diff --git a/NF.csv b/NF.csv index 0f72e9b4..eee978ab 100644 --- a/NF.csv +++ b/NF.csv @@ -91,6 +91,7 @@ Massively Parallel Reporter Assay,An assay in which multiplexing the constructio Riccardi and Ablon scales,"The Riccardi and Ablon scales score severity and visibility of disease, respectively, and are commonly used as a combined assessment for NF1 patients in clinical settings. See https://doi.org/10.1001/archderm.137.11.1421 for example usage.",,,FALSE,https://doi.org/10.1001/archderm.137.11.1421,assay,,,,Riccardi_Ablon_Scales,Class,Assay,Assay,Clinical_Assay,,, Spatial Frequency Domain Imaging,"Spatial Frequency Domain Imaging (SFDI) is a non-contact, depth-varying and wide-field optical imaging technique for measuring optical properties in a wide field-of-view on a pixel-by-pixel basis. Relevant applications include including burn assessment, skin tissue evaluation, tumor tissue detection, brain tissue monitoring.",,,FALSE,https://doi.org/10.3390/photonics8050162,assay,,,,Spatial_Frequency_Domain_Imaging,Class,Assay,Assay,Imaging_Assay,,,Note that term has no matches in OLS as of June 2022. Optical Coherence Tomography,"Optical Coherence Tomography (OCT) combines the principles of ultrasound with the imaging performance of a microscope. OCT uses infrared light waves that reflect off the internal microstructure within the biological tissues. The frequencies and bandwidths of infrared light are orders of magnitude higher than medical ultrasound signals, resulting in greatly increased image resolution, 8-25 times greater than any existing modality. In addition to providing high-level resolutions for the evaluation of microanatomic structures OCT is also able to provide information regarding tissue composition",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C20828,assay,,,,Optical_Coherence_Tomography,Class,Assay,Assay,Imaging_Assay,,, +CUT&RUN,"Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. (doi:10.7554/eLife.21856)",,,FALSE,,assay,,,,CUT_RUN,Class,Assay,Assay,Epigenetics_Assay,,, channel,Fluorescent color labeling for an array,"Cy5, Cy3","",TRUE,"",array,,"","",Channel,"",Assay,Assay_Parameter,"","","","" photograph,An image recorded by a camera.,"","",FALSE,http://purl.obolibrary.org/obo/NCIT_C86035,assay,,"","",Photograph,"",Assay,Assay_Parameter,"","","","" MRISequence,The scanning sequence/modality that is used for a conventional MRI scan.,"T1-weighted,T2-weighted,PD-weighted,Short Tau Inversion Recovery","",FALSE,Sage Bionetworks,experimentalData,,"","",MRI_Sequence,Class,Assay,Assay_Parameter,"","","","" @@ -150,52 +151,52 @@ Orbitrap Fusion Lumos Tribrid,Thermo Scientific Orbitrap Fusion Lumos Tribrid Ma Spectramax M Series,A Spectramax M Series Microplate Reader,,,FALSE,https://www.moleculardevices.com/products/microplate-readers/multi-mode-readers/spectramax-m-series-readers,platform,,,,Spectramax_M_Series,Class,Assay,Platform,Platform,,, LI-COR Odyssey CLx,A LI-COR Odyssey CLx imaging system,,,FALSE,https://www.licor.com/bio/odyssey-clx/,platform,,,,LI-COR_Odyssey_Clx,Class,Assay,Platform,Platform,,, Q Exative HF,Thermo scientific Q Exative,,,FALSE,http://purl.obolibrary.org/obo/MS_10025223,platform,,,,Q_Exative_HF,Class,Assay,Platform,Platform,,, -HiSeq3000,Illumina HiSeq 3000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21290,platform,,,,HiSeq3000,Class,Assay,Platform,Platform,,, -HiSeq2500,Illumina HiSeq 2500,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16791,platform,,,,HiSeq2500,Class,Assay,Platform,Platform,,, -HiSeq4000,Illumina HiSeq 4000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20301,platform,,,,HiSeq4000,Class,Assay,Platform,Platform,,, -NextSeq500,Illumina NextSeq 500,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18573,platform,,,,NextSeq500,Class,Assay,Platform,Platform,,, -NextSeq 550,Illumina NextSeq 550,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21697,platform,,,,NextSeq 550,Class,Assay,Platform,Platform,,, -NextSeq 1000,Illumina NextSeq 1000,,,FALSE,,platform,,,,NextSeq 1000,Class,Assay,Platform,Platform,,, -NextSeq 2000,Illumina NextSeq 2000,,,FALSE,,platform,,,,NextSeq 2000,Class,Assay,Platform,Platform,,, -HiSeq2000,Illumina HiSeq 2000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL11154,platform,,,,HiSeq2000,Class,Assay,Platform,Platform,,, -MiSeq,Illumina MiSeq,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15520,platform,,,,MiSeq,Class,Assay,Platform,Platform,,, +Illumina HiSeq 3000,Illumina HiSeq 3000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21290,platform,,,,HiSeq3000,Class,Assay,Platform,Platform,,, +Illumina HiSeq 2500,Illumina HiSeq 2500,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16791,platform,,,,HiSeq2500,Class,Assay,Platform,Platform,,, +Illumina HiSeq 4000,Illumina HiSeq 4000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20301,platform,,,,HiSeq4000,Class,Assay,Platform,Platform,,, +Illumina NextSeq 500,Illumina NextSeq 500,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18573,platform,,,,NextSeq500,Class,Assay,Platform,Platform,,, +Illumina NextSeq 550,Illumina NextSeq 550,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21697,platform,,,,NextSeq 550,Class,Assay,Platform,Platform,,, +Illumina NextSeq 1000,Illumina NextSeq 1000,,,FALSE,,platform,,,,NextSeq 1000,Class,Assay,Platform,Platform,,, +Illumina NextSeq 2000,Illumina NextSeq 2000,,,FALSE,,platform,,,,NextSeq 2000,Class,Assay,Platform,Platform,,, +Illumina HiSeq 2000,Illumina HiSeq 2000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL11154,platform,,,,HiSeq2000,Class,Assay,Platform,Platform,,, +Illumina MiSeq,Illumina MiSeq,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15520,platform,,,,MiSeq,Class,Assay,Platform,Platform,,, Zeiss LSM 980,A Zeiss Confocal Microscope,,,FALSE,https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwirj4XuwtXsAhVBrp4KHVZyARIQFjABegQIAhAC&url=https%3A%2F%2Fzeiss.ly%2Flsm980-info&usg=AOvVaw0rD50U0aMwfvt4bdfW0Yjd,platform,,,,Zeiss LSM 980,Class,Assay,Platform,Platform,,, -Affy5.0,Affymetrix Genome-Wide Human SNP 5.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6804,platform,,,,Affy5.0,Class,Assay,Platform,Platform,,, -Affy6.0,Affymetrix Genome-Wide Human SNP 6.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6801,platform,,,,Affy6.0,Class,Assay,Platform,Platform,,, -PacBioRSII,PacBio RS II,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21311,platform,,,,PacBioRSII,Class,Assay,Platform,Platform,,, -GAIIx,Illumina Genome Analyzer IIx,,,FALSE,https://support.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet_genome_analyzeriix.pdf,platform,,,,GAIIx,Class,Assay,Platform,Platform,,, -Illumina_HumanOmni1-Quadv1.0,,,,FALSE,https://www.illumina.com/documents/products/datasheets/datasheet_humanomni1_quad.pdf,platform,,,,Illumina_HumanOmni1-Quadv1.0,Class,Assay,Platform,Platform,,, -Illumina_1M,,,,FALSE,,platform,,,,Illumina_1M,Class,Assay,Platform,Platform,,, -Illumina_h650,,,,FALSE,,platform,,,,Illumina_h650,Class,Assay,Platform,Platform,,, -Illumina_Omni2pt5M,,,,FALSE,,platform,,,,Illumina_Omni2pt5M,Class,Assay,Platform,Platform,,, -Illumina_Omni5M,,,,FALSE,,platform,,,,Illumina_Omni5M,Class,Assay,Platform,Platform,,, +Affymetrix Genome-Wide Human SNP 5.0 Array,Affymetrix Genome-Wide Human SNP 5.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6804,platform,,,,Affy5.0,Class,Assay,Platform,Platform,,, +Affymetrix Genome-Wide Human SNP 6.0 Array,Affymetrix Genome-Wide Human SNP 6.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6801,platform,,,,Affy6.0,Class,Assay,Platform,Platform,,, +PacBio RS II,PacBio RS II,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21311,platform,,,,PacBioRSII,Class,Assay,Platform,Platform,,, +Illumina Genome Analyzer IIx,Illumina Genome Analyzer IIx,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16061,platform,,,,GAIIx,Class,Assay,Platform,Platform,,, +Illumina HumanOmni1-Quadv1.0,,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL24663,platform,,,,Illumina_HumanOmni1-Quadv1.0,Class,Assay,Platform,Platform,,, +Illumina 1M,,,,FALSE,,platform,,,,Illumina_1M,Class,Assay,Platform,Platform,,, +Illumina h650,,,,FALSE,,platform,,,,Illumina_h650,Class,Assay,Platform,Platform,,, +Illumina Omni2pt5M,,,,FALSE,,platform,,,,Illumina_Omni2pt5M,Class,Assay,Platform,Platform,,, +Illumina Omni5M,,,,FALSE,,platform,,,,Illumina_Omni5M,Class,Assay,Platform,Platform,,, Illumina MouseWG-6 v2.0 expression beadchip,Whole-genome expression profiling in the mouse,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6887,platform,,,,Illumina MouseWG-6_v2.0_expression_beadchip,Class,Assay,Platform,Platform,,, -Perlegen300Karray,,,,FALSE,,platform,,,,Perlegen300Karray,Class,Assay,Platform,Platform,,, -Agilent44Karray,,,,FALSE,,platform,,,,Agilent44Karray,Class,Assay,Platform,Platform,,, -IlluminaWholeGenomeDASL,Illumina Human Whole-Genome DASL HT,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13369,platform,,,,IlluminaWholeGenomeDASL,Class,Assay,Platform,Platform,,, -IlluminaHumanHap300,,,,FALSE,,platform,,,,IlluminaHumanHap300,Class,Assay,Platform,Platform,,, -NanostringnCounter,,,,FALSE,,platform,,,,NanostringnCounter,Class,Assay,Platform,Platform,,, +Perlegen 300Karray,,,,FALSE,,platform,,,,Perlegen300Karray,Class,Assay,Platform,Platform,,, +Agilent 44Karray,,,,FALSE,,platform,,,,Agilent44Karray,Class,Assay,Platform,Platform,,, +Illumina WholeGenome DASL,Illumina Human Whole-Genome DASL HT,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13369,platform,,,,IlluminaWholeGenomeDASL,Class,Assay,Platform,Platform,,, +Illumina HumanHap300,,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6083,platform,,,,IlluminaHumanHap300,Class,Assay,Platform,Platform,,, +Nanostring Counter,,,,FALSE,,platform,,,,NanostringCounter,Class,Assay,Platform,Platform,,, LTQ Orbitrap XL,LTQ Orbitrap XL Hybrid Ion Trap-Orbitrap Mass Spectrometer,,,FALSE,https://www.thermofisher.com/order/catalog/product/IQLAAEGAAPFADBMAOK,platform,,,,LTQ_Orbitrap_XL,Class,Assay,Platform,Platform,,, -IlluminaHumanMethylation450,Illumina HumanMethylation450 BeadChip,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13534,platform,,,,IlluminaHumanMethylation450,Class,Assay,Platform,Platform,,, +Illumina HumanMethylation450,Illumina HumanMethylation450 BeadChip,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13534,platform,,,,IlluminaHumanMethylation450,Class,Assay,Platform,Platform,,, Illumina Infinium MethylationEPIC BeadChip,"An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002131,platform,,,,Illumina Infinium MethylationEPIC_BeadChip,Class,Assay,Platform,Platform,,, -AffymetrixU133AB,,,,FALSE,,platform,,,,AffymetrixU133AB,Class,Assay,Platform,Platform,,, +Affymetrix U133AB,,,,FALSE,,platform,,,,AffymetrixU133AB,Class,Assay,Platform,Platform,,, Affymetrix Human Gene 1.0 ST Array,Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] in situ oligonucleotide,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6244,platform,,,,Affymetrix_Human_Gene_1.0_ST_Array,Class,Assay,Platform,Platform,,, -AffymetrixU133Plus2,Affymetrix Human Genome U133 Plus 2.