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a/current-excel-manifests/NeuropathMetadataTemplate.xlsx and b/current-excel-manifests/NeuropathMetadataTemplate.xlsx differ diff --git a/current-manifest-schemas/AD.Assay16SrRNAseqMetadataTemplate.schema.json b/current-manifest-schemas/AD.Assay16SrRNAseqMetadataTemplate.schema.json index 64fee9cb..9c0e4742 100644 --- a/current-manifest-schemas/AD.Assay16SrRNAseqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.Assay16SrRNAseqMetadataTemplate.schema.json @@ -4,376 +4,376 @@ "title": "Assay16SrRNAseqMetadataTemplate", "type": "object", "properties": { - "dnaExtractionMethod": {}, "sequencingBatch": {}, - "platform": { - "enum": [ - "Illumina_Omni2.5-8_v1.3", - "HiSeqX", - "Q Exactive HF", - "Q Exactive Plus", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "llumina Infinium General Screening Array 24-Kit v3.0", - "IlluminaHumanHap300", - "Simoa HD-1 Analyzer", - "Roche Cobas", - "HiSeq4000", - "Bionano Irys", - "time-of-flight", - "HiSeq3000", - 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"atomicForceMicroscopy", + "locomotor activation behavior", + "novelty response behavior", + "polymeraseChainReaction", "lncrnaSeq", - "microRNAcounts", - "FIA-MSMS", - "LTP", - "Biocrates p180", + "high content screen", + "FitBark", + "snATACSeq", + "methylationArray", + "scrnaSeq", + "Real Time PCR", + "frailty assessment", + "oxBS-Seq", + "in vivo bioluminescence", + "Laser Speckle Imaging", + "UPLC-ESI-QTOF-MS", "HPLC-MSMS", - "label free mass spectrometry", - "whole-cell patch clamp", + "HiChIPseq", + "Ribo-Seq", + "Immunocytochemistry", + "LFP", + "photograph", "Biocrates MxP Quant500 XL", - "Biocrates Q500", - "Rader Lipidomics", - "atomicForceMicroscopy", - "mirnaArray", + "errBisulfiteSeq", + "elevated T maze apparatus method", + "Baker Lipidomics", "Blood Chemistry Measurement", + "label free mass spectrometry", + "cellViabilityAssay", + "ATACSeq", "Sanger sequencing", - "Laser Speckle Imaging", - "ELISA", - "scirnaSeq", - "in vivo bioluminescence", - "10x multiome", + "LC-MSMS", + "anxiety-related behavior", + "immunohistochemistry", + "scwholeGenomeSeq", + "wheel running", + "scATACSeq", + "von Frey test", + "bisulfiteSeq", + "HI-C", + "snpArray", "MDMS-SL", - "mRNAcounts", - "UC Davis GCTOF", - "active avoidance learning behavior", - "oxBS-Seq", - "16SrRNAseq", - "Wishart Catecholamines", - "errBisulfiteSeq", + "sandwich ELISA", + "NOMe-Seq", + "Biocrates p180", + "MRI", + "m6A-rnaSeq", + "STARRSeq", + "whole-cell patch clamp", + "10x multiome", + "pharmacodynamics", + "Vernier Caliper", "spontaneous alternation", - "exomeSeq", - "wholeGenomeSeq", - "cellViabilityAssay", - "mirnaSeq", - "Positron Emission Tomography", - "UPLC-MSMS", - "LC-SRM", - "high content screen", - "TMT quantitation", - "DIA", "SiMoA", - "HI-C", - "MudPIT", - "scCGIseq", - "contextual conditioning behavior", - "MRI", - "Metabolon", - "Wishart High Value Metabolites", - "westernBlot", - "elevated T maze apparatus method", - "HPLC", + "scirnaSeq", + "proximity extension assay", "immunofluorescence", - "electrochemiluminescence", - "photograph", + "Biocrates Bile Acids", "nextGenerationTargetedSequencing", - "MIB/MS", - "sandwich ELISA", + "DIA", + "Zeno Electronic Walkway", + "rotarod performance test", + "LTP", + "Metabolon", "UCSD Untargeted Metabolomics", - "wheel running", - "CITESeq", - "snATACSeq", - "LFP", - "FitBark", - "NOMe-Seq", - "Ribo-Seq", - "Genotyping", - "Immunocytochemistry", + "rnaSeq", + "liquid chromatography-electrochemical detection", + "microRNAcounts", + "active avoidance learning behavior", + "Rader Lipidomics", + "memory behavior", + "MIB/MS", + "RPPA", + "UC Davis GCTOF", + "long-read rnaSeq", + "wholeGenomeSeq", + "ChIPSeq", + "CUT&Tag", + "exomeSeq", + "tractionForceMicroscopy", + "scCGIseq", + "rnaArray", + "questionnaire", "brightfieldMicroscopy", - "kinesthetic behavior", - "locomotor activation behavior", + "autoradiography", + "ISOSeq", + "LC-SRM", + "16SrRNAseq", + "pharmacokinetics", "Nightingale NMR", - "immunohistochemistry", - "Biocrates Bile Acids", - "novelty response behavior", - "Vernier Caliper", - "scrnaSeq", - "lentiMPRA", - "ChIPSeq", - "scATACSeq", + "ELISA", + "Wishart Catecholamines", + "CITESeq", "jumpingLibrary", - "STARRSeq", - "autoradiography", - "elevated plus maze test", + "UPLC-MSMS", + "open field test", + "lentiMPRA", + "mRNAcounts", + "westernBlot", + "Positron Emission Tomography", + "snrnaSeq", + "Wishart High Value Metabolites", "DNA optical mapping", - "CUT&Tag", - "anxiety-related behavior", - "UPLC-ESI-QTOF-MS", - "m6A-rnaSeq", - "proximity extension assay", - "polymeraseChainReaction", - "scwholeGenomeSeq", - "liquid chromatography-electrochemical detection", - "methylationArray", - "rotarod performance test", - "pharmacodynamics", - "pharmacokinetics", - "questionnaire", + "mirnaArray", + "electrochemiluminescence", + "elevated plus maze test", + "Leiden Oxylipins", + "TMT quantitation", "scale", - "Zeno Electronic Walkway", - "snrnaSeq", - "von Frey test", - "long-read rnaSeq", - "rnaArray", - "Baker Lipidomics", - "ISOSeq", - "HiChIPseq", - "ATACSeq" + "Biocrates Q500", + "HPLC", + "FIA-MSMS" + ] + }, + "libraryPrep": { + "enum": [ + "MULTIseq", + "STARRSeq", + "proximity ligation", + "amplicon", + "cellHashing", + "Chromium Single Cell 3'", + "multiome", + "miRNAenrichment", + "methylSeq", + "lncRNAenrichment", + "SPLITseq", + "totalRNA", + "SureCell", + "PCRfree", + "rRNAdepletion", + "polyAselection", + "snIsoSeq", + "EndItDNAEndRepairKit", + "KapaHyperPrep", + "DNALibraryConstruction" + ] + }, + "libraryBatch": {}, + "Component": {}, + "specimenID": {}, + "platform": { + "enum": [ + "OrbiTrap Fusion", + "NextSeq2000", + "Leco Pegasus IV", + "Illumina_1M", + "Orbitrap Fusion Lumos", + "MiSeq", + "Agilent44Karray", + "Illumina_HumanOmni1-Quadv1.0", + "Signa Premier AIR 3T", + "Illumina_Omni5-Quad", + "Perlegen300Karray", + "Infinium HumanOmniExpressExome", + "Infinium Omni2.5Exome-8 v1.5", + "Bruker Avance III", + "PacBio Sequel IIe", + "Xevo TQ-S", + "IlluminaMethylationEPIC", + "Xevo G2 QTOF", + "Roche Cobas", + "Affymetrix Human Gene 1.0 ST Array", + "IlluminaHumanHap300", + "time-of-flight", + "IlluminaNovaseq6000", + "Q Exactive", + "PacBioRSII", + "HiSeqX", + "IlluminaMiSeq", + "InfiniumPsychArrayBeadChip", + "NanostringnCounter", + "Orbitrap Exploris 240", + "Illumina MouseWG-6 v2.0 expression beadchip", + "Illumina NovaSeq 6000", + "IlluminaInfiniumGSAMD-24v2-0", + "LTQOrbitrapXL", + "AffymetrixU133Plus2", + "Illumina_Omni2.5-8_v1.3", + "Biocrates p180", + "HiSeq4000", + "Illumina_Omni2.5-8", + "Q Exactive HF", + "Infinium Omni2.5Exome-8 v1.4", + "SequenomMultiplex", + "Illumina_Omni5M", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "HiSeq1000", + "Olink Target 96", + "Biograph mCT", + "Illumina_Omni2pt5M", + "llumina Infinium General Screening Array 24-Kit v3.0", + "DNBSEQ", + "Simoa HD-1 Analyzer", + "NextSeq500", + "Q Exactive HF-X", + "Bionano Irys", + "Affy6.0", + "HiSeq2000", + "Illumina_h650", + "PacBio Sequel II", + "Q Exactive Plus", + "Illumina_Omni2.5-8_v1.1", + "ddSEQ Single-Cell Isolator", + "PsychChip", + "HiSeq2500", + "triple quadrupole", + "BGISEQ-500", + "IlluminaWholeGenomeDASL", + "confocalImaging", + "Infinium Omni2.5Exome-8 v1.1", + "orbitrap", + "Affy5.0", + "Infinium Omni2.5Exome-8 v1.3", + "IlluminaHumanMethylation450", + "GAIIx", + "quadrupole time-of-flight", + "HiSeq3000", + "AffymetrixU133AB", + "IlluminaHumanHap650Yv3_A", + "IlluminaHumanHT-12_V3_0_R1", + "Infinium Global Diversity Array-8", + "NanostringnCounter_MouseADPanel" ] }, - "libraryBatch": {}, + "runType": { + "enum": [ + "singleEnd", + "pairedEnd" + ] + }, + "readLength": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "assayTarget": { "enum": [ - "ZNF384", - "NCOR1", - "HCFC1", - "HNRNPK", - "H3K4me1", "CC2D1A", - "H3K27ac", - "ZNF407", - "EED", - "ZFP91", - "ASH1L", - "BCL11A", - "input", - "TAF1", - "TDP43", - "NFIB", - "BRCA1", - "YBX1", - "EGR1", "ARID1B", - "KLF5", - "PKNOX1", + "SMC3", "GMEB1", - "SP1", - "SIX4", - "DPF2", - "SREBP2", - "KAT2B", - "GATAD2B", - "H3K9ac", - "R-loops", - "BHLHE40", - "H3K9me2", - "SON", - "ZEB1", - "YBX3", - "SIN3A", - "SATB2", - "SRF", - "H3K36me3", + "REST", "CTCF", + "RAD21", + "ZNF318", + "BMI1", "ATF7", + "SIN3A", + "SRF", + "HCFC1", + "RELB", + "NCOA2", + "ZNF24", + "TBR1", + "EHMT2", + "CREM", "TRIM28", - "LaminB", - "EWSR1", + "SATB2", + "ZEB1", "ZNF592", + "SMARCA5", + "input", + "TAF1", + "ZNF207", + "H3K27me3", + "YBX1", + "NR2F2", + "H3K4me1", + "NR2F1", + "DPF2", + "H3K27ac", + "IgG", + "NR3C1", + "TDP43", + "OLIG2", + "MEF2A", + "NFIB", + "IE_V1-V3", + "ZNF407", + "TCF12", + "SIRT1", + "GATAD2A", + "ZFP91", + "ZNF143", + "CREB1", + "RB1", + "EWSR1", + "BRCA1", + "LaminB", + "CLOCK", + "ZSCAN29", + "BCL11A", + "MITF", + "DEAF1", + "FOXK2", "Pol2", + "GABPB1", + "HNRNPK", + "SIX4", + "ZEB2", "ZKSCAN1", - "IgG", - "SOX8", - "BMI1", "SP4", - "ASCL1", - "NFIC", - "BHLHE41", + "NCOR1", + "SON", "SIN3B", + "H3K9me2", + "TCF7L2", "ZBTB7B", - "ZNF207", - "IE_V1-V3", - "ZEB2", - "NEUROD1", + "YY1", "ARID3A", - "RELB", + "H3K36me3", + "KDM4A", + "SP1", + "ASCL1", + "MEIS2", + "H3K9ac", + "SREBP2", + "GATA4", + "ASH1L", + "BHLHE40", + "NRF1", + "BHLHE41", + "NFIC", + "SKIL", + "ZNF384", "ARNT", - "YY1", "BRD4", - "SMARCA5", - "H3K9me3", - "RB1", - "ZNF143", - "REST", - "TCF12", - "ZNF318", - "H3K27me3", - "RAD21", - "KLF16", - "ASH2L", - "EZH2", - "ZNF24", "MAZ", - "CREM", - "MEIS2", - "NRF1", + "R-loops", + "EED", + "EGR1", + "NONO", + "PKNOX1", + "GATAD2B", + "KLF16", + "YBX3", "E2F1", - "GABPB1", - "GATAD2A", - "NR3C1", - "CREB1", - "TCF7L2", - "H3K4me3", - "MITF", - "GATA4", - "TBR1", - "SMC3", - "OLIG2", - "NR2F1", "ZHX1", - "NONO", - "NR2F2", - "KDM4A", - "SIRT1", - "CHD4", - "EHMT2", - "CLOCK", - "NCOA2", - "DEAF1", - "MEF2A", - "FOXK2", + "ASH2L", + "H3K4me3", + "SOX8", "FOXP1", - "ZSCAN29", - "SKIL", + "EZH2", + "KLF5", + "NEUROD1", + "H3K9me3", + "CHD4", + "KAT2B", "" ] }, - "readLength": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "libraryPrep": { - "enum": [ - "STARRSeq", - "rRNAdepletion", - "Chromium Single Cell 3'", - "proximity ligation", - "EndItDNAEndRepairKit", - "DNALibraryConstruction", - "SPLITseq", - "lncRNAenrichment", - "PCRfree", - "cellHashing", - "snIsoSeq", - "miRNAenrichment", - "KapaHyperPrep", - "SureCell", - "amplicon", - "multiome", - "MULTIseq", - "methylSeq", - "polyAselection", - "totalRNA" - ] - }, - "runType": { - "enum": [ - "pairedEnd", - "singleEnd" - ] - }, - "specimenID": {}, - "Component": {} + "dnaBatch": {} }, "required": [ - "platform", "assay", - "readLength", "libraryPrep", - "runType" + "platform", + "runType", + "readLength" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.AssayATACSeqMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayATACSeqMetadataTemplate.schema.json index 267ccb91..f82b74fe 100644 --- a/current-manifest-schemas/AD.AssayATACSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayATACSeqMetadataTemplate.schema.json @@ -4,146 +4,107 @@ "title": "AssayATACSeqMetadataTemplate", "type": "object", "properties": { + "readLength": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "runType": { + "enum": [ + "singleEnd", + "pairedEnd" + ] + }, + "sequencingBatch": {}, + "meanCoverage": {}, + "meanGCContent": {}, + "libraryBatch": {}, + "pcrCycles": {}, "platform": { "enum": [ - "GAIIx", - "NextSeq500", - "Xevo TQ-S", - "Illumina_Omni2pt5M", - "Illumina_Omni2.5-8_v1.1", - "Biocrates p180", - "Infinium Omni2.5Exome-8 v1.5", - "NanostringnCounter", - "Agilent44Karray", - "InfiniumPsychArrayBeadChip", - "Illumina_1M", + "Orbitrap Exploris 240", + "HiSeq3000", + "IlluminaHumanMethylation450", + "orbitrap", + "Bruker Avance III", + "AffymetrixU133Plus2", + "MiSeq", + "Perlegen300Karray", + "Olink Target 96", + "Signa Premier AIR 3T", + "Leco Pegasus IV", "Orbitrap Fusion Lumos", - "HiSeqX", - "Illumina_Omni2.5-8", - "HiSeq1000", - "IlluminaHumanHap300", - "IlluminaNovaseq6000", - "time-of-flight", "Affy5.0", + "Agilent44Karray", + "Infinium Omni2.5Exome-8 v1.1", + "Affymetrix Human Gene 1.0 ST Array", + "NextSeq2000", + "Affy6.0", + "IlluminaInfiniumGSAMD-24v2-0", + "Infinium Omni2.5Exome-8 v1.4", + "Simoa HD-1 Analyzer", + "IlluminaHumanHap650Yv3_A", "PacBio Sequel II", - "SequenomMultiplex", + "Illumina_Omni2.5-8_v1.3", + "triple quadrupole", + "IlluminaMiSeq", + "Q Exactive", + "Infinium Omni2.5Exome-8 v1.5", + "PacBioRSII", + "Roche Cobas", "BGISEQ-500", - "HiSeq4000", - "Affy6.0", - "Leco Pegasus IV", - "Illumina NovaSeq 6000", "ddSEQ Single-Cell Isolator", - "Biograph mCT", - "AffymetrixU133Plus2", + "InfiniumPsychArrayBeadChip", "Illumina_h650", - "OrbiTrap Fusion", - "orbitrap", - "Illumina_Omni2.5-8_v1.3", - "MiSeq", - "confocalImaging", - "Illumina MouseWG-6 v2.0 expression beadchip", + "Biograph mCT", + "Illumina_Omni2.5-8_v1.1", + "Illumina_HumanOmni1-Quadv1.0", "IlluminaWholeGenomeDASL", - "Signa Premier AIR 3T", - "Olink Target 96", - "Perlegen300Karray", - "quadrupole time-of-flight", + "Illumina_Omni2.5-8", + "HiSeq1000", + "Q Exactive Plus", + "NanostringnCounter", + "Infinium Omni2.5Exome-8 v1.3", + "NextSeq500", + "GAIIx", + "NanostringnCounter_MouseADPanel", + "Illumina_1M", + "Infinium HumanOmniExpressExome", + "Xevo TQ-S", + "HiSeq2000", + "AffymetrixU133AB", + "IlluminaNovaseq6000", "DNBSEQ", - "LTQOrbitrapXL", + "time-of-flight", + "Q Exactive HF-X", "IlluminaMethylationEPIC", - "NanostringnCounter_MouseADPanel", - "IlluminaHumanHT-12_V3_0_R1", - "triple quadrupole", - "Roche Cobas", - "Illumina_Omni5M", - "Infinium Omni2.5Exome-8 v1.4", + "llumina Infinium General Screening Array 24-Kit v3.0", + "HiSeqX", + "confocalImaging", + "SequenomMultiplex", + "Illumina MouseWG-6 v2.0 expression beadchip", + "Infinium Global Diversity Array-8", "Bionano Irys", - "IlluminaHumanHap650Yv3_A", - "Q Exactive HF-X", - "HiSeq3000", - "HiSeq2000", - "IlluminaHumanMethylation450", - "Affymetrix Human Gene 1.0 ST Array", + "Illumina_Omni5M", + "Illumina NovaSeq 6000", + "Illumina_Omni2pt5M", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "quadrupole time-of-flight", "Xevo G2 QTOF", - "Q Exactive", - "Infinium Global Diversity Array-8", - "Orbitrap Exploris 240", "Q Exactive HF", + "IlluminaHumanHap300", + "Illumina_Omni5-Quad", + "Biocrates p180", + "IlluminaHumanHT-12_V3_0_R1", "HiSeq2500", - "Infinium Omni2.5Exome-8 v1.3", "PacBio Sequel IIe", - "PacBioRSII", - "Infinium Omni2.5Exome-8 v1.1", - "Simoa HD-1 Analyzer", - "Q Exactive Plus", - "AffymetrixU133AB", - "Infinium HumanOmniExpressExome", - "Bruker Avance III", "PsychChip", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "IlluminaInfiniumGSAMD-24v2-0", - "Illumina_HumanOmni1-Quadv1.0", - "Illumina_Omni5-Quad", - "NextSeq2000", - "llumina Infinium General Screening Array 24-Kit v3.0", - "IlluminaMiSeq" - ] - }, - "sequencingBatch": {}, - "isStranded": { - "enum": [ - "TRUE", - "FALSE", - "" - ] - }, - "libraryPreparationMethod": { - "enum": [ - "Omni-ATAC", - "Drop-Seq", - "10x", - "Ultralow Methyl-Seq", - "Smart-seq2", - "Accel-NGS 2S Plus", - "Smart-seq4", - "TruSeq", - "Illumina DNA PCR-Free Prep Kit", - "NexteraXT", - "NEBNext", - "SMRTbell", - "Smart-seq1", - "sac-seq", - "CEL-seq", - "Accel-NGS Methyl-Seq", - "" - ] - }, - "meanGCContent": {}, - "referenceSet": { - "enum": [ - "GRCh38", - "HRC", - "dmel_r6.06", - "GRCh37", - "1000 Genomes phase 3", - "GRCm38", - "MMUL1.0", - "" - ] - }, - "runType": { - "enum": [ - "pairedEnd", - "singleEnd" + "HiSeq4000", + "LTQOrbitrapXL", + "OrbiTrap Fusion" ] }, - "specimenID": {}, - "libraryID": {}, - "readLength": { - "not": { - "type": "null" - }, - "minLength": 1 - }, "readStrandOrigin": { "enum": [ "forward", @@ -151,138 +112,177 @@ "" ] }, - "libraryBatch": {}, - "Component": {}, - "pcrCycles": {}, - "meanCoverage": {}, "transposaseBatch": {}, "assay": { "enum": [ - "Baker Lipidomics", - "RPPA", - "in vivo bioluminescence", - "lncrnaSeq", + "CUT&Tag", + "MudPIT", + "FIA-MSMS", + "Metabolon", "Biocrates Bile Acids", - "westernBlot", - "Biocrates p180", - "immunofluorescence", - "questionnaire", - "UCSD Untargeted Metabolomics", - "wholeGenomeSeq", - "rotarod performance test", - "10x multiome", - "tractionForceMicroscopy", - "elevated T maze apparatus method", - "ChIPSeq", - "pharmacokinetics", "label free mass spectrometry", - "LC-MSMS", - "MudPIT", - "active avoidance learning behavior", - "Genotyping", + "ATACSeq", + "westernBlot", + "wheel running", + "MIB/MS", + "memory behavior", + "oxBS-Seq", + "exomeSeq", "FitBark", - "nextGenerationTargetedSequencing", - "photograph", + "rnaArray", + "active avoidance learning behavior", + "Nightingale NMR", "MDMS-SL", - "sandwich ELISA", - "proximity extension assay", + "DNA optical mapping", + "nextGenerationTargetedSequencing", + "10x multiome", + "CITESeq", + "snpArray", "m6A-rnaSeq", - "LC-MS", - "autoradiography", - "Ribo-Seq", - "HPLC-MSMS", - "long-read rnaSeq", - "mRNAcounts", - "Metabolon", - "rnaSeq", - "oxBS-Seq", - "scrnaSeq", - "Wishart High Value Metabolites", + "elevated T maze apparatus method", + "scirnaSeq", + "NOMe-Seq", "lentiMPRA", - "von Frey test", + "rotarod performance test", + "Blood Chemistry Measurement", + "sandwich ELISA", + "photograph", "bisulfiteSeq", + "16SrRNAseq", + "Sanger sequencing", + "RPPA", + "scwholeGenomeSeq", "novelty response behavior", - "atomicForceMicroscopy", - "Leiden Oxylipins", + "Genotyping", + "lncrnaSeq", + "Laser Speckle Imaging", + "UPLC-MSMS", + "scrnaSeq", + "HPLC-MSMS", + "scale", + "frailty assessment", + "LC-MS", + "whole-cell patch clamp", + "scATACSeq", "liquid chromatography-electrochemical detection", - "snATACSeq", - "Vernier Caliper", - "Nightingale NMR", - "electrochemiluminescence", - "FIA-MSMS", - "Blood Chemistry Measurement", - "UPLC-ESI-QTOF-MS", + "errBisulfiteSeq", + "locomotor activation behavior", + "proximity extension assay", + "long-read rnaSeq", + "von Frey test", + "DIA", + "Baker Lipidomics", + "Immunocytochemistry", + "atomicForceMicroscopy", + "spontaneous alternation", "LC-SRM", + "mirnaArray", + "polymeraseChainReaction", + "Leiden Oxylipins", "immunohistochemistry", - "memory behavior", - "methylationArray", - "errBisulfiteSeq", - "MIB/MS", - "mirnaSeq", - "kinesthetic behavior", - "UPLC-MSMS", - "anxiety-related behavior", - "open field test", - "frailty assessment", + "HiChIPseq", + "tractionForceMicroscopy", + "electrochemiluminescence", + "SiMoA", + "pharmacodynamics", + "Wishart Catecholamines", + "high content screen", + "HI-C", + "Ribo-Seq", + "UCSD Untargeted Metabolomics", + "MRI", + "pharmacokinetics", "ELISA", + "Positron Emission Tomography", + "contextual conditioning behavior", + "ISOSeq", + "TMT quantitation", + "Wishart High Value Metabolites", "Zeno Electronic Walkway", + "snrnaSeq", + "Biocrates Q500", + "in vivo bioluminescence", + "LC-MSMS", + "Biocrates MxP Quant500 XL", + "HPLC", "jumpingLibrary", - "pharmacodynamics", - "MRI", + "anxiety-related behavior", + "wholeGenomeSeq", + "scCGIseq", + "UC Davis GCTOF", + "methylationArray", + "mirnaSeq", "brightfieldMicroscopy", - "ATACSeq", - "16SrRNAseq", + "microRNAcounts", + "Vernier Caliper", "elevated plus maze test", - "snrnaSeq", - "TMT quantitation", - "NOMe-Seq", - "SiMoA", - "LFP", - "UC Davis GCTOF", - "spontaneous alternation", - "high content screen", - "Real Time PCR", - "scale", - "Laser Speckle Imaging", - "Biocrates MxP Quant500 XL", - "HiChIPseq", + "UPLC-ESI-QTOF-MS", "LTP", - "polymeraseChainReaction", - "Positron Emission Tomography", - "scATACSeq", - "wheel running", + "snATACSeq", + "ChIPSeq", + "open field test", + "Biocrates p180", + "immunofluorescence", + "cellViabilityAssay", + "questionnaire", + "LFP", + "autoradiography", "Rader Lipidomics", - "DIA", - "whole-cell patch clamp", - "contextual conditioning behavior", - "HPLC", - "Biocrates Q500", - "rnaArray", - "microRNAcounts", - "DNA optical mapping", "STARRSeq", - "HI-C", - "scwholeGenomeSeq", - "Sanger sequencing", - "cellViabilityAssay", - "locomotor activation behavior", - "ISOSeq", - "CUT&Tag", - "scCGIseq", - "Wishart Catecholamines", - "mirnaArray", - "exomeSeq", - "snpArray", - "scirnaSeq", - "Immunocytochemistry", - "CITESeq" + "kinesthetic behavior", + "rnaSeq", + "mRNAcounts", + "Real Time PCR" + ] + }, + "specimenID": {}, + "libraryID": {}, + "libraryPreparationMethod": { + "enum": [ + "sac-seq", + "Ultralow Methyl-Seq", + "Smart-seq2", + "TruSeq", + "NexteraXT", + "Omni-ATAC", + "10x", + "Illumina DNA PCR-Free Prep Kit", + "Smart-seq1", + "Smart-seq4", + "Accel-NGS 2S Plus", + "CEL-seq", + "Accel-NGS Methyl-Seq", + "NEBNext", + "SMRTbell", + "Drop-Seq", + "" + ] + }, + "isStranded": { + "enum": [ + "FALSE", + "TRUE", + "" + ] + }, + "Component": {}, + "referenceSet": { + "enum": [ + "GRCh38", + "GRCh37", + "GRCm38", + "HRC", + "dmel_r6.06", + "MMUL1.0", + "1000 Genomes phase 3", + "" ] } }, "required": [ - "platform", - "runType", "readLength", + "runType", + "platform", "assay" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.AssayAutoradMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayAutoradMetadataTemplate.schema.json index 75fc795d..245c3bbf 100644 --- a/current-manifest-schemas/AD.AssayAutoradMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayAutoradMetadataTemplate.schema.json @@ -4,113 +4,113 @@ "title": "AssayAutoradMetadataTemplate", "type": "object", "properties": { + "scanID": {}, + "individualID": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "ageAssessmentUnits": { + "enum": [ + "weeks", + "months", + "PCW", + "days", + "gestational weeks", + "years", + "" + ] + }, + "Component": {}, "platform": { "enum": [ - "Roche Cobas", - "PacBio Sequel IIe", - "time-of-flight", - "HiSeq1000", - "Orbitrap Exploris 240", - "PsychChip", - "Affy5.0", - "NextSeq500", - "Infinium Omni2.5Exome-8 v1.4", - "Q Exactive", - "PacBioRSII", - "Infinium Omni2.5Exome-8 v1.3", - "DNBSEQ", - "Q Exactive HF-X", - "Infinium Omni2.5Exome-8 v1.1", + "triple quadrupole", + "ddSEQ Single-Cell Isolator", "Illumina NovaSeq 6000", - "IlluminaHumanHT-12_V3_0_R1", - "LTQOrbitrapXL", - "NextSeq2000", - "Infinium HumanOmniExpressExome", - "PacBio Sequel II", + "HiSeqX", + "Illumina_Omni2.5-8_v1.1", + "Illumina MouseWG-6 v2.0 expression beadchip", "Illumina_Omni2.5-8", + "HiSeq3000", + "Infinium HumanOmniExpressExome", + "IlluminaWholeGenomeDASL", + "Bionano Irys", + "Affy6.0", + "IlluminaHumanHT-12_V3_0_R1", + "Q Exactive HF", + "AffymetrixU133AB", "BGISEQ-500", - "Xevo TQ-S", + "PacBio Sequel IIe", + "DNBSEQ", + "HiSeq4000", + "Illumina_Infinium-HumanMethylation450-BeadChip", "orbitrap", - "IlluminaWholeGenomeDASL", - "HiSeq3000", - "IlluminaNovaseq6000", - "Leco Pegasus IV", - "IlluminaMethylationEPIC", - "AffymetrixU133Plus2", - "Bruker Avance III", + "IlluminaHumanMethylation450", + "Infinium Global Diversity Array-8", + "Illumina_h650", + "Illumina_1M", + "Illumina_Omni2pt5M", + "SequenomMultiplex", + "Q Exactive HF-X", "Illumina_HumanOmni1-Quadv1.0", - "Q Exactive Plus", - "Infinium Omni2.5Exome-8 v1.5", - "confocalImaging", + "Xevo TQ-S", "quadrupole time-of-flight", + "IlluminaMiSeq", + "Orbitrap Fusion Lumos", + "MiSeq", + "Bruker Avance III", + "confocalImaging", + "Simoa HD-1 Analyzer", + "Orbitrap Exploris 240", + "Olink Target 96", + "IlluminaNovaseq6000", + "Illumina_Omni2.5-8_v1.3", + "NextSeq500", "Biocrates p180", - "IlluminaInfiniumGSAMD-24v2-0", - "triple quadrupole", - "HiSeq4000", - "AffymetrixU133AB", - "llumina Infinium General Screening Array 24-Kit v3.0", - "Illumina_h650", + "NextSeq2000", + "PacBio Sequel II", + "Roche Cobas", + "InfiniumPsychArrayBeadChip", + "NanostringnCounter_MouseADPanel", "Signa Premier AIR 3T", + "IlluminaHumanHap650Yv3_A", "OrbiTrap Fusion", - "ddSEQ Single-Cell Isolator", - "InfiniumPsychArrayBeadChip", - "Agilent44Karray", - "Olink Target 96", + "Q Exactive Plus", + "time-of-flight", + "IlluminaMethylationEPIC", + "PacBioRSII", + "GAIIx", + "Illumina_Omni5M", + "Illumina_Omni5-Quad", "Perlegen300Karray", - "IlluminaHumanHap650Yv3_A", - "MiSeq", - "Simoa HD-1 Analyzer", - "Orbitrap Fusion Lumos", + "Agilent44Karray", + "IlluminaHumanHap300", + "IlluminaInfiniumGSAMD-24v2-0", + "Infinium Omni2.5Exome-8 v1.5", "Xevo G2 QTOF", - "NanostringnCounter_MouseADPanel", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "Illumina_1M", - "IlluminaMiSeq", - "SequenomMultiplex", - "Q Exactive HF", - "Affy6.0", - "Infinium Global Diversity Array-8", - "IlluminaHumanMethylation450", - "Bionano Irys", - "Illumina_Omni2pt5M", - "GAIIx", + "llumina Infinium General Screening Array 24-Kit v3.0", + "Infinium Omni2.5Exome-8 v1.3", + "HiSeq1000", + "PsychChip", + "AffymetrixU133Plus2", + "Q Exactive", "NanostringnCounter", + "Affy5.0", "Biograph mCT", - "IlluminaHumanHap300", + "Infinium Omni2.5Exome-8 v1.1", + "Leco Pegasus IV", "HiSeq2500", - "Illumina MouseWG-6 v2.0 expression beadchip", "Affymetrix Human Gene 1.0 ST Array", - "Illumina_Omni5M", - "Illumina_Omni2.5-8_v1.3", - "Illumina_Omni2.5-8_v1.1", - "HiSeqX", - "Illumina_Omni5-Quad", - "HiSeq2000" + "HiSeq2000", + "LTQOrbitrapXL", + "Infinium Omni2.5Exome-8 v1.4" ] }, - "scanID": {}, - "individualID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "Component": {}, - "ageAssessment": {}, - "ageAssessmentUnits": { - "enum": [ - "PCW", - "gestational weeks", - "weeks", - "days", - "years", - "months", - "" - ] - } + "ageAssessment": {} }, "required": [ - "platform", - "individualID" + "individualID", + "platform" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.AssayBisulfiteSeqMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayBisulfiteSeqMetadataTemplate.schema.json index 61442c80..154e2983 100644 --- a/current-manifest-schemas/AD.AssayBisulfiteSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayBisulfiteSeqMetadataTemplate.schema.json @@ -4,299 +4,293 @@ "title": "AssayBisulfiteSeqMetadataTemplate", "type": "object", "properties": { - "lambdaDNAconc": {}, + "libraryID": {}, + "meanCoverage": {}, + "specimenID": {}, + "gDNAconc": {}, + "runType": { + "enum": [ + "singleEnd", + "pairedEnd" + ] + }, + "directionalBSseqLibrary": { + "enum": [ + "TRUE", + "FALSE", + "" + ] + }, + "Component": {}, "assay": { "enum": [ - "Biocrates p180", - "oxBS-Seq", - "autoradiography", - "wheel running", "NOMe-Seq", - "anxiety-related behavior", - "Genotyping", - "questionnaire", - "cellViabilityAssay", - "Metabolon", - "UCSD Untargeted Metabolomics", - "LC-SRM", - "microRNAcounts", - "von Frey test", - "mirnaSeq", + "immunohistochemistry", + "locomotor activation behavior", + "MudPIT", + "mRNAcounts", + "electrochemiluminescence", "SiMoA", - "Ribo-Seq", - "novelty response behavior", - "ATACSeq", - "FitBark", - "bisulfiteSeq", - "open field test", - "CITESeq", + "spontaneous alternation", + "snrnaSeq", + "UC Davis GCTOF", "snATACSeq", - "lentiMPRA", - "whole-cell patch clamp", - "elevated T maze apparatus method", - "ChIPSeq", - "lncrnaSeq", - "atomicForceMicroscopy", - "immunohistochemistry", - "FIA-MSMS", - "scirnaSeq", - "pharmacodynamics", - "polymeraseChainReaction", - "scCGIseq", + "nextGenerationTargetedSequencing", + "TMT quantitation", "snpArray", - "DIA", - "Baker Lipidomics", - "LC-MSMS", - "Leiden Oxylipins", - "16SrRNAseq", - "ELISA", + "errBisulfiteSeq", + "jumpingLibrary", + "long-read rnaSeq", + "scwholeGenomeSeq", + "oxBS-Seq", + "Sanger sequencing", "MIB/MS", - "LFP", - "MRI", - "memory behavior", - "immunofluorescence", - "pharmacokinetics", - "scrnaSeq", + "exomeSeq", + "lncrnaSeq", + "whole-cell patch clamp", + "ATACSeq", + "scCGIseq", + "Rader Lipidomics", + "high content screen", + "Vernier Caliper", + "Positron Emission Tomography", "westernBlot", - "scATACSeq", - "MDMS-SL", + "lentiMPRA", + "Wishart Catecholamines", + "mirnaSeq", + "rotarod performance test", + "immunofluorescence", + "Metabolon", "DNA optical mapping", - "CUT&Tag", - "Real Time PCR", - "methylationArray", - "STARRSeq", + "Biocrates p180", "active avoidance learning behavior", - "liquid chromatography-electrochemical detection", - "elevated plus maze test", - "HPLC-MSMS", - "contextual conditioning behavior", - "Biocrates MxP Quant500 XL", - "Biocrates Bile Acids", - "Wishart Catecholamines", - "electrochemiluminescence", - "frailty assessment", - "scwholeGenomeSeq", - "scale", - "Immunocytochemistry", - "MudPIT", - "HPLC", - "Biocrates Q500", - "nextGenerationTargetedSequencing", - "errBisulfiteSeq", - "spontaneous alternation", - "long-read rnaSeq", - "RPPA", - "Blood Chemistry Measurement", - "LTP", - "brightfieldMicroscopy", - "ISOSeq", - "UPLC-MSMS", "rnaSeq", - "rotarod performance test", - "jumpingLibrary", - "10x multiome", - "UPLC-ESI-QTOF-MS", - "high content screen", + "STARRSeq", + "m6A-rnaSeq", "mirnaArray", + "wheel running", + "16SrRNAseq", + "elevated plus maze test", + "Biocrates MxP Quant500 XL", + "FitBark", + "proximity extension assay", + "Baker Lipidomics", + "scrnaSeq", + "atomicForceMicroscopy", + "contextual conditioning behavior", "kinesthetic behavior", + "LFP", + "pharmacodynamics", + "UPLC-MSMS", + "ChIPSeq", "in vivo bioluminescence", - "Zeno Electronic Walkway", "Laser Speckle Imaging", - "Sanger sequencing", - "exomeSeq", - "m6A-rnaSeq", - "HiChIPseq", - "wholeGenomeSeq", - "proximity extension assay", - "rnaArray", - "LC-MS", - "mRNAcounts", - "Vernier Caliper", + "10x multiome", + "MDMS-SL", + "microRNAcounts", "sandwich ELISA", - "HI-C", - "Nightingale NMR", - "photograph", - "Positron Emission Tomography", + "elevated T maze apparatus method", + "LC-SRM", + "DIA", + "rnaArray", "label free mass spectrometry", - "locomotor activation behavior", - "snrnaSeq", + "photograph", + "Leiden Oxylipins", + "open field test", + "HI-C", + "frailty assessment", + "Zeno Electronic Walkway", + "CUT&Tag", + "Blood Chemistry Measurement", "tractionForceMicroscopy", - "TMT quantitation", - "UC Davis GCTOF", - "Rader Lipidomics", - "Wishart High Value Metabolites" - ] - }, - "directionalBSseqLibrary": { - "enum": [ - "FALSE", - "TRUE", - "" - ] - }, - "totalReads": {}, - "sequencingBatch": {}, - "libraryPrep": { - "enum": [ - "methylSeq", - "lncRNAenrichment", - "SureCell", - "DNALibraryConstruction", - "multiome", - "STARRSeq", - "polyAselection", - "snIsoSeq", - "proximity ligation", - "Chromium Single Cell 3'", - "rRNAdepletion", - "EndItDNAEndRepairKit", - "SPLITseq", - "amplicon", - "miRNAenrichment", - "KapaHyperPrep", - "totalRNA", - "PCRfree", - "MULTIseq", - "cellHashing" + "Wishart High Value Metabolites", + "RPPA", + "HPLC-MSMS", + "polymeraseChainReaction", + "LC-MSMS", + "Biocrates Q500", + "cellViabilityAssay", + "Nightingale NMR", + "pharmacokinetics", + "Real Time PCR", + "UPLC-ESI-QTOF-MS", + "HPLC", + "ELISA", + "brightfieldMicroscopy", + "HiChIPseq", + "Immunocytochemistry", + "von Frey test", + "memory behavior", + "methylationArray", + "FIA-MSMS", + "CITESeq", + "wholeGenomeSeq", + "MRI", + "ISOSeq", + "Biocrates Bile Acids", + "Ribo-Seq", + "bisulfiteSeq", + "autoradiography", + "LC-MS", + "anxiety-related behavior", + "scATACSeq", + "novelty response behavior", + "scale", + "LTP", + "Genotyping", + "questionnaire", + "scirnaSeq", + "liquid chromatography-electrochemical detection", + "UCSD Untargeted Metabolomics" ] }, + "lambdaDNAconc": {}, "platform": { "enum": [ - "IlluminaMethylationEPIC", - "Biocrates p180", - "Illumina_Omni2pt5M", - "Infinium Omni2.5Exome-8 v1.5", - "Illumina_Omni2.5-8_v1.1", - "AffymetrixU133AB", - "NextSeq2000", + "HiSeq3000", + "ddSEQ Single-Cell Isolator", + "IlluminaHumanHT-12_V3_0_R1", "Illumina NovaSeq 6000", - "Infinium HumanOmniExpressExome", - "llumina Infinium General Screening Array 24-Kit v3.0", + "Illumina_h650", + "IlluminaMethylationEPIC", "Illumina_Omni5-Quad", - "IlluminaHumanHap650Yv3_A", - "Q Exactive", - "HiSeq4000", - "PacBioRSII", - "Q Exactive HF-X", - "orbitrap", - "Bruker Avance III", - "HiSeq1000", + "Q Exactive Plus", + "Illumina_HumanOmni1-Quadv1.0", + "PsychChip", + "Q Exactive HF", + "IlluminaWholeGenomeDASL", + "PacBio Sequel IIe", "Agilent44Karray", "IlluminaHumanHap300", - "NanostringnCounter", - "Perlegen300Karray", - "GAIIx", - "Q Exactive HF", - "Infinium Omni2.5Exome-8 v1.1", + "PacBio Sequel II", + "Orbitrap Fusion Lumos", + "SequenomMultiplex", + "IlluminaInfiniumGSAMD-24v2-0", + "Illumina_Omni2pt5M", + "InfiniumPsychArrayBeadChip", + "Biograph mCT", + "Illumina_Omni2.5-8_v1.3", "Roche Cobas", - "DNBSEQ", + "HiSeqX", + "Biocrates p180", "Illumina_Omni2.5-8", - "AffymetrixU133Plus2", - "IlluminaWholeGenomeDASL", - "Q Exactive Plus", - "Xevo G2 QTOF", - "time-of-flight", - "Affy6.0", - "SequenomMultiplex", - "OrbiTrap Fusion", - "quadrupole time-of-flight", - "IlluminaNovaseq6000", + "confocalImaging", + "Leco Pegasus IV", "Illumina MouseWG-6 v2.0 expression beadchip", - "Signa Premier AIR 3T", + "triple quadrupole", + "LTQOrbitrapXL", + "Orbitrap Exploris 240", + "BGISEQ-500", + "Simoa HD-1 Analyzer", + "Affymetrix Human Gene 1.0 ST Array", + "Q Exactive HF-X", + "PacBioRSII", + "OrbiTrap Fusion", + "DNBSEQ", "Illumina_Infinium-HumanMethylation450-BeadChip", - "IlluminaHumanMethylation450", - "HiSeqX", + "HiSeq4000", + "Bruker Avance III", + "Affy5.0", "HiSeq2500", - "HiSeq3000", - "InfiniumPsychArrayBeadChip", - "MiSeq", - "IlluminaMiSeq", "Infinium Global Diversity Array-8", - "Illumina_1M", - "Xevo TQ-S", - "Illumina_Omni5M", - "Affy5.0", - "Affymetrix Human Gene 1.0 ST Array", + "Xevo G2 QTOF", + "AffymetrixU133Plus2", + "Perlegen300Karray", + "MiSeq", + "HiSeq1000", + "Illumina_Omni2.5-8_v1.1", + "IlluminaNovaseq6000", + "Olink Target 96", "NanostringnCounter_MouseADPanel", - "BGISEQ-500", - "Illumina_HumanOmni1-Quadv1.0", - "LTQOrbitrapXL", - "HiSeq2000", - "Illumina_h650", - "PacBio Sequel II", - "Infinium Omni2.5Exome-8 v1.4", - "Orbitrap Fusion Lumos", - "Bionano Irys", - "triple quadrupole", - "IlluminaHumanHT-12_V3_0_R1", - "IlluminaInfiniumGSAMD-24v2-0", - "Orbitrap Exploris 240", - "PacBio Sequel IIe", + "Infinium Omni2.5Exome-8 v1.1", "Infinium Omni2.5Exome-8 v1.3", + "Infinium Omni2.5Exome-8 v1.4", + "llumina Infinium General Screening Array 24-Kit v3.0", + "AffymetrixU133AB", + "Xevo TQ-S", + "HiSeq2000", + "orbitrap", "NextSeq500", - "Leco Pegasus IV", - "Simoa HD-1 Analyzer", - "Olink Target 96", - "Biograph mCT", - "ddSEQ Single-Cell Isolator", - "confocalImaging", - "PsychChip", - "Illumina_Omni2.5-8_v1.3" + "IlluminaMiSeq", + "GAIIx", + "quadrupole time-of-flight", + "Infinium Omni2.5Exome-8 v1.5", + "time-of-flight", + "Q Exactive", + "Affy6.0", + "NanostringnCounter", + "Illumina_Omni5M", + "IlluminaHumanMethylation450", + "Signa Premier AIR 3T", + "IlluminaHumanHap650Yv3_A", + "Infinium HumanOmniExpressExome", + "Bionano Irys", + "NextSeq2000", + "Illumina_1M" ] }, - "libraryBatch": {}, - "referenceSet": { + "readLength": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "libraryPrep": { "enum": [ - "HRC", - "GRCh37", - "GRCh38", - "1000 Genomes phase 3", - "MMUL1.0", - "dmel_r6.06", - "GRCm38", - "" + "proximity ligation", + "KapaHyperPrep", + "rRNAdepletion", + "miRNAenrichment", + "multiome", + "STARRSeq", + "snIsoSeq", + "SPLITseq", + "totalRNA", + "Chromium Single Cell 3'", + "MULTIseq", + "amplicon", + "cellHashing", + "lncRNAenrichment", + "DNALibraryConstruction", + "methylSeq", + "EndItDNAEndRepairKit", + "polyAselection", + "PCRfree", + "SureCell" ] }, - "libraryID": {}, "libraryPreparationMethod": { "enum": [ - "Smart-seq1", - "TruSeq", + "10x", + "Illumina DNA PCR-Free Prep Kit", + "CEL-seq", + "Smart-seq2", + "sac-seq", + "Accel-NGS 2S Plus", "Smart-seq4", + "Smart-seq1", + "SMRTbell", "Ultralow Methyl-Seq", "Drop-Seq", - "NEBNext", + "Omni-ATAC", + "TruSeq", "Accel-NGS Methyl-Seq", + "NEBNext", "NexteraXT", - "Accel-NGS 2S Plus", - "Smart-seq2", - "10x", - "CEL-seq", - "SMRTbell", - "sac-seq", - "Illumina DNA PCR-Free Prep Kit", - "Omni-ATAC", "" ] }, + "pcrCycles": {}, + "libraryBatch": {}, "dnaBatch": {}, - "Component": {}, - "runType": { - "enum": [ - "singleEnd", - "pairedEnd" - ] - }, - "gDNAconc": {}, - "specimenID": {}, "isStranded": { "enum": [ - "FALSE", "TRUE", + "FALSE", "" ] }, - "pcrCycles": {}, + "sequencingBatch": {}, "readStrandOrigin": { "enum": [ "reverse", @@ -304,19 +298,25 @@ "" ] }, - "meanCoverage": {}, - "readLength": { - "not": { - "type": "null" - }, - "minLength": 1 - } + "referenceSet": { + "enum": [ + "GRCh38", + "dmel_r6.06", + "1000 Genomes phase 3", + "GRCh37", + "HRC", + "MMUL1.0", + "GRCm38", + "" + ] + }, + "totalReads": {} }, "required": [ + "runType", "assay", - "libraryPrep", "platform", - "runType", - "readLength" + "readLength", + "libraryPrep" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.AssayChIPSeqMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayChIPSeqMetadataTemplate.schema.json index 88162429..64dd5eda 100644 --- a/current-manifest-schemas/AD.AssayChIPSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayChIPSeqMetadataTemplate.schema.json @@ -4,245 +4,354 @@ "title": "AssayChIPSeqMetadataTemplate", "type": "object", "properties": { - "assay": { - "enum": [ - "Baker Lipidomics", - "exomeSeq", - "label free mass spectrometry", - "10x multiome", - "mirnaSeq", - "HPLC", - "Sanger sequencing", - "Wishart High Value Metabolites", - "LC-MSMS", - "Blood Chemistry Measurement", - "wheel running", - "scwholeGenomeSeq", - "Positron Emission Tomography", - "westernBlot", - "HI-C", - "kinesthetic behavior", - "cellViabilityAssay", - "microRNAcounts", - "HiChIPseq", - "contextual conditioning behavior", - "LTP", - "snATACSeq", - "UPLC-MSMS", - "immunofluorescence", - "long-read rnaSeq", - "elevated plus maze test", - "ChIPSeq", - "Immunocytochemistry", - "scirnaSeq", - "MRI", - "MDMS-SL", - "nextGenerationTargetedSequencing", - "frailty assessment", - "Nightingale NMR", - "Laser Speckle Imaging", - "LC-SRM", - "methylationArray", - "atomicForceMicroscopy", - "HPLC-MSMS", - "rotarod performance test", - "snrnaSeq", - "rnaArray", - "Genotyping", - "novelty response behavior", - "sandwich ELISA", - "MudPIT", - "jumpingLibrary", - "electrochemiluminescence", - "rnaSeq", - "Real Time PCR", - "photograph", - "lentiMPRA", - "active avoidance learning behavior", - "FitBark", - "wholeGenomeSeq", - "Vernier Caliper", - "LFP", - "proximity extension assay", - "m6A-rnaSeq", - "Leiden Oxylipins", - "lncrnaSeq", - "Metabolon", - "Biocrates p180", - "pharmacokinetics", - "tractionForceMicroscopy", - "Wishart Catecholamines", - "CUT&Tag", - "scale", - "oxBS-Seq", - "errBisulfiteSeq", - "RPPA", - "von Frey test", - "whole-cell patch clamp", - "ELISA", - "TMT quantitation", - "Biocrates MxP Quant500 XL", - "DNA optical mapping", - "memory behavior", - "Zeno Electronic Walkway", - "polymeraseChainReaction", - "elevated T maze apparatus method", - "Biocrates Q500", - "mRNAcounts", - "brightfieldMicroscopy", - "Rader Lipidomics", - "STARRSeq", - "mirnaArray", - "FIA-MSMS", - "LC-MS", - "spontaneous alternation", - "questionnaire", - "CITESeq", - "snpArray", - "Ribo-Seq", - "open field test", - "scCGIseq", - "scATACSeq", - "UPLC-ESI-QTOF-MS", - "UCSD Untargeted Metabolomics", - "UC Davis GCTOF", - "pharmacodynamics", - "liquid chromatography-electrochemical detection", - "DIA", - "immunohistochemistry", - "locomotor activation behavior", - "scrnaSeq", - "Biocrates Bile Acids", - "16SrRNAseq", - "autoradiography", - "in vivo bioluminescence", - "high content screen", - "anxiety-related behavior", - "SiMoA", - "bisulfiteSeq", - "MIB/MS", - "ISOSeq", - "ATACSeq", - "NOMe-Seq" - ] + "readLength": { + "not": { + "type": "null" + }, + "minLength": 1 }, - "specimenID": {}, + "chromatinAmount": {}, + "catalogNumber": {}, + "libraryID": {}, "assayTarget": { "enum": [ - "NEUROD1", - "ZFP91", - "FOXP1", - "ASCL1", - "RAD21", + "OLIG2", + "BHLHE41", + "KAT2B", + "SP4", "EED", - "GABPB1", - "SIX4", + "CREM", "GMEB1", - "HCFC1", - "FOXK2", - "ZKSCAN1", - "REST", - "CREB1", - "CLOCK", + "SP1", + "SRF", + "H3K27me3", + "CHD4", + "DEAF1", + "SIX4", + "ZNF143", + "ZNF207", + "ASH1L", + "H3K9me2", "SIN3B", - "YBX3", - "SATB2", + "EZH2", + "FOXP1", + "SIN3A", + "NR2F1", + "BRD4", + "NONO", "SMC3", - "ZSCAN29", - "LaminB", - "H3K9ac", - "RB1", - "PKNOX1", + "KLF16", "MITF", - "RELB", + "ZNF592", + "H3K36me3", + "ASH2L", + "SKIL", "EWSR1", + "input", + "CC2D1A", + "ZEB1", + "ATF7", + "BCL11A", + "SIRT1", + "FOXK2", + "PKNOX1", + "TBR1", + "IE_V1-V3", + "E2F1", + "SATB2", + "RAD21", + "TDP43", "IgG", - "CHD4", - "BHLHE40", - "NCOA2", - "ARNT", - "ZNF143", - "SOX8", - "EGR1", + "CLOCK", + "RELB", + "MEF2A", + "ZNF407", "ZBTB7B", - "BMI1", - "CTCF", - "H3K4me3", - "R-loops", - "CC2D1A", - "YY1", - "H3K27ac", - "DEAF1", + "LaminB", "Pol2", - "KLF16", - "CREM", + "H3K9ac", + "ZEB2", + "YY1", + "KLF5", + "TCF7L2", + "ZNF24", + "YBX1", + "R-loops", + "DPF2", + "BHLHE40", + "ARNT", + "TAF1", + "ARID3A", "HNRNPK", - "KAT2B", + "EHMT2", + "NRF1", + "ZKSCAN1", + "SMARCA5", + "GABPB1", "SON", + "H3K4me3", + "KDM4A", "ZHX1", - "H3K9me3", - "NONO", - "ASH1L", - "IE_V1-V3", - "H3K4me1", + "BRCA1", + "SOX8", "NR2F2", - "NR2F1", - "H3K36me3", - "input", - "ZNF592", - "TCF7L2", + "NEUROD1", + "HCFC1", + "BMI1", "ZNF318", - "SRF", - "ZNF384", - "SKIL", - "ZNF24", - "BRCA1", - "KLF5", - "MAZ", - "E2F1", - "NFIC", - "SMARCA5", - "TBR1", - "ARID3A", - "BHLHE41", - "MEF2A", + "ZFP91", + "YBX3", + "H3K9me3", + "TCF12", + "ASCL1", + "GATA4", "GATAD2B", - "ZNF207", - "EHMT2", - "ZNF407", - "ZEB2", - "SIRT1", - "TRIM28", - "H3K9me2", - "BRD4", - "TAF1", - "EZH2", - "SREBP2", - "DPF2", - "OLIG2", - "TDP43", + "REST", + "EGR1", + "H3K27ac", + "MAZ", "MEIS2", - "GATA4", "NFIB", - "BCL11A", - "YBX1", - "ATF7", - "GATAD2A", - "TCF12", - "ARID1B", - "H3K27me3", - "SP1", - "ZEB1", + "NFIC", + "ZNF384", "NR3C1", - "KDM4A", + "TRIM28", + "H3K4me1", + "ARID1B", + "NCOA2", + "CREB1", + "GATAD2A", + "SREBP2", "NCOR1", - "ASH2L", - "NRF1", - "SIN3A", - "SP4", + "CTCF", + "RB1", + "ZSCAN29", + "" + ] + }, + "platform": { + "enum": [ + "IlluminaMethylationEPIC", + "Illumina_HumanOmni1-Quadv1.0", + "HiSeq1000", + "triple quadrupole", + "AffymetrixU133Plus2", + "quadrupole time-of-flight", + "IlluminaHumanHT-12_V3_0_R1", + "Leco Pegasus IV", + "Illumina MouseWG-6 v2.0 expression beadchip", + "LTQOrbitrapXL", + "Infinium Global Diversity Array-8", + "Orbitrap Exploris 240", + "Olink Target 96", + "Infinium Omni2.5Exome-8 v1.5", + "Illumina NovaSeq 6000", + "Orbitrap Fusion Lumos", + "PacBio Sequel IIe", + "NanostringnCounter_MouseADPanel", + "HiSeq3000", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "Infinium Omni2.5Exome-8 v1.1", + "Bionano Irys", + "DNBSEQ", + "GAIIx", + "Xevo G2 QTOF", + "HiSeqX", + "HiSeq2000", + "BGISEQ-500", + "InfiniumPsychArrayBeadChip", + "NextSeq2000", + "IlluminaHumanHap650Yv3_A", + "HiSeq4000", + "Affymetrix Human Gene 1.0 ST Array", + "Agilent44Karray", + "Infinium Omni2.5Exome-8 v1.3", + "HiSeq2500", + "IlluminaInfiniumGSAMD-24v2-0", + "Illumina_Omni2pt5M", + "NextSeq500", + "IlluminaNovaseq6000", + "Affy6.0", + "orbitrap", + "Perlegen300Karray", + "PacBioRSII", + "llumina Infinium General Screening Array 24-Kit v3.0", + "Illumina_Omni5M", + "Affy5.0", + "Infinium Omni2.5Exome-8 v1.4", + "Q Exactive Plus", + "Biograph mCT", + "Q Exactive HF-X", + "IlluminaMiSeq", + "Signa Premier AIR 3T", + "Biocrates p180", + "IlluminaHumanMethylation450", + "Illumina_Omni2.5-8", + "AffymetrixU133AB", + "PacBio Sequel II", + "Q Exactive HF", + "Infinium HumanOmniExpressExome", + "time-of-flight", + "Illumina_Omni2.5-8_v1.1", + "Illumina_Omni2.5-8_v1.3", + "OrbiTrap Fusion", + "MiSeq", + "NanostringnCounter", + "IlluminaHumanHap300", + "Simoa HD-1 Analyzer", + "Illumina_h650", + "Illumina_Omni5-Quad", + "PsychChip", + "Q Exactive", + "confocalImaging", + "SequenomMultiplex", + "ddSEQ Single-Cell Isolator", + "Xevo TQ-S", + "Bruker Avance III", + "Roche Cobas", + "IlluminaWholeGenomeDASL", + "Illumina_1M" + ] + }, + "assay": { + "enum": [ + "UPLC-MSMS", + "10x multiome", + "in vivo bioluminescence", + "rnaSeq", + "jumpingLibrary", + "NOMe-Seq", + "UC Davis GCTOF", + "CITESeq", + "snATACSeq", + "Real Time PCR", + "immunohistochemistry", + "electrochemiluminescence", + "scirnaSeq", + "FitBark", + "mirnaSeq", + "Ribo-Seq", + "ATACSeq", + "Vernier Caliper", + "ISOSeq", + "ELISA", + "locomotor activation behavior", + "m6A-rnaSeq", + "mRNAcounts", + "exomeSeq", + "FIA-MSMS", + "whole-cell patch clamp", + "spontaneous alternation", + "Biocrates Q500", + "UCSD Untargeted Metabolomics", + "microRNAcounts", + "Nightingale NMR", + "TMT quantitation", + "HPLC-MSMS", + 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"autoradiography", + "LC-MS", + "proximity extension assay", + "Biocrates p180", + "westernBlot", + "methylationArray", + "Positron Emission Tomography", + "Zeno Electronic Walkway", + "contextual conditioning behavior", + "Wishart High Value Metabolites", + "anxiety-related behavior", + "LTP", + "memory behavior", + "elevated plus maze test", + "snrnaSeq", + "UPLC-ESI-QTOF-MS", + "ChIPSeq", + "high content screen", + "CUT&Tag", + "SiMoA", + "LC-MSMS", + "Wishart Catecholamines", + "MRI", + "Laser Speckle Imaging", + "Sanger sequencing", + "kinesthetic behavior", + "active avoidance learning behavior", + "polymeraseChainReaction", + "rotarod performance test", + "novelty response behavior", + "photograph", + "Baker Lipidomics", + "Blood Chemistry Measurement", + "MudPIT", + "immunofluorescence", + "DIA" + ] + }, + "antibodyAmountUnits": {}, + "Component": {}, + "referenceSet": { + "enum": [ + "GRCh38", + "1000 Genomes phase 3", + "dmel_r6.06", + "GRCh37", + "HRC", + "GRCm38", + "MMUL1.0", "" ] }, + "antibodyAmount": {}, + "lotNumber": {}, + "chromatinAmountUnits": {}, "readStrandOrigin": { "enum": [ "reverse", @@ -250,160 +359,51 @@ "" ] }, - "readLength": { - "not": { - "type": "null" - }, - "minLength": 1 - }, + "vendor": {}, "isStranded": { "enum": [ - "TRUE", "FALSE", + "TRUE", "" ] }, "libraryPreparationMethod": { "enum": [ - "SMRTbell", - "TruSeq", - "Ultralow Methyl-Seq", - "CEL-seq", - "Drop-Seq", - "sac-seq", + "Accel-NGS 2S Plus", + "Smart-seq2", + "Smart-seq4", "Omni-ATAC", + "Drop-Seq", "Smart-seq1", - "Smart-seq4", - "Accel-NGS 2S Plus", - "NexteraXT", + "CEL-seq", + "Accel-NGS Methyl-Seq", "10x", - "NEBNext", "Illumina DNA PCR-Free Prep Kit", - "Accel-NGS Methyl-Seq", - "Smart-seq2", + "SMRTbell", + "NEBNext", + "NexteraXT", + "sac-seq", + "TruSeq", + "Ultralow Methyl-Seq", "" ] }, + "specimenID": {}, "runType": { "enum": [ "singleEnd", "pairedEnd" ] }, - "chromatinAmountUnits": {}, - "lotNumber": {}, - "totalReads": {}, - "chromatinAmount": {}, - "Component": {}, - "antibody": {}, - "antibodyAmount": {}, - "libraryID": {}, - "referenceSet": { - "enum": [ - "GRCh37", - "HRC", - "GRCh38", - "dmel_r6.06", - "GRCm38", - "1000 Genomes phase 3", - "MMUL1.0", - "" - ] - }, "sequencingBatch": {}, - "platform": { - "enum": [ - "Infinium HumanOmniExpressExome", - "Affy6.0", - "NextSeq500", - "HiSeqX", - "PacBio Sequel IIe", - "Simoa HD-1 Analyzer", - "Agilent44Karray", - "IlluminaMiSeq", - "PsychChip", - "Affy5.0", - "Biograph mCT", - "Infinium Omni2.5Exome-8 v1.5", - "Xevo G2 QTOF", - "Illumina_Omni5-Quad", - "LTQOrbitrapXL", - "Illumina_1M", - "MiSeq", - "Q Exactive HF", - "time-of-flight", - "Affymetrix Human Gene 1.0 ST Array", - "IlluminaMethylationEPIC", - "Infinium Omni2.5Exome-8 v1.1", - "IlluminaHumanHT-12_V3_0_R1", - "Olink Target 96", - "Illumina_Omni2.5-8_v1.3", - "Orbitrap Fusion Lumos", - "Infinium Global Diversity Array-8", - "IlluminaHumanHap300", - "Illumina_h650", - "IlluminaWholeGenomeDASL", - "SequenomMultiplex", - "confocalImaging", - "Roche Cobas", - "NextSeq2000", - "InfiniumPsychArrayBeadChip", - "Q Exactive", - "PacBioRSII", - "HiSeq2000", - "PacBio Sequel II", - "DNBSEQ", - "Illumina_Omni2.5-8_v1.1", - "orbitrap", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "NanostringnCounter", - "Bruker Avance III", - "Perlegen300Karray", - "triple quadrupole", - "Illumina MouseWG-6 v2.0 expression beadchip", - "IlluminaHumanHap650Yv3_A", - "Biocrates p180", - "Illumina_Omni5M", - "Infinium Omni2.5Exome-8 v1.3", - "GAIIx", - "Illumina_Omni2.5-8", - "Bionano Irys", - "Leco Pegasus IV", - "AffymetrixU133Plus2", - "IlluminaNovaseq6000", - "Illumina NovaSeq 6000", - "Illumina_Omni2pt5M", - "AffymetrixU133AB", - "Orbitrap Exploris 240", - "IlluminaHumanMethylation450", - "quadrupole time-of-flight", - "Q Exactive Plus", - "OrbiTrap Fusion", - "Signa Premier AIR 3T", - "NanostringnCounter_MouseADPanel", - "HiSeq1000", - "Q Exactive HF-X", - "HiSeq3000", - "BGISEQ-500", - "IlluminaInfiniumGSAMD-24v2-0", - "Illumina_HumanOmni1-Quadv1.0", - "ddSEQ Single-Cell Isolator", - "Infinium Omni2.5Exome-8 v1.4", - "HiSeq4000", - "llumina Infinium General Screening Array 24-Kit v3.0", - "HiSeq2500", - "Xevo TQ-S" - ] - }, - "antibodyAmountUnits": {}, "libraryBatch": {}, - "vendor": {}, - "catalogNumber": {} + "antibody": {}, + "totalReads": {} }, "required": [ - "assay", "readLength", - "runType", - "platform" + "platform", + "assay", + "runType" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.AssayHICMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayHICMetadataTemplate.schema.json index c73bd418..6bec0c9b 100644 --- a/current-manifest-schemas/AD.AssayHICMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayHICMetadataTemplate.schema.json @@ -4,295 +4,295 @@ "title": "AssayHICMetadataTemplate", "type": "object", "properties": { - "libraryPreparationMethod": { + "sequencingBatch": {}, + "Component": {}, + "platform": { "enum": [ - "CEL-seq", - "NEBNext", - "Smart-seq1", - "Ultralow Methyl-Seq", - "10x", - "sac-seq", - "Drop-Seq", - "Omni-ATAC", - "Accel-NGS 2S Plus", - "Smart-seq4", - "SMRTbell", - "TruSeq", - "Illumina DNA PCR-Free Prep Kit", - "Accel-NGS Methyl-Seq", - "NexteraXT", - "Smart-seq2", - "" + "IlluminaHumanHap650Yv3_A", + "HiSeq2000", + "Illumina MouseWG-6 v2.0 expression beadchip", + "HiSeq1000", + "IlluminaWholeGenomeDASL", + "Infinium Global Diversity Array-8", + "IlluminaNovaseq6000", + "Leco Pegasus IV", + "Q Exactive HF", + "PacBioRSII", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "HiSeq4000", + "AffymetrixU133Plus2", + "NanostringnCounter", + "PacBio Sequel IIe", + "quadrupole time-of-flight", + "Illumina_HumanOmni1-Quadv1.0", + "Illumina_Omni2.5-8", + "IlluminaMethylationEPIC", + "Perlegen300Karray", + "Illumina_Omni2.5-8_v1.3", + "IlluminaHumanHap300", + "Xevo G2 QTOF", + "NextSeq2000", + "IlluminaHumanMethylation450", + "Infinium Omni2.5Exome-8 v1.4", + "MiSeq", + "Q Exactive HF-X", + "IlluminaHumanHT-12_V3_0_R1", + "IlluminaInfiniumGSAMD-24v2-0", + "Illumina_h650", + "AffymetrixU133AB", + "SequenomMultiplex", + "Infinium Omni2.5Exome-8 v1.3", + "Affy6.0", + "Q Exactive", + "OrbiTrap Fusion", + "Roche Cobas", + "GAIIx", + "Agilent44Karray", + "DNBSEQ", + "Bionano Irys", + "orbitrap", + "NextSeq500", + "InfiniumPsychArrayBeadChip", + "PacBio Sequel II", + "llumina Infinium General Screening Array 24-Kit v3.0", + "time-of-flight", + "Affy5.0", + "Simoa HD-1 Analyzer", + "Biograph mCT", + "ddSEQ Single-Cell Isolator", + "HiSeq3000", + "HiSeqX", + "PsychChip", + "confocalImaging", + "Biocrates p180", + "Infinium Omni2.5Exome-8 v1.5", + "Bruker Avance III", + "Xevo TQ-S", + "Illumina_Omni5M", + "Affymetrix Human Gene 1.0 ST Array", + "HiSeq2500", + "LTQOrbitrapXL", + "Orbitrap Exploris 240", + "Illumina_Omni2pt5M", + "BGISEQ-500", + "Infinium Omni2.5Exome-8 v1.1", + "Q Exactive Plus", + "IlluminaMiSeq", + "Signa Premier AIR 3T", + "Orbitrap Fusion Lumos", + "Olink Target 96", + "Illumina_Omni5-Quad", + "Infinium HumanOmniExpressExome", + "Illumina_1M", + "Illumina_Omni2.5-8_v1.1", + "Illumina NovaSeq 6000", + "NanostringnCounter_MouseADPanel", + "triple quadrupole" ] }, + "specimenID": {}, "libraryID": {}, - "referenceSet": { + "libraryPrep": { "enum": [ - "1000 Genomes phase 3", - "MMUL1.0", - "GRCh37", - "HRC", - "dmel_r6.06", - "GRCm38", - "GRCh38", - "" + "multiome", + "PCRfree", + "EndItDNAEndRepairKit", + "amplicon", + "rRNAdepletion", + "DNALibraryConstruction", + "miRNAenrichment", + "lncRNAenrichment", + "polyAselection", + "Chromium Single Cell 3'", + "KapaHyperPrep", + "proximity ligation", + "totalRNA", + "STARRSeq", + "snIsoSeq", + "cellHashing", + "methylSeq", + "SPLITseq", + "SureCell", + "MULTIseq" ] }, - "sequencingBatch": {}, - "validHiCContacts": {}, - "pcrCycles": {}, - "Component": {}, - "specimenID": {}, "runType": { "enum": [ "singleEnd", "pairedEnd" ] }, - "libraryBatch": {}, + "pcrCycles": {}, "readLength": { "not": { "type": "null" }, "minLength": 1 }, + "referenceSet": { + "enum": [ + "1000 Genomes phase 3", + "GRCm38", + "GRCh38", + "dmel_r6.06", + "MMUL1.0", + "HRC", + "GRCh37", + "" + ] + }, + "totalReads": {}, + "libraryBatch": {}, + "validHiCContacts": {}, "assay": { "enum": [ - "brightfieldMicroscopy", - "UC Davis GCTOF", - "elevated T maze apparatus method", - "active avoidance learning behavior", - "ELISA", - "rotarod performance test", - "sandwich ELISA", + "snrnaSeq", + "von Frey test", + "ChIPSeq", + "CUT&Tag", + "mRNAcounts", + "rnaSeq", "UCSD Untargeted Metabolomics", - "long-read rnaSeq", - "MDMS-SL", - "contextual conditioning behavior", - "tractionForceMicroscopy", - "polymeraseChainReaction", - "scATACSeq", - "snATACSeq", - "CITESeq", - "scale", - "Ribo-Seq", - "Wishart High Value Metabolites", - "proximity extension assay", - "Sanger sequencing", - "wholeGenomeSeq", - "DNA optical mapping", - "TMT quantitation", + "active avoidance learning behavior", + "errBisulfiteSeq", + "HPLC", + "locomotor activation behavior", + "Rader Lipidomics", + "MIB/MS", + "westernBlot", + "brightfieldMicroscopy", + "LTP", + "label free mass spectrometry", "questionnaire", "exomeSeq", - "cellViabilityAssay", + "autoradiography", + "microRNAcounts", + "pharmacodynamics", + "immunohistochemistry", + "mirnaSeq", + "ATACSeq", + "UPLC-MSMS", + "Genotyping", + "LC-MS", + "lentiMPRA", + "Vernier Caliper", + "Ribo-Seq", + "kinesthetic behavior", + "contextual conditioning behavior", + "Wishart Catecholamines", + "memory behavior", + "Zeno Electronic Walkway", + "Biocrates Bile Acids", + "LFP", + "MRI", + "spontaneous alternation", "liquid chromatography-electrochemical detection", + "HI-C", + "rnaArray", + "TMT quantitation", + "Positron Emission Tomography", + "sandwich ELISA", + "scwholeGenomeSeq", + "anxiety-related behavior", + "Biocrates MxP Quant500 XL", + "10x multiome", + "FIA-MSMS", + "Biocrates Q500", + "scale", + "Laser Speckle Imaging", + "oxBS-Seq", + "DIA", + "photograph", + "frailty assessment", + "electrochemiluminescence", + "LC-MSMS", "RPPA", - "immunofluorescence", "open field test", - "snpArray", - "electrochemiluminescence", - "LC-SRM", - "Biocrates Q500", + "SiMoA", "bisulfiteSeq", - "FitBark", - "memory behavior", - "spontaneous alternation", - "UPLC-ESI-QTOF-MS", - "mirnaSeq", + "LC-SRM", + "novelty response behavior", + "rotarod performance test", + "ELISA", + "Sanger sequencing", + "MudPIT", "Baker Lipidomics", - "methylationArray", + "cellViabilityAssay", + "scrnaSeq", + "atomicForceMicroscopy", + "HiChIPseq", + "scATACSeq", + "UC Davis GCTOF", + "Wishart High Value Metabolites", "mirnaArray", - "scirnaSeq", - "HI-C", - "Biocrates Bile Acids", - "Genotyping", - "LC-MSMS", - "pharmacokinetics", - "Biocrates p180", - "high content screen", - "MRI", - "errBisulfiteSeq", + "Metabolon", + "ISOSeq", + "scCGIseq", + "m6A-rnaSeq", + "UPLC-ESI-QTOF-MS", + "snATACSeq", + "snpArray", + "Immunocytochemistry", "STARRSeq", - "Real Time PCR", - "von Frey test", - "Blood Chemistry Measurement", - "Laser Speckle Imaging", - "MudPIT", + "proximity extension assay", + "wholeGenomeSeq", + "FitBark", + "long-read rnaSeq", + "nextGenerationTargetedSequencing", + "NOMe-Seq", "in vivo bioluminescence", - "autoradiography", - "kinesthetic behavior", + "jumpingLibrary", + "Biocrates p180", + "CITESeq", + "lncrnaSeq", + "scirnaSeq", + "pharmacokinetics", + "MDMS-SL", + "tractionForceMicroscopy", + "methylationArray", "16SrRNAseq", - "pharmacodynamics", - "microRNAcounts", - "Vernier Caliper", "elevated plus maze test", - "10x multiome", - "Rader Lipidomics", - "snrnaSeq", - "oxBS-Seq", - "Biocrates MxP Quant500 XL", - "HPLC", - "westernBlot", - "nextGenerationTargetedSequencing", + "whole-cell patch clamp", + "immunofluorescence", + "elevated T maze apparatus method", "Nightingale NMR", - "HiChIPseq", - "immunohistochemistry", - "locomotor activation behavior", - "rnaSeq", - "anxiety-related behavior", - "ChIPSeq", - "Positron Emission Tomography", - "atomicForceMicroscopy", - "LFP", - "Immunocytochemistry", - "FIA-MSMS", - "scrnaSeq", - "CUT&Tag", - "scCGIseq", + "wheel running", + "Blood Chemistry Measurement", + "polymeraseChainReaction", + "high content screen", "Leiden Oxylipins", - "SiMoA", - "whole-cell patch clamp", - "photograph", - "ISOSeq", - "LC-MS", - "MIB/MS", - "UPLC-MSMS", - "rnaArray", - "Wishart Catecholamines", + "Real Time PCR", "HPLC-MSMS", - "m6A-rnaSeq", - "wheel running", - "LTP", - "novelty response behavior", - "NOMe-Seq", - "jumpingLibrary", - "mRNAcounts", - "lentiMPRA", - "ATACSeq", - "Zeno Electronic Walkway", - "frailty assessment", - "lncrnaSeq", - "DIA", - "scwholeGenomeSeq", - "label free mass spectrometry", - "Metabolon" + "DNA optical mapping" ] }, - "libraryPrep": { - "enum": [ - "PCRfree", - "SPLITseq", - "polyAselection", - "EndItDNAEndRepairKit", - "SureCell", - "KapaHyperPrep", - "MULTIseq", - "DNALibraryConstruction", - "lncRNAenrichment", - "proximity ligation", - "totalRNA", - "rRNAdepletion", - "cellHashing", - "miRNAenrichment", - "Chromium Single Cell 3'", - "methylSeq", - "snIsoSeq", - "STARRSeq", - "multiome", - "amplicon" - ] - }, - "platform": { + "libraryPreparationMethod": { "enum": [ - "BGISEQ-500", - "Illumina NovaSeq 6000", - "HiSeq2500", - "time-of-flight", - "llumina Infinium General Screening Array 24-Kit v3.0", - "IlluminaHumanHap300", - "Bruker Avance III", - "Illumina_Omni2.5-8", - "Affy6.0", - "HiSeqX", - "HiSeq2000", - "Infinium Omni2.5Exome-8 v1.3", - "Q Exactive Plus", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "DNBSEQ", - "orbitrap", - "GAIIx", - "Illumina_h650", - "IlluminaHumanMethylation450", - "Orbitrap Exploris 240", - "IlluminaNovaseq6000", - "HiSeq4000", - "LTQOrbitrapXL", - "Bionano Irys", - "Orbitrap Fusion Lumos", - "Illumina_Omni2.5-8_v1.1", - "IlluminaMiSeq", - "PacBio Sequel II", - "Illumina_1M", - "AffymetrixU133AB", - "IlluminaHumanHT-12_V3_0_R1", - "IlluminaWholeGenomeDASL", - "Infinium Omni2.5Exome-8 v1.1", - "Q Exactive HF-X", - "Biocrates p180", - "NextSeq2000", - "Affymetrix Human Gene 1.0 ST Array", - "AffymetrixU133Plus2", - "Illumina_Omni2pt5M", - "quadrupole time-of-flight", - "Olink Target 96", - "MiSeq", - "PacBioRSII", - "Illumina_Omni5-Quad", - "Illumina_Omni2.5-8_v1.3", - "confocalImaging", - "IlluminaMethylationEPIC", - "ddSEQ Single-Cell Isolator", - "NanostringnCounter", - "NextSeq500", - "Illumina_Omni5M", - "triple quadrupole", - "Infinium Omni2.5Exome-8 v1.4", - "Simoa HD-1 Analyzer", - "Signa Premier AIR 3T", - "Q Exactive", - "Roche Cobas", - "NanostringnCounter_MouseADPanel", - "Biograph mCT", - "SequenomMultiplex", - "Xevo TQ-S", - "HiSeq3000", - "Leco Pegasus IV", - "Agilent44Karray", - "PacBio Sequel IIe", - "Affy5.0", - "Infinium HumanOmniExpressExome", - "Xevo G2 QTOF", - "PsychChip", - "Illumina_HumanOmni1-Quadv1.0", - "Infinium Omni2.5Exome-8 v1.5", - "OrbiTrap Fusion", - "IlluminaInfiniumGSAMD-24v2-0", - "InfiniumPsychArrayBeadChip", - "Infinium Global Diversity Array-8", - "Illumina MouseWG-6 v2.0 expression beadchip", - "HiSeq1000", - "Perlegen300Karray", - "IlluminaHumanHap650Yv3_A", - "Q Exactive HF" + "NexteraXT", + "Smart-seq2", + "NEBNext", + "Smart-seq4", + "Ultralow Methyl-Seq", + "CEL-seq", + "Illumina DNA PCR-Free Prep Kit", + "SMRTbell", + "Accel-NGS Methyl-Seq", + "TruSeq", + "sac-seq", + "Smart-seq1", + "Accel-NGS 2S Plus", + "Drop-Seq", + "10x", + "Omni-ATAC", + "" ] - }, - "totalReads": {} + } }, "required": [ + "platform", + "libraryPrep", "runType", "readLength", - "assay", - "libraryPrep", - "platform" + "assay" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.AssayMRIMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayMRIMetadataTemplate.schema.json index efa51dda..d2b849aa 100644 --- a/current-manifest-schemas/AD.AssayMRIMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayMRIMetadataTemplate.schema.json @@ -4,120 +4,120 @@ "title": "AssayMRIMetadataTemplate", "type": "object", "properties": { + "MRItype": { + "enum": [ + "structural", + "functional", + "DTI", + "" + ] + }, "platform": { "enum": [ - "IlluminaHumanHap300", - "AffymetrixU133AB", - "Illumina_Omni2pt5M", - "HiSeq4000", - "GAIIx", - "Signa Premier AIR 3T", - "Affymetrix Human Gene 1.0 ST Array", - "Illumina_HumanOmni1-Quadv1.0", - "time-of-flight", - "Illumina MouseWG-6 v2.0 expression beadchip", - "NextSeq2000", - "Illumina_Omni2.5-8_v1.1", + "IlluminaMethylationEPIC", + "HiSeq2000", + "Olink Target 96", + "Illumina NovaSeq 6000", + "llumina Infinium General Screening Array 24-Kit v3.0", + "IlluminaNovaseq6000", + "Illumina_Omni2.5-8", + "Illumina_Omni5-Quad", + "Illumina_1M", + "Agilent44Karray", + "Illumina_Omni2.5-8_v1.3", + "IlluminaMiSeq", "Infinium HumanOmniExpressExome", + "IlluminaHumanHap300", + "PacBioRSII", + "HiSeqX", + "Infinium Global Diversity Array-8", + "Orbitrap Exploris 240", "HiSeq3000", - "llumina Infinium General Screening Array 24-Kit v3.0", "BGISEQ-500", - "Illumina_Omni2.5-8_v1.3", - "IlluminaHumanHap650Yv3_A", - "SequenomMultiplex", - "Olink Target 96", "Leco Pegasus IV", - "Q Exactive Plus", - "Infinium Global Diversity Array-8", - "Biograph mCT", - "Infinium Omni2.5Exome-8 v1.4", - "Roche Cobas", - "MiSeq", - "ddSEQ Single-Cell Isolator", - "IlluminaHumanHT-12_V3_0_R1", + "Signa Premier AIR 3T", + "NanostringnCounter_MouseADPanel", + "Illumina_Omni2.5-8_v1.1", + "Bionano Irys", "Orbitrap Fusion Lumos", + "PsychChip", + "time-of-flight", + "HiSeq4000", + "quadrupole time-of-flight", + "Xevo G2 QTOF", + "GAIIx", "InfiniumPsychArrayBeadChip", + "ddSEQ Single-Cell Isolator", + "Affy5.0", + "Xevo TQ-S", + "orbitrap", + "IlluminaHumanHT-12_V3_0_R1", + "OrbiTrap Fusion", + "AffymetrixU133AB", + "Affy6.0", + "Illumina MouseWG-6 v2.0 expression beadchip", "Infinium Omni2.5Exome-8 v1.3", - "Simoa HD-1 Analyzer", - "Q Exactive HF-X", - "HiSeq1000", - "Q Exactive", - "Infinium Omni2.5Exome-8 v1.1", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "Bionano Irys", - "Orbitrap Exploris 240", "triple quadrupole", - "NanostringnCounter", - "AffymetrixU133Plus2", - "Infinium Omni2.5Exome-8 v1.5", + "HiSeq1000", + "Biograph mCT", + "IlluminaHumanHap650Yv3_A", "LTQOrbitrapXL", - "Illumina_1M", + "IlluminaWholeGenomeDASL", "Biocrates p180", - "NanostringnCounter_MouseADPanel", + "Illumina_HumanOmni1-Quadv1.0", + "HiSeq2500", + "NanostringnCounter", + "confocalImaging", + "Simoa HD-1 Analyzer", "PacBio Sequel II", + "DNBSEQ", "NextSeq500", - "Illumina NovaSeq 6000", - "IlluminaInfiniumGSAMD-24v2-0", - "orbitrap", - "HiSeqX", - "OrbiTrap Fusion", - "Illumina_Omni2.5-8", - "HiSeq2500", + "Q Exactive Plus", + "Illumina_Omni5M", + "SequenomMultiplex", + "MiSeq", "Perlegen300Karray", - "Q Exactive HF", - "Affy6.0", - "Illumina_Omni5-Quad", "Bruker Avance III", - "IlluminaMethylationEPIC", - "IlluminaMiSeq", - "HiSeq2000", - "PsychChip", - "confocalImaging", - "PacBio Sequel IIe", - "Illumina_Omni5M", - "PacBioRSII", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "Roche Cobas", "Illumina_h650", - "DNBSEQ", - "IlluminaWholeGenomeDASL", - "Xevo G2 QTOF", - "Affy5.0", + "Illumina_Omni2pt5M", + "AffymetrixU133Plus2", + "Q Exactive", + "Infinium Omni2.5Exome-8 v1.5", + "Infinium Omni2.5Exome-8 v1.1", + "Q Exactive HF", "IlluminaHumanMethylation450", - "Xevo TQ-S", - "IlluminaNovaseq6000", - "Agilent44Karray", - "quadrupole time-of-flight" + "Infinium Omni2.5Exome-8 v1.4", + "IlluminaInfiniumGSAMD-24v2-0", + "PacBio Sequel IIe", + "Affymetrix Human Gene 1.0 ST Array", + "Q Exactive HF-X", + "NextSeq2000" ] }, - "individualID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, + "contrastAgent": {}, + "fieldStrength": {}, + "Component": {}, "ageAssessmentUnits": { "enum": [ - "days", - "years", "gestational weeks", - "months", + "days", "weeks", + "years", "PCW", + "months", "" ] }, - "scanID": {}, - "MRItype": { - "enum": [ - "DTI", - "functional", - "structural", - "" - ] + "individualID": { + "not": { + "type": "null" + }, + "minLength": 1 }, - "contrastAgent": {}, - "fieldStrength": {}, "ageAssessment": {}, - "Component": {} + "scanID": {} }, "required": [ "platform", diff --git a/current-manifest-schemas/AD.AssayMetabolomicsMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayMetabolomicsMetadataTemplate.schema.json index ee9d1926..175c211b 100644 --- a/current-manifest-schemas/AD.AssayMetabolomicsMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayMetabolomicsMetadataTemplate.schema.json @@ -4,286 +4,286 @@ "title": "AssayMetabolomicsMetadataTemplate", "type": "object", "properties": { - "batch": {}, - "spectrometerFrequency": {}, - "controlType": { + "platform": { "enum": [ - "study pool", - "water plus Baker ISTD", - "GoldenWest", - "Replicate", - "GIS", - "NIST SRM 1950", - "blank injection", - "AIBL pool", - 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"Biograph mCT", - "Leco Pegasus IV", - "OrbiTrap Fusion", - "Signa Premier AIR 3T", - "PacBio Sequel IIe", - "Bionano Irys", - "AffymetrixU133AB", - "Olink Target 96", - "Illumina MouseWG-6 v2.0 expression beadchip", - "Orbitrap Exploris 240", - "HiSeq4000", - "Biocrates p180", - "AffymetrixU133Plus2", - "Infinium Omni2.5Exome-8 v1.4", - "Infinium Omni2.5Exome-8 v1.5", - "Affy6.0", - "orbitrap", - "HiSeq2000", - "Affymetrix Human Gene 1.0 ST Array", - "MiSeq", - "Illumina_Omni2.5-8_v1.1", - "NanostringnCounter", - "Illumina_1M" + "AIBL pool", + "Replicate", + "qc mix", + "blank injection", + "Baker pool", + "study pool", + "GoldenWest", + "NIST SRM 1950", + "GIS", + "water plus Baker ISTD", + "" ] }, - "batchSize": {}, - "platformLocation": {}, "metaboliteType": { "type": "array", "items": { "enum": [ - "ketones", + "TCA cycle metabolites", + "acylglycerols", + "ceramides", + "sugars", + "steroids", + "phosphatidylcholine", + "ApoE", "bile acids", - "phosphatidylethonalamines", - 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"glycerophospholipid", + "untargeted metabolomics", + "acylcarnitines", + "glycerides", + "glycerolipid", + "biogenic amines", "" ] }, "maxItems": 39 }, - "Component": {}, - "softwareName": {}, - "ionMode": {}, - "specimenID": {} + "specimenID": {}, + "batchSize": {}, + "spectrometerFrequency": {} }, "required": [ - "assay", - "platform" + "platform", + "assay" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.AssayMethylationArrayMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayMethylationArrayMetadataTemplate.schema.json index de515f65..1b50bc99 100644 --- a/current-manifest-schemas/AD.AssayMethylationArrayMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayMethylationArrayMetadataTemplate.schema.json @@ -4,221 +4,221 @@ "title": "AssayMethylationArrayMetadataTemplate", "type": "object", "properties": { + "dnaBatch": {}, "platform": { "enum": [ + "Signa Premier AIR 3T", + "Biograph mCT", + "GAIIx", + "IlluminaHumanHT-12_V3_0_R1", + "NextSeq500", + "quadrupole time-of-flight", + "Infinium Omni2.5Exome-8 v1.1", + "HiSeq3000", + "HiSeq2500", + "IlluminaMethylationEPIC", + "Perlegen300Karray", + "Simoa HD-1 Analyzer", "PacBioRSII", - "PacBio Sequel IIe", - "llumina Infinium General Screening Array 24-Kit v3.0", + "Bionano Irys", + "Infinium HumanOmniExpressExome", + "IlluminaHumanHap300", + "AffymetrixU133Plus2", + "Illumina_Omni5-Quad", + "Illumina_Omni5M", + "Q Exactive HF-X", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "Illumina_1M", + "Affy5.0", "Xevo TQ-S", - "HiSeq4000", - "HiSeq1000", - "Olink Target 96", "DNBSEQ", - "Q Exactive HF", - "Infinium Omni2.5Exome-8 v1.3", - "Illumina_Omni5-Quad", - "IlluminaHumanHap300", - "HiSeq3000", - "IlluminaMiSeq", - "Illumina_h650", + "Orbitrap Exploris 240", + "ddSEQ Single-Cell Isolator", + "Infinium Global Diversity Array-8", + "Affy6.0", + "Illumina NovaSeq 6000", "Roche Cobas", - "Leco Pegasus IV", + "Olink Target 96", + "Illumina_h650", "OrbiTrap Fusion", - "HiSeq2000", - "GAIIx", - "Q Exactive HF-X", + "HiSeq1000", + "HiSeq4000", "Illumina_Omni2.5-8", - "Infinium Global Diversity Array-8", - "IlluminaHumanHT-12_V3_0_R1", - "ddSEQ Single-Cell Isolator", "Affymetrix Human Gene 1.0 ST Array", - "NanostringnCounter", - "BGISEQ-500", - "Agilent44Karray", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "Affy6.0", - "IlluminaHumanMethylation450", - "IlluminaMethylationEPIC", - "orbitrap", - "time-of-flight", - "triple quadrupole", - "InfiniumPsychArrayBeadChip", - "IlluminaNovaseq6000", - "confocalImaging", - "Infinium Omni2.5Exome-8 v1.5", - "Orbitrap Exploris 240", - "Infinium Omni2.5Exome-8 v1.4", - "LTQOrbitrapXL", - "Illumina MouseWG-6 v2.0 expression beadchip", - "NanostringnCounter_MouseADPanel", + "Q Exactive HF", + "Leco Pegasus IV", + "PacBio Sequel II", + "Biocrates p180", "Illumina_HumanOmni1-Quadv1.0", - "Affy5.0", - "Illumina_1M", + "IlluminaHumanHap650Yv3_A", + "InfiniumPsychArrayBeadChip", + "IlluminaMiSeq", "Illumina_Omni2.5-8_v1.1", + "MiSeq", + "NanostringnCounter", "Q Exactive", - "Simoa HD-1 Analyzer", - "Infinium Omni2.5Exome-8 v1.1", - "IlluminaHumanHap650Yv3_A", + "time-of-flight", + "Orbitrap Fusion Lumos", + "BGISEQ-500", + "HiSeq2000", + "Illumina MouseWG-6 v2.0 expression beadchip", + "Illumina_Omni2pt5M", + "HiSeqX", + "LTQOrbitrapXL", "AffymetrixU133AB", - "Illumina_Omni5M", - "SequenomMultiplex", - "Signa Premier AIR 3T", - "NextSeq500", - "Perlegen300Karray", + "IlluminaNovaseq6000", + "PacBio Sequel IIe", "Illumina_Omni2.5-8_v1.3", - "Illumina NovaSeq 6000", - "quadrupole time-of-flight", - "Biograph mCT", - "NextSeq2000", - "AffymetrixU133Plus2", - "MiSeq", - "HiSeqX", - "Bionano Irys", - "PacBio Sequel II", - "HiSeq2500", - "Bruker Avance III", - "Infinium HumanOmniExpressExome", - "IlluminaWholeGenomeDASL", - "Q Exactive Plus", + "llumina Infinium General Screening Array 24-Kit v3.0", "PsychChip", - "Illumina_Omni2pt5M", + "NanostringnCounter_MouseADPanel", + "triple quadrupole", + "IlluminaHumanMethylation450", + "SequenomMultiplex", + "Infinium Omni2.5Exome-8 v1.3", + "confocalImaging", + "Infinium Omni2.5Exome-8 v1.4", "Xevo G2 QTOF", - "Orbitrap Fusion Lumos", - "Biocrates p180", - "IlluminaInfiniumGSAMD-24v2-0" + "NextSeq2000", + "IlluminaInfiniumGSAMD-24v2-0", + "Q Exactive Plus", + "IlluminaWholeGenomeDASL", + "Infinium Omni2.5Exome-8 v1.5", + "Bruker Avance III", + "orbitrap", + "Agilent44Karray" ] }, - "arrayBatch": {}, + "ratio260over230": {}, + "ratio260over280": {}, + "Component": {}, "SentrixID": {}, + "specimenID": {}, + "GQN": {}, + "SentrixRowColumn": {}, + "arrayBatch": {}, "assay": { "enum": [ - "ATACSeq", - "TMT quantitation", - "m6A-rnaSeq", - "MIB/MS", - "UCSD Untargeted Metabolomics", - "brightfieldMicroscopy", - "polymeraseChainReaction", - "LTP", - "rnaArray", - "RPPA", - "Biocrates Bile Acids", - "MRI", - "16SrRNAseq", - "ChIPSeq", - "errBisulfiteSeq", - "scCGIseq", - "UPLC-ESI-QTOF-MS", - "von Frey test", - "Wishart 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"rotarod performance test", - "SiMoA", - "westernBlot", - "Immunocytochemistry", - "scATACSeq", - "contextual conditioning behavior", - "HI-C", - "lncrnaSeq", - "Ribo-Seq", - "immunofluorescence", - "nextGenerationTargetedSequencing", "rnaSeq", - "Nightingale NMR", "anxiety-related behavior", + "10x multiome", + "Ribo-Seq", + "methylationArray", + "DIA", + "Laser Speckle Imaging", + "lncrnaSeq", + "electrochemiluminescence", + "Leiden Oxylipins", "pharmacodynamics", - "jumpingLibrary", - "LC-MS", - "FIA-MSMS", - "long-read rnaSeq", - "open field test", - "ELISA", - "Biocrates MxP Quant500 XL", - "Blood Chemistry Measurement", - "mRNAcounts", - "Genotyping", - "LC-SRM", - "wholeGenomeSeq", - "bisulfiteSeq", - "Rader Lipidomics", - "Biocrates Q500", - "immunohistochemistry", + "proximity extension assay", + "mirnaSeq", "Baker Lipidomics", - "methylationArray", + "westernBlot", + "LC-SRM", + "von Frey test", + "UC Davis GCTOF", + "MRI", + "CUT&Tag", "scale", + "scATACSeq", + "nextGenerationTargetedSequencing", + "Blood Chemistry Measurement", + "in vivo bioluminescence", + "label free mass spectrometry", + "microRNAcounts", + "snATACSeq", + "16SrRNAseq", + "scirnaSeq", + "LC-MSMS", "high content screen", + "long-read rnaSeq", + "polymeraseChainReaction", + "RPPA", + "liquid chromatography-electrochemical detection", + "elevated T maze apparatus method", + "Wishart Catecholamines", + "photograph", + "frailty assessment", "HPLC-MSMS", - "label free mass spectrometry", - "Leiden Oxylipins", - "mirnaSeq", - "active avoidance learning behavior", - "DIA", + "HiChIPseq", + "memory behavior", + "scCGIseq", + "contextual conditioning behavior", + "Vernier Caliper", + "Genotyping", "snpArray", + "brightfieldMicroscopy", + "DNA optical mapping", "questionnaire", - "CITESeq", - "NOMe-Seq", - "LFP", - "10x multiome", - "CUT&Tag", - "lentiMPRA", + "immunofluorescence", "locomotor activation behavior", - "cellViabilityAssay", - "snATACSeq", "snrnaSeq", - "HiChIPseq", - "MudPIT", - "exomeSeq", + "open field test", + "HI-C", + "atomicForceMicroscopy", + "SiMoA", + "Zeno Electronic Walkway", + "Biocrates p180", + "Biocrates Q500", + "ISOSeq", + "Wishart High Value Metabolites", + "NOMe-Seq", + "Positron Emission Tomography", "HPLC", + "LFP", + "UPLC-ESI-QTOF-MS", + "STARRSeq", + "cellViabilityAssay", + "UPLC-MSMS", + "pharmacokinetics", + "wholeGenomeSeq", + "tractionForceMicroscopy", + "FIA-MSMS", + "m6A-rnaSeq", + "whole-cell patch clamp", + "lentiMPRA", + "sandwich ELISA", + "jumpingLibrary", + "rnaArray", + "LC-MS", + "ELISA", + "ATACSeq", + "Biocrates Bile Acids", + "mirnaArray", + "bisulfiteSeq", + "kinesthetic behavior", + "LTP", + "scrnaSeq", + "Metabolon", + "novelty response behavior", + "oxBS-Seq", + "elevated plus maze test", + "TMT quantitation", + "scwholeGenomeSeq", + "Immunocytochemistry", + "MDMS-SL", "Real Time PCR", - "frailty assessment", - "Laser Speckle Imaging", - "Biocrates p180" + "mRNAcounts", + "FitBark", + "ChIPSeq", + "Nightingale NMR", + "CITESeq", + "Biocrates MxP Quant500 XL", + "UCSD Untargeted Metabolomics", + "exomeSeq", + "MudPIT", + "Sanger sequencing", + "autoradiography", + "rotarod performance test", + "errBisulfiteSeq" ] - }, - "Component": {}, - "ratio260over230": {}, - "ratio260over280": {}, - "specimenID": {}, - "dnaBatch": {}, - "GQN": {}, - "SentrixRowColumn": {} + } }, "required": [ "platform", diff --git a/current-manifest-schemas/AD.AssayNanostringMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayNanostringMetadataTemplate.schema.json index a4c94912..0936f532 100644 --- a/current-manifest-schemas/AD.AssayNanostringMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayNanostringMetadataTemplate.schema.json @@ -4,269 +4,269 @@ "title": "AssayNanostringMetadataTemplate", "type": "object", "properties": { - "bindingDensity": {}, - "libraryPreparationMethod": { + "specimenID": {}, + "libraryPrep": { "enum": [ - "Illumina DNA PCR-Free Prep Kit", - "Accel-NGS Methyl-Seq", - "10x", - "Accel-NGS 2S Plus", - "TruSeq", - "Drop-Seq", - "Smart-seq2", - "SMRTbell", - "NEBNext", - "Ultralow Methyl-Seq", - "Smart-seq4", - "NexteraXT", - "CEL-seq", - "Smart-seq1", - "Omni-ATAC", - "sac-seq", - "" + "proximity ligation", + "snIsoSeq", + "polyAselection", + "rRNAdepletion", + "totalRNA", + "miRNAenrichment", + "lncRNAenrichment", + "cellHashing", + "MULTIseq", + "amplicon", + "STARRSeq", + "KapaHyperPrep", + "EndItDNAEndRepairKit", + "SureCell", + "methylSeq", + "DNALibraryConstruction", + "Chromium Single Cell 3'", + "PCRfree", + "multiome", + "SPLITseq" ] }, + "libraryBatch": {}, + "bindingDensity": {}, + "rnaBatch": {}, "assay": { "enum": [ - "active avoidance learning behavior", - "locomotor activation behavior", + "SiMoA", "high content screen", - "Blood Chemistry Measurement", - "UPLC-MSMS", - "tractionForceMicroscopy", - "Biocrates Q500", + "questionnaire", + "methylationArray", + "16SrRNAseq", + "ATACSeq", "MudPIT", - "Positron Emission Tomography", - "RPPA", "ISOSeq", - "LC-SRM", - "FIA-MSMS", - "whole-cell patch clamp", - "UC Davis GCTOF", - "memory behavior", - "methylationArray", - "westernBlot", - "rnaArray", - "rnaSeq", - "scATACSeq", - "MRI", + "elevated T maze apparatus method", + "wholeGenomeSeq", + "immunohistochemistry", + "Rader Lipidomics", + "Leiden Oxylipins", + "Nightingale NMR", "scrnaSeq", - "in vivo bioluminescence", - "brightfieldMicroscopy", - "ChIPSeq", + "Blood Chemistry Measurement", + "novelty response behavior", + "pharmacodynamics", + "immunofluorescence", + "contextual conditioning behavior", + "lentiMPRA", + "frailty assessment", + "tractionForceMicroscopy", "von Frey test", + "whole-cell patch clamp", + "sandwich ELISA", + "Positron Emission Tomography", + "CITESeq", + "errBisulfiteSeq", "MIB/MS", - "oxBS-Seq", - "UCSD Untargeted Metabolomics", - "atomicForceMicroscopy", - "microRNAcounts", - "LC-MSMS", - "DNA optical mapping", + "elevated plus maze test", + "rnaArray", + "pharmacokinetics", + "jumpingLibrary", "mRNAcounts", - "Wishart High Value Metabolites", - "TMT quantitation", - "scirnaSeq", - "sandwich ELISA", - "MDMS-SL", - "nextGenerationTargetedSequencing", - "rotarod performance test", - "Biocrates MxP Quant500 XL", - "anxiety-related behavior", + "photograph", + "locomotor activation behavior", + "autoradiography", + "HPLC", + "UC Davis GCTOF", + "westernBlot", "kinesthetic behavior", - "Biocrates p180", - "immunohistochemistry", - "scwholeGenomeSeq", + "Biocrates MxP Quant500 XL", + "MRI", "proximity extension assay", - "Ribo-Seq", - "mirnaArray", + "oxBS-Seq", + "Sanger sequencing", + "Wishart High Value Metabolites", + "UPLC-ESI-QTOF-MS", "liquid chromatography-electrochemical detection", + "NOMe-Seq", + "HPLC-MSMS", + "MDMS-SL", + "Biocrates Q500", "Real Time PCR", - "ATACSeq", - "scale", - "ELISA", "Biocrates Bile Acids", - "DIA", - "elevated plus maze test", - "novelty response behavior", - "Nightingale NMR", - "snpArray", - "Leiden Oxylipins", - "HI-C", - "Zeno Electronic Walkway", - "FitBark", - "errBisulfiteSeq", - "Rader Lipidomics", - "elevated T maze apparatus method", - "16SrRNAseq", - "Wishart Catecholamines", - "Sanger sequencing", - "m6A-rnaSeq", - "photograph", + "UPLC-MSMS", "LTP", - "scCGIseq", - "10x