis(deamination of 5-methyl-cytosine): null + Signature 15: null + age of cancer diagnosis: null + MismatchRepairSystemStatusEnum: + permissible_values: + Mismatch repair deficiency MMRD: null + Mismatch repair proficiency MMPP: null + Microsatellite instability high MSIH: null + Microsatellite stable MSS: null + unknown or other: null + TestAnalyteTypeEnum: + permissible_values: + unknown: null + Not Reported: null + DNA: null + mRNA: null + miRNA: null + Protein Analyte: null + Total RNA: null + ZygosityEnum: + permissible_values: + unknown: null + Not Reported: null + Heterozygous: null + Hemizygous: null + Homozygous: null + Nullizygous: null + ClinicalBiospecimenTypeEnum: + permissible_values: + Connective Tissue: null + Peritoneal Fluid: null + Not Reported: null + Saliva: null + Tissue NOS: null + Skin: null + unknown: null + Feces: null + Uninvolved Tissue NOS: null + Plasma: null + Granulocyte: null + Embryonic Tissue: null + Buccal Mucosa: null + Blood: null + Muscle Tissue: null + Cerebrospinal Fluid: null + Soft Tissue: null + Urine: null + Pleural Fluid: null + Bone Marrow: null + Serum: null + Embryonic Fluid: null + Nerve Tissue: null + Buffy Coat: null + VariantTypeEnum: + permissible_values: + Duplication: null + Conversion: null + Chrimerism: null + Not Reported: null + Partial Methylation: null + unknown: null + Substitution: null + Deletion-Insertion: null + Loss: null + Insertion: null + Hypermethylation: null + Alleles: null + Methylation: null + Inversion: null + Extension: null + Mosaicism: null + Deletion: null + Other: null + Rearrangement: null + Translocation: null + Amplification: null + Repeated Sequences: null + Splice: null + Gain: null + HistoneFamilyEnum: + permissible_values: + unknown: null + Not Reported: null + H1: null + H2A: null + H2B: null + H3: null + H4: null + ChromosomeEnum: + permissible_values: + chr7: null + chr15: null + Not Reported: null + chr3: null + chr1: null + chr18: null + unknown: null + chrY: null + chr22: null + chr14: null + chr12: null + chr11: null + chr17: null + chrM: null + chr4: null + chr21: null + chr6: null + chr10: null + chr16: null + chrX: null + chr23: null + chr8: null + chr2: null + chr13: null + chr19: null + chr20: null + chr5: null + chr9: null + TestResultEnum: + permissible_values: + Normal: null + Not Reported: null + Test Value Reported: null + unknown: null + Overexpressed: null + Intermediate: null + Not Applicable: null + Loss of Expression: null + Low: null + High: null + Equivocal: null + Copy Number Reported: null + Positive: null + Negative: null + Abnormal NOS: null + AntigenEnum: + permissible_values: + CA19-9: null + CD79A: null + CD5: null + CD30: null + Not Reported: null + CD20: null + CD14: null + CD19: null + unknown: null + CD34: null + CCND1: null + CD25: null + HLA-DR: null + Mesothelin: null + CD10: null + CD56: null + CD3: null + NSE: null + CA-125: null + CD22: null + CD23: null + Squamous Cell Carcinoma Antigen: null + CEA: null + CD33: null + CD138: null + BCL6: null + CD7: null + CD117: null + CD15: null + CD45: null + MolecularConsequenceEnum: + permissible_values: + TF Binding Site Variant: null + Transcript Amplification: null + Splice Region Variant: null + Downstream Gene Variant: null + 5 Prime UTR Variant: null + Splice Donor Variant: null + Splice Acceptor Variant: null + Stop Gain: null + Stop Retained Variant: null + TFBS Amplification: null + 3 Prime UTR Variant: null + Upstream Gene Variant: null + Intergenic Variant: null + Regulatory Region Ablation: null + NMD Transcript Variant: null + Transcript Ablation: null + Non-coding Transcript Exon Variant: null + Synonymous Variant: null + Regulatory Region Variant: null + Stop Lost: null + Mature miRNA Variant: null + Inframe Insertion: null + Inframe Deletion: null + Protein Altering Variant: null + Incomplete Terminal Codon Variant: null + TFBS Ablation: null + Intron Variant: null + Coding Sequence Variant: null + Missense Variant: null + Frameshift Variant: null + Non-coding Transcript Variant: null + Feature Truncation: null + Regulatory Region Amplification: null + Start Lost: null + Feature Elongation: null + PloidyEnum: + permissible_values: + unknown: null + Not Reported: null + Aneuploid: null + Diploid: null + Hyperdiploid: null + Hypodiploid: null + Near Diploid: null + Tetraploid: null + VariantOriginEnum: + permissible_values: + unknown: null + Germline: null + Somatic: null + HistoneVariantEnum: + permissible_values: + mH2A: null + mH2A.1: null + Not Reported: null + H2A.Z: null + H3.2: null + unknown: null + H3t (H3.4): null + H3.X: null + H2A.Z.2.2: null + H3.Y: null + H3.5: null + H3.3: null + H3.1: null + H2A-Bbd: null + mH2A.2: null + CENP-A: null + H2A.Z.2: null + H2A.X: null + H2A.Z.1: null diff --git a/modules/enums/OvarianCancerTier3.yaml b/modules/enums/OvarianCancerTier3.yaml new file mode 100644 index 0000000..3065529 --- /dev/null +++ b/modules/enums/OvarianCancerTier3.yaml @@ -0,0 +1,29 @@ +enums: + OvarianCancerPlatinumStatusEnum: + permissible_values: + unknown: null + Data not available: null + Platinum-refractory: null + Platinum-sensitive: null + Platinum-resistant: null + OvarianCancerHistologicSubtypeEnum: + permissible_values: + High-grade serous: null + Data not available: null + unknown: null + Germ cell: null + High-grade endometrioid: null + Other: null + Low-grade serous: null + Clear cell: null + Low-grade endometrioid: null + Mucinous: null + Sex-cord stromal: null + OvarianCancerSurgicalOutcomeEnum: + permissible_values: + Other: null + unknown: null + Data not available: null + R0 resection: null + Optimal cytoreduction: null + Sub-optimal cytoreduction: null diff --git a/modules/enums/Sequencing.yaml b/modules/enums/Sequencing.yaml new file mode 100644 index 0000000..86bfe6e --- /dev/null +++ b/modules/enums/Sequencing.yaml @@ -0,0 +1,74 @@ +enums: + NucleicAcidSourceEnum: + permissible_values: + Single Cell: null + Bulk Whole Cell: null + Single Nucleus: null + Bulk Nuclei: null + LibraryConstructionMethodEnum: + permissible_values: + 10xV3: null + inDropsV2: null + 10xV1.1: null + 10xV3.1: null + Drop-seq: null + 10xV2: null + 10xV1.0: null + Smart-seq2: null + Smart-SeqV4: null + sci-ATAC-seq: null + inDropsV3: null + CEL-seq2: null + TruDrop: null + SingleCellIsolationMethodEnum: + permissible_values: + Microfluidics Chip: null + Droplets: null + FACS: null + Plates: null + 10x: null + Nuclei Isolation: null + DissociationMethodEnum: + permissible_values: + Not Applicable: null + gentleMACS: null + Dounce: null + Enzymatic Digestion: null + SpikeInEnum: + permissible_values: + ERCC: null + Other Spike In: null + No Spike In: null + PhiX: null + ReverseTranscriptionPrimerEnum: + permissible_values: + Feature barcoding: null + Oligo-dT: null + Poly-dT: null + Random: null + EndBiasEnum: + permissible_values: + 3 Prime: null + 5 Prime: null + Full Length Transcript: null + SingleNucleusBufferEnum: + permissible_values: + 10x: null + NIB: null + Omni: null + TranspositionReactionEnum: + permissible_values: + Tn5: null + EZ-Tn5: null + Tn5-059: null + Nextera Tn5: null + Diagenode-unloaded Apex-Bio: null + Diagenode-loaded Apex-Bio: null + In-House: null + ReadEnum: + permissible_values: + Cell Barcode and DNA Insert: null + Sample Index and DNA Insert: null + DNA Insert: null + Sample Index: null + Cell Barcode: null diff --git a/modules/enums/Thing.yaml b/modules/enums/Thing.yaml new file mode 100644 index 0000000..9a9cfc0 --- /dev/null +++ b/modules/enums/Thing.yaml @@ -0,0 +1,91 @@ +enums: + FileFormatEnum: + permissible_values: + dat: null + R script: null + tif: null + bam: null + M: null + 7z: null + csv: null + png: null + tar: null + bai: null + OME-TIFF: null + dup: null + hic: null + cell am: null + idat: null + txt: null + raw: null + hdf5: null + bgzip: null + seg: null + rmd: null + scn: null + vcf: null + maf: null + tsv: null + pdf: null + sam: null + bedgraph: null + sra: null + abf: null + fastq: null + pzfx: null + bed narrowPeak: null + fig: null + am: null + gct: null + tagAlign: null + gzip: null + gtf: null + DICOM: null + cloupe: null + czi: null + tiff: null + powerpoint: null + zip: null + bed: null + mex: null + ab1: null + Python script: null + msf: null + mzML: null + svg: null + cel: null + mtx: null + bigwig: null + chp: null + svs: null + wiggle: null + mov: null + bcf: null + hyperlink: null + sdf: null + recal: null + idx: null + sif: null + json: null + avi: null + HEIC: null + gff3: null + bpm: null + bed broadPeak: null + excel: null + flagstat: null + mpg: null + RData: null + Sentrix descriptor file: null + jpg: null + doc: null + bed gappedPeak: null + xml: null + sqlite: null + tranches: null + plink: null + sav: null + locs: null + html: null + md: null + fasta: null diff --git a/modules/schema.csv b/modules/schema.csv deleted file mode 100644 index 9291b1b..0000000 --- a/modules/schema.csv +++ /dev/null @@ -1 +0,0 @@ -Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules diff --git a/modules/slots.yaml b/modules/slots.yaml new file mode 100644 index 0000000..b2c48c0 --- /dev/null +++ b/modules/slots.yaml @@ -0,0 +1,1823 @@ +slots: + AAChange: + title: AA Change + required: false + description: 'Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + AcquisitionMethodOtherSpecify: + title: Acquisition Method Other Specify + required: false + description: A custom acquisition method [Text - max length 100 characters] + annotations: + AdjacentBiospecimenIDs: + title: Adjacent Biospecimen IDs + required: false + description: TBD + annotations: + AdjacentSampleIDs: + title: Adjacent Sample IDs + required: false + description: List of Identifiers (separated by commas) of adjacent biospecimens cut from the same sample + annotations: + Age: + title: Age + required: true + description: Age of individual + annotations: + AgeAtMenarche: + title: Age At Menarche + required: false + description: TBD + annotations: + AgeIsObfuscated: + title: Age Is Obfuscated + required: false + description: The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified. + annotations: + range: AgeIsObfuscatedEnum + AgeatDiagnosis: + title: Age at Diagnosis + required: false + description: Age at the time of diagnosis expressed in number of days since birth. + annotations: + AlcoholDaysPerWeek: + title: Alcohol Days Per Week + required: false + description: Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage. + annotations: + AlcoholDrinksPerDay: + title: Alcohol Drinks Per Day + required: false + description: Numeric value used to describe the average number of alcoholic beverages a person consumes per day. + annotations: + AlcoholExposure: + title: Alcohol Exposure + required: false + description: Indicate if individual has alcohol exposure + annotations: + range: AlcoholExposureEnum + AlcoholHistory: + title: Alcohol History + required: false + description: A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime. + annotations: + range: HistoryEnum + AlcoholIntensity: + title: Alcohol Intensity + required: false + description: Category to describe the patient's current level of alcohol use as self-reported by the patient. + annotations: + range: AlcoholIntensityEnum + AlcoholType: + title: Alcohol Type + required: false + description: Type of alcohol use + annotations: + range: AlcoholTypeEnum + AlcoholUse: + title: Alcohol Use + required: false + description: TBD + annotations: + AnalyteType: + title: Analyte Type + required: false + description: 'The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen' + annotations: + range: AnalyteTypeEnum + AnaplasiaPresentType: + title: Anaplasia Present Type + required: false + description: The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample. + annotations: + range: AnaplasiaPresentTypeEnum + AntibioticUse: + title: Antibiotic Use + required: false + description: Antibiotic use + annotations: + range: AntibioticUseEnum + AntibodyName: + title: Antibody Name + required: false + description: TBD + annotations: + Antigen: + title: Antigen + required: false + description: 'The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + range: AntigenEnum + AppliedHardTrimming: + title: Applied Hard Trimming + required: false + description: TBD + annotations: + Authors: + title: Authors + required: false + description: TBD + annotations: + BIRADSMammographyBreastDensityCategory: + title: BIRADS Mammography Breast Density Category + required: false + description: The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines. + annotations: + range: BIRADSMammographyBreastDensityCategoryEnum + BMI: + title: BMI + required: false + description: TBD + annotations: + BiospecimenDimension1: + title: Biospecimen Dimension 1 + required: false + description: First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE + annotations: + BiospecimenDimension2: + title: Biospecimen Dimension 2 + required: false + description: Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE + annotations: + BiospecimenDimension3: + title: Biospecimen Dimension 3 + required: false + description: Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE + annotations: + BiospecimenID: + title: Biospecimen ID + required: true + description: ' Alias for Sample ID' + annotations: + BiospecimenType: + title: Biospecimen Type + required: false + description: Biospecimen Type + annotations: + range: BiospecimenTypeEnum + BloodTestNormalRangeLower: + title: Blood Test Normal Range Lower + required: false + description: Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed. + annotations: + BloodTestNormalRangeUpper: + title: Blood Test Normal Range Upper + required: false + description: Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed. + annotations: + BreastBiopsyProcedureFindingType: + title: Breast Biopsy Procedure Finding Type + required: false + description: Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease. + annotations: + range: BreastBiopsyProcedureFindingTypeEnum + BreastCancerAllredEstrogenReceptorScore: + title: Breast Cancer Allred Estrogen Receptor Score + required: false + description: The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status. + annotations: + range: BreastCancerAllredEstrogenReceptorScoreEnum + BreastCancerAssessmentTests: + title: Breast Cancer Assessment Tests + required: false + description: Text term to identify assessment tests done in participants during diagnosis + annotations: + range: BreastCancerAssessmentTestsEnum + BreastCancerGenomicTestPerformed: + title: Breast Cancer Genomic Test Performed + required: false + description: Text term that represents the name of the genomic test performed for breast cancer. + annotations: + range: BreastCancerGenomicTestPerformedEnum + BreastCarcinomaCentromere17CopyNumber: + title: Breast Carcinoma Centromere 17 Copy Number + required: false + description: Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values. + annotations: + BreastCarcinomaDetectionMethodType: + title: Breast Carcinoma Detection Method Type + required: false + description: The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer. + annotations: + range: BreastCarcinomaDetectionMethodTypeEnum + BreastCarcinomaERStatusPercentageValue: + title: Breast Carcinoma ER Status Percentage Value + required: false + description: A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer + annotations: + BreastCarcinomaHER2Centromere17CopynumberTotal: + title: Breast Carcinoma HER2 Centromere17 Copynumber