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570,platform,,,,AffymetrixU133Plus2,Class,Assay,Platform,Platform,,, -HiSeqX,Illumina HiSeq X Platform for whole-genome sequencing,,,FALSE,https://www.illumina.com/systems/sequencing-platforms/hiseq-x.html,platform,,,,HiSeqX,Class,Assay,Platform,Platform,,, +Affymetrix Human Genome U133 Plus 2.0 Array,Affymetrix Human Genome U133 Plus 2.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570,platform,,,,AffymetrixU133Plus2,Class,Assay,Platform,Platform,,, +Illumina HiSeq X,Illumina HiSeq X Platform for whole-genome sequencing,,,FALSE,https://www.illumina.com/systems/sequencing-platforms/hiseq-x.html,platform,,,,HiSeqX,Class,Assay,Platform,Platform,,, Bionano Irys,Performs whole genome mapping in a nanoscale fluidic environment enabling the structure of the genome to be imaged and then analyzed at the single molecule level,,,FALSE,https://bionanogenomics.com/products/irys/,platform,,,,Bionano_Irys,Class,Assay,Platform,Platform,,, Infinium HumanOmniExpressExome,Infinium HumanOmniExpressExome BeadChip,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18224,platform,,,,Infinium_HumanOmniExpressExome,Class,Assay,Platform,Platform,,, Illumina NovaSeq 6000,"A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002630,platform,,,,Illumina_NovaSeq_6000,Class,Assay,Platform,Platform,,, PacBio Sequel IIe System,PacBio Sequel IIe System,,,FALSE,,platform,,,,PacBio_Sequel_Iie_System,Class,Assay,Platform,Platform,,, PacBio Sequel II System,PacBio Sequel II System,,,FALSE,,platform,,,,PacBio_Sequel_II_System,Class,Assay,Platform,Platform,,, -NanostringGeoMx,NanostringGeoMx,,,FALSE,,platform,,,,Nanostring_GeoMx,Class,Assay,Platform,Platform,,, +Nanostring GeoMx,NanostringGeoMx,,,FALSE,,platform,,,,Nanostring_GeoMx,Class,Assay,Platform,Platform,,, Chromium X,"(From 10x Genomics) Single-cell platform that can analyze hundreds to hundreds of thousands of cells in single run for e.g. gene expression, chromatin accessibility, cell surface proteins, immune clonotype, antigen specificity, CRISPR perturbation screens).",,,FALSE,https://www.10xgenomics.com/chromium-x,platform,,,,Chromium_X,Class,Assay,Platform,Platform,,, 10x Visium Spatial Gene Expression,"10x Genomics product that includes special slides, reagents and technology to allow whole transcriptome profiling with morphological (spatial) context in FFPE or fresh-frozen tissues. Vendor ref: https://www.10xgenomics.com/products/spatial-gene-expression",,,FALSE,http://www.ebi.ac.uk/efo/EFO_0010961,platform,,,,10x_Visium_Spatial_Gene_Expression,Class,Assay,Platform,Platform,,, EnVision 2103 Multiplate Reader,EnVision 2103 Multiplate Reader,,,FALSE,,platform,,,,EnVision_2103,Class,Assay,Platform,Platform,,, Vectra H1 3D Imaging System,"(From vendor) Handheld imaging system for clinical-quality 3D imaging; applications for facial aesthetics and clinical documention.",,,FALSE,https://www.canfieldsci.com/imaging-systems/vectra-h1-3d-imaging-system/,platform,,,,Vectra_H1,Class,Assay,Platform,Platform,,, Vevo 3100 Imaging System,"(From vendor) A micro-ultrasound imaging system for anatomical, hemodynamic, functional, and molecular data all in one platform.",,,FALSE,https://www.visualsonics.com/product/imaging-systems/vevo-3100,platform,,,,Vectra_H1,Class,Assay,Platform,Platform,,, drugScreenType,String describing general class of drug screen,"singleMolecule, smallMoleculeLibraryScreen, combinationLibraryScreen, combinationScreen",,FALSE,,compoundScreen,,,,drugScreenType,Property,Assay,annotationProperty,,,, -assay,The technology used to generate the data in this file,"elevated plus maze test, open field test, rotarod performance test, mRNAcounts, high content screen, Immunocytochemistry, immunofluorescence, autoradiography, electrochemiluminescence, Real Time PCR, in vivo tumor growth, scale, Blood Chemistry Measurement, in vivo bioluminescence, immunohistochemistry, NOMe-Seq, FIA-MSMS, UPLC-MSMS, HPLC-MSMS, liquid chromatography-electrochemical detection, rnaSeq, mirnaSeq, LC-MSMS, LC-MS, lncrnaSeq, Whole Exome Sequencing, Sanger sequencing, ChIPSeq, rnaArray, snpArray, methylationArray, mirnaArray, bisulfiteSeq, ATACSeq, HI-C, errBisulfiteSeq, ISOSeq, westernBlot, wholeGenomeSeq, polymeraseChainReaction, cellViabilityAssay, atomicForceMicroscopy, brightfieldMicroscopy, tractionForceMicroscopy, nextGenerationTargetedSequencing, jumpingLibrary, MIB/MS, scCGIseq, MudPIT, questionnaire, DNA optical mapping, oxBS-Seq, Ribo-Seq, Positron Emission Tomography, RPPA, ELISA, LTP, LFP, whole-cell patch clamp, sandwich ELISA, Laser Speckle Imaging, Genotyping, TMT quantitation, label free mass spectrometry, cell count, reporter gene assay, Single Cell RNA Sequencing, spatial transcriptomics, Conventional MRI, Functional MRI, Magnetic Resonance Spectroscopy, 2D Incucyte, 2D CellTiter-Glo, 3D microtissue viability, in vivo PDX viability, 2D AlamarBlue fluorescence, 2D AlamarBlue absorbance, rheometry, FTIR Spectroscopy, differential scanning calorimetry, Gel filtration chromatography, Massively Parallel Reporter Assay,Riccardi and Ablon scales,Spatial Frequency Domain Imaging,Optical Coherence Tomography",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one, -platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","HiSeq3000, HiSeq2500, HiSeq4000, NextSeq500, HiSeq2000, MiSeq, Zeiss LSM 980, Affy5.0, Affy6.0, PacBioRSII, GAIIx, Illumina_HumanOmni1-Quadv1.0, Illumina_1M, Illumina_h650, Illumina_Omni2pt5M, Illumina_Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen300Karray, Agilent44Karray, IlluminaWholeGenomeDASL, IlluminaHumanHap300, NanostringnCounter, LTQOrbitrapXL, IlluminaHumanMethylation450, Illumina Infinium MethylationEPIC BeadChip, AffymetrixU133AB, Affymetrix Human Gene 1.0 ST Array, AffymetrixU133Plus2, HiSeqX, Bionano Irys, Infinium HumanOmniExpressExome, NextSeq 550, NextSeq 1000, NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, NanostringGeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader,Vectra H1 3D Imaging System,Vevo 3100 Imaging System,10x Visium Spatial Gene Expression",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,, +assay,The technology used to generate the data in this file,"elevated plus maze test, open field test, rotarod performance test, mRNAcounts, high content screen, Immunocytochemistry, immunofluorescence, autoradiography, electrochemiluminescence, Real Time PCR, in vivo tumor growth, scale, Blood Chemistry Measurement, in vivo bioluminescence, immunohistochemistry, NOMe-Seq, FIA-MSMS, UPLC-MSMS, HPLC-MSMS, liquid chromatography-electrochemical detection, rnaSeq, mirnaSeq, LC-MSMS, LC-MS, lncrnaSeq, Whole Exome Sequencing, Sanger sequencing, ChIPSeq, rnaArray, snpArray, methylationArray, mirnaArray, bisulfiteSeq, ATACSeq, HI-C, errBisulfiteSeq, ISOSeq, westernBlot, wholeGenomeSeq, polymeraseChainReaction, cellViabilityAssay, atomicForceMicroscopy, brightfieldMicroscopy, tractionForceMicroscopy, nextGenerationTargetedSequencing, jumpingLibrary, MIB/MS, scCGIseq, MudPIT, questionnaire, DNA optical mapping, oxBS-Seq, Ribo-Seq, Positron Emission Tomography, RPPA, ELISA, LTP, LFP, whole-cell patch clamp, sandwich ELISA, Laser Speckle Imaging, Genotyping, TMT quantitation, label free mass spectrometry, cell count, reporter gene assay, Single Cell RNA Sequencing, spatial transcriptomics, Conventional MRI, Functional MRI, Magnetic Resonance Spectroscopy, 2D Incucyte, 2D CellTiter-Glo, 3D microtissue viability, in vivo PDX viability, 2D AlamarBlue fluorescence, 2D AlamarBlue absorbance, rheometry, FTIR Spectroscopy, differential scanning calorimetry, Gel filtration chromatography, Massively Parallel Reporter Assay,Riccardi and Ablon scales,Spatial Frequency Domain Imaging,Optical Coherence Tomography,CUT&RUN",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one, +platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","Illumina HiSeq 3000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina NextSeq 500, Illumina HiSeq 2000, Illumina MiSeq, Zeiss LSM 980, Affymetrix Genome-Wide Human SNP 5.0 Array, Affymetrix Genome-Wide Human SNP 6.0 Array, PacBio RS II, Illumina Genome Analyzer IIx, Illumina HumanOmni1-Quadv1.0, Illumina 1M, Illumina h650, Illumina Omni2pt5M, Illumina Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen 300Karray, Agilent 44Karray, Illumina WholeGenome DASL, Illumina HumanHap300, Nanostring Counter, LTQ Orbitrap XL, Illumina HumanMethylation450, Illumina Infinium MethylationEPIC BeadChip, Affymetrix U133AB, Affymetrix Human Gene 1.0 ST Array, Affymetrix Human Genome U133 Plus 2.0 Array, Illumina HiSeq X, Bionano Irys, Infinium HumanOmniExpressExome, Illumina NextSeq 550, Illumina NextSeq 1000, Illumina NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, Nanostring GeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader,Vectra H1 3D Imaging System,Vevo 3100 Imaging System,10x Visium Spatial Gene Expression",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,, targetCaptureKitID,"A unique identifier for the kit used to construct a genomic library using target capture-based techniques, which should be composed of the vendor name, kit name and kit version.",,,TRUE,http://purl.obolibrary.org/obo/NCIT_C177583,experimentalData,,,,targetCaptureKitID,Property,Assay,annotationProperty,,,,"For WES processing, the target BED used could be provided based on the target capture kit." libraryID,,,,TRUE,,experimentalData,,,,libraryID,Property,Assay,annotationProperty,,,, assayTarget,The HUGO gene symbol that represents the target analyte assayed.,,,FALSE,Sage Bionetworks,experimentalData,,,,assayTarget,Property,Assay,annotationProperty,,,, @@ -394,6 +395,7 @@ AC007-hTERT,"Human arachnoid cell line","","",FALSE,"",modelSystemName,,"","",AC NF2-/- AC007-hTERT,"Knock-out cell line developed by CRISPR targeting NF2 exon 8 in AC007-hTERT","","",FALSE,"",modelSystemName,,"","",hTERT_NF2_arachnoid,Class,Biosample,Model_System,Cell_Line_Model,"","","" Ben-Men-1,"Human meningioma cell line (RRID:CVCL_1959)","","",FALSE,"https://web.expasy.org/cellosaurus/CVCL_1959",modelSystemName,,"","",Ben-Men-1,Class,Biosample,Model_System,Cell_Line_Model,"","","" human foreskin fibroblasts,"generic human foreskin fibroblasts, often used as a control cell in toxicology experiments","","",FALSE,Sage Bionetworks,modelSystemName,,"","",human foreskin fibroblasts,Class,Biosample,Cell,fibroblasts,"","","" +M3 MPNST,"A patient-derived MPNST cell line","","",FALSE,Sage Bionetworks,modelSystemName,,"","",M3_MPNST,Class,Biosample,Cell,Cell_Line_Model,"","","" Male,"A person who belongs to the sex that normally produces sperm. The term is used to indicate biological sex distinctions, cultural gender role distinctions, or both.","","",FALSE,http://purl.obolibrary.org/obo/NCIT_C20197,sex,,"","",Male,Class,Biosample,Sex,"","","","" Female,"A person who belongs to the sex that normally produces ova. The term is used to indicate biological sex distinctions, or cultural gender