multiome", + "FitBark", + "anxiety-related behavior", + "TMT quantitation", + "lncrnaSeq", + "active avoidance learning behavior", + "LC-SRM", "Baker Lipidomics", - "immunofluorescence", - "HPLC", - "CUT&Tag", + "RPPA", "spontaneous alternation", - "Vernier Caliper", - "frailty assessment", - "LC-MS", - "pharmacokinetics", - "polymeraseChainReaction", - "Genotyping", - "cellViabilityAssay", + "DNA optical mapping", + "memory behavior", + "10x multiome", + "open field test", "snrnaSeq", - "mirnaSeq", - "wholeGenomeSeq", + "LC-MSMS", + "Biocrates p180", + "nextGenerationTargetedSequencing", + "Ribo-Seq", + "FIA-MSMS", + "brightfieldMicroscopy", + "Genotyping", + "LFP", "electrochemiluminescence", - "autoradiography", - "jumpingLibrary", + "scCGIseq", + "cellViabilityAssay", + "Laser Speckle Imaging", + "bisulfiteSeq", + "scATACSeq", "label free mass spectrometry", - "exomeSeq", - "STARRSeq", - "lncrnaSeq", - "pharmacodynamics", - "UPLC-ESI-QTOF-MS", - "HPLC-MSMS", - "HiChIPseq", - "CITESeq", - "lentiMPRA", - "wheel running", - "contextual conditioning behavior", + "Wishart Catecholamines", + "Vernier Caliper", + "scirnaSeq", "long-read rnaSeq", - "bisulfiteSeq", - "NOMe-Seq", - "open field test", + "Zeno Electronic Walkway", + "DIA", + "ELISA", + "in vivo bioluminescence", + "scwholeGenomeSeq", + "microRNAcounts", + "mirnaArray", + "UCSD Untargeted Metabolomics", + "mirnaSeq", + "ChIPSeq", "snATACSeq", - "Laser Speckle Imaging", - "LFP", - "questionnaire", - "SiMoA", - "Immunocytochemistry", - "Metabolon" - ] - }, - "libraryPrep": { - "enum": [ - "Chromium Single Cell 3'", - "proximity ligation", - "methylSeq", - "miRNAenrichment", - "DNALibraryConstruction", - "rRNAdepletion", - "SPLITseq", "STARRSeq", - "KapaHyperPrep", - "totalRNA", - "cellHashing", - "EndItDNAEndRepairKit", - "PCRfree", - "snIsoSeq", - "amplicon", - "lncRNAenrichment", - "polyAselection", - "SureCell", - "MULTIseq", - "multiome" + "atomicForceMicroscopy", + "LC-MS", + "snpArray", + "Metabolon", + "CUT&Tag", + "polymeraseChainReaction", + "exomeSeq", + "HI-C", + "wheel running", + "Immunocytochemistry", + "rnaSeq", + "m6A-rnaSeq", + "rotarod performance test", + "HiChIPseq", + "scale" ] }, + "nanostringBatch": {}, + "Component": {}, "platform": { "enum": [ - "Agilent44Karray", - "Leco Pegasus IV", - "Illumina_Omni5M", + "Infinium Omni2.5Exome-8 v1.3", + "ddSEQ Single-Cell Isolator", + "Infinium HumanOmniExpressExome", + "NextSeq2000", + "Infinium Global Diversity Array-8", + "MiSeq", + "Orbitrap Fusion Lumos", + "Simoa HD-1 Analyzer", + "GAIIx", + "IlluminaInfiniumGSAMD-24v2-0", + "IlluminaWholeGenomeDASL", "quadrupole time-of-flight", - "Biograph mCT", - "confocalImaging", - "Orbitrap Exploris 240", - "Infinium Omni2.5Exome-8 v1.5", - "Illumina MouseWG-6 v2.0 expression beadchip", - "HiSeq2500", - "Illumina_h650", - "PacBio Sequel IIe", - "SequenomMultiplex", - "IlluminaMiSeq", + "triple quadrupole", "PsychChip", - "Q Exactive HF", - "HiSeq4000", + "Leco Pegasus IV", + "AffymetrixU133Plus2", "Bruker Avance III", - "IlluminaInfiniumGSAMD-24v2-0", - "Simoa HD-1 Analyzer", - "Olink Target 96", + "llumina Infinium General Screening Array 24-Kit v3.0", + "Illumina_HumanOmni1-Quadv1.0", + "IlluminaHumanMethylation450", + "HiSeq4000", + "HiSeq2500", + "Biograph mCT", + "NanostringnCounter", "time-of-flight", - "HiSeq3000", - "IlluminaNovaseq6000", - "OrbiTrap Fusion", - "Illumina_1M", + "Illumina_Omni2.5-8_v1.1", + "IlluminaMiSeq", + "PacBioRSII", + "HiSeq1000", "HiSeqX", - "IlluminaHumanHap300", "Q Exactive Plus", - "NextSeq500", - "AffymetrixU133Plus2", - "orbitrap", - "Signa Premier AIR 3T", + "LTQOrbitrapXL", + "InfiniumPsychArrayBeadChip", + "Q Exactive", "Affymetrix Human Gene 1.0 ST Array", + "PacBio Sequel IIe", + "Roche Cobas", + "IlluminaMethylationEPIC", + "Affy6.0", + "Illumina_Omni2.5-8_v1.3", "Illumina_Omni2pt5M", - "Biocrates p180", - "Xevo TQ-S", - "Infinium HumanOmniExpressExome", + "DNBSEQ", "Infinium Omni2.5Exome-8 v1.1", - "Illumina_Omni5-Quad", - "Q Exactive", - "llumina Infinium General Screening Array 24-Kit v3.0", - "Illumina_Omni2.5-8", - "Illumina_HumanOmni1-Quadv1.0", - "HiSeq2000", - "Illumina NovaSeq 6000", + "PacBio Sequel II", + "Infinium Omni2.5Exome-8 v1.4", "NanostringnCounter_MouseADPanel", - "PacBioRSII", - "IlluminaHumanHap650Yv3_A", "Bionano Irys", - "Affy5.0", + "Olink Target 96", + "Agilent44Karray", + "Orbitrap Exploris 240", + "HiSeq3000", "AffymetrixU133AB", - "Illumina_Omni2.5-8_v1.3", - "InfiniumPsychArrayBeadChip", + "BGISEQ-500", + "SequenomMultiplex", + "Illumina MouseWG-6 v2.0 expression beadchip", + "Biocrates p180", + "Illumina_Omni5M", + "OrbiTrap Fusion", + "Illumina_Omni5-Quad", + "HiSeq2000", "Perlegen300Karray", - "Roche Cobas", - "ddSEQ Single-Cell Isolator", - "IlluminaMethylationEPIC", - "Orbitrap Fusion Lumos", - "DNBSEQ", - "Affy6.0", + "Illumina_h650", + "IlluminaHumanHap650Yv3_A", + "confocalImaging", + "Illumina_Omni2.5-8", + "IlluminaNovaseq6000", + "Signa Premier AIR 3T", + "IlluminaHumanHap300", + "Xevo G2 QTOF", + "Xevo TQ-S", + "Affy5.0", + "Illumina_1M", + "Illumina NovaSeq 6000", + "orbitrap", + "Q Exactive HF", "Illumina_Infinium-HumanMethylation450-BeadChip", - "Illumina_Omni2.5-8_v1.1", - "IlluminaHumanHT-12_V3_0_R1", - "HiSeq1000", - "IlluminaWholeGenomeDASL", - "Infinium Global Diversity Array-8", "Q Exactive HF-X", - "Infinium Omni2.5Exome-8 v1.4", - "GAIIx", - "IlluminaHumanMethylation450", - "LTQOrbitrapXL", - "BGISEQ-500", - "Xevo G2 QTOF", - "PacBio Sequel II", - "NanostringnCounter", - "MiSeq", - "triple quadrupole", - "Infinium Omni2.5Exome-8 v1.3", - "NextSeq2000" + "Infinium Omni2.5Exome-8 v1.5", + "NextSeq500", + "IlluminaHumanHT-12_V3_0_R1" + ] + }, + "libraryPreparationMethod": { + "enum": [ + "CEL-seq", + "Ultralow Methyl-Seq", + "SMRTbell", + "10x", + "sac-seq", + "Omni-ATAC", + "Accel-NGS Methyl-Seq", + "Smart-seq2", + "TruSeq", + "Smart-seq4", + "NexteraXT", + "Illumina DNA PCR-Free Prep Kit", + "NEBNext", + "Smart-seq1", + "Accel-NGS 2S Plus", + "Drop-Seq", + "" ] }, "geneRLF": {}, - "Component": {}, - "libraryBatch": {}, - "specimenID": {}, - "nanostringBatch": {}, - "rnaBatch": {}, "RIN": {} }, "required": [ - "assay", "libraryPrep", + "assay", "platform" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.AssayPETMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayPETMetadataTemplate.schema.json index a3db63a0..6e441c2e 100644 --- a/current-manifest-schemas/AD.AssayPETMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayPETMetadataTemplate.schema.json @@ -4,101 +4,99 @@ "title": "AssayPETMetadataTemplate", "type": "object", "properties": { - "Component": {}, "scanID": {}, - "ageAssessment": {}, - "ligand": {}, "platform": { "enum": [ - "ddSEQ Single-Cell Isolator", - "Perlegen300Karray", "Orbitrap Exploris 240", - "llumina Infinium General Screening Array 24-Kit v3.0", - "Leco Pegasus IV", - "Illumina_Omni2pt5M", - "HiSeqX", - "PsychChip", - "IlluminaHumanHT-12_V3_0_R1", - "IlluminaNovaseq6000", - "Illumina_Omni2.5-8", + "IlluminaHumanMethylation450", + "Orbitrap Fusion Lumos", + "Infinium Global Diversity Array-8", + "Simoa HD-1 Analyzer", "PacBio Sequel II", - "NextSeq500", + "Illumina_Omni2pt5M", + "Infinium Omni2.5Exome-8 v1.3", "Illumina_1M", - "AffymetrixU133AB", - "Bionano Irys", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "IlluminaMiSeq", - "Olink Target 96", - "InfiniumPsychArrayBeadChip", + "HiSeq3000", + "Q Exactive", + "Affy5.0", "Xevo G2 QTOF", - "confocalImaging", - "Infinium Omni2.5Exome-8 v1.1", - "MiSeq", - "PacBio Sequel IIe", - "Illumina_Omni5-Quad", - "Infinium Omni2.5Exome-8 v1.3", - "HiSeq4000", - "Illumina_HumanOmni1-Quadv1.0", - "DNBSEQ", - "Illumina MouseWG-6 v2.0 expression beadchip", - "AffymetrixU133Plus2", - "HiSeq2500", - "Biocrates p180", + "NextSeq2000", + "GAIIx", "IlluminaHumanHap300", - "IlluminaInfiniumGSAMD-24v2-0", - "Illumina_Omni2.5-8_v1.3", + "IlluminaHumanHap650Yv3_A", + "HiSeqX", + "InfiniumPsychArrayBeadChip", + "triple quadrupole", + "Biograph mCT", + "IlluminaHumanHT-12_V3_0_R1", + "PacBioRSII", + "AffymetrixU133Plus2", + "IlluminaMethylationEPIC", + "Infinium HumanOmniExpressExome", + "Illumina_Omni5-Quad", + "MiSeq", "Illumina_Omni5M", - "Affy5.0", - "HiSeq3000", + "HiSeq2500", "Infinium Omni2.5Exome-8 v1.4", - "Infinium Omni2.5Exome-8 v1.5", - "triple quadrupole", - "HiSeq2000", - "Illumina_h650", - "Q Exactive HF-X", - "Simoa HD-1 Analyzer", - "IlluminaHumanMethylation450", - "BGISEQ-500", + "IlluminaInfiniumGSAMD-24v2-0", + "ddSEQ Single-Cell Isolator", + "Illumina_Omni2.5-8", + "time-of-flight", + "Olink Target 96", + "Perlegen300Karray", + "NanostringnCounter", + "quadrupole time-of-flight", + "IlluminaWholeGenomeDASL", "Roche Cobas", - "IlluminaHumanHap650Yv3_A", - "NanostringnCounter_MouseADPanel", + "Bionano Irys", + "Xevo TQ-S", + "IlluminaNovaseq6000", + "PsychChip", + "NextSeq500", + "Q Exactive HF-X", + "HiSeq2000", + "Illumina NovaSeq 6000", + "Illumina MouseWG-6 v2.0 expression beadchip", "Affy6.0", - "Orbitrap Fusion Lumos", + "Illumina_h650", + "Illumina_HumanOmni1-Quadv1.0", + "IlluminaMiSeq", + "orbitrap", "Q Exactive Plus", - "GAIIx", - "Infinium HumanOmniExpressExome", - "IlluminaMethylationEPIC", - "Illumina NovaSeq 6000", - "PacBioRSII", - "time-of-flight", - "Signa Premier AIR 3T", + "DNBSEQ", "Agilent44Karray", - "Q Exactive HF", - "NextSeq2000", - "Q Exactive", - "Xevo TQ-S", - "Bruker Avance III", + "PacBio Sequel IIe", + "Illumina_Infinium-HumanMethylation450-BeadChip", "Illumina_Omni2.5-8_v1.1", - "LTQOrbitrapXL", - "quadrupole time-of-flight", - "Affymetrix Human Gene 1.0 ST Array", + "NanostringnCounter_MouseADPanel", + "Infinium Omni2.5Exome-8 v1.1", "OrbiTrap Fusion", - "Biograph mCT", - "Infinium Global Diversity Array-8", + "llumina Infinium General Screening Array 24-Kit v3.0", + "Bruker Avance III", + "Q Exactive HF", + "Infinium Omni2.5Exome-8 v1.5", "HiSeq1000", - "NanostringnCounter", - "IlluminaWholeGenomeDASL", - "orbitrap", - "SequenomMultiplex" + "LTQOrbitrapXL", + "Signa Premier AIR 3T", + "AffymetrixU133AB", + "Biocrates p180", + "Affymetrix Human Gene 1.0 ST Array", + "Leco Pegasus IV", + "BGISEQ-500", + "HiSeq4000", + "SequenomMultiplex", + "Illumina_Omni2.5-8_v1.3", + "confocalImaging" ] }, + "Component": {}, "ageAssessmentUnits": { "enum": [ "weeks", - "gestational weeks", + "years", "days", + "gestational weeks", "months", - "years", "PCW", "" ] @@ -108,7 +106,9 @@ "type": "null" }, "minLength": 1 - } + }, + "ligand": {}, + "ageAssessment": {} }, "required": [ "platform", diff --git a/current-manifest-schemas/AD.AssayRnaArrayMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayRnaArrayMetadataTemplate.schema.json index 292d8030..8e114338 100644 --- a/current-manifest-schemas/AD.AssayRnaArrayMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayRnaArrayMetadataTemplate.schema.json @@ -4,217 +4,217 @@ "title": "AssayRnaArrayMetadataTemplate", "type": "object", "properties": { - "specimenID": {}, "platform": { "enum": [ - "BGISEQ-500", - "Xevo TQ-S", - "Illumina_Omni5M", - "NanostringnCounter", - "time-of-flight", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "Illumina_Omni2pt5M", - "IlluminaHumanHap650Yv3_A", - "HiSeq4000", - "IlluminaHumanMethylation450", - "Roche Cobas", - "llumina Infinium General Screening Array 24-Kit v3.0", - "IlluminaInfiniumGSAMD-24v2-0", - "HiSeq1000", "AffymetrixU133AB", - "ddSEQ Single-Cell Isolator", - "Infinium Omni2.5Exome-8 v1.4", - "NanostringnCounter_MouseADPanel", - "Q Exactive HF-X", - "NextSeq2000", - "Signa Premier AIR 3T", "HiSeq3000", + "IlluminaInfiniumGSAMD-24v2-0", + "Agilent44Karray", + "orbitrap", "Illumina_Omni5-Quad", - "PsychChip", - "Orbitrap Exploris 240", - "quadrupole time-of-flight", - "Affymetrix Human Gene 1.0 ST Array", - "Illumina_Omni2.5-8_v1.1", - "Q Exactive", - "Infinium Omni2.5Exome-8 v1.5", - "Illumina_1M", - "Q Exactive HF", - "Biograph mCT", - "HiSeq2500", - "PacBioRSII", - "Simoa HD-1 Analyzer", "Xevo G2 QTOF", - "Illumina_Omni2.5-8", - "Bruker Avance III", - "Infinium Omni2.5Exome-8 v1.3", - "LTQOrbitrapXL", - "Q Exactive Plus", + "Leco Pegasus IV", "Biocrates p180", - "IlluminaWholeGenomeDASL", - "Perlegen300Karray", - "NextSeq500", - "OrbiTrap Fusion", + "IlluminaMiSeq", + "Bionano Irys", + "Roche Cobas", + "NanostringnCounter", + "Q Exactive HF", + "Xevo TQ-S", + "Illumina_1M", + "HiSeqX", + "HiSeq1000", + "Illumina_Omni5M", + "Q Exactive Plus", + "IlluminaHumanHT-12_V3_0_R1", + "Infinium HumanOmniExpressExome", + "Orbitrap Exploris 240", + "confocalImaging", + "HiSeq2000", "Orbitrap Fusion Lumos", + "Infinium Omni2.5Exome-8 v1.5", + "Infinium Omni2.5Exome-8 v1.4", "DNBSEQ", - "IlluminaMiSeq", - "IlluminaMethylationEPIC", "Olink Target 96", + "NanostringnCounter_MouseADPanel", + "NextSeq2000", + "PacBio Sequel IIe", + "time-of-flight", + "Illumina_Omni2.5-8", + "Simoa HD-1 Analyzer", + "Affy6.0", + "HiSeq2500", + "IlluminaHumanMethylation450", + "Infinium Global Diversity Array-8", + "Illumina MouseWG-6 v2.0 expression beadchip", + "Q Exactive", + "Infinium Omni2.5Exome-8 v1.3", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "Illumina_HumanOmni1-Quadv1.0", + "IlluminaMethylationEPIC", + "quadrupole time-of-flight", "PacBio Sequel II", - "MiSeq", + "triple quadrupole", + "BGISEQ-500", + "IlluminaHumanHap300", + "Biograph mCT", + "Infinium Omni2.5Exome-8 v1.1", + "Q Exactive HF-X", + "Bruker Avance III", "Illumina NovaSeq 6000", - "InfiniumPsychArrayBeadChip", - "IlluminaHumanHT-12_V3_0_R1", - "confocalImaging", "GAIIx", - "Illumina_h650", - "triple quadrupole", - "Bionano Irys", + "InfiniumPsychArrayBeadChip", + "Illumina_Omni2.5-8_v1.1", + "PacBioRSII", + "IlluminaWholeGenomeDASL", + "AffymetrixU133Plus2", + "Signa Premier AIR 3T", + "HiSeq4000", + "Affymetrix Human Gene 1.0 ST Array", + "LTQOrbitrapXL", + "llumina Infinium General Screening Array 24-Kit v3.0", + "Perlegen300Karray", + "SequenomMultiplex", "IlluminaNovaseq6000", + "PsychChip", + "Illumina_Omni2.5-8_v1.3", + "IlluminaHumanHap650Yv3_A", + "MiSeq", + "Illumina_h650", + "OrbiTrap Fusion", "Affy5.0", - "SequenomMultiplex", - "IlluminaHumanHap300", - "orbitrap", - "AffymetrixU133Plus2", - "PacBio Sequel IIe", - "HiSeq2000", - "HiSeqX", - "Illumina_HumanOmni1-Quadv1.0", - "Leco Pegasus IV", - "Infinium Global Diversity Array-8", - "Illumina MouseWG-6 v2.0 expression beadchip", - "Infinium HumanOmniExpressExome", - "Infinium Omni2.5Exome-8 v1.1", - "Agilent44Karray", - "Affy6.0", - "Illumina_Omni2.5-8_v1.3" + "Illumina_Omni2pt5M", + "ddSEQ Single-Cell Isolator", + "NextSeq500" ] }, + "rnaBatch": {}, + "arrayBatch": {}, + "specimenID": {}, + "RIN": {}, "assay": { "enum": [ - "lentiMPRA", - "von Frey test", - "Genotyping", - "immunohistochemistry", - "LC-SRM", - "pharmacokinetics", - "NOMe-Seq", + "rnaArray", + "scwholeGenomeSeq", + "Metabolon", + "UCSD Untargeted Metabolomics", + "methylationArray", "TMT quantitation", - "Laser Speckle Imaging", - "exomeSeq", - "MIB/MS", "microRNAcounts", - "immunofluorescence", - "snATACSeq", - "scale", - "jumpingLibrary", - "Immunocytochemistry", - "proximity extension assay", + "spontaneous alternation", + "lncrnaSeq", + "westernBlot", + "pharmacodynamics", + "NOMe-Seq", + "lentiMPRA", + "frailty assessment", "mirnaArray", - "Blood Chemistry Measurement", - "nextGenerationTargetedSequencing", - "HI-C", - "novelty response behavior", - "anxiety-related behavior", "long-read rnaSeq", - "oxBS-Seq", + "Nightingale NMR", + "Biocrates p180", + "DIA", + "STARRSeq", + "Ribo-Seq", + "scale", + "scrnaSeq", + "Sanger sequencing", + "ChIPSeq", + "electrochemiluminescence", + "elevated plus maze test", + "MDMS-SL", + "FitBark", + "proximity extension assay", + "LTP", + "UPLC-ESI-QTOF-MS", + "Immunocytochemistry", + "10x multiome", + "bisulfiteSeq", + "LC-MS", + "brightfieldMicroscopy", + "rnaSeq", + "liquid chromatography-electrochemical detection", + "atomicForceMicroscopy", + "cellViabilityAssay", "scATACSeq", - "MudPIT", - "DNA optical mapping", - "methylationArray", - "pharmacodynamics", + "UPLC-MSMS", + "Leiden Oxylipins", + "active avoidance learning behavior", + "anxiety-related behavior", + "contextual conditioning behavior", + "autoradiography", + "mRNAcounts", + "pharmacokinetics", + "memory behavior", + "Biocrates Bile Acids", + "errBisulfiteSeq", + "immunohistochemistry", + "snrnaSeq", "wheel running", - "ELISA", + "RPPA", + "elevated T maze apparatus method", + "Biocrates MxP Quant500 XL", + "nextGenerationTargetedSequencing", + "Zeno Electronic Walkway", + "Vernier Caliper", + "oxBS-Seq", + "label free mass spectrometry", "LFP", - "westernBlot", + "Blood Chemistry Measurement", + "UC Davis GCTOF", + "mirnaSeq", + "ATACSeq", "ISOSeq", + "SiMoA", + "scCGIseq", + "locomotor activation behavior", + "scirnaSeq", "Biocrates Q500", - "Wishart High Value Metabolites", + "Positron Emission Tomography", + "HI-C", + "snpArray", "questionnaire", - "LTP", - "in vivo bioluminescence", - "mRNAcounts", - "kinesthetic behavior", - "Sanger sequencing", - "scrnaSeq", - "bisulfiteSeq", - "mirnaSeq", - "scCGIseq", - "ATACSeq", - "rotarod performance test", - "MDMS-SL", + "LC-SRM", "m6A-rnaSeq", - "Biocrates p180", - "Biocrates MxP Quant500 XL", - "spontaneous alternation", + "whole-cell patch clamp", "Baker Lipidomics", - "active avoidance learning behavior", - "elevated plus maze test", - "sandwich ELISA", - "scwholeGenomeSeq", - "Leiden Oxylipins", + "CITESeq", + "von Frey test", + "ELISA", + "jumpingLibrary", "open field test", - "CUT&Tag", - "high content screen", - "snpArray", - "UC Davis GCTOF", - "polymeraseChainReaction", - "errBisulfiteSeq", - "Vernier Caliper", - "Positron Emission Tomography", - "UPLC-ESI-QTOF-MS", - "HPLC-MSMS", + "rotarod performance test", + "16SrRNAseq", "HPLC", - "ChIPSeq", - "Metabolon", - "RPPA", - "electrochemiluminescence", - "frailty assessment", - "CITESeq", - "autoradiography", - "memory behavior", - "tractionForceMicroscopy", - "HiChIPseq", - "UCSD Untargeted Metabolomics", - "whole-cell patch clamp", - "photograph", - "contextual conditioning behavior", - "atomicForceMicroscopy", - "label free mass spectrometry", - "scirnaSeq", - "STARRSeq", - "LC-MS", - "brightfieldMicroscopy", - "MRI", - "Zeno Electronic Walkway", - "Rader Lipidomics", - "UPLC-MSMS", - "snrnaSeq", - "Real Time PCR", + "kinesthetic behavior", + "Genotyping", "FIA-MSMS", - "rnaArray", - "rnaSeq", + "sandwich ELISA", + "Laser Speckle Imaging", "wholeGenomeSeq", - "DIA", - "SiMoA", - "Ribo-Seq", - "liquid chromatography-electrochemical detection", - "FitBark", + "HPLC-MSMS", + "HiChIPseq", + "Rader Lipidomics", + "MRI", + "polymeraseChainReaction", + "CUT&Tag", + "exomeSeq", "Wishart Catecholamines", + "novelty response behavior", + "DNA optical mapping", "LC-MSMS", - "elevated T maze apparatus method", - "lncrnaSeq", - "locomotor activation behavior", - "Nightingale NMR", - "16SrRNAseq", - "10x multiome", - "cellViabilityAssay", - "Biocrates Bile Acids" + "high content screen", + "tractionForceMicroscopy", + "Wishart High Value Metabolites", + "MIB/MS", + "Real Time PCR", + "snATACSeq", + "in vivo bioluminescence", + "photograph", + "immunofluorescence", + "MudPIT" ] }, - "rnaBatch": {}, - "Component": {}, - "arrayBatch": {}, - "RIN": {} + "Component": {} }, "required": [ "platform", diff --git a/current-manifest-schemas/AD.AssayRnaSeqMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayRnaSeqMetadataTemplate.schema.json index e5c3c1cc..f2268ff5 100644 --- a/current-manifest-schemas/AD.AssayRnaSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayRnaSeqMetadataTemplate.schema.json @@ -4,148 +4,31 @@ "title": "AssayRnaSeqMetadataTemplate", "type": "object", "properties": { - "RIN": {}, - "assay": { + "libraryPrep": { "enum": [ - "immunohistochemistry", - "von Frey test", - "Wishart Catecholamines", - "Blood Chemistry Measurement", - "anxiety-related behavior", - "NOMe-Seq", - "ELISA", - "Biocrates Bile Acids", - "LC-MS", - "HI-C", - "LTP", - "DNA optical mapping", - "CITESeq", - "nextGenerationTargetedSequencing", - "Zeno Electronic Walkway", - "FitBark", - "in vivo bioluminescence", - "Biocrates Q500", - "errBisulfiteSeq", - "Sanger sequencing", - "snrnaSeq", - "Ribo-Seq", - "MudPIT", - "pharmacodynamics", - "snpArray", - "wholeGenomeSeq", - "spontaneous alternation", - "m6A-rnaSeq", - "scwholeGenomeSeq", - "UC Davis GCTOF", - "westernBlot", - "tractionForceMicroscopy", - "mirnaArray", - "jumpingLibrary", - "methylationArray", - "MRI", - "ATACSeq", - "contextual conditioning behavior", - "UCSD Untargeted Metabolomics", - "whole-cell patch clamp", - "microRNAcounts", - "Rader Lipidomics", - "MDMS-SL", - "ChIPSeq", - "UPLC-MSMS", - "rotarod performance test", - "brightfieldMicroscopy", - "SiMoA", - "snATACSeq", - "RPPA", - "scrnaSeq", - "FIA-MSMS", - "LC-MSMS", - "liquid chromatography-electrochemical detection", - "atomicForceMicroscopy", - "elevated plus maze test", - "Biocrates MxP Quant500 XL", - "label free mass spectrometry", - "HiChIPseq", - "Leiden Oxylipins", - "active avoidance learning behavior", - "memory behavior", - "long-read rnaSeq", - "Laser Speckle Imaging", - "mirnaSeq", - "16SrRNAseq", - "high content screen", - "TMT quantitation", - "Vernier Caliper", - "DIA", - "lentiMPRA", - "polymeraseChainReaction", - "scale", - "ISOSeq", - "CUT&Tag", - "exomeSeq", - "frailty assessment", - "photograph", - "autoradiography", - "novelty response behavior", - "kinesthetic behavior", - "sandwich ELISA", - "Real Time PCR", - "bisulfiteSeq", - "mRNAcounts", - "electrochemiluminescence", - "scirnaSeq", - "Genotyping", - "Baker Lipidomics", - "10x multiome", - "Wishart High Value Metabolites", - "open field test", + "totalRNA", + "lncRNAenrichment", + "cellHashing", + "Chromium Single Cell 3'", + "polyAselection", + "KapaHyperPrep", + "multiome", + "MULTIseq", "STARRSeq", - "elevated T maze apparatus method", - "pharmacokinetics", - "oxBS-Seq", - "UPLC-ESI-QTOF-MS", - "HPLC-MSMS", - "Positron Emission Tomography", - "Biocrates p180", - "Immunocytochemistry", - "lncrnaSeq", - "Nightingale NMR", - "questionnaire", - "scATACSeq", - "cellViabilityAssay", - "scCGIseq", - "locomotor activation behavior", - "LFP", - "rnaArray", - "HPLC", - "rnaSeq", - "proximity extension assay", - "immunofluorescence", - "MIB/MS", - "wheel running", - "Metabolon", - "LC-SRM" - ] - }, - "referenceSet": { - "enum": [ - "dmel_r6.06", - "1000 Genomes phase 3", - "MMUL1.0", - "GRCh38", - "GRCh37", - "GRCm38", - "HRC", - "" + "proximity ligation", + "DNALibraryConstruction", + "EndItDNAEndRepairKit", + "methylSeq", + "SureCell", + "PCRfree", + "rRNAdepletion", + "snIsoSeq", + "amplicon", + "SPLITseq", + "miRNAenrichment" ] }, - "readLength": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "Component": {}, + "libraryID": {}, "isStranded": { "enum": [ "TRUE", @@ -153,163 +36,280 @@ "" ] }, - "sequencingBatch": {}, - "totalReads": {}, - "runType": { - "enum": [ - "singleEnd", - "pairedEnd" - ] - }, - "specimenID": {}, "platform": { "enum": [ + "Orbitrap Fusion Lumos", + "ddSEQ Single-Cell Isolator", + "GAIIx", + "PsychChip", + "Bruker Avance III", + "Q Exactive HF", + "IlluminaMethylationEPIC", + "Q Exactive Plus", + "Leco Pegasus IV", + "PacBio Sequel II", + "Infinium Omni2.5Exome-8 v1.1", "NextSeq2000", - "IlluminaHumanHap300", - "time-of-flight", + "quadrupole time-of-flight", + "Simoa HD-1 Analyzer", "Affy6.0", - "Illumina MouseWG-6 v2.0 expression beadchip", - "SequenomMultiplex", - "PsychChip", - "IlluminaInfiniumGSAMD-24v2-0", - "Xevo TQ-S", - "Illumina_Omni5M", - "Illumina_Omni2.5-8", - "Infinium Omni2.5Exome-8 v1.5", - "Roche Cobas", - "MiSeq", - "HiSeqX", + "HiSeq2500", + "Infinium Omni2.5Exome-8 v1.4", "IlluminaWholeGenomeDASL", - "Q Exactive HF-X", - "DNBSEQ", - "Infinium Omni2.5Exome-8 v1.3", - "Olink Target 96", - "IlluminaNovaseq6000", - "PacBio Sequel II", - "Illumina_Omni2.5-8_v1.1", - "IlluminaHumanMethylation450", - "GAIIx", - "IlluminaMiSeq", - "Orbitrap Fusion Lumos", - "triple quadrupole", - "IlluminaHumanHT-12_V3_0_R1", - "Infinium HumanOmniExpressExome", + "NanostringnCounter_MouseADPanel", + "IlluminaHumanHap650Yv3_A", "HiSeq1000", - "Orbitrap Exploris 240", - "Bionano Irys", - "Biograph mCT", - "BGISEQ-500", - "llumina Infinium General Screening Array 24-Kit v3.0", "LTQOrbitrapXL", - "Illumina_Omni2.5-8_v1.3", + "Illumina_Omni5M", + "Olink Target 96", + "Illumina_HumanOmni1-Quadv1.0", + "Affymetrix Human Gene 1.0 ST Array", + "llumina Infinium General Screening Array 24-Kit v3.0", + "MiSeq", + "HiSeqX", + "InfiniumPsychArrayBeadChip", + "Infinium Omni2.5Exome-8 v1.5", + "Affy5.0", + "Illumina_1M", + "Illumina_Omni2.5-8", + "Illumina MouseWG-6 v2.0 expression beadchip", + "Biocrates p180", "HiSeq4000", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "Illumina_Omni2.5-8_v1.1", "Illumina_h650", - "InfiniumPsychArrayBeadChip", - "Illumina_HumanOmni1-Quadv1.0", + "IlluminaNovaseq6000", + "Q Exactive HF-X", "Infinium Global Diversity Array-8", - "Perlegen300Karray", - "quadrupole time-of-flight", - "Q Exactive HF", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "Xevo G2 QTOF", - "Illumina_Omni2pt5M", - "Affy5.0", - "ddSEQ Single-Cell Isolator", - "Infinium Omni2.5Exome-8 v1.1", - "HiSeq3000", "Agilent44Karray", - "OrbiTrap Fusion", - "HiSeq2500", - "HiSeq2000", - "IlluminaMethylationEPIC", - "Affymetrix Human Gene 1.0 ST Array", - "NanostringnCounter", + "BGISEQ-500", + "time-of-flight", + "Xevo TQ-S", + "PacBio Sequel IIe", + "DNBSEQ", + "AffymetrixU133Plus2", "orbitrap", + "NanostringnCounter", + "IlluminaHumanHT-12_V3_0_R1", + "IlluminaInfiniumGSAMD-24v2-0", "AffymetrixU133AB", - "Q Exactive Plus", - "PacBio Sequel IIe", - "Biocrates p180", - "Infinium Omni2.5Exome-8 v1.4", - "Bruker Avance III", - "Q Exactive", - "Leco Pegasus IV", + "IlluminaHumanHap300", + "SequenomMultiplex", + "HiSeq3000", + "OrbiTrap Fusion", + "HiSeq2000", + "Infinium HumanOmniExpressExome", + "Roche Cobas", + "triple quadrupole", + "Illumina_Omni2.5-8_v1.3", "NextSeq500", + "IlluminaHumanMethylation450", + "Perlegen300Karray", + "Bionano Irys", + "Infinium Omni2.5Exome-8 v1.3", + "Signa Premier AIR 3T", + "Orbitrap Exploris 240", + "Biograph mCT", "Illumina_Omni5-Quad", + "Xevo