Total + required: false + description: Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer + annotations: + BreastCarcinomaHER2Chromosome17Ratio: + title: Breast Carcinoma HER2 Chromosome17 Ratio + required: false + description: HER2 chromosome 17 ratio in participants with breast cancer + annotations: + BreastCarcinomaHER2RatioDiagnosis: + title: Breast Carcinoma HER2 Ratio Diagnosis + required: false + description: HER2 ratio of the participant at diagnosis + annotations: + BreastCarcinomaHER2Status: + title: Breast Carcinoma HER2 Status + required: false + description: Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 in a participant with breast cancer + annotations: + range: BreastCarcinomaHER2StatusEnum + BreastCarcinomaHistologyCategory: + title: Breast Carcinoma Histology Category + required: false + description: Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes. + annotations: + range: BreastCarcinomaHistologyCategoryEnum + BreastCarcinomaPRStatusPercentageValue: + title: Breast Carcinoma PR Status Percentage Value + required: false + description: A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer + annotations: + BreastCarcinomaSurgicalProcedureName: + title: Breast Carcinoma Surgical Procedure Name + required: false + description: Text name of a surgical procedure performed for a person with a diagnosis of breast cancer + annotations: + range: BreastCarcinomaSurgicalProcedureNameEnum + BreastImagingPerformedType: + title: Breast Imaging Performed Type + required: false + description: The kind of technology or method performed for screening, diagnosis, surgical procedures or therapy that aids in the visualization of the breast(s). + annotations: + range: BreastImagingPerformedTypeEnum + BreastQuadrantSite: + title: Breast Quadrant Site + required: false + description: The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination. + annotations: + range: BreastQuadrantSiteEnum + COVID19AntibodyTesting: + title: COVID19 Antibody Testing + required: false + description: TBD + annotations: + COVID19CancerTreatmentFollowup: + title: COVID19 Cancer Treatment Followup + required: false + description: TBD + annotations: + COVID19ComplicationsSeverity: + title: COVID19 Complications Severity + required: false + description: TBD + annotations: + COVID19CurrentStatus: + title: COVID19 Current Status + required: false + description: TBD + annotations: + COVID19OccurrenceIndicator: + title: COVID19 Occurrence Indicator + required: false + description: TBD + annotations: + COVID19PositiveLabTestIndicator: + title: COVID19 Positive Lab Test Indicator + required: false + description: TBD + annotations: + CancerAssociatedGeneMutations: + title: Cancer Associated Gene Mutations + required: false + description: Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history + annotations: + range: CancerAssociatedGeneMutationsEnum + CancerIncidence: + title: Cancer Incidence + required: false + description: TBD + annotations: + CancerIncidenceLocation: + title: Cancer Incidence Location + required: false + description: TBD + annotations: + CatalogNumber: + title: Catalog Number + required: false + description: TBD + annotations: + CauseofDeath: + title: Cause of Death + required: false + description: The cause of death + annotations: + range: CauseofDeathEnum + CauseofDeathSource: + title: Cause of Death Source + required: false + description: TBD + annotations: + CellBarcodeLength: + title: Cell Barcode Length + required: false + description: 'Length of cell barcode read (in bp): number' + annotations: + CellBarcodeOffset: + title: Cell Barcode Offset + required: false + description: 'Offset in sequence for cell barcode read (in bp): number' + annotations: + CellBarcodeTag: + title: Cell Barcode Tag + required: false + description: TBD + annotations: + CellCount: + title: Cell Count + required: false + description: 'Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + CellMedianNumberGenes: + title: Cell Median Number Genes + required: false + description: Median number of genes detected per cell. Number + annotations: + CellMedianNumberReads: + title: Cell Median Number Reads + required: false + description: Median number of reads per cell. Number + annotations: + CellTotal: + title: Cell Total + required: false + description: Number of sequenced cells. Applies to raw counts matrix only. + annotations: + ChannelID: + title: Channel ID + required: false + description: TBD + annotations: + ChannelMetadataFilename: + title: Channel Metadata Filename + required: false + description: Full path of uploaded companion CSV file containing channel-level metadata details + annotations: + ChannelName: + title: Channel Name + required: false + description: TBD + annotations: + ChannelPassedQC: + title: Channel Passed QC + required: false + description: TBD + annotations: + Chewingtobaccodailyusecount: + title: Chewing tobacco daily use count + required: false + description: TBD + annotations: + Chromosome: + title: Chromosome + required: false + description: 'The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + range: ChromosomeEnum + CigarettesperDay: + title: Cigarettes per Day + required: false + description: The average number of cigarettes smoked per day. + annotations: + ClassBRCA1: + title: Class BRCA1 + required: false + description: TBD + annotations: + ClassBRCA2: + title: Class BRCA2 + required: false + description: TBD + annotations: + ClinicalBiospecimenType: + title: Clinical Biospecimen Type + required: false + description: 'The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + range: ClinicalBiospecimenTypeEnum + Clonality: + title: Clonality + required: false + description: 'The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + range: ClonalityEnum + Clone: + title: Clone + required: false + description: TBD + annotations: + Comment: + title: Comment + required: false + description: Free text field (generally for QC comment) + annotations: + Component: + title: Component + required: false + description: TBD + annotations: + Concentration: + title: Concentration + required: false + description: TBD + annotations: + ConcomitantMedicationReceivedType: + title: Concomitant Medication Received Type + required: false + description: TBD + annotations: + CopyNumber: + title: Copy Number + required: false + description: 'Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + CountryofBirth: + title: Country of Birth + required: false + description: TBD + annotations: + CountryofResidence: + title: Country of Residence + required: false + description: Country of Residence at enrollment + annotations: + range: CountryofResidenceEnum + CryopreservedCellsinSample: + title: Cryopreserved Cells in Sample + required: true + description: Indicate if library preparation was based on revived frozen cells. + annotations: + range: CryopreservedCellsinSampleEnum + CycleNumber: + title: Cycle Number + required: false + description: TBD + annotations: + Cytoband: + title: Cytoband + required: false + description: 'Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + DataCategory: + title: Data Category + required: false + description: TBD + annotations: + DaystoBirth: + title: Days to Birth + required: false + description: Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days. + annotations: + DaystoDeath: + title: Days to Death + required: false + description: Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days. + annotations: + DaystoProgression: + title: Days to Progression + required: false + description: Number of days between the date used for index and the date the patient's disease progressed. + annotations: + DaystoProgressionFree: + title: Days to Progression Free + required: false + description: Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free. + annotations: + DaystoRecurrence: + title: Days to Recurrence + required: false + description: TBD + annotations: + DetailedSampleID: + title: Detailed Sample ID + required: false + description: ' Additional alternative ID associated with a biosample' + annotations: + DiagnosisStatusType: + title: Diagnosis Status Type + required: false + description: TBD + annotations: + Dilution: + title: Dilution + required: false + description: TBD + annotations: + DimensionOrder: + title: DimensionOrder + required: false + description: The order in which the individual planes of data are interleaved. + annotations: + range: DimensionOrderEnum + DimensionsUnit: + title: Dimensions Unit + required: false + description: Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc) + annotations: + range: DimensionsUnitEnum + DissociationMethod: + title: Dissociation Method + required: true + description: The tissue dissociation method used for scRNASeq or scATAC-seq assays + annotations: + range: DissociationMethodEnum + ERReceptorStatus: + title: Breast Carcinoma Estrogen Receptor Status + required: false + description: Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer + annotations: + range: ReceptorStatusEnum + ERStainingIntensity: + title: Breast Carcinoma ER Staining Intensity + required: false + description: Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer + annotations: + range: StainingIntensityEnum + ERStatus: + title: ER Status + required: false + description: TBD + annotations: + Ecigvape30dayusenum: + title: Ecig vape 30 day use num + required: false + description: TBD + annotations: + Ecigvapetimesperday: + title: Ecig vape times per day + required: false + description: TBD + annotations: + Ecigvapeuse: + title: Ecig vape use + required: false + description: TBD + annotations: + EducationLevel: + title: Education Level + required: false + description: TBD + annotations: + EmissionBandwidth: + title: Emission Bandwidth + required: false + description: TBD + annotations: + EmissionWavelength: + title: Emission Wavelength + required: false + description: TBD + annotations: + EmptyWellBarcode: + title: Empty Well Barcode + required: false + description: Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays. + annotations: + EndBias: + title: End Bias + required: false + description: The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript + annotations: + range: EndBiasEnum + EnvironmentalTobaccoSmokeExposure: + title: Environmental Tobacco Smoke Exposure + required: false + description: The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers. + annotations: + range: IndicatorEnum + Ethnicity: + title: Ethnicity + required: true + description: An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. + annotations: + range: EthnicityEnum + ExcitationBandwidth: + title: Excitation Bandwidth + required: false + description: TBD + annotations: + ExcitationWavelength: + title: Excitation Wavelength + required: false + description: TBD + annotations: + Exon: + title: Exon + required: false + description: 'Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + ExtentofTumorResection: + title: Extent of Tumor Resection + required: false + description: The degree to which the lesion has been cut out, or resected. + annotations: + range: ExtentofTumorResectionEnum + FOVX: + title: FOVX + required: false + description: Field of view X dimension. Floating point + annotations: + FOVXUnit: + title: FOVXUnit + required: false + description: 'Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)' + annotations: + range: MicroscopyUnitEnum + FOVY: + title: FOVY + required: false + description: Field of view Y dimension. Floating point value + annotations: + FOVYUnit: + title: FOVYUnit + required: false + description: 'Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)' + annotations: + range: MicroscopyUnitEnum + FOVnumber: + title: FOV number + required: false + description: Index of FOV (as it pertains to its sequence order). Integer >= 1 + annotations: + FamilyMemberVitalStatusIndicator: + title: Family Member Vital Status Indicator + required: false + description: The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1) + annotations: + range: IndicatorEnum + FeatureReferenceId: + title: Feature Reference Id + required: false + description: Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref] + annotations: + FileFormat: + title: File Format + required: false + description: Format of a file (e.g. txt, csv, fastq, bam, etc.) + annotations: + range: FileFormatEnum + Filename: + title: Filename + required: false + description: TBD + annotations: + FixationDuration: + title: Fixation Duration + required: false + description: The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes) + annotations: + Fluorophore: + title: Fluorophore + required: false + description: TBD + annotations: + FrameAveraging: + title: Frame Averaging + required: false + description: Number of frames averaged together (if no averaging, set to 1). Integer >= 1 + annotations: + Gender: + title: Gender + required: false + description: Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.] + annotations: + range: SexEnum + GeneSymbol: + title: Gene Symbol + required: false + description: 'The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + GenomeAnnotationURL: + title: Genome Annotation URL + required: false + description: TBD + annotations: + GenomicCoverageType: + title: Genomic Coverage Type + required: true + description: Genomic coverage + enum_range: + - Whole Genome + - Targeted Genome + - Beadchip Array + GenomicReference: + title: Genomic Reference + required: false + description: TBD + annotations: + GenomicReferenceURL: + title: Genomic Reference URL + required: false + description: TBD + annotations: + Gravidity: + title: Gravidity + required: false + description: Total number of pregnancies regardless of outcome + annotations: + HER2BreastCarcinomaCopyNumberTotal: + title: HER2 Breast Carcinoma Copy Number Total + required: false + description: Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values. + annotations: + HER2Status: + title: HER2 Status + required: false + description: TBD + annotations: + Height: + title: Height + required: false + description: TBD + annotations: + HereditaryCancerPredispositionSyndrome: + title: Hereditary Cancer Predisposition Syndrome + required: false + description: History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient. + annotations: + range: HereditaryCancerPredispositionSyndromeEnum + HistologicMorphologyCode: + title: Histologic Morphology Code + required: false + description: 'Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510' + annotations: + HistoneFamily: + title: Histone Family + required: false + description: The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones. + annotations: + range: HistoneFamilyEnum + HistoneVariant: + title: Histone Variant + required: false + description: The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones. + annotations: + range: HistoneVariantEnum + HormoneTherapyBreastCancerPreventionIndicator: + title: Hormone Therapy Breast Cancer Prevention Indicator + required: false + description: Did the patient receive hormonal therapy for prevention of breast cancer? + annotations: + range: HormoneTherapyBreastCancerPreventionIndicatorEnum + ImageID: + title: Image ID + required: false + description: Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML) + annotations: + ImagingAssayType: + title: Imaging Assay Type + required: false + description: Type of imaging assay + annotations: + range: ImagingAssayTypeEnum + Immersion: + title: Immersion + required: false + description: Immersion medium + annotations: + range: ImmersionEnum + Immunosuppression: + title: Immunosuppression + required: false + description: TBD + annotations: + InputCellsandNuclei: + title: Input Cells and Nuclei + required: false + description: 'Number of cells and number of nuclei input; entry format: number, number' + annotations: + Intron: + title: Intron + required: false + description: Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located. + annotations: + InvasiveDuctalBreastCarcinomaHistologicCategory: + title: Invasive Ductal Breast Carcinoma Histologic Category + required: false + description: The histologic subtype for the most common type of invasive breast carcinoma. + annotations: + range: InvasiveDuctalBreastCarcinomaHistologicCategoryEnum + InvasiveLobularBreastCarcinomaHistologicCategory: + title: Invasive Lobular Breast Carcinoma Histologic Category + required: false + description: The histologic subtype for an infiltrating lobular carcinoma of the breast. + annotations: + range: InvasiveLobularBreastCarcinomaHistologicCategoryEnum + IschemicTemperature: + title: Ischemic Temperature + required: false + description: Specify whether specimen experienced warm or cold ischemia. + annotations: + range: IschemicTemperatureEnum + IschemicTime: + title: Ischemic Time + required: false + description: Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value. + annotations: + KnownGeneticPredispositionMutation: + title: Known Genetic Predisposition Mutation + required: false + description: A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient. + annotations: + range: IndicatorEnum + LabID: + title: Lab ID + required: false + description: TBD + annotations: + LabTestsforMMRStatus: + title: Lab Tests for MMR Status + required: false + description: Laboratory tests used to evaluate the status of mismatch repair pathways + annotations: + range: LabTestsforMMRStatusEnum + LaboratoryTest: + title: Laboratory Test + required: false + description: The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease. + annotations: + range: LaboratoryTestEnum + Laterality: + title: Sample Laterality + required: false + description: For samples in paired organs, designates the side from which obtained. + annotations: + range: SpecimenLateralityEnum + LensNA: + title: LensNA + required: false + description: The numerical aperture of the lens. Floating point value > 0. + annotations: + LibraryConstructionMethod: + title: Library Construction Method + required: true + description: Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711] + annotations: + range: LibraryConstructionMethodEnum + LinkedDatasets: + title: Linked Datasets + required: false + description: TBD + annotations: + LinkedMatrices: + title: Linked Matrices + required: false + description: TBD + annotations: + LinkedProject: + title: Linked Project + required: false + description: TBD + annotations: + LociAbnormalCount: + title: Loci Abnormal Count + required: false + description: Numeric value used to describe the number of loci determined to be abnormal. + annotations: + LociCount: + title: Loci Count + required: false + description: Numeric value used to describe the number of loci tested. + annotations: + Locus: + title: Locus + required: false + description: 'Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.' + annotations: + Lot: + title: Lot + required: false + description: TBD + annotations: + MammaprintRiskGroup: + title: Mammaprint Risk Group + required: false + description: Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test. + annotations: + range: OncotypeRiskGroupEnum + MatrixType: + title: Matrix Type + required: false + description: TBD + annotations: + MedianFractionofReadsinAnnotatedcisDNAElements: + title: Median Fraction of Reads in Annotated cis DNA Elements + required: false + description: Median fraction of reads in annotated cis-DNA elements (FRIADE) + annotations: + MedianFractionofReadsinPeaks: + title: Median Fraction of Reads in Peaks + required: false + description: Median fraction of reads in peaks (FRIP) + annotations: + MedianPassingReadPercentage: + title: Median Passing Read Percentage + required: false + description: Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode + annotations: + MedianPercentageofMitochondrialReadsperNucleus: + title: Median Percentage of Mitochondrial Reads per Nucleus + required: false + description: Contamination from mitochondrial sequences + annotations: + MedianUMIsperCellNumber: + title: Median UMIs per Cell Number + required: false + description: Number + annotations: + MedicallyUnderservedArea: + title: Medically Underserved Area + required: false + description: TBD + annotations: + MenopauseStatus: + title: Menopause Status + required: false + description: TBD + annotations: + MenstrualCyclePhase: + title: Menstrual Cycle Phase + required: false + description: TBD + annotations: + MetalIsotopeElement: + title: Metal Isotope Element + required: false + description: TBD + annotations: + MetalIsotopeMass: + title: Metal Isotope Mass + required: false + description: TBD + annotations: + Microscope: + title: Microscope + required: false + description: Microscope type (manufacturer, model, etc) used for this experiment + annotations: + MismatchRepairMutation: + title: Mismatch Repair Mutation + required: false + description: 'The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + range: IndicatorEnum + MismatchRepairSystemStatus: + title: Mismatch Repair System Status + required: false + description: The text that best describes the condition or state of MMR (mismatch repair system) in the patient + annotations: + range: MismatchRepairSystemStatusEnum + ModeofCancerDetection: + title: Mode of Cancer Detection + required: false + description: Text term used to describe the mode of cancer detection, like standard of care screening or random detection + annotations: + range: ModeofCancerDetectionEnum + MolecularAnalysisMethod: + title: Molecular Analysis Method + required: false + description: 'The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + range: MolecularAnalysisMethodEnum + MolecularConsequence: + title: Molecular Consequence + required: false + description: 'The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + range: MolecularConsequenceEnum + MulticentricBreastCarcinomaPresentIndicator: + title: Multicentric Breast Carcinoma Present Indicator + required: false + description: A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from different clones and usually located in different quadrants of the breast. + annotations: + range: IndicatorEnum + MultifocalBreastCarcinomaPresentIndicator: + title: Multifocal Breast Carcinoma Present Indicator + required: false + description: A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from the same clone and usually located in the same quadrant of the breast. + annotations: + range: IndicatorEnum + MutationalSignatures: + title: Mutational Signatures + required: false + description: 'Mutational signatures identified in the patient, includes signatures linked to selected exogenous carcinogens, endogenous and enzymatic modification of DNA or defective DNA repair. Note: Include only outputs of tests that were completed clinically for the participant and only include data from a diagnostic array that was completed prior to research sequencing was done. ' + annotations: + range: MutationalSignaturesEnum + NominalMagnification: + title: NominalMagnification + required: false + description: The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units) + annotations: + NucleiBarcodeLength: + title: Nuclei Barcode Length + required: false + description: Nuclei Barcode Length + annotations: + NucleiBarcodeRead: + title: Nuclei Barcode Read + required: false + description: Nuclei Barcode Read + annotations: + NucleicAcidSource: + title: Nucleic Acid Source + required: false + description: The source of the input nucleic molecule + annotations: + range: NucleicAcidSourceEnum + NucleusIdentifier: + title: Nucleus Identifier + required: false + description: Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from + annotations: + range: NucleusIdentifierEnum + NumberofDrinksPerWeek: + title: Number of Drinks Per Week + required: false + description: TBD + annotations: + Objective: + title: Objective + required: false + description: Objective + annotations: + OligoBarcodeLowerStrand: + title: Oligo Barcode Lower Strand + required: false + description: TBD + annotations: + OligoBarcodeUpperStrand: + title: Oligo Barcode Upper Strand + required: false + description: TBD + annotations: + OncotypeRiskGroup: + title: Oncotype Risk Group + required: false + description: Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score. + annotations: + range: OncotypeRiskGroupEnum + OncotypeScore: + title: Oncotype Score + required: false + description: OncotypeDX recurrence score + annotations: + OtherBiopsyResectionSite: + title: Other Biopsy Resection Site + required: false + description: A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under Clinical Data Tier 1) + annotations: + OvarianCancerHistologicSubtype: + title: Ovarian Cancer Histologic Subtype + required: false + description: Text term to describe the histological subtype of ovarian cancer in the participant + annotations: + range: OvarianCancerHistologicSubtypeEnum + OvarianCancerPlatinumStatus: + title: Ovarian Cancer Platinum Status + required: false + description: Text term to indicate the status of treatment with platinum in participant with ovarian cancer + annotations: + range: OvarianCancerPlatinumStatusEnum + OvarianCancerSurgicalOutcome: + title: Ovarian Cancer Surgical Outcome + required: false + description: Text term that describes the kind of surgical treatment administered. + annotations: + range: OvarianCancerSurgicalOutcomeEnum + PRReceptorStatus: + title: Breast Carcinoma Progesterone Receptor Status + required: false + description: Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer + annotations: + range: ReceptorStatusEnum + PRStainingIntensity: + title: Breast Carcinoma PR Staining Intensity + required: false + description: Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer + annotations: + range: StainingIntensityEnum + PRStatus: + title: PR Status + required: false + description: TBD + annotations: + PackYearsSmoked: + title: Pack Years Smoked + required: false + description: Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20. + annotations: + ParentBiospecimenID: + title: Parent Biospecimen ID + required: false + description: ' Biospecimen identifier indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated' + annotations: + ParentID: + title: Parent ID + required: false + description: ' ID of parent biospecimen' + annotations: + Parity: + title: Parity + required: false + description: Number of pregnancies carried over the threshold of viability + annotations: + ParticipantID: + title: Participant ID + required: true + description: ' ID associated with a patient' + annotations: + PassedQC: + title: Passed QC + required: false + description: Did all channels pass QC (if not add free text Comment) + annotations: + range: PassedQCEnum + Pathogenicity: + title: Pathogenicity + required: false + description: The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG). + annotations: + range: PathogenicityEnum + PeaksCallingSoftware: + title: Peaks Calling Software + required: false + description: TBD + annotations: + PhysicalSizeX: + title: PhysicalSizeX + required: false + description: Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0. + annotations: + PhysicalSizeXUnit: + title: PhysicalSizeXUnit + required: false + description: 'The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)' + annotations: + range: MicroscopyUnitEnum + PhysicalSizeY: + title: PhysicalSizeY + required: false + description: Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0. + annotations: + PhysicalSizeYUnit: + title: PhysicalSizeYUnit + required: false + description: 'The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)' + annotations: + range: MicroscopyUnitEnum + PhysicalSizeZ: + title: PhysicalSizeZ + required: false + description: Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0. + annotations: + PhysicalSizeZUnit: + title: PhysicalSizeZUnit + required: false + description: 'The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)' + annotations: + range: MicroscopyUnitEnum + PixelType: + title: PixelType + required: false + description: Data type for each pixel value. E.g. ""uint16"" + annotations: + range: PixelTypeEnum + PixelsBigEndian: + title: Pixels BigEndian + required: false + description: Boolean (True/False) + annotations: + range: PixelsBigEndianEnum + PlaneCount: + title: PlaneCount + required: false + description: Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1 + annotations: + Ploidy: + title: Ploidy + required: false + description: Text term used to describe the number of sets of homologous chromosomes. + annotations: + range: PloidyEnum + PortionWeight: + title: Portion Weight + required: false + description: Numeric value that represents the sample portion weight, measured in milligrams. + annotations: + PrecancerousConditionType: + title: Precancerous Condition Type + required: false + description: The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL). + annotations: + range: PrecancerousConditionTypeEnum + PreservationMethod: + title: Preservation Method + required: false + description: Text term that represents the method used to preserve the sample. + annotations: + range: PreservationMethodEnum + PrimaryDiagnosis: + title: Primary Diagnosis + required: false + description: Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O). + annotations: + range: PrimaryDiagnosisEnum + PriorInvasiveBreastDisease: + title: Prior Invasive Breast Disease + required: false + description: Text term to indicate prior invasive breast condition in the participant + annotations: + range: PriorInvasiveBreastDiseaseEnum + PriorSitesofRadiation: + title: Prior Sites of Radiation + required: false + description: TBD + annotations: + ProgressionorRecurrenceAnatomicSite: + title: Progression or Recurrence Anatomic Site + required: false + description: TBD + annotations: + ProgressionorRecurrenceType: + title: Progression or Recurrence Type + required: false + description: TBD + annotations: + ProtocolLink: + title: Protocol Link + required: false + description: URL to a free/open protocol resource describing 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 sample was obtained or generated. + annotations: + PublicationDOI: + title: Publication DOI + required: false + description: TBD + annotations: + Pyramid: + title: Pyramid + required: false + description: Does data file contain pyramid of images + annotations: + range: PyramidEnum + RRIDidentifier: + title: RRID identifier + required: false + description: TBD + annotations: + Race: + title: Race + required: true + description: An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. + annotations: + range: RaceEnum + Read1: + title: Read1 + required: true + description: Read 1 content description + annotations: + range: ReadEnum + Read2: + title: Read2 + required: true + description: Read 2 content description + annotations: + range: ReadEnum + Read3: + title: Read3 + required: true + description: Read 3 content description + annotations: + range: ReadEnum + ReadIndicator: + title: Read Indicator + required: false + description: TBD + annotations: + RelationshipAgeatDiagnosis: + title: Relationship Age at Diagnosis + required: false + description: The age (in years) when the patient's relative was first diagnosed. + annotations: + RelationshipGender: + title: Relationship Gender + required: false + description: The text term used to describe the gender of the patient's relative with a history of cancer. + annotations: + range: SexEnum + RelationshipPrimaryDiagnosis: + title: Relationship Primary Diagnosis + required: false + description: The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer. + annotations: + range: RelationshipPrimaryDiagnosisEnum + RelationshipType: + title: Relationship Type + required: false + description: The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties. + annotations: + RelativeswithCancerHistoryCount: + title: Relatives with Cancer History Count + required: false + description: The number of relatives the patient has with a known history of cancer. + annotations: + RelativewithCancerHistory: + title: Relative with Cancer History + required: false + description: The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer. + annotations: + range: RelativewithCancerHistoryEnum + ReverseTranscriptionPrimer: + title: Reverse Transcription Primer + required: false + description: An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA + annotations: + range: ReverseTranscriptionPrimerEnum + RuralvsUrban: + title: Rural vs Urban + required: false + description: TBD + annotations: + SampleCollectionCenter: + title: Sample Collection Center + required: false + description: TBD + annotations: + SampleCollectionYear: + title: Sample Collection Year + required: false + description: TBD + annotations: + SampleID: + title: Sample ID + required: true + description: ' ID associated with a biosample' + annotations: + SampleSite: + title: Sample Site + required: false + description: TBD + annotations: + SatelliteMetastasisPresentIndicator: + title: Satellite Metastasis Present Indicator + required: false + description: A yes/no indicator to ask if intransit metastases or satellite lesions are present. + annotations: + range: SatelliteMetastasisPresentIndicatorEnum + ScATACseqLibraryLayout: + title: scATACseq Library Layout + required: false + description: Sequencing read type + annotations: + range: ScATACseqLibraryLayoutEnum + ScRNAseqWorkflowParametersDescription: + title: scRNAseq Workflow Parameters Description + required: false + description: TBD + annotations: + ScRNAseqWorkflowType: + title: scRNAseq Workflow Type + required: false + description: TBD + annotations: + SecondExon: + title: Second Exon + required: false + description: The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation. + annotations: + SecondGeneSymbol: + title: Second Gene Symbol + required: false + description: 'The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + SecondhandSmokeasChild: + title: Secondhand Smoke as Child + required: false + description: The text term used to indicate whether the patient was exposed to secondhand smoke as a child. + annotations: + range: HistoryEnum + Secondhandsmokeexposureyears: + title: Second hand smoke exposure years + required: false + description: TBD + annotations: + SectionNumberinSequence: + title: Section Number in Sequence + required: false + description: Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field) + annotations: + SectionThicknessValue: + title: Section Thickness Value + required: false + description: Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um). + annotations: + SectioningDaysfromIndex: + title: Sectioning Days from Index + required: false + description: Number of days from the research participant's index date that the biospecimen was sectioned after collection + annotations: + SentinelLymphNodeCount: + title: Sentinel Lymph Node Count + required: false + description: Numeric count of sentinel lymph nodes. + annotations: + SentinelNodePositiveAssessmentCount: + title: Sentinel Node Positive Assessment Count + required: false + description: The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor. + annotations: + SequencingPlatform: + title: Sequencing Platform + required: true + description: A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument. + annotations: + range: SequencingPlatformEnum + Sex: + title: Sex + required: true + description: Sex of individual + annotations: + range: SexEnum + ShippingConditionType: + title: Shipping Condition Type + required: false + description: Text descriptor of the shipping environment of a biospecimen. + annotations: + range: ShippingConditionTypeEnum + SingleCellIsolationMethod: + title: Single Cell Isolation Method + required: true + description: The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets) + annotations: + range: SingleCellIsolationMethodEnum + SingleNucleusBuffer: + title: Single Nucleus Buffer + required: false + description: Nuclei isolation buffer + annotations: + range: SingleNucleusBufferEnum + SiteofResectionorBiopsy: + title: Site of Resection or Biopsy + required: false + description: The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O). + annotations: + range: SiteofResectionorBiopsyEnum + SizeC: + title: SizeC + required: false + description: Number of channels. Integer >= 1 + annotations: + SizeT: + title: SizeT + required: false + description: Number of time points. Integer >= 1 + annotations: + SizeX: + title: SizeX + required: false + description: 'Size of image: X dimension (in pixels). Integer >= 1' + annotations: + SizeY: + title: SizeY + required: false + description: 'Size of image: Y dimension (in pixels). Integer >= 1' + annotations: + SizeZ: + title: SizeZ + required: false + description: 'Size of image: Z dimension (in pixels). Integer >= 1' + annotations: + SlideChargeType: + title: Slide Charge Type + required: false + description: A description of the charge on the glass slide. + annotations: + range: SlideChargeTypeEnum + SmokeExposureDuration: + title: Smoke Exposure Duration + required: false + description: TBD + annotations: + SmokelessTobaccoQuitAge: + title: Smokeless Tobacco Quit Age + required: false + description: TBD + annotations: + SmokingExposure: + title: Smoking Exposure + required: false + description: Indicate if individual has smoking exposure + annotations: + range: SmokingExposureEnum + SmokingFrequency: + title: Smoking Frequency + required: false + description: The text term used to generally decribe how often the patient smokes. + annotations: + range: SmokingFrequencyEnum + SoftwareandVersion: + title: Software and Version + required: false + description: TBD + annotations: + SpecializedMolecularTest: + title: Specialized Molecular Test + required: false + description: 'Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + SpecimenLaterality: + title: Specimen Laterality + required: false + description: For samples in paired organs, designates the side from which obtained. + annotations: + range: SpecimenLateralityEnum + SpikeIn: + title: Spike In + required: true + description: A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix + annotations: + range: SpikeInEnum + StartDaysfromIndex: + title: Start Days from Index + required: false + description: Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable' + annotations: + StopDaysfromIndex: + title: Stop Days from Index + required: false + description: 'Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is ''Not Applicable''' + annotations: + SubCycleNumber: + title: Sub Cycle Number + required: false + description: TBD + annotations: + TargetName: + title: Target Name + required: false + description: TBD + annotations: + TechnicalReplicateGroup: + title: Technical Replicate Group + required: false + description: A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch) + annotations: + TestAnalyteType: + title: Test Analyte Type + required: false + description: 'The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + range: TestAnalyteTypeEnum + TestResult: + title: Test Result + required: false + description: 'The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + range: TestResultEnum + TestUnits: + title: Test Units + required: false + description: 'The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + TestValue: + title: Test Value + required: false + description: 'The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here' + annotations: + ThresholdforMinimumPassingReads: + title: Threshold for Minimum Passing Reads + required: false + description: Threshold for calling cells + annotations: + TimebetweenWakingandFirstSmoke: + title: Time between Waking and First Smoke + required: false + description: TBD + annotations: + TimepointLabel: + title: Timepoint Label + required: false + description: Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED. + annotations: + Title: + title: Title + required: false + description: TBD + annotations: + TobaccoSmokingOnsetYear: + title: Tobacco Smoking Onset Year + required: false + description: TBD + annotations: + TobaccoSmokingQuitYear: + title: Tobacco Smoking Quit Year + required: false + description: TBD + annotations: + TobaccoSmokingStatus: + title: Tobacco Smoking Status + required: false + description: Category describing current smoking status and smoking history as self-reported by a patient + annotations: + range: TobaccoSmokingStatusEnum + TobaccoUse: + title: Tobacco Use + required: false + description: TBD + annotations: + TobaccoUseperDay: + title: Tobacco Use per Day + required: false + description: Numeric value that represents the number of times the patient uses tobacco each day. + annotations: + TotalNumberofInputCells: + title: Total Number of Input Cells + required: false + description: Number of cells loaded/placed on plates + annotations: + TotalNumberofPassingNuclei: + title: Total Number of Passing Nuclei + required: false + description: Number of nuclei sequenced + annotations: + TotalReads: + title: Total Reads + required: false + description: Total number of reads per sample. Integer + annotations: + TotalVolume: + title: Total Volume + required: false + description: Numeric value for the total amount of sample or specimen + annotations: + TotalVolumeUnit: + title: Total Volume Unit + required: false + description: Unit of measurement used for the total amount of sample or specimen + annotations: + range: TotalVolumeUnitEnum + Transcript: + title: Transcript + required: false + description: 'Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + TranspositionReaction: + title: Transposition Reaction + required: false + description: Name of the transposase, transposon sequences + annotations: + range: TranspositionReactionEnum + Tseries: + title: Tseries + required: false + description: Does data file contain a time-series of images + annotations: + range: TseriesEnum + TumorExtranodalExtensionIndicator: + title: Tumor Extranodal Extension Indicator + required: false + description: The indicator to determine extranodal involvement or extent of the disease. + annotations: + range: TumorExtranodalExtensionIndicatorEnum + TumorTissueType: + title: Tumor Tissue Type + required: false + description: 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) + annotations: + range: TumorTissueTypeEnum + TypeofSmokeExposure: + title: Type of Smoke Exposure + required: false + description: TBD + annotations: + TypeofTobaccoUsed: + title: Type of Tobacco Used + required: false + description: TBD + annotations: + Typeofsmokeexposurecumulativeyears: + title: Type of smoke exposure cumulative years + required: false + description: TBD + annotations: + UMIBarcodeLength: + title: UMI Barcode Length + required: false + description: 'Length of UMI barcode read (in bp): number' + annotations: + UMIBarcodeOffset: + title: UMI Barcode Offset + required: false + description: 'Start position of UMI barcode in the sequence. Values: number, 0 for start of read' + annotations: + UMITag: + title: UMI Tag + required: false + description: TBD + annotations: + ValidBarcodesCellNumber: + title: Valid Barcodes Cell Number + required: false + description: Number + annotations: + VariantOrigin: + title: Variant Origin + required: false + description: 'The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.' + annotations: + range: VariantOriginEnum + VariantType: + title: Variant Type + required: false + description: The text term used to describe the type of genetic variation. + annotations: + range: VariantTypeEnum + VascularInvasionType: + title: Vascular Invasion Type + required: false + description: Text term that represents the type of vascular tumor invasion. + annotations: + range: VascularInvasionTypeEnum + Vendor: + title: Vendor + required: false + description: TBD + annotations: + VitalStatus: + title: Vital Status + required: false + description: The survival state of the person registered on the protocol. + annotations: + range: VitalStatusEnum + Weight: + title: Weight + required: false + description: TBD + annotations: + WellIndex: + title: Well Index + required: false + description: Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays + annotations: + range: WellIndexEnum + WhitelistCellBarcodeFileLink: + title: Whitelist Cell Barcode File Link + required: false + description: TBD + annotations: + WorkflowLink: + title: Workflow Link + required: false + description: TBD + annotations: + WorkflowVersion: + title: Workflow Version + required: false + description: TBD + annotations: + WorkingDistance: + title: WorkingDistance + required: false + description: The working distance of the lens, expressed as a floating point number. Floating point > 0. + annotations: + WorkingDistanceUnit: + title: WorkingDistanceUnit + required: false + description: 'The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)' + annotations: + range: MicroscopyUnitEnum + YearOfBirth: + title: Year Of Birth + required: false + description: Numeric value to represent the calendar year in which an individual was born. + annotations: + YearofDeath: + title: Year of Death + required: false + description: Numeric value to represent the year of the death of an individual. + annotations: + YearsSmoked: + title: Years Smoked + required: false + description: Numeric value (or unknown) to represent the number of years a person has been smoking. + annotations: + Zstack: + title: Zstack + required: false + description: Does data file contain a Z-stack of images + annotations: + range: ZstackEnum + Zygosity: + title: Zygosity + required: false + description: The text term used to describe the zygosity of a specific genetic variant. + annotations: + range: ZygosityEnum diff --git a/tests/generate/basic_templates.sh b/tests/generate/basic_templates.sh index c7ae29b..e592441 100755 --- a/tests/generate/basic_templates.sh +++ b/tests/generate/basic_templates.sh @@ -24,8 +24,12 @@ else fi # Setup config -echo "Getting $CONFIG to use as test config..." -wget $CONFIG -O $TEST_CONFIG +if [ -f "$TEST_CONFIG" ]; then + echo "Local $TEST_CONFIG present, running test with this local config..." +else + echo "Getting $CONFIG to use as test config..." + wget $CONFIG -O $TEST_CONFIG +fi TEMPLATES=($(jq '.manifest_schemas[] | .schema_name' $TEST_CONFIG | tr -d '"')) #TITLES=($(jq '.manifest_schemas[] | .display_name' $TEST_CONFIG | tr -d '"'))