role distinctions, or both.","","",FALSE,http://purl.obolibrary.org/obo/NCIT_C16576,sex,,"","",Female,Class,Biosample,Sex,"","","","" Unknown,"Not known, observed, recorded; or reported as unknown by the data contributor.","","",FALSE,http://purl.obolibrary.org/obo/NCIT_C17998,sex,,"","",Unknown_Sex,Class,Biosample,Sex,"","","","" @@ -512,7 +514,7 @@ parentSpecimenID,"A unique identifier (non-PII) that represents the parent speci specimenID,"A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the",,,FALSE,,experimentalData,,,,specimenID,Property,Biosample,annotationProperty,,,many,"Typically annotated with a single ID, but many allowed for summary data." specimenIDSource,"Optional annotation describing where the specimen ID source derived from, e.g. the biobank providing samples or a providing lab.",,,FALSE,,,,,,,Property,Biosample,annotationProperty,,,,This is not officially part of the template and only used as needed. aliquotID,A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ,,,FALSE,,,,,,,Property,Biosample,annotationProperty,,,, -modelSystemName,"A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","C57BL/6J,NOD scid gamma,B6;129S2-Trp53tm1Tyj Nf1tm1Tyj/J,B6;129-Trp53tm1Tyj Nf1tm1Tyj Suz12Gt(Betageo)1Khe/KcichJ,B6.129S2-Nf1tm1Tyj/J,B6.129S1-Nf1tm1Cbr/J,B6.129(Cg)-Nf1tm1Par/J,hiPSC-SCP,hiPSC,JHU 2-103-CL,JHU 2-002-CL,JHU 2-079-CL,JHU 2-103-PDX,JHU 2-002-PDX,JHU 2-079-PDX,human foreskin fibroblasts,hTERT NF1 ipNF05.5,hTERT NF1 ipNF05.5 (Mixed clones),hTERT NF1 ipn06.2 A,hTERT NF1 ipNF95.11b C/T,hTERT NF1 ipNF95.6,hTERT SC ipn02.8,hTERT NF1 ipnNF95.11c,hTERT NF1 ipNF95.11b C,hTERT NF1 ipnNF09.4,hTERT NF1 ipNF04.4,hTERT NF1 sipnNF95.12B,hTERT NF1 ipNF00.6,hTERT NF1 ipNF03.3,hTERT NF1 ipn02.3 2λ,hTERT SC ipn02.8,SZ-NF1,SZ-NF2,SZ-NF4,NF1,Lis42_NF1_1N,Lis47_NF1_2N,ST88-14,sNF96.2,sNF02.2,sNF94.3,GM11602,GM11601,KCL024,KCL025,5PNF_TdiPSsv_PM_6,5PNF_TdiPSsv_MM_4,7PNF_SiPSrv_PM_12,6PNF_SiPSrv_PM_2,3PNF_SiPSsv_MM_11,3PNF_FiPSsv_PM_2,NCC-MPNST5-C1,NCC-MPNST3-C1,NCC-MPNST4-C1,NCC-MPNST3-X2-C1,NCC-MPNST2-C1,STS-26T,YST-1,90-8,S520,S462,S462.TY,sc93.1,Fb93.1, JH-2-002-CL, JH-2-079-CL, JH-2-103-CL, icNF00.10a, cNF00.10a, icNF97.2a, cNF97.2a, icNF97.2b, cNF97.2b, icNF98.4d, cNF98.4d, i28NF, 28NF, icNF04.9a, cNF04.9a, icNF98.4c, cNF98.4c, Nf2-/- Schwann SC (mouse) (PMID26554010), SC4 [Mouse schwannoma], AC007-hTERT, NF2-/- AC007-hTERT, Ben-Men-1",,FALSE,http://purl.obolibrary.org/obo/NCIT_C94171,neuro,,,list,modelSystemName,Property,Biosample,annotationProperty,annotationProperty,Model_System,, +modelSystemName,"A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","C57BL/6J,NOD scid gamma,B6;129S2-Trp53tm1Tyj Nf1tm1Tyj/J,B6;129-Trp53tm1Tyj Nf1tm1Tyj Suz12Gt(Betageo)1Khe/KcichJ,B6.129S2-Nf1tm1Tyj/J,B6.129S1-Nf1tm1Cbr/J,B6.129(Cg)-Nf1tm1Par/J,hiPSC-SCP,hiPSC,JHU 2-103-CL,JHU 2-002-CL,JHU 2-079-CL,JHU 2-103-PDX,JHU 2-002-PDX,JHU 2-079-PDX,human foreskin fibroblasts,hTERT NF1 ipNF05.5,hTERT NF1 ipNF05.5 (Mixed clones),hTERT NF1 ipn06.2 A,hTERT NF1 ipNF95.11b C/T,hTERT NF1 ipNF95.6,hTERT SC ipn02.8,hTERT NF1 ipnNF95.11c,hTERT NF1 ipNF95.11b C,hTERT NF1 ipnNF09.4,hTERT NF1 ipNF04.4,hTERT NF1 sipnNF95.12B,hTERT NF1 ipNF00.6,hTERT NF1 ipNF03.3,hTERT NF1 ipn02.3 2λ,hTERT SC ipn02.8,SZ-NF1,SZ-NF2,SZ-NF4,NF1,Lis42_NF1_1N,Lis47_NF1_2N,ST88-14,sNF96.2,sNF02.2,sNF94.3,GM11602,GM11601,KCL024,KCL025,5PNF_TdiPSsv_PM_6,5PNF_TdiPSsv_MM_4,7PNF_SiPSrv_PM_12,6PNF_SiPSrv_PM_2,3PNF_SiPSsv_MM_11,3PNF_FiPSsv_PM_2,NCC-MPNST5-C1,NCC-MPNST3-C1,NCC-MPNST4-C1,NCC-MPNST3-X2-C1,NCC-MPNST2-C1,STS-26T,YST-1,90-8,S520,S462,S462.TY,sc93.1,Fb93.1, JH-2-002-CL, JH-2-079-CL, JH-2-103-CL, icNF00.10a, cNF00.10a, icNF97.2a, cNF97.2a, icNF97.2b, cNF97.2b, icNF98.4d, cNF98.4d, i28NF, 28NF, icNF04.9a, cNF04.9a, icNF98.4c, cNF98.4c, Nf2-/- Schwann SC (mouse) (PMID26554010), SC4 [Mouse schwannoma], AC007-hTERT, NF2-/- AC007-hTERT, Ben-Men-1,M3 MPNST",,FALSE,http://purl.obolibrary.org/obo/NCIT_C94171,neuro,,,list,modelSystemName,Property,Biosample,annotationProperty,annotationProperty,Model_System,, nf2Genotype,"Genotype of NF2 gene in the biospecimen from which the data were derived, if known","-/-, +/-, +/+, +/?, -/?, Unknown",,FALSE,,neurofibromatosis,,,,nf2Genotype,Property,Biosample,annotationProperty,,Genotype,, nf1Genotype,"Genotype of NF1 gene in the biospecimen from which the data were derived, if known","-/-, +/-, +/+, +/?, -/?, Unknown",,FALSE,,neurofibromatosis,,,,nf1Genotype,Property,Biosample,annotationProperty,,Genotype,, specimenPreparationMethod,"Term that represents preservation of the sample before usage in, e.g. sequencing","Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNAlater, formalin-fixed, ethanol, Viably frozen",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=sample&anchor=preservation_method,ngs,,,,specimenPreparationMethod,Property,Biosample,annotationProperty,,Specimen_State,, @@ -738,9 +740,9 @@ meanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage proportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=proportion_coverage_10x,,,,,proportionCoverage10x,Property,Processing,annotationProperty,,,, proportionCoverage30x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=proportion_coverage_30x,,,,,proportionCoverage30x,Property,Processing,annotationProperty,,,, Component,"Category of metadata manifest; provide the same one for all items/rows.",,,TRUE,https://w3id.org/biolink/vocab/category,,,,,,,,,,,, -genomicsAssayTemplate_Normalized,"Generic template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) WITHOUT full individual and biospecimen data. To link individual and biospecimen metadata, an additional “biospecimenTemplate_Default” must be additionally completed with either specimenID or aliquotID available for joining. This is a two-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,specimenID,aliquotID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Normalized,Class,Template,Template,Assay_Template,,, +genomicsAssayTemplateNormalized,"Generic template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) WITHOUT full individual and biospecimen data. To link individual and biospecimen metadata, an additional “biospecimenTemplate_Default” must be additionally completed with either specimenID or aliquotID available for joining. This is a two-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,specimenID,aliquotID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Normalized,Class,Template,Template,Assay_Template,,, genomicsAssayTemplate,"Generic denormalized template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) along with individual, biospecimen and experimental metadata. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template,Class,Template,Template,Assay_Template,,, -genomicsAssayTemplate_Extended,"Template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,runType,libraryPrep,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, +genomicsAssayTemplateExtended,"Template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,runType,libraryPrep,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, WGSTemplate,"Template for describing raw data from Whole Genome Sequencing (WGS)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,WGS_Template,Class,Template,Template,Assay_Template,,, WESTemplate,"Template for describing raw data from Whole Exome Sequencing (WES)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,targetCaptureKitID,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,WES_Template,Class,Template,Template,Assay_Template,,, RNASeqTemplate,"Template for describing raw data from (bulk) RNA-sequencing",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,targetDepth,comments",TRUE,Sage Bionetworks,template,,,,RNA_Seq_Template,Class,Template,Template,Assay_Template,,, @@ -749,7 +751,7 @@ ProcessedAlignedReadsTemplate,"Template for describing aligned reads output data ProcessedVariantCallsTemplate,"Template for describing either germline or variant calls output data (i.e. VCF/MAF)",,"Component,Filename,resourceType,progressReportNumber,specimenID,dataType,assay,individualID,workflow,comments",TRUE,Sage Bionetworks,template,,,,Processed_Variant_Calls_Template,Class,Template,Template,Assay_Template,,, ProcessedExpressionTemplate,"Template for describing expression output data",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,individualID,specimenID,workflow,expressionUnit,comments",TRUE,Sage Bionetworks,template,,,,Processed_Expression_Template,Class,Template,Template,Assay_Template,,, imagingAssayTemplate,"Generic template for describing data from an imaging type assay (IHC, etc). This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,comments",TRUE,Sage Bionetworks,template,,,,Imaging_Assay_Template,Class,Template,Template,Assay_Template,,, -imagingAssayTemplate_Extended,"Template for describing data from an imaging type assay (IHC, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Imaging_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, +imagingAssayTemplateExtended,"Template for describing data from an imaging type assay (IHC, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Imaging_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, MRIAssayTemplate,Generic template for describing data from an MRI assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,MRISequence,comments",TRUE,Sage Bionetworks,template,,,,MRI_Assay_Template,Class,Template,Template,Assay_Template,,, epigeneticsAssayTemplate,Generic template for describing data from an epigenetics assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Epigenetics_Assay_Template,Class,Template,Template,Assay_Template,,, pharmacokineticsAssayTemplate,Generic template for describing data from a pharmacokinetics assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Pharmacokinetics_Assay_Template,Class,Template,Template,Assay_Template,,, @@ -757,7 +759,7 @@ proteomicsAssayTemplate,Generic template for describing data from a proteomics a plateBasedReporterAssayTemplate,Generic template for describing data from a plate-based reporter assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,reporterGene,reporterSubstance,comments",TRUE,Sage Bionetworks,template,,,,Plate_Based_Reporter_Assay_Template,Class,Template,Template,Assay_Template,,, patientTimepointsTemplate,Template for capturing individual-level metadata with time points. Do not use for data file annotation.,,"Component,individualID,experimentalTimepoint",TRUE,Sage Bionetworks,template,,,,Patient_Timepoints_Template,Class,Template,Template,Non_Assay_Template,,, clinicalAssayTemplate,"Annotation template for simple endpoint data from clinical assays often used in diagnostic practice or clinical trials; may include repeated measures and a treatment/intervention context. Examples include bloodwork results (creatine assay, serum antibody assay), tumor size measurements, or medication adherence. Note that clinical data are from human individuals, therefore species should be “human”. ",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,comments",TRUE,Sage Bionetworks,template,,,,Clinical_Assay_Template,Class,Template,Template,Assay_Template,,, -clinicalAssayTemplate_Extended,Annotation template for simple endpoint data from clinical assays often used in diagnostic practice or clinical trials; may include repeated measures and a treatment/intervention context. Extended to capture additional drug/treatment parameters.