G2 QTOF", + "Illumina NovaSeq 6000", + "Q Exactive", "confocalImaging", - "Signa Premier AIR 3T", - "AffymetrixU133Plus2", - "IlluminaHumanHap650Yv3_A", "PacBioRSII", - "Simoa HD-1 Analyzer", - "Illumina NovaSeq 6000", - "NanostringnCounter_MouseADPanel", - "Illumina_1M" + "Illumina_Omni2pt5M", + "IlluminaMiSeq" ] }, - "rnaBatch": {}, "libraryPreparationMethod": { "enum": [ - "NEBNext", - "Illumina DNA PCR-Free Prep Kit", + "Ultralow Methyl-Seq", "sac-seq", - "Smart-seq1", - "Accel-NGS Methyl-Seq", - "Smart-seq2", "Accel-NGS 2S Plus", - "Smart-seq4", - "TruSeq", - "Omni-ATAC", - "SMRTbell", + "NEBNext", "Drop-Seq", + "Omni-ATAC", "10x", + "Smart-seq2", "CEL-seq", - "Ultralow Methyl-Seq", + "Smart-seq4", + "SMRTbell", + "TruSeq", + "Illumina DNA PCR-Free Prep Kit", + "Smart-seq1", + "Accel-NGS Methyl-Seq", "NexteraXT", "" ] }, - "libraryID": {}, + "Component": {}, + "validBarcodeReads": {}, "readStrandOrigin": { "enum": [ - "reverse", "forward", + "reverse", "" ] }, + "rnaBatch": {}, + "sequencingBatch": {}, + "runType": { + "enum": [ + "pairedEnd", + "singleEnd" + ] + }, + "totalReads": {}, "DV200": {}, - "libraryPrep": { + "libraryVersion": {}, + "referenceSet": { "enum": [ - "KapaHyperPrep", + "HRC", + "GRCh37", + "GRCh38", + "MMUL1.0", + "1000 Genomes phase 3", + "dmel_r6.06", + "GRCm38", + "" + ] + }, + "libraryBatch": {}, + "readLength": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "RIN": {}, + "assay": { + "enum": [ + "SiMoA", + "Ribo-Seq", + "Biocrates Bile Acids", + "Wishart High Value Metabolites", + "LC-MSMS", + "MIB/MS", + "scrnaSeq", + "snpArray", + "LTP", + "photograph", + "high content screen", + "Immunocytochemistry", + "exomeSeq", + "active avoidance learning behavior", + "cellViabilityAssay", + "Rader Lipidomics", + "electrochemiluminescence", + "jumpingLibrary", + "scirnaSeq", + "Real Time PCR", + "rnaSeq", + "oxBS-Seq", + "m6A-rnaSeq", + "kinesthetic behavior", + "Positron Emission Tomography", + "scCGIseq", + "immunohistochemistry", + "scwholeGenomeSeq", + "immunofluorescence", + "ELISA", + "HPLC-MSMS", + "pharmacokinetics", + "Biocrates Q500", + "open field test", + "in vivo bioluminescence", + "TMT quantitation", + "mirnaSeq", + "von Frey test", + "Zeno Electronic Walkway", + "ATACSeq", + "ISOSeq", + "wheel running", + "MDMS-SL", + "sandwich ELISA", + "methylationArray", + "spontaneous alternation", + "UPLC-ESI-QTOF-MS", + "pharmacodynamics", + "UPLC-MSMS", + "CUT&Tag", + "RPPA", + "MudPIT", + "questionnaire", + "atomicForceMicroscopy", + "contextual conditioning behavior", + "HPLC", + "long-read rnaSeq", + "Nightingale NMR", + "snrnaSeq", + "Leiden Oxylipins", + "anxiety-related behavior", + "UC Davis GCTOF", + "Biocrates p180", + "mRNAcounts", + "Blood Chemistry Measurement", + "nextGenerationTargetedSequencing", + "snATACSeq", + "Sanger sequencing", + "10x multiome", + "LC-SRM", + "proximity extension assay", "STARRSeq", - "DNALibraryConstruction", - "amplicon", - "miRNAenrichment", - "PCRfree", - "SureCell", - "lncRNAenrichment", - "Chromium Single Cell 3'", - "SPLITseq", - "totalRNA", - "snIsoSeq", - "multiome", - "rRNAdepletion", - "methylSeq", - "polyAselection", - "EndItDNAEndRepairKit", - "cellHashing", - "MULTIseq", - "proximity ligation" + "ChIPSeq", + "Wishart Catecholamines", + "frailty assessment", + "NOMe-Seq", + "FitBark", + "tractionForceMicroscopy", + "DNA optical mapping", + "FIA-MSMS", + "liquid chromatography-electrochemical detection", + "mirnaArray", + "westernBlot", + "whole-cell patch clamp", + "scATACSeq", + "UCSD Untargeted Metabolomics", + "errBisulfiteSeq", + "wholeGenomeSeq", + "Vernier Caliper", + "lncrnaSeq", + "CITESeq", + "polymeraseChainReaction", + "elevated plus maze test", + "locomotor activation behavior", + "autoradiography", + "MRI", + "DIA", + "scale", + "Laser Speckle Imaging", + "16SrRNAseq", + "HiChIPseq", + "Metabolon", + "elevated T maze apparatus method", + "HI-C", + "Biocrates MxP Quant500 XL", + "rotarod performance test", + "LC-MS", + "rnaArray", + "Baker Lipidomics", + "LFP", + "lentiMPRA", + "label free mass spectrometry", + "brightfieldMicroscopy", + "Genotyping", + "bisulfiteSeq", + "memory behavior", + "microRNAcounts", + "novelty response behavior" ] }, - "validBarcodeReads": {}, - "libraryVersion": {}, - "libraryBatch": {} + "specimenID": {} }, "required": [ - "assay", - "readLength", - "runType", + "libraryPrep", "platform", - "libraryPrep" + "runType", + "readLength", + "assay" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.AssaySTARRSeqMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssaySTARRSeqMetadataTemplate.schema.json index 00bce389..cc767659 100644 --- a/current-manifest-schemas/AD.AssaySTARRSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssaySTARRSeqMetadataTemplate.schema.json @@ -4,317 +4,317 @@ "title": "AssaySTARRSeqMetadataTemplate", "type": "object", "properties": { - "isStranded": { - "enum": [ - "TRUE", - "FALSE", - "" - ] - }, - "GQN": {}, "libraryPrep": { "enum": [ - "totalRNA", + "Chromium Single Cell 3'", "DNALibraryConstruction", + "rRNAdepletion", + "polyAselection", + "lncRNAenrichment", + "cellHashing", "EndItDNAEndRepairKit", + "snIsoSeq", + "amplicon", "STARRSeq", - "lncRNAenrichment", - "proximity ligation", "PCRfree", - "SureCell", - "rRNAdepletion", - "cellHashing", - "MULTIseq", "multiome", - "KapaHyperPrep", - "snIsoSeq", "methylSeq", - "amplicon", - "miRNAenrichment", + "MULTIseq", "SPLITseq", - "polyAselection", - "Chromium Single Cell 3'" - ] - }, - "totalReads": {}, - "libraryVersion": {}, - "ratio260over280": {}, - "dnaBatch": {}, - "validBarcodeReads": {}, - "numberCells": {}, - "runType": { - "enum": [ - "pairedEnd", - "singleEnd" - ] - }, - "libraryPreparationMethod": { - "enum": [ - "NEBNext", - "10x", - "Smart-seq1", - "Smart-seq2", - "sac-seq", - "TruSeq", - "Drop-Seq", - "Illumina DNA PCR-Free Prep Kit", - "Accel-NGS Methyl-Seq", - "NexteraXT", - "CEL-seq", - "Ultralow Methyl-Seq", - "Smart-seq4", - "Omni-ATAC", - "Accel-NGS 2S Plus", - "SMRTbell", - "" + "KapaHyperPrep", + "SureCell", + "proximity ligation", + "miRNAenrichment", + "totalRNA" ] }, - "RIN": {}, - "sequencingBatch": {}, + "medianGenes": {}, "platform": { "enum": [ - "HiSeq3000", - "IlluminaHumanMethylation450", - "Bionano Irys", - "Roche Cobas", - "PacBio Sequel II", - "PacBio Sequel IIe", - "SequenomMultiplex", - "Illumina_Omni2.5-8_v1.3", - "IlluminaMiSeq", - "Infinium Omni2.5Exome-8 v1.1", - "DNBSEQ", "Xevo G2 QTOF", - "Illumina_Omni5M", + "HiSeq4000", + "IlluminaHumanHap650Yv3_A", + "Bruker Avance III", + "Illumina_Omni2.5-8_v1.3", + "IlluminaHumanHT-12_V3_0_R1", + "quadrupole time-of-flight", + "AffymetrixU133AB", + "Illumina_Omni2pt5M", + "IlluminaWholeGenomeDASL", + "Infinium Omni2.5Exome-8 v1.4", + "Infinium Omni2.5Exome-8 v1.5", "HiSeq1000", - "Illumina_Omni5-Quad", - "LTQOrbitrapXL", - "triple quadrupole", - "PacBioRSII", + "Illumina NovaSeq 6000", + "Orbitrap Fusion Lumos", + "Illumina_Omni5M", + "time-of-flight", + "Illumina_Omni2.5-8", + "Perlegen300Karray", + "Simoa HD-1 Analyzer", "confocalImaging", - "Biograph mCT", - "Infinium Omni2.5Exome-8 v1.4", + "triple quadrupole", + "IlluminaNovaseq6000", + "Affymetrix Human Gene 1.0 ST Array", + "Illumina MouseWG-6 v2.0 expression beadchip", + "Illumina_h650", + "orbitrap", + "NanostringnCounter_MouseADPanel", "NextSeq2000", - "llumina Infinium General Screening Array 24-Kit v3.0", + "PacBio Sequel IIe", "Q Exactive Plus", - "Agilent44Karray", + "IlluminaInfiniumGSAMD-24v2-0", + "HiSeqX", + "SequenomMultiplex", "Illumina_Infinium-HumanMethylation450-BeadChip", - "Infinium Global Diversity Array-8", - "IlluminaHumanHap300", "Infinium Omni2.5Exome-8 v1.3", - "GAIIx", - "HiSeq2500", - "Q Exactive", - "ddSEQ Single-Cell Isolator", - "time-of-flight", - "HiSeq4000", - "Olink Target 96", - "Perlegen300Karray", - "PsychChip", - "Illumina_Omni2.5-8_v1.1", - "orbitrap", - "Affymetrix Human Gene 1.0 ST Array", - "IlluminaNovaseq6000", - "OrbiTrap Fusion", + "IlluminaHumanHap300", + "IlluminaHumanMethylation450", "NanostringnCounter", - "Illumina_1M", - "AffymetrixU133Plus2", - "Illumina_Omni2.5-8", - "InfiniumPsychArrayBeadChip", - "Biocrates p180", "Signa Premier AIR 3T", - "NextSeq500", - "Orbitrap Exploris 240", - "Illumina_h650", - "IlluminaHumanHap650Yv3_A", - "Q Exactive HF", - "Simoa HD-1 Analyzer", - "IlluminaMethylationEPIC", - "Illumina_Omni2pt5M", + "BGISEQ-500", + "HiSeq2000", "Xevo TQ-S", + "Infinium Omni2.5Exome-8 v1.1", + "OrbiTrap Fusion", + "Q Exactive HF", + "Q Exactive HF-X", + "LTQOrbitrapXL", + "HiSeq3000", "Affy6.0", - "AffymetrixU133AB", - "IlluminaHumanHT-12_V3_0_R1", - "HiSeqX", - "Illumina NovaSeq 6000", - "quadrupole time-of-flight", - "Bruker Avance III", - "Infinium Omni2.5Exome-8 v1.5", + "Q Exactive", + "Illumina_Omni5-Quad", + "PsychChip", + "Roche Cobas", + "PacBio Sequel II", + "Orbitrap Exploris 240", + "Affy5.0", + "GAIIx", + "Agilent44Karray", + "NextSeq500", + "ddSEQ Single-Cell Isolator", + "InfiniumPsychArrayBeadChip", + "IlluminaMethylationEPIC", + "Biograph mCT", + "Illumina_1M", + "Illumina_Omni2.5-8_v1.1", + "IlluminaMiSeq", "MiSeq", - "Orbitrap Fusion Lumos", - "IlluminaInfiniumGSAMD-24v2-0", - "HiSeq2000", - "Q Exactive HF-X", + "Infinium Global Diversity Array-8", "Infinium HumanOmniExpressExome", - "NanostringnCounter_MouseADPanel", + "Olink Target 96", "Illumina_HumanOmni1-Quadv1.0", + "llumina Infinium General Screening Array 24-Kit v3.0", + "DNBSEQ", "Leco Pegasus IV", - "IlluminaWholeGenomeDASL", - "Illumina MouseWG-6 v2.0 expression beadchip", - "BGISEQ-500", - "Affy5.0" + "Biocrates p180", + "PacBioRSII", + "Bionano Irys", + "AffymetrixU133Plus2", + "HiSeq2500" + ] + }, + "GQN": {}, + "libraryBatch": {}, + "libraryID": {}, + "isStranded": { + "enum": [ + "TRUE", + "FALSE", + "" + ] + }, + "referenceSet": { + "enum": [ + "HRC", + "GRCh37", + "dmel_r6.06", + "MMUL1.0", + "1000 Genomes phase 3", + "GRCh38", + "GRCm38", + "" + ] + }, + "numberCells": {}, + "runType": { + "enum": [ + "singleEnd", + "pairedEnd" + ] + }, + "validBarcodeReads": {}, + "readStrandOrigin": { + "enum": [ + "reverse", + "forward", + "" + ] + }, + "libraryPreparationMethod": { + "enum": [ + "Accel-NGS Methyl-Seq", + "Smart-seq2", + "sac-seq", + "TruSeq", + "Accel-NGS 2S Plus", + "Drop-Seq", + "Ultralow Methyl-Seq", + "Illumina DNA PCR-Free Prep Kit", + "CEL-seq", + "SMRTbell", + "NEBNext", + "NexteraXT", + "10x", + "Smart-seq4", + "Smart-seq1", + "Omni-ATAC", + "" ] }, + "Component": {}, + "RIN": {}, "assay": { "enum": [ - "scale", - "kinesthetic behavior", - "label free mass spectrometry", - "wheel running", - "liquid chromatography-electrochemical detection", + "exomeSeq", + "atomicForceMicroscopy", + "mirnaArray", + "16SrRNAseq", + "locomotor activation behavior", + "contextual conditioning behavior", + "autoradiography", + "scATACSeq", + "jumpingLibrary", + "active avoidance learning behavior", + "rotarod performance test", + "LC-SRM", + "snATACSeq", "UPLC-ESI-QTOF-MS", - "Nightingale NMR", - "pharmacodynamics", - "methylationArray", + "electrochemiluminescence", + "westernBlot", + "Biocrates MxP Quant500 XL", + "Wishart Catecholamines", "anxiety-related behavior", - "16SrRNAseq", + "methylationArray", + "tractionForceMicroscopy", + "errBisulfiteSeq", + "rnaSeq", "novelty response behavior", - "mirnaSeq", + "FIA-MSMS", + "frailty assessment", + "high content screen", + "immunohistochemistry", + "mRNAcounts", + "wheel running", "LFP", - "tractionForceMicroscopy", - "snrnaSeq", + "UCSD Untargeted Metabolomics", + "immunofluorescence", "microRNAcounts", - "MIB/MS", - "RPPA", - "HI-C", - "HPLC", - "LC-MSMS", - "UPLC-MSMS", - "MRI", - "Vernier Caliper", + "pharmacodynamics", "wholeGenomeSeq", - "pharmacokinetics", - "scrnaSeq", - "long-read rnaSeq", - "von Frey test", - "cellViabilityAssay", - "brightfieldMicroscopy", - "scATACSeq", - "Metabolon", - "jumpingLibrary", - "immunohistochemistry", - "elevated plus maze test", - "scirnaSeq", + "Rader Lipidomics", "scCGIseq", - "Biocrates Bile Acids", - "LC-SRM", - "mirnaArray", - "snATACSeq", - "open field test", - "Zeno Electronic Walkway", - "photograph", - "UCSD Untargeted Metabolomics", + "HPLC", + "ISOSeq", + "DIA", + "TMT quantitation", + "STARRSeq", + "LTP", "DNA optical mapping", - "rotarod performance test", - "snpArray", - "rnaArray", - "Wishart Catecholamines", - "memory behavior", - "MDMS-SL", - "high content screen", + "spontaneous alternation", + "scrnaSeq", + "SiMoA", + "m6A-rnaSeq", + "scwholeGenomeSeq", "FitBark", - "active avoidance learning behavior", - "exomeSeq", - "LC-MS", - "polymeraseChainReaction", - "MudPIT", - "contextual conditioning behavior", - "oxBS-Seq", - "immunofluorescence", + "NOMe-Seq", + "snrnaSeq", + "proximity extension assay", + "sandwich ELISA", + "Wishart High Value Metabolites", + "liquid chromatography-electrochemical detection", + "kinesthetic behavior", + "ChIPSeq", + "Ribo-Seq", + "CITESeq", "HiChIPseq", + "MRI", + "open field test", + "HPLC-MSMS", + "Vernier Caliper", + "scale", "lncrnaSeq", - "Biocrates p180", "CUT&Tag", - "atomicForceMicroscopy", - "frailty assessment", - "m6A-rnaSeq", - "elevated T maze apparatus method", "UC Davis GCTOF", - "ChIPSeq", - "LTP", - "Blood Chemistry Measurement", - "Rader Lipidomics", - "Baker Lipidomics", - "Positron Emission Tomography", - "CITESeq", "Immunocytochemistry", - "errBisulfiteSeq", - "ISOSeq", - "nextGenerationTargetedSequencing", - "Wishart High Value Metabolites", - "NOMe-Seq", - "DIA", - "FIA-MSMS", - "proximity extension assay", + "von Frey test", + "in vivo bioluminescence", + "UPLC-MSMS", + "label free mass spectrometry", + "lentiMPRA", + "Positron Emission Tomography", + "oxBS-Seq", + "Zeno Electronic Walkway", + "brightfieldMicroscopy", + "HI-C", "Laser Speckle Imaging", - "locomotor activation behavior", - "ELISA", + "LC-MSMS", + "Biocrates Q500", + "MIB/MS", + "Blood Chemistry Measurement", + "whole-cell patch clamp", + "Biocrates Bile Acids", + "mirnaSeq", "questionnaire", - "scwholeGenomeSeq", - "10x multiome", - "electrochemiluminescence", - "Ribo-Seq", - "westernBlot", - "HPLC-MSMS", - "autoradiography", - "bisulfiteSeq", - "sandwich ELISA", - "lentiMPRA", - "SiMoA", - "Sanger sequencing", + "Baker Lipidomics", + "polymeraseChainReaction", + "snpArray", + "Genotyping", + "Metabolon", + "Nightingale NMR", + "photograph", + "rnaArray", "ATACSeq", - "whole-cell patch clamp", - "rnaSeq", - "TMT quantitation", - "in vivo bioluminescence", - "Biocrates Q500", - "mRNAcounts", + "cellViabilityAssay", + "long-read rnaSeq", + "LC-MS", + "Sanger sequencing", "Leiden Oxylipins", - "spontaneous alternation", - "Genotyping", - "Biocrates MxP Quant500 XL", - "STARRSeq", - "Real Time PCR" + "MDMS-SL", + "Biocrates p180", + "memory behavior", + "MudPIT", + "nextGenerationTargetedSequencing", + "scirnaSeq", + "Real Time PCR", + "pharmacokinetics", + "10x multiome", + "elevated T maze apparatus method", + "elevated plus maze test", + "ELISA", + "bisulfiteSeq", + "RPPA" ] }, - "rnaBatch": {}, + "ratio260over280": {}, + "totalReads": {}, + "sequencingBatch": {}, "readLength": { "not": { "type": "null" }, "minLength": 1 }, - "libraryBatch": {}, - "referenceSet": { - "enum": [ - "dmel_r6.06", - "GRCm38", - "MMUL1.0", - "1000 Genomes phase 3", - "GRCh37", - "HRC", - "GRCh38", - "" - ] - }, - "libraryID": {}, - "readStrandOrigin": { - "enum": [ - "reverse", - "forward", - "" - ] - }, - "medianUMIs": {}, - "medianGenes": {}, + "ratio260over230": {}, + "rnaBatch": {}, + "dnaBatch": {}, + "libraryVersion": {}, "specimenID": {}, - "Component": {}, - "ratio260over230": {} + "medianUMIs": {} }, "required": [ "libraryPrep", - "runType", "platform", + "runType", "assay", "readLength" ] diff --git a/current-manifest-schemas/AD.AssayScrnaSeqMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayScrnaSeqMetadataTemplate.schema.json index 39753cc5..d44541bd 100644 --- a/current-manifest-schemas/AD.AssayScrnaSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayScrnaSeqMetadataTemplate.schema.json @@ -4,326 +4,326 @@ "title": "AssayScrnaSeqMetadataTemplate", "type": "object", "properties": { - "runType": { + "isStranded": { "enum": [ - "singleEnd", - "pairedEnd" + "TRUE", + "FALSE", + "" ] }, - "sequencingBatch": {}, - "medianUMIs": {}, - "libraryVersion": {}, + "libraryID": {}, + "medianGenes": {}, + "RIN": {}, "Component": {}, - "libraryType": { + "readStrandOrigin": { "enum": [ - "cDNA", - "ADT", - "plasmid DNA", - "HTO", - "CMO", - "LMO", + "reverse", + "forward", "" ] }, - "medianGenes": {}, - "validBarcodeReads": {}, - "rnaBatch": {}, + "sequencingBatch": {}, + "runType": { + "enum": [ + "singleEnd", + "pairedEnd" + ] + }, + "numberCells": {}, "libraryPreparationMethod": { "enum": [ - "Accel-NGS 2S Plus", - "sac-seq", + "NexteraXT", + "Smart-seq1", "SMRTbell", "10x", - "Omni-ATAC", - "Smart-seq1", - "NexteraXT", - "CEL-seq", "Drop-Seq", + "Ultralow Methyl-Seq", + "CEL-seq", + "Accel-NGS 2S Plus", "NEBNext", - "Smart-seq2", "Illumina DNA PCR-Free Prep Kit", + "Omni-ATAC", + "sac-seq", + "Smart-seq2", + "Smart-seq4", "TruSeq", "Accel-NGS Methyl-Seq", - "Ultralow Methyl-Seq", - "Smart-seq4", "" ] }, - "libraryID": {}, - "sampleBarcode": {}, - "libraryPrep": { - "enum": [ - "multiome", - "totalRNA", - "STARRSeq", - "amplicon", - "MULTIseq", - "cellHashing", - "miRNAenrichment", - "proximity ligation", - "KapaHyperPrep", - "snIsoSeq", - "methylSeq", - "DNALibraryConstruction", - "lncRNAenrichment", - "EndItDNAEndRepairKit", - "PCRfree", - "rRNAdepletion", - "SureCell", - "Chromium Single Cell 3'", - "SPLITseq", - "polyAselection" - ] - }, - "isStranded": { - "enum": [ - "FALSE", - "TRUE", - "" - ] - }, - "referenceSet": { - "enum": [ - "GRCh37", - "dmel_r6.06", - "1000 Genomes phase 3", - "HRC", - "GRCh38", - "GRCm38", - "MMUL1.0", - "" - ] - }, - "readLength": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "RIN": {}, + "medianUMIs": {}, + "libraryVersion": {}, + "rnaBatch": {}, "libraryBatch": {}, "assay": { "enum": [ - "10x multiome", - "TMT quantitation", - "HI-C", - "atomicForceMicroscopy", - 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"electrochemiluminescence", + "in vivo bioluminescence", + "tractionForceMicroscopy", + "DIA", + "ISOSeq", + "kinesthetic behavior", + "DNA optical mapping", + "whole-cell patch clamp", + "ChIPSeq", + "scCGIseq", + "HI-C", "Ribo-Seq", - "proximity extension assay", "von Frey test", - "contextual conditioning behavior", - "HPLC-MSMS", - "scrnaSeq", - "snpArray", + "NOMe-Seq", + "UPLC-MSMS", + "locomotor activation behavior", + "high content screen", + "sandwich ELISA", + "STARRSeq", "polymeraseChainReaction", + "LC-MS", + "scATACSeq", + "Real Time PCR", + "Laser Speckle Imaging", + "HPLC", + "proximity extension assay", + "LTP", + "Sanger sequencing", + "snATACSeq", + "TMT quantitation", "16SrRNAseq", - "Rader Lipidomics", - "MIB/MS", - "rnaArray", - "scirnaSeq", - "elevated plus maze test", - "UCSD Untargeted Metabolomics", - "Wishart Catecholamines", + "LFP", + "microRNAcounts", + "Nightingale NMR", + "brightfieldMicroscopy", + "scale", + "Baker Lipidomics", "active avoidance learning behavior", - "questionnaire", - "Blood Chemistry Measurement", - "high content screen", - "open field test", - "Laser Speckle Imaging" - ] - }, - "numberCells": {}, - "specimenID": {}, - "totalReads": {}, - "readStrandOrigin": { - "enum": [ - "reverse", - "forward", - "" + "methylationArray", + "wheel running", + "Wishart Catecholamines", + "label free mass spectrometry", + "Metabolon", + "mirnaArray", + "mirnaSeq", + "Positron Emission Tomography" ] }, + "validBarcodeReads": {}, "platform": { "enum": [ - "quadrupole time-of-flight", - "HiSeq1000", - "OrbiTrap Fusion", - "IlluminaMiSeq", - "Illumina MouseWG-6 v2.0 expression beadchip", - "PacBioRSII", - "Agilent44Karray", - "Infinium Omni2.5Exome-8 v1.5", - "Infinium Global Diversity Array-8", - "ddSEQ Single-Cell Isolator", - "confocalImaging", - "IlluminaHumanHap650Yv3_A", - "Infinium HumanOmniExpressExome", - "Illumina_HumanOmni1-Quadv1.0", "LTQOrbitrapXL", - "NanostringnCounter_MouseADPanel", - "Infinium Omni2.5Exome-8 v1.1", - 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+ "IlluminaMethylationEPIC", + "Infinium HumanOmniExpressExome", + "HiSeq1000", + "IlluminaHumanHT-12_V3_0_R1", + "Agilent44Karray", + "Illumina NovaSeq 6000", + "Biograph mCT", "Illumina_Omni2.5-8_v1.3", - "HiSeqX", - "IlluminaInfiniumGSAMD-24v2-0", + "Q Exactive HF-X", "Illumina_Omni2.5-8", - "Affy6.0", - "Signa Premier AIR 3T", - "triple quadrupole", + "Orbitrap Exploris 240", + "Illumina_h650", + "Illumina_Omni2.5-8_v1.1", + "IlluminaNovaseq6000", + "IlluminaInfiniumGSAMD-24v2-0", "HiSeq2500", - "NextSeq500", - "HiSeq3000", - "Leco Pegasus IV", - "Bruker Avance III", - "Biocrates p180", - "PsychChip", - "Roche Cobas", - "Xevo TQ-S", + "NextSeq2000", + "Infinium Global Diversity Array-8", "Infinium Omni2.5Exome-8 v1.3", - "DNBSEQ", - "NanostringnCounter", - "PacBio Sequel II", - "Q Exactive Plus", - "Illumina_h650", "GAIIx", - "SequenomMultiplex", - "BGISEQ-500", - "Orbitrap Exploris 240", - "Biograph mCT", - "Affy5.0" + "Simoa HD-1 Analyzer", + "Bruker Avance III" ] - } + }, + "referenceSet": { + "enum": [ + "1000 Genomes phase 3", + "GRCh38", + "dmel_r6.06", + "GRCm38", + "GRCh37", + "MMUL1.0", + "HRC", + "" + ] + }, + "libraryType": { + "enum": [ + "plasmid DNA", + "cDNA", + "ADT", + "HTO", + "CMO", + "LMO", + "" + ] + }, + "libraryPrep": { + "enum": [ + "lncRNAenrichment", + "SPLITseq", + "DNALibraryConstruction", + "totalRNA", + "proximity ligation", + "methylSeq", + "PCRfree", + "multiome", + "MULTIseq", + "cellHashing", + "miRNAenrichment", + "snIsoSeq", + "polyAselection", + "Chromium Single Cell 3'", + "STARRSeq", + "SureCell", + "amplicon", + "KapaHyperPrep", + "rRNAdepletion", + "EndItDNAEndRepairKit" + ] + }, + "totalReads": {}, + "sampleBarcode": {}, + "readLength": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "specimenID": {} }, "required": [ "runType", - "libraryPrep", - "readLength", "assay", - "platform" + "platform", + "libraryPrep", + "readLength" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.AssaySnpArrayMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssaySnpArrayMetadataTemplate.schema.json index b30f4d8a..fe476638 100644 --- a/current-manifest-schemas/AD.AssaySnpArrayMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssaySnpArrayMetadataTemplate.schema.json @@ -4,222 +4,222 @@ "title": "AssaySnpArrayMetadataTemplate", "type": "object", "properties": { - "ratio260over280": {}, - "ratio260over230": {}, "Component": {}, - "platform": { - "enum": [ - "Illumina_Omni2.5-8_v1.3", - "time-of-flight", - "HiSeq1000", - "Illumina NovaSeq 6000", - "Orbitrap Exploris 240", - "Illumina_Omni2pt5M", - "MiSeq", - "Q Exactive Plus", - "IlluminaHumanHT-12_V3_0_R1", - "PacBio Sequel IIe", - "IlluminaMethylationEPIC", - "Olink Target 96", - "IlluminaNovaseq6000", - "Xevo TQ-S", - "llumina Infinium General Screening Array 24-Kit v3.0", - "NextSeq2000", - "PsychChip", - "Biograph mCT", - "GAIIx", - "AffymetrixU133Plus2", - "DNBSEQ", - 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Speckle Imaging", + "ISOSeq", + "Rader Lipidomics", + "scATACSeq", + "nextGenerationTargetedSequencing", + "label free mass spectrometry", + "locomotor activation behavior", + "Blood Chemistry Measurement", + "in vivo bioluminescence", "m6A-rnaSeq", + "Metabolon", + "Biocrates p180", + "sandwich ELISA", + "brightfieldMicroscopy", + "Biocrates Bile Acids", "atomicForceMicroscopy", - "UC Davis GCTOF", - "RPPA", + "elevated T maze apparatus method", + "MDMS-SL", + "Ribo-Seq", + "jumpingLibrary", + "von Frey test", + "tractionForceMicroscopy", "snrnaSeq", - "Wishart Catecholamines", - "MudPIT", - "mRNAcounts", + "active avoidance learning behavior", + "scCGIseq", + "immunohistochemistry", "rnaSeq", - "16SrRNAseq", - "errBisulfiteSeq", - "HI-C", - "open field test", - "proximity extension assay", - "liquid chromatography-electrochemical detection", - "DNA optical mapping", - "bisulfiteSeq", - "CUT&Tag", - "whole-cell patch clamp", - "oxBS-Seq", "snATACSeq", - "brightfieldMicroscopy", - 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"Positron Emission Tomography", + "high content screen", + "exomeSeq", + "HI-C", + "Real Time PCR", "NOMe-Seq", - "pharmacokinetics", - "STARRSeq", + "proximity extension assay", + "scwholeGenomeSeq", + "Baker Lipidomics", + "Nightingale NMR", + "Sanger sequencing", + "Biocrates MxP Quant500 XL", + "CUT&Tag", + "Wishart Catecholamines", + "snpArray", + "Biocrates Q500", + "ATACSeq", + "bisulfiteSeq", + "westernBlot", + "microRNAcounts", + "DIA", + "mRNAcounts", + "LC-MSMS", + "UPLC-MSMS", "ChIPSeq", + "polymeraseChainReaction", + "rnaArray", + "liquid chromatography-electrochemical detection", + "scrnaSeq", + "MudPIT", + "FIA-MSMS", + "errBisulfiteSeq", + "mirnaSeq", + "16SrRNAseq", + "contextual conditioning behavior", + "scirnaSeq", + "CITESeq", "scale", - "ATACSeq" + "UCSD Untargeted Metabolomics", + "ELISA", + "TMT quantitation", + "electrochemiluminescence", + "HPLC-MSMS", + "Laser Speckle Imaging", + "kinesthetic behavior", + "whole-cell patch clamp", + "pharmacokinetics", + "wheel running", + "Zeno Electronic Walkway" ] }, - "dnaBatch": {}, - "specimenID": {}, - "GQN": {} + "platform": { + "enum": [ + "Bruker Avance III", + "NextSeq500", + "Infinium Global Diversity Array-8", + "Xevo TQ-S", + "GAIIx", + "SequenomMultiplex", + "Bionano Irys", + "NanostringnCounter_MouseADPanel", + "HiSeq2500", + "Affymetrix Human Gene 1.0 ST Array", + "OrbiTrap Fusion", + "IlluminaMethylationEPIC", + "Leco Pegasus IV", + "ddSEQ Single-Cell Isolator", + "Orbitrap Exploris 240", + "Perlegen300Karray", + "Illumina NovaSeq 6000", + "MiSeq", + "Biocrates p180", + "time-of-flight", + "AffymetrixU133Plus2", + "Illumina MouseWG-6 v2.0 expression beadchip", + "Roche Cobas", + "Infinium HumanOmniExpressExome", + "Q Exactive HF", + "NanostringnCounter", + "HiSeq2000", + "Olink Target 96", + "AffymetrixU133AB", + "Illumina_Omni5M", + "Illumina_1M", + "Illumina_Omni2pt5M", + "Q Exactive HF-X", + "HiSeq3000", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "triple quadrupole", + 