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,compoundName,compoundDose,comments",TRUE,Sage Bionetworks,template,,,,Clinical_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, +clinicalAssayTemplateExtended,Annotation template for simple endpoint data from clinical assays often used in diagnostic practice or clinical trials; may include repeated measures and a treatment/intervention context. Extended to capture additional drug/treatment parameters.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,compoundName,compoundDose,comments",TRUE,Sage Bionetworks,template,,,,Clinical_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, behavioralAssayTemplate,"Generic template for describing data from behavioral assays such as “adaptive n-back task” (for humans) or “shock-probe defensive burying test” (for mice). If another modality is used as part of the behavioral assay, e.g. fMRI, that data can be linked.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,experimentalCondition,experimentalTimepoint,comments",TRUE,Sage Bionetworks,template,,,,Behavioral_Assay_Template,Class,Template,Template,Assay_Template,,, sourceCodeTemplate,Template for describing scripts or source code files for a software application.,,"Component,Filename,resourceType,programmingLanguage,documentation,runtimePlatform,comments",TRUE,Sage Bionetworks,template,,,,Source_Code_Template,Class,Template,Template,Non_Assay_Template,,, protocolTemplate,Template for describing a protocol document. (BETA) Adapted from https://bioschema.org/profiles/LabProtocol/0.6-DRAFT-2020_12_08,,"Component,Filename,resourceType,author,citation,license,comments",TRUE,Sage Bionetworks,template,,,,Protocol_Template,Class,Template,Template,Non_Assay_Template,,, @@ -765,7 +767,7 @@ pdxGenomicsAssay,Template for describing PDX assay data that extends genomicsAss updateMilestoneReport,Defines a metadata template for updating milestone report values in NF studies -- currently a supported feature for NTAP and GFF.,,"Component,Filename,resourceType,progressReportNumber",FALSE,Sage Bionetworks,template,,,,Update_Milestone_Report,Class,Template,Template,Non_Assay_Template,,, template,Parent attribute for the manifest template attributes.,,,FALSE,Sage Bionetworks,template,,,,Template,Class,Template,Template,,,, individualTemplate,Base template for minimal information describing individual-level data within the NF scope. Not called “patientTemplate_Default” because individuals can be a non-human organism.,"individualID,sex,age,ageUnit,species,diagnosis,nf1Genotype,nf2Genotype","Component,individualID,sex,age,ageUnit,species,diagnosis,nf1Genotype,nf2Genotype",FALSE,Sage Bionetworks,template,,,,Individual_Template,Class,Template,Template,Non_Assay_Template,,, -biospecimenTemplate_Normalized,Base template for describing biospecimen-level data.,"parentSpecimenID,specimenID,aliquotID,organ,tissue,isCellLine,isPrimaryCell,cellType,tumorType,specimenPreparationMethod,modelSystemName","Component,parentSpecimenID,specimenID,aliquotID,organ,tissue,isCellLine,isPrimaryCell,cellType,tumorType,specimenPreparationMethod,modelSystemName",FALSE,Sage Bionetworks,template,,,,Biospecimen_Template_Normalized,Class,Template,Template,Non_Assay_Template,,, +biospecimenTemplateNormalized,Base template for describing biospecimen-level data.,"parentSpecimenID,specimenID,aliquotID,organ,tissue,isCellLine,isPrimaryCell,cellType,tumorType,specimenPreparationMethod,modelSystemName","Component,parentSpecimenID,specimenID,aliquotID,organ,tissue,isCellLine,isPrimaryCell,cellType,tumorType,specimenPreparationMethod,modelSystemName",FALSE,Sage Bionetworks,template,,,,Biospecimen_Template_Normalized,Class,Template,Template,Non_Assay_Template,,, biospecimenTemplate,Denormalized template for describing biospecimen data that includes all individual-level data as well.,,"Component,individualID,parentSpecimenID",FALSE,Sage Bionetworks,template,,,,Biospecimen_Template,Class,Template,Template,Non_Assay_Template,,, dataFileComponent,Template component for describing a data file resource that extends fileTemplate_Default with required properties dataType and dataSubtype.,"Filename,entityId,fileFormat,resourceType,dataType,dataSubtype","Filename,entityId,fileFormat,resourceType,dataType,dataSubtype",FALSE,Sage Bionetworks,template,,,,Data_File_Component,Class,Template,TemplateComponent,,,, experimentComponent,Template component for describing core experimental parameters.,"experimentalCondition,experimentalTimepoint","experimentalCondition,experimentalTimepoint",FALSE,Sage Bionetworks,template,,,,Experiment_Component,Class,Template,TemplateComponent,,,, diff --git a/NF.jsonld b/NF.jsonld index c00d9ecb..ac4edbf8 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -3541,6 +3541,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:CUT&RUN", + "@type": "rdfs:Class", + "rdfs:comment": "Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. (doi:10.7554/eLife.21856)", + "rdfs:label": "CUT&RUN", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "CUT&RUN", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Channel", "@type": "rdfs:Class", @@ -4567,10 +4584,10 @@ "sms:validationRules": [] }, { - "@id": "bts:HiSeq3000", + "@id": "bts:IlluminaHiSeq3000", "@type": "rdfs:Class", "rdfs:comment": "Illumina HiSeq 3000", - "rdfs:label": "HiSeq3000", + "rdfs:label": "IlluminaHiSeq3000", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -4579,15 +4596,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HiSeq3000", + "sms:displayName": "Illumina HiSeq 3000", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HiSeq2500", + "@id": "bts:IlluminaHiSeq2500", "@type": "rdfs:Class", "rdfs:comment": "Illumina HiSeq 2500", - "rdfs:label": "HiSeq2500", + "rdfs:label": "IlluminaHiSeq2500", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -4596,15 +4613,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HiSeq2500", + "sms:displayName": "Illumina HiSeq 2500", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HiSeq4000", + "@id": "bts:IlluminaHiSeq4000", "@type": "rdfs:Class", "rdfs:comment": "Illumina HiSeq 4000", - "rdfs:label": "HiSeq4000", + "rdfs:label": "IlluminaHiSeq4000", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -4613,15 +4630,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HiSeq4000", + "sms:displayName": "Illumina HiSeq 4000", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NextSeq500", + "@id": "bts:IlluminaNextSeq500", "@type": "rdfs:Class", "rdfs:comment": "Illumina NextSeq 500", - "rdfs:label": "NextSeq500", + "rdfs:label": "IlluminaNextSeq500", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -4630,15 +4647,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NextSeq500", + "sms:displayName": "Illumina NextSeq 500", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NextSeq550", + "@id": "bts:IlluminaNextSeq550", "@type": "rdfs:Class", "rdfs:comment": "Illumina NextSeq 550", - "rdfs:label": "NextSeq550", + "rdfs:label": "IlluminaNextSeq550", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -4647,15 +4664,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NextSeq 550", + "sms:displayName": "Illumina NextSeq 550", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NextSeq1000", + "@id": "bts:IlluminaNextSeq1000", "@type": "rdfs:Class", "rdfs:comment": "Illumina NextSeq 1000", - "rdfs:label": "NextSeq1000", + "rdfs:label": "IlluminaNextSeq1000", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -4664,15 +4681,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NextSeq 1000", + "sms:displayName": "Illumina NextSeq 1000", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NextSeq2000", + "@id": "bts:IlluminaNextSeq2000", "@type": "rdfs:Class", "rdfs:comment": "Illumina NextSeq 2000", - "rdfs:label": "NextSeq2000", + "rdfs:label": "IlluminaNextSeq2000", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -4681,15 +4698,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NextSeq 2000", + "sms:displayName": "Illumina NextSeq 2000", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HiSeq2000", + "@id": "bts:IlluminaHiSeq2000", "@type": "rdfs:Class", "rdfs:comment": "Illumina HiSeq 2000", - "rdfs:label": "HiSeq2000", + "rdfs:label": "IlluminaHiSeq2000", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -4698,15 +4715,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HiSeq2000", + "sms:displayName": "Illumina HiSeq 2000", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MiSeq", + "@id": "bts:IlluminaMiSeq", "@type": "rdfs:Class", "rdfs:comment": "Illumina MiSeq", - "rdfs:label": "MiSeq", + "rdfs:label": "IlluminaMiSeq", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -4715,7 +4732,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MiSeq", + "sms:displayName": "Illumina MiSeq", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -4737,10 +4754,10 @@ "sms:validationRules": [] }, { - "@id": "bts:Affy5.0", + "@id": "bts:AffymetrixGenome-WideHumanSNP5.0Array", "@type": "rdfs:Class", "rdfs:comment": "Affymetrix Genome-Wide Human SNP 5.0 Array", - "rdfs:label": "Affy5.0", + "rdfs:label": "AffymetrixGenome-WideHumanSNP5.0Array", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -4749,15 +4766,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Affy5.0", + "sms:displayName": "Affymetrix Genome-Wide Human SNP 5.0 Array", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Affy6.0", + "@id": "bts:AffymetrixGenome-WideHumanSNP6.0Array", "@type": "rdfs:Class", "rdfs:comment": "Affymetrix Genome-Wide Human SNP 6.0 Array", - "rdfs:label": "Affy6.0", + "rdfs:label": "AffymetrixGenome-WideHumanSNP6.0Array", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -4766,7 +4783,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Affy6.0", + "sms:displayName": "Affymetrix Genome-Wide Human SNP 6.0 Array", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -4783,15 +4800,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PacBioRSII", + "sms:displayName": "PacBio RS II", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GAIIx", + "@id": "bts:IlluminaGenomeAnalyzerIIx", "@type": "rdfs:Class", "rdfs:comment": "Illumina Genome Analyzer IIx", - "rdfs:label": "GAIIx", + "rdfs:label": "IlluminaGenomeAnalyzerIIx", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -4800,7 +4817,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GAIIx", + "sms:displayName": "Illumina Genome Analyzer IIx", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -4817,7 +4834,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Illumina_HumanOmni1-Quadv1.0", + "sms:displayName": "Illumina HumanOmni1-Quadv1.0", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -4834,15 +4851,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Illumina_1M", + "sms:displayName": "Illumina 1M", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:IlluminaH650", + "@id": "bts:Illuminah650", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "IlluminaH650", + "rdfs:label": "Illuminah650", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -4851,7 +4868,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Illumina_h650", + "sms:displayName": "Illumina h650", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -4868,7 +4885,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Illumina_Omni2pt5M", + "sms:displayName": "Illumina Omni2pt5M", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -4885,7 +4902,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Illumina_Omni5M", + "sms:displayName": "Illumina Omni5M", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -4919,7 +4936,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Perlegen300Karray", + "sms:displayName": "Perlegen 300Karray", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -4936,7 +4953,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Agilent44Karray", + "sms:displayName": "Agilent 44Karray", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -4953,7 +4970,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "IlluminaWholeGenomeDASL", + "sms:displayName": "Illumina WholeGenome DASL", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -4970,15 +4987,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "IlluminaHumanHap300", + "sms:displayName": "Illumina HumanHap300", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NanostringnCounter", + "@id": "bts:NanostringCounter", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "NanostringnCounter", + "rdfs:label": "NanostringCounter", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -4987,7 +5004,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanostringnCounter", + "sms:displayName": "Nanostring Counter", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -5021,7 +5038,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "IlluminaHumanMethylation450", + "sms:displayName": "Illumina HumanMethylation450", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -5055,7 +5072,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "AffymetrixU133AB", + "sms:displayName": "Affymetrix U133AB", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -5077,10 +5094,10 @@ "sms:validationRules": [] }, { - "@id": "bts:AffymetrixU133Plus2", + "@id": "bts:AffymetrixHumanGenomeU133Plus2.0Array", "@type": "rdfs:Class", "rdfs:comment": "Affymetrix Human Genome U133 Plus 2.0 Array", - "rdfs:label": "AffymetrixU133Plus2", + "rdfs:label": "AffymetrixHumanGenomeU133Plus2.0Array", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -5089,15 +5106,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "AffymetrixU133Plus2", + "sms:displayName": "Affymetrix Human Genome U133 Plus 2.0 Array", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HiSeqX", + "@id": "bts:IlluminaHiSeqX", "@type": "rdfs:Class", "rdfs:comment": "Illumina HiSeq X Platform for whole-genome sequencing", - "rdfs:label": "HiSeqX", + "rdfs:label": "IlluminaHiSeqX", "rdfs:subClassOf": [ { "@id": "bts:Platform" @@ -5106,7 +5123,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HiSeqX", + "sms:displayName": "Illumina HiSeq X", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -5208,7 +5225,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanostringGeoMx", + "sms:displayName": "Nanostring GeoMx", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -5596,6 +5613,9 @@ }, { "@id": "bts:OpticalCoherenceTomography" + }, + { + "@id": "bts:CUT&RUN" } ], "sms:displayName": "assay", @@ -5605,7 +5625,7 @@ { "@id": "bts:Platform", "@type": "rdfs:Class", - "rdfs:comment": "A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ", + "rdfs:comment": "A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.", "rdfs:label": "Platform", "rdfs:subClassOf": [ { @@ -5617,37 +5637,37 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:HiSeq3000" + "@id": "bts:IlluminaHiSeq3000" }, { - "@id": "bts:HiSeq2500" + "@id": "bts:IlluminaHiSeq2500" }, { - "@id": "bts:HiSeq4000" + "@id": "bts:IlluminaHiSeq4000" }, { - "@id": "bts:NextSeq500" + "@id": "bts:IlluminaNextSeq500" }, { - "@id": "bts:HiSeq2000" + "@id": "bts:IlluminaHiSeq2000" }, { - "@id": "bts:MiSeq" + "@id": "bts:IlluminaMiSeq" }, { "@id": "bts:ZeissLSM980" }, { - "@id": "bts:Affy5.0" + "@id": "bts:AffymetrixGenome-WideHumanSNP5.0Array" }, { - "@id": "bts:Affy6.0" + "@id": "bts:AffymetrixGenome-WideHumanSNP6.0Array" }, { "@id": "bts:PacBioRSII" }, { - "@id": "bts:GAIIx" + "@id": "bts:IlluminaGenomeAnalyzerIIx" }, { "@id": "bts:IlluminaHumanOmni1-Quadv1.0" @@ -5656,7 +5676,7 @@ "@id": "bts:Illumina1M" }, { - "@id": "bts:IlluminaH650" + "@id": "bts:Illuminah650" }, { "@id": "bts:IlluminaOmni2pt5M" @@ -5680,7 +5700,7 @@ "@id": "bts:IlluminaHumanHap300" }, { - "@id": "bts:NanostringnCounter" + "@id": "bts:NanostringCounter" }, { "@id": "bts:LTQOrbitrapXL" @@ -5698,10 +5718,10 @@ "@id": "bts:AffymetrixHumanGene1.0STArray" }, { - "@id": "bts:AffymetrixU133Plus2" + "@id": "bts:AffymetrixHumanGenomeU133Plus2.0Array" }, { - "@id": "bts:HiSeqX" + "@id": "bts:IlluminaHiSeqX" }, { "@id": "bts:BionanoIrys" @@ -5710,13 +5730,13 @@ "@id": "bts:InfiniumHumanOmniExpressExome" }, { - "@id": "bts:NextSeq550" + "@id": "bts:IlluminaNextSeq550" }, { - "@id": "bts:NextSeq1000" + "@id": "bts:IlluminaNextSeq1000" }, { - "@id": "bts:NextSeq2000" + "@id": "bts:IlluminaNextSeq2000" }, { "@id": "bts:PacBioSequelIIeSystem" @@ -9336,6 +9356,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:M3MPNST", + "@type": "rdfs:Class", + "rdfs:comment": "A patient-derived MPNST cell line", + "rdfs:label": "M3MPNST", + "rdfs:subClassOf": [ + { + "@id": "bts:ModelSystemName" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "M3 MPNST", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Male", "@type": "rdfs:Class", @@ -12278,6 +12315,9 @@ }, { "@id": "bts:Ben-Men-1" + }, + { + "@id": "bts:M3MPNST" } ], "sms:displayName": "modelSystemName", @@ -16993,7 +17033,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "genomicsAssayTemplate_Normalized", + "sms:displayName": "genomicsAssayTemplateNormalized", "sms:required": "sms:true", "sms:requiresDependency": [ { @@ -17103,7 +17143,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "genomicsAssayTemplate_Extended", + "sms:displayName": "genomicsAssayTemplateExtended", "sms:required": "sms:true", "sms:requiresDependency": [ { @@ -17637,7 +17677,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "imagingAssayTemplate_Extended", + "sms:displayName": "imagingAssayTemplateExtended", "sms:required": "sms:true", "sms:requiresDependency": [ { @@ -18089,7 +18129,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "clinicalAssayTemplate_Extended", + "sms:displayName": "clinicalAssayTemplateExtended", "sms:required": "sms:true", "sms:requiresDependency": [ { @@ -18504,7 +18544,7 @@ "@id": "bts:ModelSystemName" } ], - "sms:displayName": "biospecimenTemplate_Normalized", + "sms:displayName": "biospecimenTemplateNormalized", "sms:required": "sms:false", "sms:requiresDependency": [ { diff --git a/modules/Assay/Assay.csv b/modules/Assay/Assay.csv index 26679da5..1ebd33e4 100644 --- a/modules/Assay/Assay.csv +++ b/modules/Assay/Assay.csv @@ -91,3 +91,4 @@ Massively Parallel Reporter Assay,An assay in which multiplexing the constructio Riccardi and Ablon scales,"The Riccardi and Ablon scales score severity and visibility of disease, respectively, and are commonly used as a combined assessment for NF1 patients in clinical settings. See https://doi.org/10.1001/archderm.137.11.1421 for example usage.",,,FALSE,https://doi.org/10.1001/archderm.137.11.1421,assay,,,,Riccardi_Ablon_Scales,Class,Assay,Assay,Clinical_Assay,,, Spatial Frequency Domain Imaging,"Spatial Frequency Domain Imaging (SFDI) is a non-contact, depth-varying and wide-field optical imaging technique for measuring optical properties in a wide field-of-view on a pixel-by-pixel basis. Relevant applications include including burn assessment, skin tissue evaluation, tumor tissue detection, brain tissue monitoring.",,,FALSE,https://doi.org/10.3390/photonics8050162,assay,,,,Spatial_Frequency_Domain_Imaging,Class,Assay,Assay,Imaging_Assay,,,Note that term has no matches in OLS as of June 2022. Optical Coherence Tomography,"Optical Coherence Tomography (OCT) combines the principles of ultrasound with the imaging performance of a microscope. OCT uses infrared light waves that reflect off the internal microstructure within the biological tissues. The frequencies and bandwidths of infrared light are orders of magnitude higher than medical ultrasound signals, resulting in greatly increased image resolution, 8-25 times greater than any existing modality. In addition to providing high-level resolutions for the evaluation of microanatomic structures OCT is also able to provide information regarding tissue composition",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C20828,assay,,,,Optical_Coherence_Tomography,Class,Assay,Assay,Imaging_Assay,,, +CUT&RUN,"Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. (doi:10.7554/eLife.21856)",,,FALSE,,assay,,,,CUT_RUN,Class,Assay,Assay,Epigenetics_Assay,,, diff --git a/modules/Assay/Platform.csv b/modules/Assay/Platform.csv index 0d8152cb..7b4b5181 100644 --- a/modules/Assay/Platform.csv +++ b/modules/Assay/Platform.csv @@ -5,44 +5,44 @@ Orbitrap Fusion Lumos Tribrid,Thermo Scientific Orbitrap Fusion Lumos Tribrid Ma Spectramax M Series,A Spectramax M Series Microplate Reader,,,FALSE,https://www.moleculardevices.com/products/microplate-readers/multi-mode-readers/spectramax-m-series-readers,platform,,,,Spectramax_M_Series,Class,Assay,Platform,Platform,,, LI-COR Odyssey CLx,A LI-COR Odyssey CLx imaging system,,,FALSE,https://www.licor.com/bio/odyssey-clx/,platform,,,,LI-COR_Odyssey_Clx,Class,Assay,Platform,Platform,,, Q Exative HF,Thermo scientific Q Exative,,,FALSE,http://purl.obolibrary.org/obo/MS_10025223,platform,,,,Q_Exative_HF,Class,Assay,Platform,Platform,,, -HiSeq3000,Illumina HiSeq 3000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21290,platform,,,,HiSeq3000,Class,Assay,Platform,Platform,,, -HiSeq2500,Illumina HiSeq 2500,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16791,platform,,,,HiSeq2500,Class,Assay,Platform,Platform,,, -HiSeq4000,Illumina HiSeq 4000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20301,platform,,,,HiSeq4000,Class,Assay,Platform,Platform,,, -NextSeq500,Illumina NextSeq 500,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18573,platform,,,,NextSeq500,Class,Assay,Platform,Platform,,, -NextSeq 550,Illumina NextSeq 550,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21697,platform,,,,NextSeq 550,Class,Assay,Platform,Platform,,, -NextSeq 1000,Illumina NextSeq 1000,,,FALSE,,platform,,,,NextSeq 1000,Class,Assay,Platform,Platform,,, -NextSeq 2000,Illumina NextSeq 2000,,,FALSE,,platform,,,,NextSeq 2000,Class,Assay,Platform,Platform,,, -HiSeq2000,Illumina