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"IlluminaWholeGenomeDASL", + "NextSeq2000", + "IlluminaHumanMethylation450" + ] + }, + "GQN": {}, + "dnaBatch": {} }, "required": [ - "platform", - "assay" + "assay", + "platform" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.AssayTMTquantitationMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayTMTquantitationMetadataTemplate.schema.json index 3791a849..5d75462f 100644 --- a/current-manifest-schemas/AD.AssayTMTquantitationMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayTMTquantitationMetadataTemplate.schema.json @@ -4,238 +4,238 @@ "title": "AssayTMTquantitationMetadataTemplate", "type": "object", "properties": { - "specimenID": {}, "batch": {}, "resolution": {}, - "TMTType": {}, + "Component": {}, "multiconsensusStudyFileID": {}, - "batchChannel": {}, - "assay": { + "fragmentation": {}, + "specimenID": {}, + "controlType": { "enum": [ - "Ribo-Seq", - "MDMS-SL", - "Vernier Caliper", - "snpArray", - "10x multiome", - "frailty assessment", - "scale", - "NOMe-Seq", - "snATACSeq", - "rnaSeq", - "oxBS-Seq", - "MIB/MS", - "UC Davis GCTOF", - "open field test", - "elevated plus maze test", - "ATACSeq", - "lncrnaSeq", - "Metabolon", - "Positron Emission Tomography", - "rnaArray", - "mRNAcounts", - "m6A-rnaSeq", - "whole-cell patch clamp", - "CUT&Tag", - "Rader Lipidomics", - "sandwich ELISA", - "TMT quantitation", - "nextGenerationTargetedSequencing", - "ChIPSeq", - "active avoidance learning behavior", - "SiMoA", - "FitBark", - "Baker Lipidomics", - "scrnaSeq", - "autoradiography", - "DIA", - "MudPIT", - "HI-C", - "RPPA", - "microRNAcounts", - "bisulfiteSeq", - "Laser Speckle Imaging", - "Biocrates MxP Quant500 XL", - "LC-SRM", - "Biocrates Q500", - "Biocrates Bile Acids", - "scwholeGenomeSeq", - "UCSD Untargeted Metabolomics", - "long-read rnaSeq", - "in vivo bioluminescence", - "novelty response behavior", - "von Frey test", - "proximity extension assay", - "contextual conditioning behavior", - "scCGIseq", - "UPLC-MSMS", - "Blood Chemistry Measurement", - "high content screen", - "exomeSeq", - "elevated T maze apparatus method", - "lentiMPRA", - "immunofluorescence", - "locomotor activation behavior", - "anxiety-related behavior", - "cellViabilityAssay", - "DNA optical mapping", - "Leiden Oxylipins", - "westernBlot", - "immunohistochemistry", - "Genotyping", - "wholeGenomeSeq", - "Wishart High Value Metabolites", - "ISOSeq", - "STARRSeq", - "spontaneous alternation", - "HiChIPseq", - "ELISA", - "LFP", - "scATACSeq", - "LC-MSMS", - "polymeraseChainReaction", - "Wishart Catecholamines", - "HPLC-MSMS", - "electrochemiluminescence", - "brightfieldMicroscopy", - "photograph", - "snrnaSeq", - "Zeno Electronic Walkway", - "Real Time PCR", - "Nightingale NMR", - "errBisulfiteSeq", - "jumpingLibrary", - "scirnaSeq", - "memory behavior", - "16SrRNAseq", - "rotarod performance test", - "wheel running", - "pharmacodynamics", - "CITESeq", - "atomicForceMicroscopy", - "Biocrates p180", - "methylationArray", - "Sanger sequencing", - "liquid chromatography-electrochemical detection", - "kinesthetic behavior", - "mirnaArray", - "UPLC-ESI-QTOF-MS", - "HPLC", - "label free mass spectrometry", - "mirnaSeq", - "tractionForceMicroscopy", - "Immunocytochemistry", - "pharmacokinetics", - "LC-MS", - "questionnaire", - "FIA-MSMS", - "MRI", - "LTP" + "Baker pool", + "GIS", + "NIST SRM 1950", + "Replicate", + "study pool", + "AIBL pool", + "qc mix", + "water plus Baker ISTD", + "GoldenWest", + "blank injection", + "" ] }, - "Component": {}, - "fragmentation": {}, + "TMTType": {}, "platform": { "enum": [ + "IlluminaNovaseq6000", + "Illumina_h650", + "Bionano Irys", + "Agilent44Karray", + "HiSeq3000", + "llumina Infinium General Screening Array 24-Kit v3.0", + "HiSeq2000", + "Affy6.0", + "Illumina MouseWG-6 v2.0 expression beadchip", + "Q Exactive Plus", "NanostringnCounter", + "IlluminaHumanHT-12_V3_0_R1", + "IlluminaHumanHap300", + "Affy5.0", + "PacBio Sequel IIe", "InfiniumPsychArrayBeadChip", + "PacBio Sequel II", + "Illumina_1M", + "DNBSEQ", + "HiSeq4000", "Signa Premier AIR 3T", + "Illumina NovaSeq 6000", + "NextSeq2000", + "Simoa HD-1 Analyzer", + "IlluminaMiSeq", + "PsychChip", + "Orbitrap Fusion Lumos", + "Olink Target 96", + "IlluminaMethylationEPIC", + "Illumina_Omni2.5-8", + "Q Exactive HF-X", + "GAIIx", "Illumina_HumanOmni1-Quadv1.0", - "Illumina_Omni2.5-8_v1.3", + "Orbitrap Exploris 240", + "BGISEQ-500", "Infinium Omni2.5Exome-8 v1.4", - "Affymetrix Human Gene 1.0 ST Array", - "Xevo TQ-S", - "Olink Target 96", - "Infinium Omni2.5Exome-8 v1.5", - "IlluminaWholeGenomeDASL", - "Q Exactive Plus", - "Q Exactive HF", + "AffymetrixU133AB", "confocalImaging", - "BGISEQ-500", + "IlluminaHumanMethylation450", + "orbitrap", "IlluminaHumanHap650Yv3_A", - "Illumina NovaSeq 6000", - "HiSeq2000", - "IlluminaMethylationEPIC", + "Biocrates p180", + "LTQOrbitrapXL", "ddSEQ Single-Cell Isolator", - "HiSeq4000", - "Illumina_Omni2.5-8", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "Bionano Irys", - "Illumina_1M", - "PacBio Sequel II", - "triple quadrupole", - "Illumina MouseWG-6 v2.0 expression beadchip", - "MiSeq", - "Illumina_Omni5-Quad", - "PsychChip", + "Illumina_Omni2.5-8_v1.3", + "Illumina_Omni5M", + "quadrupole time-of-flight", + "Leco Pegasus IV", "HiSeq2500", - "Affy5.0", - "llumina Infinium General Screening Array 24-Kit v3.0", - "IlluminaMiSeq", - "Biograph mCT", - "Illumina_h650", "time-of-flight", - "HiSeq1000", - "HiSeq3000", - "quadrupole time-of-flight", - "DNBSEQ", - "IlluminaHumanHap300", + "Biograph mCT", "Infinium Omni2.5Exome-8 v1.1", - "AffymetrixU133AB", - "OrbiTrap Fusion", - "Q Exactive", - "IlluminaHumanMethylation450", - "Bruker Avance III", - "Roche Cobas", - "GAIIx", - "Infinium Global Diversity Array-8", - "AffymetrixU133Plus2", - "Infinium Omni2.5Exome-8 v1.3", - "LTQOrbitrapXL", - "Infinium HumanOmniExpressExome", - "Illumina_Omni5M", "Illumina_Omni2.5-8_v1.1", - "IlluminaHumanHT-12_V3_0_R1", + "Infinium HumanOmniExpressExome", + "HiSeq1000", + "OrbiTrap Fusion", + "Affymetrix Human Gene 1.0 ST Array", + "Illumina_Omni2pt5M", + "triple quadrupole", "PacBioRSII", - "Orbitrap Exploris 240", - "HiSeqX", + "Q Exactive HF", + "Roche Cobas", "Perlegen300Karray", - "Biocrates p180", - "IlluminaNovaseq6000", - "Orbitrap Fusion Lumos", - "NextSeq500", + "NanostringnCounter_MouseADPanel", "SequenomMultiplex", - "Affy6.0", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "Infinium Omni2.5Exome-8 v1.3", + "NextSeq500", "Xevo G2 QTOF", - "Q Exactive HF-X", - "NextSeq2000", - "Illumina_Omni2pt5M", - "Agilent44Karray", - "Simoa HD-1 Analyzer", "IlluminaInfiniumGSAMD-24v2-0", - "Leco Pegasus IV", - "NanostringnCounter_MouseADPanel", - "PacBio Sequel IIe", - "orbitrap" + "Infinium Omni2.5Exome-8 v1.5", + "HiSeqX", + "Illumina_Omni5-Quad", + "AffymetrixU133Plus2", + "MiSeq", + "Xevo TQ-S", + "Infinium Global Diversity Array-8", + "Q Exactive", + "IlluminaWholeGenomeDASL", + "Bruker Avance III" ] }, - "controlType": { + "batchChannel": {}, + "assay": { "enum": [ - "Baker pool", - "GoldenWest", - "NIST SRM 1950", - "AIBL pool", - "qc mix", - "blank injection", - "water plus Baker ISTD", - "Replicate", - "study pool", - "GIS", - "" + "jumpingLibrary", + "high content screen", + "CUT&Tag", + "tractionForceMicroscopy", + "UPLC-ESI-QTOF-MS", + "scATACSeq", + "Immunocytochemistry", + "SiMoA", + "contextual conditioning behavior", + "electrochemiluminescence", + "pharmacokinetics", + "scwholeGenomeSeq", + "LTP", + "Zeno Electronic Walkway", + "brightfieldMicroscopy", + "oxBS-Seq", + "TMT quantitation", + "microRNAcounts", + "ChIPSeq", + "proximity extension assay", + "scirnaSeq", + "LC-MSMS", + "Genotyping", + "pharmacodynamics", + "atomicForceMicroscopy", + "m6A-rnaSeq", + "rotarod performance test", + "UPLC-MSMS", + "elevated plus maze test", + "Blood Chemistry Measurement", + "ATACSeq", + "nextGenerationTargetedSequencing", + "photograph", + "elevated T maze apparatus method", + "methylationArray", + "Real Time PCR", + "sandwich ELISA", + "LFP", + "STARRSeq", + "open field test", + "scale", + "Laser Speckle Imaging", + "MIB/MS", + "memory behavior", + "RPPA", + "Sanger sequencing", + "errBisulfiteSeq", + "snpArray", + "Rader Lipidomics", + "Vernier Caliper", + "Wishart Catecholamines", + "snrnaSeq", + "HPLC-MSMS", + "rnaArray", + "in vivo bioluminescence", + "LC-MS", + "MDMS-SL", + "mRNAcounts", + "rnaSeq", + "autoradiography", + "exomeSeq", + "Biocrates p180", + "Biocrates Bile Acids", + "MudPIT", + "active avoidance learning behavior", + "kinesthetic behavior", + "cellViabilityAssay", + "westernBlot", + "Positron Emission Tomography", + "LC-SRM", + "von Frey test", + "Biocrates Q500", + "snATACSeq", + "UCSD Untargeted Metabolomics", + "frailty assessment", + "CITESeq", + "bisulfiteSeq", + "mirnaSeq", + "DIA", + "16SrRNAseq", + "spontaneous alternation", + "Wishart High Value Metabolites", + "locomotor activation behavior", + "FitBark", + "scCGIseq", + "UC Davis GCTOF", + "lncrnaSeq", + "10x multiome", + "mirnaArray", + "long-read rnaSeq", + "ISOSeq", + "HPLC", + "lentiMPRA", + "Metabolon", + "NOMe-Seq", + "HiChIPseq", + "immunofluorescence", + "wholeGenomeSeq", + "Leiden Oxylipins", + "Baker Lipidomics", + "immunohistochemistry", + "DNA optical mapping", + "label free mass spectrometry", + "novelty response behavior", + "ELISA", + "Biocrates MxP Quant500 XL", + "whole-cell patch clamp", + "anxiety-related behavior", + "polymeraseChainReaction", + "scrnaSeq", + "liquid chromatography-electrochemical detection", + "wheel running", + "Ribo-Seq", + "FIA-MSMS", + "HI-C", + "questionnaire", + "Nightingale NMR", + "MRI" ] } }, "required": [ - "assay", - "platform" + "platform", + "assay" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.AssayWholeExomeSeqMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayWholeExomeSeqMetadataTemplate.schema.json index 9337a272..5f5d0a4e 100644 --- a/current-manifest-schemas/AD.AssayWholeExomeSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayWholeExomeSeqMetadataTemplate.schema.json @@ -4,296 +4,296 @@ "title": "AssayWholeExomeSeqMetadataTemplate", "type": "object", "properties": { - "libraryID": {}, - "sequencingBatch": {}, - "libraryPrep": { + "specimenID": {}, + "ratio260over280": {}, + "runType": { "enum": [ - "miRNAenrichment", - "amplicon", - "Chromium Single Cell 3'", - "PCRfree", - "proximity ligation", - "STARRSeq", - "KapaHyperPrep", - "snIsoSeq", - "EndItDNAEndRepairKit", - "MULTIseq", - "cellHashing", - "methylSeq", - "lncRNAenrichment", - "totalRNA", - "polyAselection", - "SPLITseq", - "SureCell", - "DNALibraryConstruction", - "multiome", - "rRNAdepletion" + "singleEnd", + "pairedEnd" ] }, - "runType": { + "referenceSet": { "enum": [ - "pairedEnd", - "singleEnd" + "GRCh37", + "GRCm38", + "dmel_r6.06", + "MMUL1.0", + "1000 Genomes phase 3", + "GRCh38", + "HRC", + "" ] }, "libraryPreparationMethod": { "enum": [ - "TruSeq", - "Smart-seq4", - "sac-seq", - "Illumina DNA PCR-Free Prep Kit", "Accel-NGS Methyl-Seq", + "10x", + "Omni-ATAC", "Ultralow Methyl-Seq", - "NexteraXT", "Drop-Seq", - "Omni-ATAC", - "SMRTbell", - "10x", - "Smart-seq1", - "NEBNext", - "CEL-seq", + "Smart-seq4", + "NexteraXT", + "sac-seq", "Accel-NGS 2S Plus", + "SMRTbell", "Smart-seq2", + "TruSeq", + "Illumina DNA PCR-Free Prep Kit", + "CEL-seq", + "NEBNext", + "Smart-seq1", "" ] }, - "totalReads": {}, - "dnaBatch": {}, - "referenceSet": { - "enum": [ - "HRC", - "MMUL1.0", - "GRCh37", - "GRCh38", - "dmel_r6.06", - "1000 Genomes phase 3", - "GRCm38", - "" - ] - }, - "platform": { - "enum": [ - "Illumina_Omni2.5-8_v1.1", - "IlluminaWholeGenomeDASL", - "Infinium Omni2.5Exome-8 v1.1", - "Q Exactive HF", - "Perlegen300Karray", - "Orbitrap Fusion Lumos", - "Affy6.0", - "LTQOrbitrapXL", - "AffymetrixU133Plus2", - "NextSeq500", - "HiSeqX", - "Bruker Avance III", - "MiSeq", - "IlluminaHumanHT-12_V3_0_R1", - "DNBSEQ", - "Simoa HD-1 Analyzer", - "Bionano Irys", - "IlluminaMethylationEPIC", - "confocalImaging", - "Infinium Global Diversity Array-8", - "NextSeq2000", - "HiSeq1000", - "Affymetrix Human Gene 1.0 ST Array", - "NanostringnCounter_MouseADPanel", - "IlluminaHumanMethylation450", - "Q Exactive", - "Signa Premier AIR 3T", - "Illumina_Omni2pt5M", - "Illumina_HumanOmni1-Quadv1.0", - "HiSeq3000", - "PacBio Sequel II", - "Xevo TQ-S", - "Biocrates p180", - "Infinium Omni2.5Exome-8 v1.5", - "Biograph mCT", - "Leco Pegasus IV", - "quadrupole time-of-flight", - "Illumina_Omni2.5-8", - "Infinium Omni2.5Exome-8 v1.4", - "HiSeq2000", - "Q Exactive HF-X", - "Illumina_1M", - "llumina Infinium General Screening Array 24-Kit v3.0", - "Infinium Omni2.5Exome-8 v1.3", - "IlluminaInfiniumGSAMD-24v2-0", - "Infinium HumanOmniExpressExome", - "PsychChip", - "IlluminaMiSeq", - "HiSeq4000", - "IlluminaNovaseq6000", - "InfiniumPsychArrayBeadChip", - "time-of-flight", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "Q Exactive Plus", - "PacBioRSII", - "ddSEQ Single-Cell Isolator", - "NanostringnCounter", - "Illumina MouseWG-6 v2.0 expression beadchip", - "PacBio Sequel IIe", - "Agilent44Karray", - "Orbitrap Exploris 240", - "Illumina_Omni2.5-8_v1.3", - "HiSeq2500", - "Illumina_Omni5M", - "Illumina NovaSeq 6000", - "OrbiTrap Fusion", - "IlluminaHumanHap650Yv3_A", - "Illumina_h650", - "BGISEQ-500", - "Roche Cobas", - "Olink Target 96", - "Affy5.0", - "Xevo G2 QTOF", - "SequenomMultiplex", - "Illumina_Omni5-Quad", - "IlluminaHumanHap300", - "orbitrap", - "triple quadrupole", - "GAIIx", - "AffymetrixU133AB" - ] - }, - "ratio260over230": {}, "assay": { "enum": [ - "MIB/MS", - "mRNAcounts", - "elevated plus maze test", - "scirnaSeq", - "Wishart High Value Metabolites", - "mirnaSeq", - "spontaneous alternation", - "methylationArray", - "tractionForceMicroscopy", - "in vivo bioluminescence", - "m6A-rnaSeq", - "von Frey test", - "cellViabilityAssay", - "ChIPSeq", + "LTP", + "long-read rnaSeq", + "polymeraseChainReaction", "ELISA", - "photograph", + "RPPA", + "bisulfiteSeq", + "ISOSeq", + "FIA-MSMS", + "snATACSeq", + "frailty assessment", + "Vernier Caliper", + "wheel running", + "kinesthetic behavior", + "HPLC-MSMS", + "lncrnaSeq", + "brightfieldMicroscopy", + "Sanger sequencing", + "scCGIseq", + "snpArray", + "Leiden Oxylipins", + "locomotor activation behavior", + "UPLC-MSMS", + "mRNAcounts", "Rader Lipidomics", - "open field test", + "spontaneous alternation", + "anxiety-related behavior", + "TMT quantitation", + "elevated plus maze test", + "DIA", + "elevated T maze apparatus method", + "Blood Chemistry Measurement", + "rnaSeq", + "memory behavior", + "proximity extension assay", "Genotyping", - "lentiMPRA", - "nextGenerationTargetedSequencing", - "immunofluorescence", "Real Time PCR", - "ATACSeq", - "scale", + "ChIPSeq", + "high content screen", "Zeno Electronic Walkway", - "frailty assessment", - "wholeGenomeSeq", - "10x multiome", - "FIA-MSMS", - "wheel running", - "lncrnaSeq", - "bisulfiteSeq", - "Vernier Caliper", + "ATACSeq", + "atomicForceMicroscopy", + "MDMS-SL", + "Nightingale NMR", + "sandwich ELISA", + "MIB/MS", + "in vivo bioluminescence", + "mirnaArray", + "CUT&Tag", + "HI-C", "HiChIPseq", - "TMT quantitation", - "LC-SRM", - "pharmacokinetics", - "LFP", - "DNA optical mapping", - "SiMoA", + "scale", + "photograph", + "oxBS-Seq", + "immunofluorescence", "microRNAcounts", + "NOMe-Seq", "jumpingLibrary", - "DIA", - "autoradiography", - "HI-C", + "16SrRNAseq", + "Biocrates p180", "whole-cell patch clamp", - "snpArray", - "atomicForceMicroscopy", - "Baker Lipidomics", - "HPLC", - "Ribo-Seq", + "label free mass spectrometry", "questionnaire", - "Biocrates p180", - "contextual conditioning behavior", - "NOMe-Seq", - "westernBlot", - "pharmacodynamics", - "ISOSeq", - "locomotor activation behavior", - "UPLC-ESI-QTOF-MS", - "immunohistochemistry", - "Metabolon", - "memory behavior", - "LTP", - "RPPA", - "MDMS-SL", - "Blood Chemistry Measurement", - "Sanger sequencing", - "UPLC-MSMS", - "UCSD Untargeted Metabolomics", + "nextGenerationTargetedSequencing", + "tractionForceMicroscopy", + "lentiMPRA", "LC-MSMS", - "elevated T maze apparatus method", - "electrochemiluminescence", + "LC-SRM", + "Ribo-Seq", + "Biocrates Bile Acids", + "immunohistochemistry", "Biocrates MxP Quant500 XL", - "scCGIseq", - "oxBS-Seq", - "CUT&Tag", - "sandwich ELISA", - "brightfieldMicroscopy", - "Laser Speckle Imaging", - "exomeSeq", - "kinesthetic behavior", - "active avoidance learning behavior", - "long-read rnaSeq", - "liquid chromatography-electrochemical detection", + "m6A-rnaSeq", + "electrochemiluminescence", + "mirnaSeq", + "scrnaSeq", "scATACSeq", + "active avoidance learning behavior", + "MudPIT", "CITESeq", + "Wishart High Value Metabolites", + "cellViabilityAssay", + "von Frey test", + "LC-MS", + "westernBlot", + "errBisulfiteSeq", + "liquid chromatography-electrochemical detection", + "DNA optical mapping", + "Immunocytochemistry", + "UCSD Untargeted Metabolomics", + "contextual conditioning behavior", "rotarod performance test", - "16SrRNAseq", - "scwholeGenomeSeq", - "Leiden Oxylipins", - "snATACSeq", - "FitBark", - "Nightingale NMR", "Wishart Catecholamines", - "Immunocytochemistry", - "STARRSeq", - "polymeraseChainReaction", - "errBisulfiteSeq", - "novelty response behavior", - "high content screen", - "LC-MS", + "snrnaSeq", + "Metabolon", "rnaArray", - "Biocrates Bile Acids", - "rnaSeq", - "label free mass spectrometry", - "MudPIT", - "HPLC-MSMS", - "mirnaArray", - "anxiety-related behavior", + "scwholeGenomeSeq", + "open field test", + "HPLC", + "FitBark", + "autoradiography", + "Positron Emission Tomography", + "pharmacokinetics", + "wholeGenomeSeq", "Biocrates Q500", + "novelty response behavior", + "Laser Speckle Imaging", + "LFP", + "10x multiome", + "pharmacodynamics", + "methylationArray", "MRI", - "UC Davis GCTOF", - "snrnaSeq", - "Positron Emission Tomography", - "proximity extension assay", - "scrnaSeq" + "exomeSeq", + "UPLC-ESI-QTOF-MS", + "Baker Lipidomics", + "SiMoA", + "scirnaSeq", + "STARRSeq", + "UC Davis GCTOF" ] }, - "specimenID": {}, + "GQN": {}, + "dnaBatch": {}, "readLength": { "not": { "type": "null" }, "minLength": 1 }, + "platform": { + "enum": [ + "PacBio Sequel IIe", + "Illumina MouseWG-6 v2.0 expression beadchip", + "IlluminaNovaseq6000", + "IlluminaMiSeq", + "AffymetrixU133Plus2", + "Illumina_Omni2pt5M", + "Q Exactive HF-X", + "NanostringnCounter_MouseADPanel", + "GAIIx", + "Leco Pegasus IV", + "Bionano Irys", + "IlluminaMethylationEPIC", + "LTQOrbitrapXL", + "NanostringnCounter", + "IlluminaWholeGenomeDASL", + "HiSeq2500", + "Illumina_Omni5-Quad", + "Illumina_Omni2.5-8_v1.1", + "confocalImaging", + "Infinium Global Diversity Array-8", + "IlluminaHumanHap300", + "PacBioRSII", + "llumina Infinium General Screening Array 24-Kit v3.0", + "MiSeq", + "DNBSEQ", + "HiSeq2000", + "HiSeqX", + "Infinium Omni2.5Exome-8 v1.1", + "PsychChip", + "IlluminaHumanHap650Yv3_A", + "NextSeq500", + "Illumina_Omni2.5-8_v1.3", + "Illumina_Omni2.5-8", + "Infinium Omni2.5Exome-8 v1.4", + "Infinium Omni2.5Exome-8 v1.3", + "Q Exactive HF", + "Xevo TQ-S", + "Biocrates p180", + "Agilent44Karray", + "Illumina_1M", + "Orbitrap Fusion Lumos", + "Q Exactive", + "quadrupole time-of-flight", + "Signa Premier AIR 3T", + "Affy6.0", + "AffymetrixU133AB", + "Olink Target 96", + "Affy5.0", + "PacBio Sequel II", + "IlluminaInfiniumGSAMD-24v2-0", + "HiSeq3000", + "OrbiTrap Fusion", + "Perlegen300Karray", + "Illumina NovaSeq 6000", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "NextSeq2000", + "Roche Cobas", + "orbitrap", + "Affymetrix Human Gene 1.0 ST Array", + "Illumina_h650", + "triple quadrupole", + "Orbitrap Exploris 240", + "IlluminaHumanMethylation450", + "Bruker Avance III", + "ddSEQ Single-Cell Isolator", + "Q Exactive Plus", + "SequenomMultiplex", + "time-of-flight", + "Infinium Omni2.5Exome-8 v1.5", + "Infinium HumanOmniExpressExome", + "HiSeq1000", + "Xevo G2 QTOF", + "Biograph mCT", + "Simoa HD-1 Analyzer", + "InfiniumPsychArrayBeadChip", + "BGISEQ-500", + "Illumina_Omni5M", + "HiSeq4000", + "IlluminaHumanHT-12_V3_0_R1", + "Illumina_HumanOmni1-Quadv1.0" + ] + }, + "libraryPrep": { + "enum": [ + "SPLITseq", + "multiome", + "EndItDNAEndRepairKit", + "totalRNA", + "MULTIseq", + "cellHashing", + "methylSeq", + "SureCell", + "lncRNAenrichment", + "Chromium Single Cell 3'", + "proximity ligation", + "DNALibraryConstruction", + "KapaHyperPrep", + "miRNAenrichment", + "rRNAdepletion", + "PCRfree", + "amplicon", + "polyAselection", + "snIsoSeq", + "STARRSeq" + ] + }, + "libraryID": {}, + "ratio260over230": {}, + "sequencingBatch": {}, "Component": {}, - "ratio260over280": {}, - "GQN": {} + "totalReads": {} }, "required": [ - "libraryPrep", "runType", - "platform", "assay", - "readLength" + "readLength", + "platform", + "libraryPrep" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.AssayWholeGenomeSeqMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayWholeGenomeSeqMetadataTemplate.schema.json index 9101dcfb..04ac01db 100644 --- a/current-manifest-schemas/AD.AssayWholeGenomeSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayWholeGenomeSeqMetadataTemplate.schema.json @@ -4,8 +4,6 @@ "title": "AssayWholeGenomeSeqMetadataTemplate", "type": "object", "properties": { - "totalReads": {}, - "GQN": {}, "sequencingBatch": {}, "readLength": { "not": { @@ -13,288 +11,290 @@ }, "minLength": 1 }, - "ratio260over230": {}, - "specimenID": {}, - "referenceSet": { + "dnaBatch": {}, + "libraryPrep": { "enum": [ - "GRCh37", - "1000 Genomes phase 3", - "MMUL1.0", - "HRC", - "dmel_r6.06", - "GRCh38", - "GRCm38", - "" + "lncRNAenrichment", + "totalRNA", + "MULTIseq", + "methylSeq", + "Chromium Single Cell 3'", + "proximity ligation", + "EndItDNAEndRepairKit", + "SureCell", + "rRNAdepletion", + "multiome", + "cellHashing", + "STARRSeq", + "miRNAenrichment", + "polyAselection", + "SPLITseq", + "PCRfree", + "amplicon", + "KapaHyperPrep", + "DNALibraryConstruction", + "snIsoSeq" ] }, - "dnaBatch": {}, + "assay": { + "enum": [ + "10x multiome", + "rnaSeq", + "MDMS-SL", + "HPLC-MSMS", + "Biocrates MxP Quant500 XL", + "TMT quantitation", + "spontaneous alternation", + "microRNAcounts", + "liquid chromatography-electrochemical detection", + "snpArray", + "Biocrates Bile Acids", + "Real Time PCR", + "LFP", + "CUT&Tag", + "UCSD Untargeted Metabolomics", + "brightfieldMicroscopy", + "LC-SRM", + "mRNAcounts", + "NOMe-Seq", + "m6A-rnaSeq", + "ELISA", + "pharmacodynamics", + "FIA-MSMS", + "DNA optical mapping", + "jumpingLibrary", + "scale", + "locomotor activation behavior", + "immunofluorescence", + "elevated plus maze test", + "atomicForceMicroscopy", + "scwholeGenomeSeq", + "kinesthetic behavior", + "Ribo-Seq", + "errBisulfiteSeq", + "Positron Emission Tomography", + "tractionForceMicroscopy", + "photograph", + "contextual conditioning behavior", + "HPLC", + "MIB/MS", + "RPPA", + "Blood Chemistry Measurement", + "mirnaArray", + "Sanger sequencing", + "Biocrates p180", + "snATACSeq", + "Vernier Caliper", + "DIA", + "whole-cell patch clamp", + "Biocrates Q500", + "immunohistochemistry", + "16SrRNAseq", + "wholeGenomeSeq", + "exomeSeq", + "HI-C", + "mirnaSeq", + "proximity extension assay", + "nextGenerationTargetedSequencing", + "rnaArray", + "UPLC-MSMS", + "LC-MSMS", + "Baker Lipidomics", + "oxBS-Seq", + "cellViabilityAssay", + "HiChIPseq", + "lncrnaSeq", + "autoradiography", + "STARRSeq", + "pharmacokinetics", + "memory behavior", + "label free mass spectrometry", + "novelty response behavior", + "open field test", + "scirnaSeq", + "snrnaSeq", + "active avoidance learning behavior", + "frailty assessment", + "scCGIseq", + "electrochemiluminescence", + "Zeno Electronic Walkway", + "MRI", + "LTP", + "sandwich ELISA", + "Rader Lipidomics", + "lentiMPRA", + "scATACSeq", + "Genotyping", + "high content screen", + "ATACSeq", + "ChIPSeq", + "methylationArray", + "Immunocytochemistry", + "scrnaSeq", + "ISOSeq", + "LC-MS", + "polymeraseChainReaction", + "Wishart High Value Metabolites", + "UC Davis GCTOF", + "anxiety-related behavior", + "von Frey test", + "Nightingale NMR", + "bisulfiteSeq", + "FitBark", + "Metabolon", + "wheel running", + "in vivo bioluminescence", + "SiMoA", + "MudPIT", + "elevated T maze apparatus method", + "long-read rnaSeq", + "Leiden Oxylipins", + "CITESeq", + "westernBlot", + "Wishart Catecholamines", + "UPLC-ESI-QTOF-MS", + "Laser Speckle Imaging", + "rotarod performance test", + "questionnaire" + ] + }, + "libraryID": {}, + "specimenID": {}, "platform": { "enum": [ - "Affy5.0", - "PsychChip", - "Xevo TQ-S", - "PacBio Sequel IIe", - "AffymetrixU133Plus2", - "Q Exactive HF", - "Signa Premier AIR 3T", - "ddSEQ Single-Cell Isolator", - "HiSeq2000", - "Simoa HD-1 Analyzer", - "Illumina_Omni2.5-8", - "Illumina_h650", - "Leco Pegasus IV", + "Infinium Omni2.5Exome-8 v1.5", "IlluminaNovaseq6000", - "IlluminaMethylationEPIC", - "Illumina NovaSeq 6000", - "IlluminaHumanHap650Yv3_A", "MiSeq", - "Illumina_1M", - "Agilent44Karray", - "IlluminaMiSeq", - "Perlegen300Karray", - "confocalImaging", + "GAIIx", + "Orbitrap Fusion Lumos", + "HiSeq2500", "SequenomMultiplex", + "NextSeq2000", + "LTQOrbitrapXL", + "ddSEQ Single-Cell Isolator", + "PsychChip", + "Infinium Omni2.5Exome-8 v1.1", + "Illumina NovaSeq 6000", + "Q Exactive HF-X", + "Perlegen300Karray", + "Xevo TQ-S", + "NextSeq500", "IlluminaHumanHap300", - "PacBioRSII", - "Q Exactive", - "Biocrates p180", - "DNBSEQ", - "Bruker Avance III", - "Roche Cobas", - "IlluminaHumanHT-12_V3_0_R1", + "llumina Infinium General Screening Array 24-Kit v3.0", + "Affy6.0", + "InfiniumPsychArrayBeadChip", "Q Exactive Plus", - "HiSeq2500", - "Infinium HumanOmniExpressExome", - "Illumina_Omni2.5-8_v1.1", - "HiSeq1000", - "LTQOrbitrapXL", - "Affymetrix Human Gene 1.0 ST Array", - "Bionano Irys", - "Biograph mCT", - "GAIIx", + "Olink Target 96", + "Simoa HD-1 Analyzer", "quadrupole time-of-flight", - "IlluminaInfiniumGSAMD-24v2-0", + "time-of-flight", + "IlluminaMethylationEPIC", + "Q Exactive", + "Illumina_Omni2pt5M", + "Roche Cobas", "AffymetrixU133AB", - "NextSeq500", - "HiSeqX", + "PacBioRSII", + "BGISEQ-500", "Infinium Omni2.5Exome-8 v1.3", - "Q Exactive HF-X", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "Illumina_Omni2pt5M", - "NextSeq2000", + "Biograph mCT", + "triple quadrupole", + "Illumina_Omni2.5-8", + "NanostringnCounter_MouseADPanel", + "Biocrates p180", + "Illumina_Omni5-Quad", + "HiSeq1000", + "Illumina_Omni2.5-8_v1.1", + "PacBio Sequel II", "HiSeq3000", - "Illumina_Omni2.5-8_v1.3", + "IlluminaHumanMethylation450", + "orbitrap", + "Signa Premier AIR 3T", + "Affy5.0", "OrbiTrap Fusion", - "time-of-flight", - "NanostringnCounter", - "llumina Infinium General Screening Array 24-Kit v3.0", - "InfiniumPsychArrayBeadChip", + "IlluminaHumanHap650Yv3_A", "Xevo G2 QTOF", - "Olink Target 96", - "Infinium Omni2.5Exome-8 v1.4", - "BGISEQ-500", - "IlluminaHumanMethylation450", - "Illumina_HumanOmni1-Quadv1.0", - "Infinium Omni2.5Exome-8 v1.5", - "Illumina_Omni5-Quad", "IlluminaWholeGenomeDASL", - "NanostringnCounter_MouseADPanel", - "Orbitrap Exploris 240", - "HiSeq4000", - "Infinium Global Diversity Array-8", - "orbitrap", - "Infinium Omni2.5Exome-8 v1.1", - "Affy6.0", - "PacBio Sequel II", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "IlluminaHumanHT-12_V3_0_R1", + "HiSeq2000", + "Illumina_Omni2.5-8_v1.3", + "Leco Pegasus IV", + "confocalImaging", "Illumina_Omni5M", + "PacBio Sequel IIe", + "Infinium Global Diversity Array-8", + "NanostringnCounter", + "Bionano Irys", + "Q Exactive HF", + "DNBSEQ", + "Illumina_h650", + "HiSeqX", + "HiSeq4000", + "Orbitrap Exploris 240", + "Agilent44Karray", + "Infinium Omni2.5Exome-8 v1.4", + "Illumina_HumanOmni1-Quadv1.0", "Illumina MouseWG-6 v2.0 expression beadchip", - "triple quadrupole", - "Orbitrap Fusion Lumos" + "AffymetrixU133Plus2", + "Affymetrix Human Gene 1.0 ST Array", + "Infinium HumanOmniExpressExome", + "Illumina_1M", + "Bruker Avance III", + "IlluminaMiSeq", + "IlluminaInfiniumGSAMD-24v2-0" ] }, - "Component": {}, + "GQN": {}, + "ratio260over280": {}, "runType": { "enum": [ - "pairedEnd", - "singleEnd" + "singleEnd", + "pairedEnd" ] }, - "assay": { + "numberCells": {}, + "totalReads": {}, + "Component": {}, + "referenceSet": { "enum": [ - "rnaArray", - "snATACSeq", - "Biocrates Bile Acids", - "STARRSeq", - "exomeSeq", - "Biocrates MxP Quant500 XL", - "electrochemiluminescence", - "snrnaSeq", - "Wishart High Value Metabolites", - "autoradiography", - "tractionForceMicroscopy", - "cellViabilityAssay", - "HPLC", - "MDMS-SL", - "pharmacodynamics", - "errBisulfiteSeq", - "DNA optical mapping", - "Nightingale NMR", - "kinesthetic behavior", - "questionnaire", - "Immunocytochemistry", - "immunofluorescence", - "bisulfiteSeq", - "ELISA", - "CITESeq", - "mirnaArray", - "Real Time PCR", - "scCGIseq", - "brightfieldMicroscopy", - "elevated plus maze test", - "novelty response behavior", - "Vernier Caliper", - "wholeGenomeSeq", - "ATACSeq", - "UPLC-ESI-QTOF-MS", - "liquid chromatography-electrochemical detection", - "TMT quantitation", - "LFP", - "elevated T maze apparatus method", - "frailty assessment", - "HiChIPseq", - "Sanger sequencing", - "contextual conditioning behavior", - "spontaneous alternation", - "Wishart Catecholamines", - "Biocrates p180", - "scrnaSeq", - "ISOSeq", - "microRNAcounts", - "rnaSeq", - "rotarod performance test", - "Zeno Electronic Walkway", - "scwholeGenomeSeq", - "Positron Emission Tomography", - "wheel running", - "Blood Chemistry Measurement", - "16SrRNAseq", - "CUT&Tag", - "Baker Lipidomics", - "active avoidance learning behavior", - "whole-cell patch clamp", - "methylationArray", - "LTP", - "m6A-rnaSeq", - "lentiMPRA", - "mRNAcounts", - "jumpingLibrary", - "MRI", - "FitBark", - "UPLC-MSMS", - "long-read rnaSeq", - "Rader Lipidomics", - "Metabolon", - "UCSD Untargeted Metabolomics", - "westernBlot", - "LC-MSMS", - "sandwich ELISA", - "Ribo-Seq", - "anxiety-related behavior", - "locomotor activation behavior", - "UC Davis GCTOF", - "FIA-MSMS", - "proximity extension assay", - "ChIPSeq", - "polymeraseChainReaction", - "label free mass spectrometry", - "LC-SRM", - "NOMe-Seq", - "scale", - "10x multiome", - "SiMoA", - "scirnaSeq", - "HPLC-MSMS", - "scATACSeq", - "snpArray", - "oxBS-Seq", - "HI-C", - "LC-MS", - "photograph", - "Genotyping", - "mirnaSeq", - "MIB/MS", - "von Frey test", - "Biocrates Q500", - "lncrnaSeq", - "DIA", - "high content screen", - "in vivo bioluminescence", - "open field test", - "pharmacokinetics", - "MudPIT", - "Laser Speckle Imaging", - "nextGenerationTargetedSequencing", - "immunohistochemistry", - "memory behavior", - "atomicForceMicroscopy", - "Leiden Oxylipins", - "RPPA" + "dmel_r6.06", + "GRCh37", + "GRCm38", + "HRC", + "1000 Genomes phase 3", + "MMUL1.0", + "GRCh38", + "" ] }, "libraryPreparationMethod": { "enum": [ + "10x", "NEBNext", - "Smart-seq4", - "Smart-seq2", - "TruSeq", + "sac-seq", "Accel-NGS 2S Plus", - "10x", + "Drop-Seq", "Smart-seq1", - "SMRTbell", + "Smart-seq2", + "Omni-ATAC", + "Smart-seq4", "Illumina DNA PCR-Free Prep Kit", - "Drop-Seq", + "Accel-NGS Methyl-Seq", "Ultralow Methyl-Seq", "CEL-seq", - "sac-seq", + "SMRTbell", + "TruSeq", "NexteraXT", - "Accel-NGS Methyl-Seq", - "Omni-ATAC", "" ] }, - "libraryPrep": { - "enum": [ - "MULTIseq", - "EndItDNAEndRepairKit", - "SureCell", - "polyAselection", - "STARRSeq", - "PCRfree", - "proximity ligation", - "snIsoSeq", - "miRNAenrichment", - "totalRNA", - "DNALibraryConstruction", - "Chromium Single Cell 3'", - "multiome", - "SPLITseq", - "lncRNAenrichment", - "rRNAdepletion", - "methylSeq", - "cellHashing", - "amplicon", - "KapaHyperPrep" - ] - }, - "libraryID": {}, - "numberCells": {}, - "ratio260over280": {} + "ratio260over230": {} }, "required": [ "readLength", - "platform", - "runType", + "libraryPrep", "assay", - "libraryPrep" + "platform", + "runType" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.BiospecimenDrosophilaMetadataTemplate.schema.json b/current-manifest-schemas/AD.BiospecimenDrosophilaMetadataTemplate.schema.json index 559d49ed..470098c6 100644 --- a/current-manifest-schemas/AD.BiospecimenDrosophilaMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.BiospecimenDrosophilaMetadataTemplate.schema.json @@ -4,41 +4,41 @@ "title": "BiospecimenDrosophilaMetadataTemplate", "type": "object", "properties": { - "nucleicAcidSource": { - "enum": [ - "single nucleus", - "mitochondria", - "sorted nuclei", - "sorted cells", - "cfDNA", - "bulk cell", - "not applicable", - "single cell", - "bulk nuclei", - "" - ] - }, + "nMale": {}, "bodyPart": { "enum": [ - "head", "brain", + "head", "" ] }, - "tissueWeight": {}, - "ageDays": {}, - "nIndividuals": {}, - "nFemale": {}, - "temperature": {}, - "nMale": {}, - "specimenID": {}, - "Component": {}, "genotype": { "not": { "type": "null" }, "minLength": 1 - } + }, + "temperature": {}, + "Component": {}, + "ageDays": {}, + "nFemale": {}, + "nucleicAcidSource": { + "enum": [ + "cfDNA", + "sorted cells", + "sorted nuclei", + "bulk nuclei", + "single cell", + "single nucleus", + "bulk cell", + "not applicable", + "mitochondria", + "" + ] + }, + "specimenID": {}, + "tissueWeight": {}, + "nIndividuals": {} }, "required": [ "genotype" diff --git a/current-manifest-schemas/AD.BiospecimenInvitroMetadataTemplate.schema.json b/current-manifest-schemas/AD.BiospecimenInvitroMetadataTemplate.schema.json index afbd7231..7dd44ba6 100644 --- a/current-manifest-schemas/AD.BiospecimenInvitroMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.BiospecimenInvitroMetadataTemplate.schema.json @@ -4,265 +4,265 @@ "title": "BiospecimenInvitroMetadataTemplate", "type": "object", "properties": { - "Component": {}, + "modelSystemType": { + "enum": [ + "cerebral organoid", + "primary cell culture", + "animal", + "iPSC", + "organoid", + "immortalized cell line", + "" + ] + }, "individualID": { "not": { "type": "null" }, "minLength": 1 }, - "specimenIdSource": {}, - "treatmentType": { - "enum": [ - "Control", - "Abeta42 oligomer", - "Abeta42 fibril", - "levetiracetam", - "haloperidol", - "verubecestat", - "clozapine", - "placebo", - "cuprizone", - "" - ] - }, - "differentiationMethod": { - "enum": [ - "directed differentiation", - "Ngn2 induction", - "" - ] - }, - "passage": {}, "assay": { "enum": [ - "Nightingale NMR", - "exomeSeq", + "Leiden Oxylipins", + "Sanger sequencing", + "pharmacokinetics", + "long-read rnaSeq", + "scCGIseq", + "whole-cell patch clamp", + "atomicForceMicroscopy", + "sandwich ELISA", + "m6A-rnaSeq", "immunofluorescence", - "memory behavior", + "ChIPSeq", + "nextGenerationTargetedSequencing", + "proximity extension assay", "pharmacodynamics", - "westernBlot", - "Baker Lipidomics", - "brightfieldMicroscopy", - "scwholeGenomeSeq", - "snrnaSeq", - "LC-SRM", - "MIB/MS", - "Vernier Caliper", - "immunohistochemistry", - "ATACSeq", - "mirnaArray", - "Zeno Electronic Walkway", - "scCGIseq", - "LTP", - "ISOSeq", + "bisulfiteSeq", + "anxiety-related behavior", + "electrochemiluminescence", + "HiChIPseq", + "polymeraseChainReaction", + "STARRSeq", + "in vivo bioluminescence", + "cellViabilityAssay", + "UCSD Untargeted Metabolomics", + "Immunocytochemistry", + "kinesthetic behavior", "elevated T maze apparatus method", - "active avoidance learning behavior", - "Genotyping", + "questionnaire", + "Ribo-Seq", + "snrnaSeq", + "Metabolon", + "scwholeGenomeSeq", + "westernBlot", + "CITESeq", + "jumpingLibrary", + "mRNAcounts", + "microRNAcounts", + "TMT quantitation", + "UPLC-MSMS", + "ELISA", + "CUT&Tag", + "snpArray", + "novelty response behavior", + "Biocrates Q500", + "UC Davis GCTOF", + "Biocrates MxP Quant500 XL", + "exomeSeq", + "autoradiography", + "MRI", + "lncrnaSeq", + "Positron Emission Tomography", "LC-MSMS", - "methylationArray", + "rnaSeq", + "scirnaSeq", + "wheel running", + "UPLC-ESI-QTOF-MS", + "16SrRNAseq", + "ATACSeq", "locomotor activation behavior", - "SiMoA", - "Biocrates MxP Quant500 XL", - "MudPIT", - "UPLC-MSMS", - "label free mass spectrometry", + "brightfieldMicroscopy", + "active avoidance learning behavior", + "lentiMPRA", + "RPPA", "Biocrates Bile Acids", - "Positron Emission Tomography", + "mirnaSeq", + "FIA-MSMS", + "tractionForceMicroscopy", + "scrnaSeq", + "errBisulfiteSeq", + "Rader Lipidomics", + "10x multiome", + "methylationArray", "elevated plus maze test", - "photograph", - "MRI", - "high content screen", - "long-read rnaSeq", + "Blood Chemistry Measurement", "Wishart High Value Metabolites", - "Leiden Oxylipins", - "10x multiome", - "Immunocytochemistry", - "Laser Speckle Imaging", - "Metabolon", - "Sanger sequencing", - "16SrRNAseq", - "HPLC-MSMS", - "mirnaSeq", - "liquid chromatography-electrochemical detection", - "frailty assessment", - "DIA", "Real Time PCR", - "LFP", - "pharmacokinetics", - "UC Davis GCTOF", "scATACSeq", - "STARRSeq", - "sandwich ELISA", - "snpArray", - "bisulfiteSeq", - "TMT quantitation", - "microRNAcounts", - "mRNAcounts", - "lentiMPRA", - "cellViabilityAssay", - "wheel running", - "FIA-MSMS", - "electrochemiluminescence", - "m6A-rnaSeq", - "atomicForceMicroscopy", - "oxBS-Seq", - "spontaneous alternation", + "Zeno Electronic Walkway", "LC-MS", + "MDMS-SL", + "spontaneous alternation", "wholeGenomeSeq", - "UCSD Untargeted Metabolomics", - "novelty response behavior", - "RPPA", - "jumpingLibrary", - "HI-C", - "snATACSeq", - "Rader Lipidomics", - "scrnaSeq", - "Biocrates Q500", - "ChIPSeq", - "HiChIPseq", - "NOMe-Seq", "open field test", - "Biocrates p180", - "questionnaire", - "rotarod performance test", + "NOMe-Seq", + "Vernier Caliper", "Wishart Catecholamines", + "Laser Speckle Imaging", + "rnaArray", "HPLC", - "errBisulfiteSeq", - "CITESeq", - "rnaSeq", - "scirnaSeq", - "MDMS-SL", - "DNA optical mapping", - "nextGenerationTargetedSequencing", - "kinesthetic behavior", + "oxBS-Seq", "FitBark", - "whole-cell patch clamp", - "Ribo-Seq", + "Nightingale NMR", + "photograph", "contextual conditioning behavior", - "lncrnaSeq", - "ELISA", - "Blood Chemistry Measurement", - "CUT&Tag", - "UPLC-ESI-QTOF-MS", - "scale", - "rnaArray", - "in vivo bioluminescence", + "MudPIT", + "immunohistochemistry", + "HI-C", + "ISOSeq", + "Baker Lipidomics", + "HPLC-MSMS", + "rotarod performance test", + "DIA", + "frailty assessment", + "DNA optical mapping", + "LFP", + "high content screen", + "label free mass spectrometry", + "Biocrates p180", + "MIB/MS", "von Frey test", - "polymeraseChainReaction", - "tractionForceMicroscopy", - "anxiety-related behavior", - "autoradiography", - "proximity extension assay" - ] - }, - "specimenID": {}, - "terminalDifferentiationPoint": {}, - "nucleicAcidSource": { - "enum": [ - "single nucleus", - "mitochondria", - "bulk nuclei", - "sorted cells", - "bulk cell", - "single cell", - "cfDNA", - "sorted nuclei", - "not applicable", - "" + "LTP", + "memory behavior", + "scale", + "liquid chromatography-electrochemical detection", + "mirnaArray", + "snATACSeq", + "LC-SRM", + "Genotyping", + "SiMoA" ] }, - "samplingAge": {}, - "reprogrammingMethod": { + "samplingAgeUnits": { "enum": [ - "episomal vectors", - "CytoTune iPS 2.0 Sendai Reprogramming Kit", - "Sendai virus", + "PCW", + "gestational weeks", + "days", + "months", + "years", + "weeks", "" ] }, - "modelSystemType": { + "specimenIdSource": {}, + "differentiationMethod": { "enum": [ - "animal", - "organoid", - "primary cell culture", - "cerebral organoid", - "immortalized cell line", - "iPSC", + "directed differentiation", + "Ngn2 induction", "" ] }, "sourceCell": { "enum": [ + "embryonic stem cells", + "astrocytes", "cord blood stem cells", + "B-lymphocytes", + "peripheral blood mononuclear cell", "fibroblast", "lymphoblast", - "embryonic stem cells", - "peripheral blood mononuclear cell", - "astrocytes", "iPSC", - "B-lymphocytes", "" ] }, - "samplingAgeUnits": { + "reprogrammingMethod": { "enum": [ - "months", - "PCW", - "days", - "weeks", - "years", - "gestational weeks", + "CytoTune iPS 2.0 Sendai Reprogramming Kit", + "Sendai virus", + "episomal vectors", + "" + ] + }, + "samplingAge": {}, + "specimenID": {}, + "terminalDifferentiationPoint": {}, + "Component": {}, + "treatmentType": { + "enum": [ + "Abeta42 fibril", + "placebo", + "haloperidol", + "levetiracetam", + "clozapine", + "cuprizone", + "Control", + "verubecestat", + "Abeta42 oligomer", "" ] }, "cellType": { "enum": [ "dopaminergic neurons", - "lymphoblast", - "neuron", - "macrophages", - "iPSC", - "schwann", - "fibroblast", - "lymphoblastoid cell line", + "CNON", + "embryonic stem cells", + "iPSC-derived telencephalic organoids", + "B-lymphocytes", "CD8+ T-Cells", - "immune cell", - "Schwann cell precusor", + "round", "polygonal", - "SH-SY5Y", "A549", - "NCX NES", - "NeuN+", - "embryonic stem cells", - "iPSC-derived neuron", - "peripheral blood mononuclear cell", - "monocytes", + "Schwann cell precusor", + "neural progenitor cell", "schwannoma", - "epithelial-like", - "astrocytes", + "SH-SY5Y", + "monocytes", + "immune cell", + "lymphoblast", + "iPSC", + "NeuN-", + "iPSC-derived neuronal progenitor cell", + "microglia", "iPSC-derived astrocytes", - "neural progenitor cell", - "iPSC-derived glia", - "CNON", - "GLUtamatergic neurons", - "monocyte-derived microglia", + "iPSC-derived neuron", + "lymphoblastoid cell line", + "NeuN+", + "oligodendrocyte", + "epithelial-like", + "NCX NES", "GABAergic neurons", - "CD138+", "meningioma", - "iPSC-derived neuronal progenitor cell", - "round", - "arachnoid", - "iPSC-derived telencephalic organoids", - "oligodendrocyte", - "NeuN-", + "CD138+", + "fibroblast", + "neuron", "epithelial", - "microglia", - "B-lymphocytes", + "GLUtamatergic neurons", "glia", + "arachnoid", + "monocyte-derived microglia", + "macrophages", + "astrocytes", + "schwann", + "peripheral blood mononuclear cell", + "iPSC-derived glia", + "" + ] + }, + "nucleicAcidSource": { + "enum": [ + "bulk cell", + "not applicable", + "single nucleus", + "cfDNA", + "sorted nuclei", + "single cell", + "sorted cells", + "bulk nuclei", + "mitochondria", "" ] - } + }, + "passage": {} }, "required": [ "individualID", diff --git a/current-manifest-schemas/AD.BiospecimenMetadataTemplate.schema.json b/current-manifest-schemas/AD.BiospecimenMetadataTemplate.schema.json index 96c65723..9e2c4272 100644 --- a/current-manifest-schemas/AD.BiospecimenMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.BiospecimenMetadataTemplate.schema.json @@ -4,372 +4,372 @@ "title": "BiospecimenMetadataTemplate", "type": "object", "properties": { - "individualID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "organ": { - "enum": [ - "skin", - "cerebrospinal fluid", - "kidney", - "prostate", - "brain", - "pancreas", - "lymph node", - "bone marrow", - "breast", - "Bursa Of Fabricius", - "colon", - "lung", - "mammary gland", - "liver", - "large intestine", - "ovary", - "blood", - "spleen", - "nerves", - "nose" - ] - }, - "visitNumber": {}, "treatmentType": { "enum": [ - "Control", "clozapine", - "cuprizone", - "Abeta42 fibril", - "haloperidol", - "Abeta42 oligomer", - "verubecestat", "placebo", + "Abeta42 oligomer", "levetiracetam", + "verubecestat", + "cuprizone", + "Control", + "haloperidol", + "Abeta42 fibril", "" ] }, - "BrodmannArea": {}, - "fastingState": { + "isPostMortem": { "enum": [ "TRUE", "FALSE", "" ] }, - "nucleicAcidSource": { - "enum": [ - "bulk nuclei", - "single cell", - "mitochondria", - "sorted cells", - "sorted nuclei", - "single nucleus", - "cfDNA", - "not applicable", - "bulk cell", - "" - ] - }, + "visitNumber": {}, "tissue": { "enum": [ - "meninges", - "occipital visual cortex", - "amygdaloid complex", - "splenocyte", - "subgenual cingulate cortex", - "midbrain", - "bone marrow", - "temporal cortex", - "subgenual anterior cingulate cortex", - "hippocampus", - "right cerebral hemisphere", - "frontal pole", - "inferolateral temporal cortex", - "medial frontal cortex", - "posterior superior temporal cortex", - "head of caudate nucleus", - "primary somatosensory cortex", - "Not Applicable", - "mammillary body", - "medial ganglionic eminence", - "nerve tissue", + "superior parietal lobe", "frontal cortex", - "primary tumor", + "entorhinal cortex", + "lateral entorhinal cortex", + "insula", + "hippocampus", + "putamen", "temporal pole", - "primary auditory cortex", + "blood", + "anterior cingulate cortex", "caudate nucleus", - "dorsolateral prefrontal cortex", - "liver", - "Buffy Coat", - "Dorsal Root Ganglion", - "ventricular zone", - "cerebral cortex", - "cortical plate", + "primary somatosensory cortex", "middle temporal gyrus", - "medial orbital frontal cortex", - "anterior cingulate cortex", - "posterior cingulate cortex", + "midbrain", + "fusiform gyrus", + "occipital lobe", + "Not Applicable", + "primary visual cortex", + "middle frontal gyrus", "dorsal anterior cingulate cortex", - "thalamus", - "frontal lobe", - "insular cortex", - "parietal cortex", - "parietal lobe", - "insula", - "prefrontal cortex", - "temporal lobe", - "olfactory neuroepithelium", - "entorhinal cortex", - "dorsal pallium", + "VZ/SVZ", + "mammillary body", + "nerve tissue", "orbitofrontal cortex", - "Buccal Mucosa", - "cerebellar cortex", + "parahippocampal gyrus", + "unspecified", "angular gyrus", - "middle frontal gyrus", - "posterior inferior parietal cortex", - "serum", + "insular cortex", + "fecal material", + "cerebellar cortex", + "posteroinferior parietal cortex", + "primary auditory cortex", + "dorsolateral prefrontal cortex", "dorsomedial prefrontal cortex", - "lateral entorhinal cortex", - "inferior temporal gyrus", - "superior temporal gyrus", - "fusiform gyrus", - "precentral gyrus", - "nucleus accumbens", + "Buccal Mucosa", + "inferior frontal gyrus", + "dorsal pallium", + "head of caudate nucleus", "forebrain", - "occipital lobe", - "plasma", - "primary visual cortex", - "left cerebral hemisphere", + "nucleus accumbens", "amygdala", - "primary motor cortex", + "cerebral cortex", + "olfactory neuroepithelium", + "inferior temporal gyrus", "ventrolateral prefrontal cortex", - "parahippocampal gyrus", - "posteroinferior parietal cortex", - "cecum derived fecal material", - "medial entorhinal cortex", - "fecal material", - "unspecified", - "superior parietal lobe", + "meninges", "medial dorsal nucleus of thalamus", "inferior temporal cortex", + "occipital visual cortex", + "liver", + "bone marrow", + "primary motor cortex", + "posterior cingulate cortex", + "prefrontal cortex", + "frontal lobe", + "left cerebral hemisphere", + "subgenual cingulate cortex", + "subgenual anterior cingulate cortex", + "medial ganglionic eminence", + "parietal cortex", "whole brain", + "serum", + "medial orbital frontal cortex", + "precentral gyrus", + "splenocyte", + "medial entorhinal cortex", + "cecum derived fecal material", + "primary tumor", + "temporal cortex", + "parietal lobe", + "Buffy Coat", + "Dorsal Root Ganglion", + "cortical plate", + "amygdaloid complex", + "right cerebral hemisphere", + "thalamus", + "posterior superior temporal cortex", + "frontal pole", + "striatum", "cerebellum", + "ventricular zone", + "inferolateral temporal cortex", + "plasma", "embryonic tissue", - "blood", - "striatum", - "inferior frontal gyrus", - "putamen", + "medial frontal cortex", "medial prefrontal cortex", - "VZ/SVZ" + "temporal lobe", + "posterior inferior parietal cortex", + "superior temporal gyrus" ] }, - "isPostMortem": { + "specimenID": {}, + "Component": {}, + "treatmentDose": {}, + "individualID": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "cellType": { "enum": [ - "TRUE", - "FALSE", + "GABAergic neurons", + "monocytes", + "NeuN+", + "oligodendrocyte", + "meningioma", + "astrocytes", + "iPSC", + "schwann", + "lymphoblast", + "SH-SY5Y", + "CD8+ T-Cells", + "polygonal", + "monocyte-derived microglia", + "Schwann cell precusor", + "iPSC-derived neuronal progenitor cell", + "immune cell", + "iPSC-derived astrocytes", + "arachnoid", + "macrophages", + "embryonic stem cells", + "A549", + "neuron", + "round", + "CNON", + "schwannoma", + "dopaminergic neurons", + "lymphoblastoid cell line", + "glia", + "peripheral blood mononuclear cell", + "epithelial-like", + "neural progenitor cell", + "epithelial", + "microglia", + "fibroblast", + "NeuN-", + "iPSC-derived glia", + "B-lymphocytes", + "iPSC-derived telencephalic organoids", + "iPSC-derived neuron", + "GLUtamatergic neurons", + "NCX NES", + "CD138+", "" ] }, - "Component": {}, - "assay": { + "sampleStatus": { "enum": [ - "MDMS-SL", - "ChIPSeq", - "DNA optical mapping", - "oxBS-Seq", - "UC Davis GCTOF", - "scirnaSeq", - "snATACSeq", - "HPLC-MSMS", - "Wishart Catecholamines", - "anxiety-related behavior", - "mirnaSeq", - "HiChIPseq", - "UCSD Untargeted Metabolomics", - "cellViabilityAssay", - "Immunocytochemistry", - "immunofluorescence", - "immunohistochemistry", + "formalin-fixed", + "fresh", + "paxgene", + "frozen", + "" + ] + }, + "BrodmannArea": {}, + "samplingAgeUnits": { + "enum": [ + "days", + "weeks", + "gestational weeks", + "years", + "PCW", + "months", + "" + ] + }, + "nucleicAcidSource": { + "enum": [ + "single cell", + "cfDNA", + "sorted nuclei", + "sorted cells", + "single nucleus", + "mitochondria", + "not applicable", + "bulk nuclei", + "bulk cell", + "" + ] + }, + "samplingAge": {}, + "organ": { + "enum": [ + "large intestine", + "nose", + "ovary", + "Bursa Of Fabricius", + "cerebrospinal fluid", + "lung", + "blood", + "prostate", + "colon", + "skin", + "spleen", + "nerves", + "breast", + "mammary gland", + "brain", + "kidney", + "bone marrow", + "liver", + "lymph node", + "pancreas" + ] + }, + "assay": { + "enum": [ + "ATACSeq", "NOMe-Seq", - "Rader Lipidomics", - "kinesthetic behavior", - "proximity extension assay", + "Vernier Caliper", "rotarod performance test", - "DIA", - "von Frey test", - "nextGenerationTargetedSequencing", - "ISOSeq", - "Wishart High Value Metabolites", - "Baker Lipidomics", - "SiMoA", - "mirnaArray", - "HPLC", - "spontaneous alternation", + "Rader Lipidomics", + "memory behavior", + "Leiden Oxylipins", "LC-MSMS", - "Blood Chemistry Measurement", - "STARRSeq", - "Zeno Electronic Walkway", - "CITESeq", - "scale", + "16SrRNAseq", "scATACSeq", - "Biocrates Bile Acids", - "rnaSeq", + "HPLC-MSMS", + "mirnaArray", + "Positron Emission Tomography", + "UCSD Untargeted Metabolomics", + "electrochemiluminescence", + "jumpingLibrary", + "ELISA", + "LC-SRM", + "scirnaSeq", + "UPLC-ESI-QTOF-MS", + "TMT quantitation", + "HPLC", + "snpArray", + "von Frey test", + "MRI", + "pharmacokinetics", "MIB/MS", - "open field test", + "spontaneous alternation", + "LFP", + "in vivo bioluminescence", + "tractionForceMicroscopy", + "bisulfiteSeq", + "label free mass spectrometry", + "immunohistochemistry", + "nextGenerationTargetedSequencing", + "Nightingale NMR", + "mRNAcounts", + "SiMoA", + "snrnaSeq", + "HI-C", + "oxBS-Seq", + "Laser Speckle Imaging", + "HiChIPseq", "scrnaSeq", - "wholeGenomeSeq", - "MRI", - "lentiMPRA", - "liquid chromatography-electrochemical detection", "elevated T maze apparatus method", + "CITESeq", + "brightfieldMicroscopy", + "elevated plus maze test", "autoradiography", - "contextual conditioning behavior", + "FitBark", + "Biocrates MxP Quant500 XL", + "polymeraseChainReaction", + "LTP", + "whole-cell patch clamp", + "rnaArray", + "active avoidance learning behavior", + "atomicForceMicroscopy", + "scCGIseq", + "snATACSeq", + "microRNAcounts", + "ISOSeq", + "kinesthetic behavior", + "Wishart High Value Metabolites", + "Biocrates Q500", + "Blood Chemistry Measurement", + "CUT&Tag", + "LC-MS", "long-read rnaSeq", - "brightfieldMicroscopy", - "MudPIT", - "sandwich ELISA", "novelty response behavior", - "scCGIseq", - "methylationArray", - "tractionForceMicroscopy", - "UPLC-ESI-QTOF-MS", + "m6A-rnaSeq", "Metabolon", - "Biocrates Q500", - "questionnaire", - "16SrRNAseq", - "mRNAcounts", - "microRNAcounts", - "rnaArray", - "pharmacokinetics", "high content screen", - "LC-MS", - "bisulfiteSeq", - "electrochemiluminescence", - "locomotor activation behavior", - "pharmacodynamics", + "photograph", + "open field test", + "Immunocytochemistry", + "contextual conditioning behavior", + "MudPIT", + "lncrnaSeq", + "proximity extension assay", + "rnaSeq", "RPPA", + "Real Time PCR", + "Zeno Electronic Walkway", + "wholeGenomeSeq", + "DNA optical mapping", + "wheel running", + "10x multiome", + "Genotyping", + "Baker Lipidomics", + "DIA", + "liquid chromatography-electrochemical detection", "Biocrates p180", - "atomicForceMicroscopy", - "in vivo bioluminescence", - "FIA-MSMS", - "m6A-rnaSeq", - "ELISA", - "photograph", - "snpArray", - "ATACSeq", - "Laser