HiSeq 2000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL11154,platform,,,,HiSeq2000,Class,Assay,Platform,Platform,,, -MiSeq,Illumina MiSeq,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15520,platform,,,,MiSeq,Class,Assay,Platform,Platform,,, +Illumina HiSeq 3000,Illumina HiSeq 3000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21290,platform,,,,HiSeq3000,Class,Assay,Platform,Platform,,, +Illumina HiSeq 2500,Illumina HiSeq 2500,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16791,platform,,,,HiSeq2500,Class,Assay,Platform,Platform,,, +Illumina HiSeq 4000,Illumina HiSeq 4000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20301,platform,,,,HiSeq4000,Class,Assay,Platform,Platform,,, +Illumina NextSeq 500,Illumina NextSeq 500,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18573,platform,,,,NextSeq500,Class,Assay,Platform,Platform,,, +Illumina NextSeq 550,Illumina NextSeq 550,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21697,platform,,,,NextSeq 550,Class,Assay,Platform,Platform,,, +Illumina NextSeq 1000,Illumina NextSeq 1000,,,FALSE,,platform,,,,NextSeq 1000,Class,Assay,Platform,Platform,,, +Illumina NextSeq 2000,Illumina NextSeq 2000,,,FALSE,,platform,,,,NextSeq 2000,Class,Assay,Platform,Platform,,, +Illumina HiSeq 2000,Illumina HiSeq 2000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL11154,platform,,,,HiSeq2000,Class,Assay,Platform,Platform,,, +Illumina MiSeq,Illumina MiSeq,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15520,platform,,,,MiSeq,Class,Assay,Platform,Platform,,, Zeiss LSM 980,A Zeiss Confocal Microscope,,,FALSE,https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwirj4XuwtXsAhVBrp4KHVZyARIQFjABegQIAhAC&url=https%3A%2F%2Fzeiss.ly%2Flsm980-info&usg=AOvVaw0rD50U0aMwfvt4bdfW0Yjd,platform,,,,Zeiss LSM 980,Class,Assay,Platform,Platform,,, -Affy5.0,Affymetrix Genome-Wide Human SNP 5.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6804,platform,,,,Affy5.0,Class,Assay,Platform,Platform,,, -Affy6.0,Affymetrix Genome-Wide Human SNP 6.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6801,platform,,,,Affy6.0,Class,Assay,Platform,Platform,,, -PacBioRSII,PacBio RS II,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21311,platform,,,,PacBioRSII,Class,Assay,Platform,Platform,,, -GAIIx,Illumina Genome Analyzer IIx,,,FALSE,https://support.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet_genome_analyzeriix.pdf,platform,,,,GAIIx,Class,Assay,Platform,Platform,,, -Illumina_HumanOmni1-Quadv1.0,,,,FALSE,https://www.illumina.com/documents/products/datasheets/datasheet_humanomni1_quad.pdf,platform,,,,Illumina_HumanOmni1-Quadv1.0,Class,Assay,Platform,Platform,,, -Illumina_1M,,,,FALSE,,platform,,,,Illumina_1M,Class,Assay,Platform,Platform,,, -Illumina_h650,,,,FALSE,,platform,,,,Illumina_h650,Class,Assay,Platform,Platform,,, -Illumina_Omni2pt5M,,,,FALSE,,platform,,,,Illumina_Omni2pt5M,Class,Assay,Platform,Platform,,, -Illumina_Omni5M,,,,FALSE,,platform,,,,Illumina_Omni5M,Class,Assay,Platform,Platform,,, +Affymetrix Genome-Wide Human SNP 5.0 Array,Affymetrix Genome-Wide Human SNP 5.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6804,platform,,,,Affy5.0,Class,Assay,Platform,Platform,,, +Affymetrix Genome-Wide Human SNP 6.0 Array,Affymetrix Genome-Wide Human SNP 6.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6801,platform,,,,Affy6.0,Class,Assay,Platform,Platform,,, +PacBio RS II,PacBio RS II,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21311,platform,,,,PacBioRSII,Class,Assay,Platform,Platform,,, +Illumina Genome Analyzer IIx,Illumina Genome Analyzer IIx,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16061,platform,,,,GAIIx,Class,Assay,Platform,Platform,,, +Illumina HumanOmni1-Quadv1.0,,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL24663,platform,,,,Illumina_HumanOmni1-Quadv1.0,Class,Assay,Platform,Platform,,, +Illumina 1M,,,,FALSE,,platform,,,,Illumina_1M,Class,Assay,Platform,Platform,,, +Illumina h650,,,,FALSE,,platform,,,,Illumina_h650,Class,Assay,Platform,Platform,,, +Illumina Omni2pt5M,,,,FALSE,,platform,,,,Illumina_Omni2pt5M,Class,Assay,Platform,Platform,,, +Illumina Omni5M,,,,FALSE,,platform,,,,Illumina_Omni5M,Class,Assay,Platform,Platform,,, Illumina MouseWG-6 v2.0 expression beadchip,Whole-genome expression profiling in the mouse,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6887,platform,,,,Illumina MouseWG-6_v2.0_expression_beadchip,Class,Assay,Platform,Platform,,, -Perlegen300Karray,,,,FALSE,,platform,,,,Perlegen300Karray,Class,Assay,Platform,Platform,,, -Agilent44Karray,,,,FALSE,,platform,,,,Agilent44Karray,Class,Assay,Platform,Platform,,, -IlluminaWholeGenomeDASL,Illumina Human Whole-Genome DASL HT,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13369,platform,,,,IlluminaWholeGenomeDASL,Class,Assay,Platform,Platform,,, -IlluminaHumanHap300,,,,FALSE,,platform,,,,IlluminaHumanHap300,Class,Assay,Platform,Platform,,, -NanostringnCounter,,,,FALSE,,platform,,,,NanostringnCounter,Class,Assay,Platform,Platform,,, +Perlegen 300Karray,,,,FALSE,,platform,,,,Perlegen300Karray,Class,Assay,Platform,Platform,,, +Agilent 44Karray,,,,FALSE,,platform,,,,Agilent44Karray,Class,Assay,Platform,Platform,,, +Illumina WholeGenome DASL,Illumina Human Whole-Genome DASL HT,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13369,platform,,,,IlluminaWholeGenomeDASL,Class,Assay,Platform,Platform,,, +Illumina HumanHap300,,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6083,platform,,,,IlluminaHumanHap300,Class,Assay,Platform,Platform,,, +Nanostring Counter,,,,FALSE,,platform,,,,NanostringCounter,Class,Assay,Platform,Platform,,, LTQ Orbitrap XL,LTQ Orbitrap XL Hybrid Ion Trap-Orbitrap Mass Spectrometer,,,FALSE,https://www.thermofisher.com/order/catalog/product/IQLAAEGAAPFADBMAOK,platform,,,,LTQ_Orbitrap_XL,Class,Assay,Platform,Platform,,, -IlluminaHumanMethylation450,Illumina HumanMethylation450 BeadChip,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13534,platform,,,,IlluminaHumanMethylation450,Class,Assay,Platform,Platform,,, +Illumina HumanMethylation450,Illumina HumanMethylation450 BeadChip,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13534,platform,,,,IlluminaHumanMethylation450,Class,Assay,Platform,Platform,,, Illumina Infinium MethylationEPIC BeadChip,"An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002131,platform,,,,Illumina Infinium MethylationEPIC_BeadChip,Class,Assay,Platform,Platform,,, -AffymetrixU133AB,,,,FALSE,,platform,,,,AffymetrixU133AB,Class,Assay,Platform,Platform,,, +Affymetrix U133AB,,,,FALSE,,platform,,,,AffymetrixU133AB,Class,Assay,Platform,Platform,,, Affymetrix Human Gene 1.0 ST Array,Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] in situ oligonucleotide,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6244,platform,,,,Affymetrix_Human_Gene_1.0_ST_Array,Class,Assay,Platform,Platform,,, -AffymetrixU133Plus2,Affymetrix Human Genome U133 Plus 2.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570,platform,,,,AffymetrixU133Plus2,Class,Assay,Platform,Platform,,, -HiSeqX,Illumina HiSeq X Platform for whole-genome sequencing,,,FALSE,https://www.illumina.com/systems/sequencing-platforms/hiseq-x.html,platform,,,,HiSeqX,Class,Assay,Platform,Platform,,, +Affymetrix Human Genome U133 Plus 2.0 Array,Affymetrix Human Genome U133 Plus 2.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570,platform,,,,AffymetrixU133Plus2,Class,Assay,Platform,Platform,,, +Illumina HiSeq X,Illumina HiSeq X Platform for whole-genome sequencing,,,FALSE,https://www.illumina.com/systems/sequencing-platforms/hiseq-x.html,platform,,,,HiSeqX,Class,Assay,Platform,Platform,,, Bionano Irys,Performs whole genome mapping in a nanoscale fluidic environment enabling the structure of the genome to be imaged and then analyzed at the single molecule level,,,FALSE,https://bionanogenomics.com/products/irys/,platform,,,,Bionano_Irys,Class,Assay,Platform,Platform,,, Infinium HumanOmniExpressExome,Infinium HumanOmniExpressExome BeadChip,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18224,platform,,,,Infinium_HumanOmniExpressExome,Class,Assay,Platform,Platform,,, Illumina NovaSeq 6000,"A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002630,platform,,,,Illumina_NovaSeq_6000,Class,Assay,Platform,Platform,,, PacBio Sequel IIe System,PacBio Sequel IIe System,,,FALSE,,platform,,,,PacBio_Sequel_Iie_System,Class,Assay,Platform,Platform,,, PacBio Sequel II System,PacBio Sequel II System,,,FALSE,,platform,,,,PacBio_Sequel_II_System,Class,Assay,Platform,Platform,,, -NanostringGeoMx,NanostringGeoMx,,,FALSE,,platform,,,,Nanostring_GeoMx,Class,Assay,Platform,Platform,,, +Nanostring GeoMx,NanostringGeoMx,,,FALSE,,platform,,,,Nanostring_GeoMx,Class,Assay,Platform,Platform,,, Chromium X,"(From 10x Genomics) Single-cell platform that can analyze hundreds to hundreds of thousands of cells in single run for e.g. gene expression, chromatin accessibility, cell surface proteins, immune clonotype, antigen specificity, CRISPR perturbation screens).",,,FALSE,https://www.10xgenomics.com/chromium-x,platform,,,,Chromium_X,Class,Assay,Platform,Platform,,, 10x Visium Spatial Gene Expression,"10x Genomics product that includes special slides, reagents and technology to allow whole transcriptome profiling with morphological (spatial) context in FFPE or fresh-frozen tissues. Vendor ref: https://www.10xgenomics.com/products/spatial-gene-expression",,,FALSE,http://www.ebi.ac.uk/efo/EFO_0010961,platform,,,,10x_Visium_Spatial_Gene_Expression,Class,Assay,Platform,Platform,,, EnVision 2103 Multiplate Reader,EnVision 2103 Multiplate Reader,,,FALSE,,platform,,,,EnVision_2103,Class,Assay,Platform,Platform,,, diff --git a/modules/Assay/annotationProperty.csv b/modules/Assay/annotationProperty.csv index 6c9fefc1..9c3d0c8e 100644 --- a/modules/Assay/annotationProperty.csv +++ b/modules/Assay/annotationProperty.csv @@ -1,7 +1,7 @@ Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules,.ID,.Type,.Module,.Root,.SubOf,.Range,.Cardinality,.EditorNote drugScreenType,String describing general class of drug screen,"singleMolecule, smallMoleculeLibraryScreen, combinationLibraryScreen, combinationScreen",,FALSE,,compoundScreen,,,,drugScreenType,Property,Assay,annotationProperty,,,, -assay,The technology used to generate the data in this file,"elevated plus maze test, open field test, rotarod performance test, mRNAcounts, high content screen, Immunocytochemistry, immunofluorescence, autoradiography, electrochemiluminescence, Real Time PCR, in vivo tumor growth, scale, Blood Chemistry Measurement, in vivo bioluminescence, immunohistochemistry, NOMe-Seq, FIA-MSMS, UPLC-MSMS, HPLC-MSMS, liquid chromatography-electrochemical detection, rnaSeq, mirnaSeq, LC-MSMS, LC-MS, lncrnaSeq, Whole Exome Sequencing, Sanger sequencing, ChIPSeq, rnaArray, snpArray, methylationArray, mirnaArray, bisulfiteSeq, ATACSeq, HI-C, errBisulfiteSeq, ISOSeq, westernBlot, wholeGenomeSeq, polymeraseChainReaction, cellViabilityAssay, atomicForceMicroscopy, brightfieldMicroscopy, tractionForceMicroscopy, nextGenerationTargetedSequencing, jumpingLibrary, MIB/MS, scCGIseq, MudPIT, questionnaire, DNA optical mapping, oxBS-Seq, Ribo-Seq, Positron Emission Tomography, RPPA, ELISA, LTP, LFP, whole-cell patch clamp, sandwich ELISA, Laser Speckle Imaging, Genotyping, TMT quantitation, label free mass spectrometry, cell count, reporter gene assay, Single Cell RNA Sequencing, spatial transcriptomics, Conventional MRI, Functional MRI, Magnetic Resonance Spectroscopy, 2D Incucyte, 2D CellTiter-Glo, 3D microtissue viability, in vivo PDX viability, 2D AlamarBlue fluorescence, 2D AlamarBlue absorbance, rheometry, FTIR Spectroscopy, differential scanning calorimetry, Gel filtration chromatography, Massively Parallel Reporter Assay,Riccardi and Ablon scales,Spatial Frequency Domain Imaging,Optical Coherence Tomography",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one, -platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","HiSeq3000, HiSeq2500, HiSeq4000, NextSeq500, HiSeq2000, MiSeq, Zeiss LSM 980, Affy5.0, Affy6.0, PacBioRSII, GAIIx, Illumina_HumanOmni1-Quadv1.0, Illumina_1M, Illumina_h650, Illumina_Omni2pt5M, Illumina_Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen300Karray, Agilent44Karray, IlluminaWholeGenomeDASL, IlluminaHumanHap300, NanostringnCounter, LTQOrbitrapXL, IlluminaHumanMethylation450, Illumina Infinium MethylationEPIC BeadChip, AffymetrixU133AB, Affymetrix Human Gene 1.0 ST Array, AffymetrixU133Plus2, HiSeqX, Bionano Irys, Infinium HumanOmniExpressExome, NextSeq 550, NextSeq 1000, NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, NanostringGeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader,Vectra H1 3D Imaging System,Vevo 3100 Imaging System,10x Visium Spatial Gene Expression",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,, +assay,The technology used to generate the data in this file,"elevated plus maze test, open field test, rotarod performance test, mRNAcounts, high content screen, Immunocytochemistry, immunofluorescence, autoradiography, electrochemiluminescence, Real Time PCR, in vivo tumor growth, scale, Blood Chemistry Measurement, in vivo bioluminescence, immunohistochemistry, NOMe-Seq, FIA-MSMS, UPLC-MSMS, HPLC-MSMS, liquid chromatography-electrochemical detection, rnaSeq, mirnaSeq, LC-MSMS, LC-MS, lncrnaSeq, Whole Exome Sequencing, Sanger sequencing, ChIPSeq, rnaArray, snpArray, methylationArray, mirnaArray, bisulfiteSeq, ATACSeq, HI-C, errBisulfiteSeq, ISOSeq, westernBlot, wholeGenomeSeq, polymeraseChainReaction, cellViabilityAssay, atomicForceMicroscopy, brightfieldMicroscopy, tractionForceMicroscopy, nextGenerationTargetedSequencing, jumpingLibrary, MIB/MS, scCGIseq, MudPIT, questionnaire, DNA optical mapping, oxBS-Seq, Ribo-Seq, Positron Emission Tomography, RPPA, ELISA, LTP, LFP, whole-cell patch clamp, sandwich ELISA, Laser Speckle Imaging, Genotyping, TMT quantitation, label free mass spectrometry, cell count, reporter gene assay, Single Cell RNA Sequencing, spatial transcriptomics, Conventional MRI, Functional MRI, Magnetic Resonance Spectroscopy, 2D Incucyte, 2D CellTiter-Glo, 3D microtissue viability, in vivo PDX viability, 2D AlamarBlue fluorescence, 2D AlamarBlue absorbance, rheometry, FTIR Spectroscopy, differential scanning calorimetry, Gel filtration chromatography, Massively Parallel Reporter Assay,Riccardi and Ablon scales,Spatial Frequency Domain Imaging,Optical Coherence Tomography,CUT&RUN",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one, +platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","Illumina HiSeq 3000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina NextSeq 500, Illumina HiSeq 2000, Illumina MiSeq, Zeiss LSM 980, Affymetrix Genome-Wide Human SNP 5.0 Array, Affymetrix Genome-Wide Human SNP 6.0 Array, PacBio RS II, Illumina Genome Analyzer IIx, Illumina HumanOmni1-Quadv1.0, Illumina 1M, Illumina h650, Illumina Omni2pt5M, Illumina Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen 300Karray, Agilent 44Karray, Illumina WholeGenome DASL, Illumina HumanHap300, Nanostring Counter, LTQ Orbitrap XL, Illumina HumanMethylation450, Illumina Infinium MethylationEPIC BeadChip, Affymetrix U133AB, Affymetrix Human Gene 1.0 ST Array, Affymetrix Human Genome U133 Plus 2.0 Array, Illumina HiSeq X, Bionano Irys, Infinium HumanOmniExpressExome, Illumina NextSeq 550, Illumina NextSeq 1000, Illumina NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, Nanostring GeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader,Vectra H1 3D Imaging System,Vevo 3100 Imaging System,10x Visium Spatial Gene Expression",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,, targetCaptureKitID,"A unique identifier for the kit used to construct a genomic library using target capture-based techniques, which should be composed of the vendor name, kit name and kit version.",,,TRUE,http://purl.obolibrary.org/obo/NCIT_C177583,experimentalData,,,,targetCaptureKitID,Property,Assay,annotationProperty,,,,"For WES processing, the target BED used could be provided based on the target capture kit." libraryID,,,,TRUE,,experimentalData,,,,libraryID,Property,Assay,annotationProperty,,,, assayTarget,The HUGO gene symbol that represents the target analyte assayed.,,,FALSE,Sage Bionetworks,experimentalData,,,,assayTarget,Property,Assay,annotationProperty,,,, diff --git a/modules/Biosample/Model_System.csv b/modules/Biosample/Model_System.csv index 2c0c747b..6452ac91 100644 --- a/modules/Biosample/Model_System.csv +++ b/modules/Biosample/Model_System.csv @@ -89,3 +89,4 @@ AC007-hTERT,"Human arachnoid cell line","","",FALSE,"",modelSystemName,,"","",AC NF2-/- AC007-hTERT,"Knock-out cell line developed by CRISPR targeting NF2 exon 8 in AC007-hTERT","","",FALSE,"",modelSystemName,,"","",hTERT_NF2_arachnoid,Class,Biosample,Model_System,Cell_Line_Model,"","","" Ben-Men-1,"Human meningioma cell line (RRID:CVCL_1959)","","",FALSE,"https://web.expasy.org/cellosaurus/CVCL_1959",modelSystemName,,"","",Ben-Men-1,Class,Biosample,Model_System,Cell_Line_Model,"","","" human foreskin fibroblasts,"generic human foreskin fibroblasts, often used as a control cell in toxicology experiments","","",FALSE,Sage Bionetworks,modelSystemName,,"","",human foreskin fibroblasts,Class,Biosample,Cell,fibroblasts,"","","" +M3 MPNST,"A patient-derived MPNST cell line","","",FALSE,Sage Bionetworks,modelSystemName,,"","",M3_MPNST,Class,Biosample,Cell,Cell_Line_Model,"","","" diff --git a/modules/Biosample/annotationProperty.csv b/modules/Biosample/annotationProperty.csv index 4bd00d79..89337f05 100644 --- a/modules/Biosample/annotationProperty.csv +++ b/modules/Biosample/annotationProperty.csv @@ -18,7 +18,7 @@ parentSpecimenID,"A unique identifier (non-PII) that represents the parent speci specimenID,"A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the",,,FALSE,,experimentalData,,,,specimenID,Property,Biosample,annotationProperty,,,many,"Typically annotated with a single ID, but many allowed for summary data." specimenIDSource,"Optional annotation describing where the specimen ID source derived from, e.g. the biobank providing samples or a providing lab.",,,FALSE,,,,,,,Property,Biosample,annotationProperty,,,,This is not officially part of the template and only used as needed. aliquotID,A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ,,,FALSE,,,,,,,Property,Biosample,annotationProperty,,,, -modelSystemName,"A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","C57BL/6J,NOD scid gamma,B6;129S2-Trp53tm1Tyj Nf1tm1Tyj/J,B6;129-Trp53tm1Tyj Nf1tm1Tyj Suz12Gt(Betageo)1Khe/KcichJ,B6.129S2-Nf1tm1Tyj/J,B6.129S1-Nf1tm1Cbr/J,B6.129(Cg)-Nf1tm1Par/J,hiPSC-SCP,hiPSC,JHU 2-103-CL,JHU 2-002-CL,JHU 2-079-CL,JHU 2-103-PDX,JHU 2-002-PDX,JHU 2-079-PDX,human foreskin fibroblasts,hTERT NF1 ipNF05.5,hTERT NF1 ipNF05.5 (Mixed clones),hTERT NF1 ipn06.2 A,hTERT NF1 ipNF95.11b C/T,hTERT NF1 ipNF95.6,hTERT SC ipn02.8,hTERT NF1 ipnNF95.11c,hTERT NF1 ipNF95.11b C,hTERT NF1 ipnNF09.4,hTERT NF1 ipNF04.4,hTERT NF1 sipnNF95.12B,hTERT NF1 ipNF00.6,hTERT NF1 ipNF03.3,hTERT NF1 ipn02.3 2λ,hTERT SC ipn02.8,SZ-NF1,SZ-NF2,SZ-NF4,NF1,Lis42_NF1_1N,Lis47_NF1_2N,ST88-14,sNF96.2,sNF02.2,sNF94.3,GM11602,GM11601,KCL024,KCL025,5PNF_TdiPSsv_PM_6,5PNF_TdiPSsv_MM_4,7PNF_SiPSrv_PM_12,6PNF_SiPSrv_PM_2,3PNF_SiPSsv_MM_11,3PNF_FiPSsv_PM_2,NCC-MPNST5-C1,NCC-MPNST3-C1,NCC-MPNST4-C1,NCC-MPNST3-X2-C1,NCC-MPNST2-C1,STS-26T,YST-1,90-8,S520,S462,S462.TY,sc93.1,Fb93.1, JH-2-002-CL, JH-2-079-CL, JH-2-103-CL, icNF00.10a, cNF00.10a, icNF97.2a, cNF97.2a, icNF97.2b, cNF97.2b, icNF98.4d, cNF98.4d, i28NF, 28NF, icNF04.9a, cNF04.9a, icNF98.4c, cNF98.4c, Nf2-/- Schwann SC (mouse) (PMID26554010), SC4 [Mouse schwannoma], AC007-hTERT, NF2-/- AC007-hTERT, Ben-Men-1",,FALSE,http://purl.obolibrary.org/obo/NCIT_C94171,neuro,,,list,modelSystemName,Property,Biosample,annotationProperty,annotationProperty,Model_System,, +modelSystemName,"A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","C57BL/6J,NOD scid gamma,B6;129S2-Trp53tm1Tyj Nf1tm1Tyj/J,B6;129-Trp53tm1Tyj Nf1tm1Tyj Suz12Gt(Betageo)1Khe/KcichJ,B6.129S2-Nf1tm1Tyj/J,B6.129S1-Nf1tm1Cbr/J,B6.129(Cg)-Nf1tm1Par/J,hiPSC-SCP,hiPSC,JHU 2-103-CL,JHU 2-002-CL,JHU 2-079-CL,JHU 2-103-PDX,JHU 2-002-PDX,JHU 2-079-PDX,human foreskin fibroblasts,hTERT NF1 ipNF05.5,hTERT NF1 ipNF05.5 (Mixed clones),hTERT NF1 ipn06.2 A,hTERT NF1 ipNF95.11b C/T,hTERT NF1 ipNF95.6,hTERT SC ipn02.8,hTERT NF1 ipnNF95.11c,hTERT NF1 ipNF95.11b C,hTERT NF1 ipnNF09.4,hTERT NF1 ipNF04.4,hTERT NF1 sipnNF95.12B,hTERT NF1 ipNF00.6,hTERT NF1 ipNF03.3,hTERT NF1 ipn02.3 2λ,hTERT SC ipn02.8,SZ-NF1,SZ-NF2,SZ-NF4,NF1,Lis42_NF1_1N,Lis47_NF1_2N,ST88-14,sNF96.2,sNF02.2,sNF94.3,GM11602,GM11601,KCL024,KCL025,5PNF_TdiPSsv_PM_6,5PNF_TdiPSsv_MM_4,7PNF_SiPSrv_PM_12,6PNF_SiPSrv_PM_2,3PNF_SiPSsv_MM_11,3PNF_FiPSsv_PM_2,NCC-MPNST5-C1,NCC-MPNST3-C1,NCC-MPNST4-C1,NCC-MPNST3-X2-C1,NCC-MPNST2-C1,STS-26T,YST-1,90-8,S520,S462,S462.TY,sc93.1,Fb93.1, JH-2-002-CL, JH-2-079-CL, JH-2-103-CL, icNF00.10a, cNF00.10a, icNF97.2a, cNF97.2a, icNF97.2b, cNF97.2b, icNF98.4d, cNF98.4d, i28NF, 28NF, icNF04.9a, cNF04.9a, icNF98.4c, cNF98.4c, Nf2-/- Schwann SC (mouse) (PMID26554010), SC4 [Mouse schwannoma], AC007-hTERT, NF2-/- AC007-hTERT, Ben-Men-1,M3 MPNST",,FALSE,http://purl.obolibrary.org/obo/NCIT_C94171,neuro,,,list,modelSystemName,Property,Biosample,annotationProperty,annotationProperty,Model_System,, nf2Genotype,"Genotype of NF2 gene in the biospecimen from which the data were derived, if known","-/-, +/-, +/+, +/?, -/?, Unknown",,FALSE,,neurofibromatosis,,,,nf2Genotype,Property,Biosample,annotationProperty,,Genotype,, nf1Genotype,"Genotype of NF1 gene in the biospecimen from which the data were derived, if known","-/-, +/-, +/+, +/?, -/?, Unknown",,FALSE,,neurofibromatosis,,,,nf1Genotype,Property,Biosample,annotationProperty,,Genotype,, specimenPreparationMethod,"Term that represents preservation of the sample before usage in, e.g. sequencing","Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNAlater, formalin-fixed, ethanol, Viably frozen",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=sample&anchor=preservation_method,ngs,,,,specimenPreparationMethod,Property,Biosample,annotationProperty,,Specimen_State,, diff --git a/modules/Template/Template.csv b/modules/Template/Template.csv index b93160f8..2bfad170 100644 --- a/modules/Template/Template.csv +++ b/modules/Template/Template.csv @@ -1,7 +1,7 @@ Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules,.ID,.Type,.Module,.Root,.SubOf,.Range,.Cardinality,.EditorNote -genomicsAssayTemplate_Normalized,"Generic template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) WITHOUT full individual and biospecimen data. To link individual and biospecimen metadata, an additional “biospecimenTemplate_Default” must be additionally completed with either specimenID or aliquotID available for joining. This is a two-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,specimenID,aliquotID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Normalized,Class,Template,Template,Assay_Template,,, +genomicsAssayTemplateNormalized,"Generic template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) WITHOUT full individual and biospecimen data. To link individual and biospecimen metadata, an additional “biospecimenTemplate_Default” must be additionally completed with either specimenID or aliquotID available for joining. This is a two-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,specimenID,aliquotID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Normalized,Class,Template,Template,Assay_Template,,, genomicsAssayTemplate,"Generic denormalized template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) along with individual, biospecimen and experimental metadata. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template,Class,Template,Template,Assay_Template,,, -genomicsAssayTemplate_Extended,"Template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,runType,libraryPrep,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, +genomicsAssayTemplateExtended,"Template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,runType,libraryPrep,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, WGSTemplate,"Template for describing raw data from Whole Genome Sequencing (WGS)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,WGS_Template,Class,Template,Template,Assay_Template,,, WESTemplate,"Template for describing raw data from Whole Exome Sequencing (WES)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,targetCaptureKitID,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,WES_Template,Class,Template,Template,Assay_Template,,, RNASeqTemplate,"Template for describing raw data from (bulk) RNA-sequencing",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,targetDepth,comments",TRUE,Sage Bionetworks,template,,,,RNA_Seq_Template,Class,Template,Template,Assay_Template,,, @@ -10,7 +10,7 @@ ProcessedAlignedReadsTemplate,"Template for describing aligned reads output data ProcessedVariantCallsTemplate,"Template for describing either germline or variant calls output data (i.e. VCF/MAF)",,"Component,Filename,resourceType,progressReportNumber,specimenID,dataType,assay,individualID,workflow,comments",TRUE,Sage Bionetworks,template,,,,Processed_Variant_Calls_Template,Class,Template,Template,Assay_Template,,, ProcessedExpressionTemplate,"Template for describing expression output data",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,individualID,specimenID,workflow,expressionUnit,comments",TRUE,Sage Bionetworks,template,,,,Processed_Expression_Template,Class,Template,Template,Assay_Template,,, imagingAssayTemplate,"Generic template for describing data from an imaging type assay (IHC, etc). This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,comments",TRUE,Sage Bionetworks,template,,,,Imaging_Assay_Template,Class,Template,Template,Assay_Template,,, -imagingAssayTemplate_Extended,"Template for describing data from an imaging type assay (IHC, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Imaging_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, +imagingAssayTemplateExtended,"Template for describing data from an imaging type assay (IHC, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Imaging_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, MRIAssayTemplate,Generic template for describing data from an MRI assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,MRISequence,comments",TRUE,Sage Bionetworks,template,,,,MRI_Assay_Template,Class,Template,Template,Assay_Template,,, epigeneticsAssayTemplate,Generic template for describing data from an epigenetics assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Epigenetics_Assay_Template,Class,Template,Template,Assay_Template,,, pharmacokineticsAssayTemplate,Generic template for describing data from a pharmacokinetics assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Pharmacokinetics_Assay_Template,Class,Template,Template,Assay_Template,,, @@ -18,7 +18,7 @@ proteomicsAssayTemplate,Generic template for describing data from a proteomics a plateBasedReporterAssayTemplate,Generic template for describing data from a plate-based reporter assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,reporterGene,reporterSubstance,comments",TRUE,Sage Bionetworks,template,,,,Plate_Based_Reporter_Assay_Template,Class,Template,Template,Assay_Template,,, patientTimepointsTemplate,Template for capturing individual-level metadata with time points. Do not use for data file annotation.,,"Component,individualID,experimentalTimepoint",TRUE,Sage Bionetworks,template,,,,Patient_Timepoints_Template,Class,Template,Template,Non_Assay_Template,,, clinicalAssayTemplate,"Annotation template for simple endpoint data from clinical assays often used in diagnostic practice or clinical trials; may include repeated measures and a treatment/intervention context. Examples include bloodwork results (creatine assay, serum antibody assay), tumor size measurements, or medication adherence. Note that clinical data are from human individuals, therefore species should be “human”. ",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,comments",TRUE,Sage Bionetworks,template,,,,Clinical_Assay_Template,Class,Template,Template,Assay_Template,,, -clinicalAssayTemplate_Extended,Annotation template for simple endpoint data from clinical assays often used in diagnostic practice or clinical trials; may include repeated measures and a treatment/intervention context. Extended to capture additional drug/treatment parameters.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,compoundName,compoundDose,comments",TRUE,Sage Bionetworks,template,,,,Clinical_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, +clinicalAssayTemplateExtended,Annotation template for simple endpoint data from clinical assays often used in diagnostic practice or clinical trials; may include repeated measures and a treatment/intervention context. Extended to capture additional drug/treatment parameters.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,compoundName,compoundDose,comments",TRUE,Sage Bionetworks,template,,,,Clinical_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, behavioralAssayTemplate,"Generic template for describing data from behavioral assays such as “adaptive n-back task” (for humans) or “shock-probe defensive burying test” (for mice). If another modality is used as part of the behavioral assay, e.g. fMRI, that data can be linked.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,experimentalCondition,experimentalTimepoint,comments",TRUE,Sage Bionetworks,template,,,,Behavioral_Assay_Template,Class,Template,Template,Assay_Template,,, sourceCodeTemplate,Template for describing scripts or source code files for a software application.,,"Component,Filename,resourceType,programmingLanguage,documentation,runtimePlatform,comments",TRUE,Sage Bionetworks,template,,,,Source_Code_Template,Class,Template,Template,Non_Assay_Template,,, protocolTemplate,Template for describing a protocol document. (BETA) Adapted from https://bioschema.org/profiles/LabProtocol/0.6-DRAFT-2020_12_08,,"Component,Filename,resourceType,author,citation,license,comments",TRUE,Sage Bionetworks,template,,,,Protocol_Template,Class,Template,Template,Non_Assay_Template,,, @@ -26,7 +26,7 @@ pdxGenomicsAssay,Template for describing PDX assay data that extends genomicsAss updateMilestoneReport,Defines a metadata template for updating milestone report values in NF studies -- currently a supported feature for NTAP and GFF.,,"Component,Filename,resourceType,progressReportNumber",FALSE,Sage Bionetworks,template,,,,Update_Milestone_Report,Class,Template,Template,Non_Assay_Template,,, template,Parent attribute for the manifest template attributes.,,,FALSE,Sage Bionetworks,template,,,,Template,Class,Template,Template,,,, individualTemplate,Base template for minimal information describing individual-level data within the NF scope. Not called “patientTemplate_Default” because individuals can be a non-human organism.,"individualID,sex,age,ageUnit,species,diagnosis,nf1Genotype,nf2Genotype","Component,individualID,sex,age,ageUnit,species,diagnosis,nf1Genotype,nf2Genotype",FALSE,Sage Bionetworks,template,,,,Individual_Template,Class,Template,Template,Non_Assay_Template,,, -biospecimenTemplate_Normalized,Base template for describing biospecimen-level data.,"parentSpecimenID,specimenID,aliquotID,organ,tissue,isCellLine,isPrimaryCell,cellType,tumorType,specimenPreparationMethod,modelSystemName","Component,parentSpecimenID,specimenID,aliquotID,organ,tissue,isCellLine,isPrimaryCell,cellType,tumorType,specimenPreparationMethod,modelSystemName",FALSE,Sage Bionetworks,template,,,,Biospecimen_Template_Normalized,Class,Template,Template,Non_Assay_Template,,, +biospecimenTemplateNormalized,Base template for describing biospecimen-level data.,"parentSpecimenID,specimenID,aliquotID,organ,tissue,isCellLine,isPrimaryCell,cellType,tumorType,specimenPreparationMethod,modelSystemName","Component,parentSpecimenID,specimenID,aliquotID,organ,tissue,isCellLine,isPrimaryCell,cellType,tumorType,specimenPreparationMethod,modelSystemName",FALSE,Sage Bionetworks,template,,,,Biospecimen_Template_Normalized,Class,Template,Template,Non_Assay_Template,,, biospecimenTemplate,Denormalized template for describing biospecimen data that includes all individual-level data as well.,,"Component,individualID,parentSpecimenID",FALSE,Sage Bionetworks,template,,,,Biospecimen_Template,Class,Template,Template,Non_Assay_Template,,, dataFileComponent,Template component for describing a data file resource that extends fileTemplate_Default with required properties dataType and dataSubtype.,"Filename,entityId,fileFormat,resourceType,dataType,dataSubtype","Filename,entityId,fileFormat,resourceType,dataType,dataSubtype",FALSE,Sage Bionetworks,template,,,,Data_File_Component,Class,Template,TemplateComponent,,,, experimentComponent,Template component for describing core experimental parameters.,"experimentalCondition,experimentalTimepoint","experimentalCondition,experimentalTimepoint",FALSE,Sage Bionetworks,template,,,,Experiment_Component,Class,Template,TemplateComponent,,,,