Speckle Imaging", - "LC-SRM", - "Leiden Oxylipins", - "Nightingale NMR", - "memory behavior", - "HI-C", + "UC Davis GCTOF", + "sandwich ELISA", + "methylationArray", + "MDMS-SL", + "pharmacodynamics", "frailty assessment", + "questionnaire", + "Biocrates Bile Acids", + "locomotor activation behavior", + "lentiMPRA", "scwholeGenomeSeq", - "whole-cell patch clamp", - "Biocrates MxP Quant500 XL", - "jumpingLibrary", - "snrnaSeq", - "lncrnaSeq", - "Positron Emission Tomography", - "wheel running", - "elevated plus maze test", - "Sanger sequencing", - "Vernier Caliper", - "CUT&Tag", + "scale", + "ChIPSeq", + "FIA-MSMS", + "mirnaSeq", + "UPLC-MSMS", + "STARRSeq", "exomeSeq", - "Real Time PCR", - "LTP", - "active avoidance learning behavior", - "polymeraseChainReaction", - "Ribo-Seq", - "LFP", - "10x multiome", - "FitBark", - "TMT quantitation", - "label free mass spectrometry", "errBisulfiteSeq", - "UPLC-MSMS", + "immunofluorescence", + "cellViabilityAssay", + "Sanger sequencing", + "Wishart Catecholamines", + "anxiety-related behavior", "westernBlot", - "Genotyping" - ] - }, - "treatmentDose": {}, - "specimenID": {}, - "samplingAge": {}, - "samplingAgeUnits": { - "enum": [ - "weeks", - "years", - "PCW", - "months", - "gestational weeks", - "days", - "" + "Ribo-Seq" ] }, - "specimenIdSource": {}, - "sampleStatus": { + "fastingState": { "enum": [ - "paxgene", - "fresh", - "frozen", - "formalin-fixed", + "TRUE", + "FALSE", "" ] }, - "cellType": { - "enum": [ - "monocytes", - "peripheral blood mononuclear cell", - "CD8+ T-Cells", - "microglia", - "arachnoid", - "GLUtamatergic neurons", - "iPSC-derived glia", - "monocyte-derived microglia", - "iPSC-derived telencephalic organoids", - "immune cell", - "NeuN+", - "lymphoblastoid cell line", - "oligodendrocyte", - "glia", - "NCX NES", - "iPSC-derived neuron", - "astrocytes", - "CD138+", - "epithelial-like", - "lymphoblast", - "polygonal", - "macrophages", - "schwann", - "Schwann cell precusor", - "iPSC-derived astrocytes", - "epithelial", - "A549", - "schwannoma", - "NeuN-", - "meningioma", - "dopaminergic neurons", - "round", - 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"minLength": 1 + }, + "assay": { + "enum": [ + "scATACSeq", + "Metabolon", + "scale", + "MIB/MS", + "immunohistochemistry", + "snATACSeq", + "Zeno Electronic Walkway", + "HPLC", + "Baker Lipidomics", + "questionnaire", + "snpArray", + "Wishart Catecholamines", + "mirnaArray", + "von Frey test", + "CITESeq", + "methylationArray", + "MudPIT", + "ELISA", + "westernBlot", + "cellViabilityAssay", + "DIA", + "MRI", + "Biocrates p180", + "tractionForceMicroscopy", + "Real Time PCR", + "ISOSeq", + "pharmacokinetics", + "MDMS-SL", + "CUT&Tag", + "FIA-MSMS", + "spontaneous alternation", + "mRNAcounts", + "active avoidance learning behavior", + "LFP", + "Genotyping", + "Rader Lipidomics", + "wheel running", + "liquid chromatography-electrochemical detection", + "Biocrates MxP Quant500 XL", + "scrnaSeq", + "snrnaSeq", + "Leiden Oxylipins", + "wholeGenomeSeq", + "whole-cell patch clamp", + "label free mass spectrometry", + "Wishart High Value Metabolites", + "m6A-rnaSeq", + "Vernier Caliper", + "lncrnaSeq", + "16SrRNAseq", + "TMT quantitation", + "photograph", + "frailty assessment", + "STARRSeq", + "Positron Emission Tomography", + "Biocrates Q500", + "Ribo-Seq", + "autoradiography", + "microRNAcounts", + "scwholeGenomeSeq", + "polymeraseChainReaction", + "Sanger sequencing", + "bisulfiteSeq", + "oxBS-Seq", + "immunofluorescence", + "pharmacodynamics", + "UCSD Untargeted Metabolomics", + "Blood Chemistry Measurement", + "proximity extension assay", + "Immunocytochemistry", + "long-read rnaSeq", + "HI-C", + "UPLC-MSMS", + "errBisulfiteSeq", + "elevated T maze apparatus method", + "RPPA", + "UPLC-ESI-QTOF-MS", + "novelty response behavior", + "locomotor activation behavior", + "ATACSeq", + "rnaArray", + "SiMoA", + "high content screen", + "LC-MSMS", + "scCGIseq", + "scirnaSeq", + "Laser Speckle Imaging", + "UC Davis GCTOF", + "in vivo bioluminescence", + "atomicForceMicroscopy", + "nextGenerationTargetedSequencing", + "electrochemiluminescence", + "sandwich ELISA", + "FitBark", + "mirnaSeq", + "rotarod performance test", + "Biocrates Bile Acids", + "jumpingLibrary", + "HiChIPseq", + "LC-MS", + "LC-SRM", + "brightfieldMicroscopy", + "open field test", + "contextual conditioning behavior", + "kinesthetic behavior", + "lentiMPRA", + "Nightingale NMR", + "elevated plus maze test", + "DNA optical mapping", + "LTP", + "HPLC-MSMS", + "rnaSeq", + "memory behavior", + "NOMe-Seq", + "exomeSeq", + "ChIPSeq", + "anxiety-related behavior", + "10x multiome" ] }, + "Component": {}, "dataSubtype": { "enum": [ - "normalized", - "processed", - "raw", - "metadata", "dataMatrix", + "raw", + "processed", "residualized", + "normalized", + "metadata", "" ] }, "specimenID": {}, "species": { "enum": [ - "Drosophila melanogaster", - "Rhesus macaque", + "Rat", "Sus scrofa", - "Pan troglodytes", + "Drosophila melanogaster", + "Human", "Mouse", + "Pan troglodytes", "Gallus gallus", - "Rat", - "Human", + "Rhesus macaque", "" ] } }, "required": [ - "resourceType", - "fileFormat", - "assay", - "isMultiSpecimen", + "grant", "consortium", "isModelSystem", + "fileFormat", + "resourceType", + "isMultiSpecimen", + "study", "Filename", - "grant", - "study" + "assay" ], "allOf": [ { @@ -638,14 +639,14 @@ "properties": { "species": { "enum": [ - "Drosophila melanogaster", - "Rhesus macaque", + "Rat", "Sus scrofa", - "Pan troglodytes", + "Drosophila melanogaster", + "Human", "Mouse", + "Pan troglodytes", "Gallus gallus", - "Rat", - "Human" + "Rhesus macaque" ] } }, diff --git a/current-manifest-schemas/AD.IndividualAnimalMODEL-ADMetadataTemplate.schema.json b/current-manifest-schemas/AD.IndividualAnimalMODEL-ADMetadataTemplate.schema.json index 8f07bd85..a17b1fbf 100644 --- a/current-manifest-schemas/AD.IndividualAnimalMODEL-ADMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.IndividualAnimalMODEL-ADMetadataTemplate.schema.json @@ -4,127 +4,60 @@ "title": "IndividualAnimalMODEL-ADMetadataTemplate", "type": "object", "properties": { - "materialOrigin": { - "enum": [ - "UCI_TMF", - "IU", - "JAX", - "Pitt" - ] - }, - "modelSystemName": { + "bedding": { "enum": [ - "Bin1.B6", - "3xTg-AD", - "APPKM670", - "Trem2R47H", - "Abca7KO", - "Trem2R47H_NSS", - "Trem2flox", - "Snx1D465NSNP", - "APOE4KI", - "hTauTrem2", - "BRI2-AB42", - "CRND8", - "PicalmH458R", - "Cd2ap.B6", - "AB42", - "APOE2KI", - "Plexin-B1-KO", - "TYROBP_KO.KO", - "MAPT-P301K", - "TYROBP_WT.KO", - "Abca7V1599M_rs117187003", - "Ceacam1KO", - "APOE4Trem2R47H", - "Plcg2KO", - "TYROBP_WT", - "Abca7A1527GAPOE4Trem2R47H", - "C57BL6J", - "5XFAD", - "Abi3S209F_Aduci", - "MthfrC677TSNP", - "Sorl1A528TSNP", - "APPPS1", - "hCR1KIAPOE4Trem2", - "APPKM670-671NL-PSEN1deltaexon9", - "Kif21bT82TSNP", - "Mtmr4V297GSNP", - "ApoEKO", - "Trem2KO", - "APOE3KI", - "AppKOAPOE4Trem2R47H", - "TYROBP", - "Clasp2L163PSNP", - "Trem2Y38C", - "Il1rapKO", - "rTg4510", - "hTau", - "APPS1_Plexin-B1-KO", - "B6.Gfap-APOE4", - "Meox2KOHET", - "Spi1rs1377416", - "TAUPS19_Plexin-B1-KO", - "TREM2", - "hAbetaKI", - "B6.Clu", - "TAUPS19", - "APPKM650", - "hAPPAPOE4Trem2R47H", - "APPE693Q", - "Bin1K358R_Aduci", - "Plcg2M28LSNP" + "aspen", + "pine", + "aspen sanichip", + "sanichip", + "Alpha-dri", + "corn cob" ] }, "species": { "enum": [ - "Human", + "Pan troglodytes", + "Rhesus macaque", "Rat", "Sus scrofa", - "Pan troglodytes", - "Mouse", + "Drosophila melanogaster", "Gallus gallus", - "Rhesus macaque", - "Drosophila melanogaster" + "Mouse", + "Human" ] }, + "ageDeath": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "waterpH": {}, - "dateBirth": { + "genotypeBackground": { "not": { "type": "null" }, "minLength": 1 }, - "brainWeight": {}, - "rodentWeight": {}, - "matingID": {}, - "generation": {}, - "stockNumber": {}, - "Component": {}, + "treatmentDose": {}, "ageDeathUnits": { "enum": [ - "weeks", - "days", "PCW", - "months", + "days", + "gestational weeks", + "weeks", "years", - "gestational weeks" + "months" ] }, - "strainOfficialName": {}, - "climbID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, "genotype": { "not": { "type": "null" }, "minLength": 1 }, - "ageDeath": { + "strainOfficialName": {}, + "individualID": { "not": { "type": "null" }, @@ -132,122 +65,190 @@ }, "individualIdSource": { "enum": [ - "Clotomics_PAIKEA_MSSM", - "Rush", - "UW-CDL", - "NIMH-HBCC", + "MayoBrainBank", + "Penn", "DongLab", + "PGP", + "MSSM", + "Novogenix", + "XCell Science", "Mayo Clinic", + "UCI_TMF", + "Clotomics_PAIKEA_MSSM", + "Oxford", "ABR", - "Pritzker", + "NICHD", + "BEB_Miller", + "Geschwind", + "IU", + "JAX", + "ABN", "Einstein", - "MayoBrainBank", - "Newcastle", - "HBSFRC", - "TAA", + "UCSF", + "Rush", + "UW-CDL", + "UM-BTB", "NYBB", - "UCI_TMF", - "JAX", - "NDRI", - "XCell Science", - "Oxford", + "LIBD", + "Caltech", "Vaccarino", + "TAA", + "Newcastle", "BannerSun", - "ABN", + "Pitt", + "SMRI", + "ADNI", "AIBS", + "Pritzker", "Sestan", - "BEB_Miller", - "Yale", - "NICHD", - "Geschwind", - "UM-BTB", - "Pitt", - "MSSM", - "LIBD", - "LivingBrainProject_MSSM", "StemExpress", - "Novogenix", - "IU", - "PGP", - "Penn", + "HBSFRC", + "NIMH-HBCC", + "LivingBrainProject_MSSM", + "Yale", + "NDRI", "HBTRC", - "Emory", - "ADNI", - "SMRI", - "UCSF" + "Emory" ] }, - "bedding": { + "climbID": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "dateBirth": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "room": {}, + "materialOrigin": { "enum": [ - "corn cob", - "pine", - "aspen", - "aspen sanichip", - "sanichip", - "Alpha-dri" + "UCI_TMF", + "Pitt", + "JAX", + "IU" + ] + }, + "rodentWeight": {}, + "brainWeight": {}, + "generation": {}, + "microchipID": {}, + "rodentDiet": { + "enum": [ + "4% standard", + "7% standard", + "5W80 western diet", + "45% high-fat diet", + "6% standard" ] }, "treatmentType": { "enum": [ - "clozapine", - "cuprizone", - "verubecestat", - "levetiracetam", - "Abeta42 fibril", "haloperidol", - "Abeta42 oligomer", "Control", + "levetiracetam", + "Abeta42 fibril", + "verubecestat", "placebo", + "clozapine", + "cuprizone", + "Abeta42 oligomer", "" ] }, - "microchipID": {}, - "treatmentDose": {}, "birthID": {}, - "room": {}, - "sex": { + "matingID": {}, + "Component": {}, + "modelSystemName": { "enum": [ - "missing or unknown", - "male", - "female" + "AB42", + "APOE4Trem2R47H", + "Bin1K358R_Aduci", + "Plcg2KO", + "TAUPS19_Plexin-B1-KO", + "MAPT-P301K", + "3xTg-AD", + "Trem2flox", + "Plexin-B1-KO", + "rTg4510", + "CRND8", + "C57BL6J", + "hTau", + "PicalmH458R", + "hCR1KIAPOE4Trem2", + "Trem2R47H_NSS", + "APPKM670-671NL-PSEN1deltaexon9", + "Cd2ap.B6", + "ApoEKO", + "Trem2Y38C", + "APPKM650", + "Snx1D465NSNP", + "Trem2R47H", + "Sorl1A528TSNP", + "TYROBP_WT.KO", + "Clasp2L163PSNP", + "Mtmr4V297GSNP", + "Bin1.B6", + "Abca7KO", + "Spi1rs1377416", + "MthfrC677TSNP", + "APOE3KI", + "hAPPAPOE4Trem2R47H", + "Ceacam1KO", + "Plcg2M28LSNP", + "5XFAD", + "TYROBP", + "TYROBP_WT", + "Abca7A1527GAPOE4Trem2R47H", + "hTauTrem2", + "TAUPS19", + "APPS1_Plexin-B1-KO", + "hAbetaKI", + "TREM2", + "Abi3S209F_Aduci", + "Il1rapKO", + "APOE2KI", + "APPKM670", + "APPE693Q", + "Abca7V1599M_rs117187003", + "B6.Clu", + "Meox2KOHET", + "AppKOAPOE4Trem2R47H", + "B6.Gfap-APOE4", + "Trem2KO", + "APOE4KI", + "APPPS1", + "TYROBP_KO.KO", + "BRI2-AB42", + "Kif21bT82TSNP" ] }, - "rodentDiet": { + "stockNumber": {}, + "sex": { "enum": [ - "4% standard", - "45% high-fat diet", - "6% standard", - "5W80 western diet", - "7% standard" + "female", + "male", + "missing or unknown" ] - }, - "individualID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "genotypeBackground": { - "not": { - "type": "null" - }, - "minLength": 1 } }, "required": [ - "materialOrigin", - "modelSystemName", + "bedding", "species", - "dateBirth", + "ageDeath", + "genotypeBackground", "ageDeathUnits", - "climbID", "genotype", - "ageDeath", + "individualID", "individualIdSource", - "bedding", - "sex", + "climbID", + "dateBirth", + "materialOrigin", "rodentDiet", - "individualID", - "genotypeBackground" + "modelSystemName", + "sex" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.IndividualAnimalMetadataTemplate.schema.json b/current-manifest-schemas/AD.IndividualAnimalMetadataTemplate.schema.json index a7520ff1..cef1d673 100644 --- a/current-manifest-schemas/AD.IndividualAnimalMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.IndividualAnimalMetadataTemplate.schema.json @@ -4,30 +4,88 @@ "title": "IndividualAnimalMetadataTemplate", "type": "object", "properties": { - "dateDeath": {}, - "genotype": { - "not": { - "type": "null" - }, - "minLength": 1 - }, "matingID": {}, - "genotypeBackground": { + "dateDeath": {}, + "litter": {}, + "dateBirth": { "not": { "type": "null" }, "minLength": 1 }, - "individualID": { + "genotype": { "not": { "type": "null" }, "minLength": 1 }, - "sexChromosome": {}, "treatmentDose": {}, - "Component": {}, - "dateBirth": { + "room": {}, + "modelSystemName": { + "enum": [ + "TAUPS19_Plexin-B1-KO", + "Trem2R47H", + "AB42", + "Mtmr4V297GSNP", + "APOE2KI", + "Clasp2L163PSNP", + "APOE4Trem2R47H", + "B6.Gfap-APOE4", + "APPKM650", + "C57BL6J", + "Abi3S209F_Aduci", + "APOE3KI", + "Bin1.B6", + "hAPPAPOE4Trem2R47H", + "Plcg2KO", + "rTg4510", + "Bin1K358R_Aduci", + "Abca7A1527GAPOE4Trem2R47H", + "TYROBP_KO.KO", + "AppKOAPOE4Trem2R47H", + "PicalmH458R", + "BRI2-AB42", + "hAbetaKI", + "Snx1D465NSNP", + "hTau", + "TYROBP_WT.KO", + "Spi1rs1377416", + "TYROBP", + "CRND8", + "APPS1_Plexin-B1-KO", + "Il1rapKO", + "APPKM670", + "hTauTrem2", + "3xTg-AD", + "MAPT-P301K", + "APOE4KI", + "Plcg2M28LSNP", + "TYROBP_WT", + "Ceacam1KO", + "TREM2", + "Cd2ap.B6", + "Abca7V1599M_rs117187003", + "APPKM670-671NL-PSEN1deltaexon9", + "Kif21bT82TSNP", + "APPPS1", + "APPE693Q", + "MthfrC677TSNP", + "Meox2KOHET", + "5XFAD", + "Abca7KO", + "B6.Clu", + "Trem2Y38C", + "Trem2R47H_NSS", + "Trem2flox", + "hCR1KIAPOE4Trem2", + "Plexin-B1-KO", + "Sorl1A528TSNP", + "TAUPS19", + "ApoEKO", + "Trem2KO" + ] + }, + "genotypeBackground": { "not": { "type": "null" }, @@ -35,145 +93,88 @@ }, "sex": { "enum": [ - "missing or unknown", + "female", "male", - "female" + "missing or unknown" ] }, "species": { "enum": [ - "Pan troglodytes", - "Drosophila melanogaster", - "Sus scrofa", "Rhesus macaque", - "Rat", - "Gallus gallus", + "Sus scrofa", "Human", - "Mouse" + "Mouse", + "Drosophila melanogaster", + "Rat", + "Pan troglodytes", + "Gallus gallus" ] }, + "Component": {}, + "individualID": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "individualIdSource": { "enum": [ - "ABN", - "LIBD", - "XCell Science", - "AIBS", - "Oxford", - "NYBB", - "NICHD", - "NIMH-HBCC", - "Mayo Clinic", + "PGP", + "ABR", "Yale", - "UM-BTB", - "DongLab", - "TAA", - "SMRI", - "BEB_Miller", - "Sestan", - "StemExpress", - "LivingBrainProject_MSSM", - "MSSM", - "JAX", + "LIBD", "Geschwind", + "UW-CDL", + "BEB_Miller", + "NICHD", "BannerSun", - "PGP", "MayoBrainBank", - "NDRI", + "TAA", + "UCSF", + "UM-BTB", + "ABN", + "AIBS", + "HBSFRC", + "Pritzker", "Penn", - "Emory", - "ABR", - "Clotomics_PAIKEA_MSSM", - "HBTRC", + "Mayo Clinic", + "Caltech", + "IU", "Novogenix", + "UCI_TMF", + "LivingBrainProject_MSSM", + "Oxford", + "Sestan", + "Clotomics_PAIKEA_MSSM", + "ADNI", + "Einstein", + "XCell Science", + "JAX", + "MSSM", "Rush", - "UCSF", - "HBSFRC", - "UW-CDL", + "NDRI", + "DongLab", + "StemExpress", + "Emory", "Pitt", + "NIMH-HBCC", + "HBTRC", "Vaccarino", - "Einstein", + "NYBB", "Newcastle", - "IU", - "UCI_TMF", - "Pritzker", - "ADNI" + "SMRI" ] }, - "room": {}, - "litter": {}, - "modelSystemName": { - "enum": [ - "TAUPS19_Plexin-B1-KO", - "APPPS1", - "AB42", - "Abca7KO", - "APPKM650", - "APPKM670-671NL-PSEN1deltaexon9", - "B6.Gfap-APOE4", - "hAPPAPOE4Trem2R47H", - "MAPT-P301K", - "ApoEKO", - "Plcg2KO", - "Snx1D465NSNP", - "Spi1rs1377416", - "Trem2flox", - "TYROBP_WT.KO", - "Trem2Y38C", - "Plexin-B1-KO", - "rTg4510", - "Trem2KO", - "Cd2ap.B6", - "3xTg-AD", - "MthfrC677TSNP", - "APPS1_Plexin-B1-KO", - "hCR1KIAPOE4Trem2", - "AppKOAPOE4Trem2R47H", - "TYROBP_KO.KO", - "C57BL6J", - "PicalmH458R", - "hAbetaKI", - "hTauTrem2", - "Meox2KOHET", - "Trem2R47H", - "APOE4KI", - "TYROBP", - "APOE3KI", - "Plcg2M28LSNP", - "APPE693Q", - "hTau", - "Bin1K358R_Aduci", - "Kif21bT82TSNP", - "Abi3S209F_Aduci", - "Clasp2L163PSNP", - "Sorl1A528TSNP", - "5XFAD", - "Bin1.B6", - "Abca7V1599M_rs117187003", - "Trem2R47H_NSS", - "APOE2KI", - "Ceacam1KO", - "TYROBP_WT", - "Il1rapKO", - "APOE4Trem2R47H", - "TAUPS19", - "B6.Clu", - "BRI2-AB42", - "APPKM670", - "TREM2", - "CRND8", - "Abca7A1527GAPOE4Trem2R47H", - "Mtmr4V297GSNP" - ] - } + "sexChromosome": {} }, "required": [ + "dateBirth", "genotype", + "modelSystemName", "genotypeBackground", - "individualID", - "dateBirth", "sex", "species", - "individualIdSource", - "modelSystemName" + "individualID", + "individualIdSource" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.IndividualHumanMetadataTemplate.schema.json b/current-manifest-schemas/AD.IndividualHumanMetadataTemplate.schema.json index ad59a5ce..a3f83d26 100644 --- a/current-manifest-schemas/AD.IndividualHumanMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.IndividualHumanMetadataTemplate.schema.json @@ -4,229 +4,229 @@ "title": "IndividualHumanMetadataTemplate", "type": "object", "properties": { - "race": { + "causeDeath": {}, + "mannerDeath": { "enum": [ - "American Indian or Alaska Native", - "Native Hawaiian or Other Pacific Islander", - "White", - "Black or African American", - "Asian", + "homicide", + "natural causes", + "suicide", + "accident", + "undetermined", "" ] }, - "Component": {}, - "pmiUnits": { + "sex": { "enum": [ - "minutes", - "hours", + "male", + "missing or unknown", + "female" + ] + }, + "Braak": { + "enum": [ + "BRAAK Stage 2", + "BRAAK Stage 6", + "BRAAK Stage 3", + "No BRAAK stage", + "BRAAK Stage 4", + "BRAAK Stage 1", + "missing or unknown", + "BRAAK Stage 5", "" ] }, - "species": { + "ethnicity": {}, + "apoeGenotype": { "enum": [ - "Sus scrofa", - "Pan troglodytes", - "Gallus gallus", - "Rat", - "Mouse", - "Rhesus macaque", - "Human", - "Drosophila melanogaster" + "23", + "24", + "22", + "44", + "33", + "34", + "" ] }, - "diagnosisCriteria": {}, - "CERAD": { + "ageDeathUnits": { "enum": [ - "Frequent Definite C3", - "Sparse Possible C1", - "Moderate Probable C2", - "missing or unknown", - "No AD C0", + "weeks", + "PCW", + "gestational weeks", + "months", + "years", + "days", "" ] }, - "mannerDeath": { + "PMI": {}, + "cohort": { "enum": [ - "natural causes", - "accident", - "suicide", - "homicide", - "undetermined", + "MC", + "MCJ", + "FBS", + "HBTRC", + "ROSMAP", + "EFIGA", + "Pitt ADRC", + "MARS-WI", + "POINTER", + "Columbia ADRC", + "MIND", + "HUP", + "HPGP", + "UW ADRC", + "Banner", + "MSBB", + "CLINCOR", + "MARS", + "BEB-Miller", + "Tulsa LIBR-1000", + "BLSA", + "NYBB", + "UFL", + "MCR", + "DiCAD", + "LBP", + "ADRC", + "UPBB", + "ABC-DS", + "RADC", + "Biggs Institute Brain Bank", + "HBCC", + "ACT", + "CHDWB", + "Framingham", + "EHBS", + "ADNI", + "Mayo Clinic", + "UPenn", + "BEAM", + "SMRI", + "WHICAP", + "Emory_ADRC", + "UK Biobank", "" ] }, + "ageDeath": {}, "diagnosis": { "enum": [ - "Breast Cancer", - "Fibrocystic Breast Disease", - "multiple system atrophy", - "Substance Related Disorder", - "Skin Cancer", - "traumatic brain injury", - "Alzheimer disease with psychosis", - "vascular dementia", - "hypoxia", + "Lung Cancer", "CS-DS", - "anxiety", - "Lewy body disease", - "AD-DS", - "pathological aging", - "Not Applicable", - "Brain Cancer", - "Colon Cancer", - "dystonia", - "Juvenile Myelomonocytic Leukemia", + "Ovary Cancer", "Prostate Cancer", - "Neurofibromatosis 2", - "MCI-DS", + "Control", + "Not Applicable", + "Major Depressive Disorder", "no cognitive impairment", - "Pancreatic Cancer", "progressive supranuclear palsy", - "Cervical Cancer", "Williams Syndrome", - "frontotemporal dementia", - "Major Depressive Disorder", - "essential tremor", + "anxiety", + "Lewy body disease", + "type 2 diabetes mellitus", + "dementia", "Bladder Cancer", - "Ovary Cancer", + "Juvenile Myelomonocytic Leukemia", + "multiple system atrophy", + "Skin Cancer", + "Substance Related Disorder", + "Schizophrenia", + "Neurofibromatosis 1", + "mild cognitive impairment", + "Parkinson's disease", + "Breast Cancer", + "Alzheimer disease with psychosis", + "Cervical Cancer", + "Pancreatic Cancer", + "Neurofibromatosis 2", + "Brain Cancer", "Affective Disorder", - "Bipolar Disorder", + "amyotrophic lateral sclerosis", + "Colon Cancer", + "dystonia", + "frontotemporal dementia", + "hypoxia", + "Tourette Syndrome", "corticobasal degeneration disorder", - "gliosis", + "essential tremor", "Leukemia", - "mild cognitive impairment", - "obesity", - "Parkinson's disease", "Alzheimer Disease", + "pathological aging", + "Bipolar Disorder", + "MCI-DS", + "obesity", + "traumatic brain injury", + "Fibrocystic Breast Disease", "Autism Spectrum Disorder", - "type 2 diabetes mellitus", - "Control", - "Lung Cancer", - "Tourette Syndrome", - "amyotrophic lateral sclerosis", - "Schizophrenia", - "dementia", + "AD-DS", + "vascular dementia", + "gliosis", "obsessive compulsive disorder", - "Neurofibromatosis 1", "" ] }, - "causeDeath": {}, - "PMI": {}, "apoe4Status": { "enum": [ - "missing or unknown", - "one or two E4", "no E4", - "" - ] - }, - "ageDeathUnits": { - "enum": [ - "PCW", - "days", - "months", - "weeks", - "gestational weeks", - "years", - "" - ] - }, - "ethnicity": {}, - "brainWeight": {}, - "sex": { - "enum": [ - "male", + "one or two E4", "missing or unknown", - "female" + "" ] }, - "cohort": { + "pH": {}, + "yearsEducation": {}, + "race": { "enum": [ - "HUP", - "CHDWB", - "ACT", - "MCR", - "UPBB", - "NYBB", - "UK Biobank", - "HBTRC", - "WHICAP", - "Emory_ADRC", - "EFIGA", - "LBP", - "Framingham", - "BLSA", - "Tulsa LIBR-1000", - "ADRC", - "SMRI", - "MSBB", - "MARS-WI", - "MCJ", - "Pitt ADRC", - "HBCC", - "EHBS", - "CLINCOR", - "UW ADRC", - "BEB-Miller", - "MIND", - "FBS", - "Mayo Clinic", - "Banner", - "MARS", - "ADNI", - "ABC-DS", - "Biggs Institute Brain Bank", - "UPenn", - "HPGP", - "UFL", - "RADC", - "MC", - "ROSMAP", - "BEAM", - "POINTER", - "DiCAD", - "Columbia ADRC", + "White", + "American Indian or Alaska Native", + "Native Hawaiian or Other Pacific Islander", + "Asian", + "Black or African American", "" ] }, - "pH": {}, + "diagnosisCriteria": {}, "individualID": { "not": { "type": "null" }, "minLength": 1 }, - "Braak": { + "Component": {}, + "CERAD": { "enum": [ - "BRAAK Stage 3", - "BRAAK Stage 2", - "BRAAK Stage 5", - "BRAAK Stage 4", - "BRAAK Stage 6", + "Sparse Possible C1", + "No AD C0", + "Frequent Definite C3", + "Moderate Probable C2", "missing or unknown", - "BRAAK Stage 1", - "No BRAAK stage", "" ] }, - "apoeGenotype": { + "species": { "enum": [ - "22", - "44", - "33", - "24", - "23", - "34", - "" + "Gallus gallus", + "Human", + "Pan troglodytes", + "Rat", + "Rhesus macaque", + "Mouse", + "Sus scrofa", + "Drosophila melanogaster" ] }, - "ageDeath": {}, - "yearsEducation": {} + "brainWeight": {}, + "pmiUnits": { + "enum": [ + "hours", + "minutes", + "" + ] + } }, "required": [ - "species", "sex", - "individualID" + "individualID", + "species" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.ModeladStrainAnimalMetadataTemplate.schema.json b/current-manifest-schemas/AD.ModeladStrainAnimalMetadataTemplate.schema.json index 091fbe04..92393a11 100644 --- a/current-manifest-schemas/AD.ModeladStrainAnimalMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.ModeladStrainAnimalMetadataTemplate.schema.json @@ -5,17 +5,11 @@ "type": "object", "properties": { "strainOfficialName": {}, - "Component": {}, + "geneticMutations": {}, + "geneticBackground": {}, "registryAbbreviation": {}, "stockNumber": {}, - "geneticBackground": {}, - "strainCommonName": {}, - "individualID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, + "Component": {}, "modelType": { "enum": [ "Early-onset AD (EOAD)", @@ -25,8 +19,14 @@ "" ] }, - "geneticMutations": {}, - "specimenID": {} + "specimenID": {}, + "strainCommonName": {}, + "individualID": { + "not": { + "type": "null" + }, + "minLength": 1 + } }, "required": [ "individualID" diff --git a/current-manifest-schemas/AD.NeuropathMetadataTemplate.schema.json b/current-manifest-schemas/AD.NeuropathMetadataTemplate.schema.json index 68e65248..a9ac73bf 100644 --- a/current-manifest-schemas/AD.NeuropathMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.NeuropathMetadataTemplate.schema.json @@ -4,358 +4,358 @@ "title": "NeuropathMetadataTemplate", "type": "object", "properties": { - "Braak": { + "CERAD": { "enum": [ - "BRAAK Stage 2", "missing or unknown", - "BRAAK Stage 4", - "BRAAK Stage 3", - "BRAAK Stage 6", - "No BRAAK stage", - "BRAAK Stage 5", - "BRAAK Stage 1" + "Moderate Probable C2", + "Frequent Definite C3", + "No AD C0", + "Sparse Possible C1" ] }, - "AMY_THAL": { + "CVD_S": { "enum": [ - "Phase 2", - "Phase 3", - "Phase 1", - "Phase 5", + "No CVD_S", + "Presence", "missing or unknown", - "No Thal Phase", - "Phase 4" + "" ] }, - "CVD_CAA": { + "MICR": { "enum": [ - "No CVD_CAA", + "Yes", + "No", "missing or unknown", - "Severe", - "Moderate", - "Mild", "" ] }, - "Component": {}, - "AMY_A": { + "TDP_5": { "enum": [ - "Thal Phase 4 or 5", "missing or unknown", - "Thal Phase 3", - "Thal Phase 1 or 2", - "No A Score" + "No TDP_5", + "hippocampus", + "Neocortex", + "Entorhinal", + "Brainstem/Spinal Cord", + "amygdala", + "" ] }, - "alt_LEWY_full": { + "WMRCAL": { "enum": [ - "Brainstem predominant", + "Yes", + "No", "missing or unknown", - "No alt_LEWY_full", - "Olfactory bulb only", - "Neocortical diffuse", - "Amygdala only", - "Limbic transitional", "" ] }, - "INT": { + "PMI": { "not": { "type": "null" }, "minLength": 1 }, - "CVD_ATH": { + "WBVD": { "enum": [ + "Yes", + "No", "missing or unknown", - "Severe", - "No CVD_ATH", - "Moderate", - "Mild", "" ] }, - "B_SCORE": { - "enum": [ - "BRAAK Stage 1-2", - "missing or unknown", - "BRAAK Stage 3-4", - "No B score", - "BRAAK Stage 5-6" - ] - }, - "INFA": { + "CVD_ART": { "enum": [ - "No", + "Moderate", "missing or unknown", - "Yes", + "No CVD_ART", + "Mild", + "Severe", "" ] }, - "WBVD": { + "CVD_ART_ANY": { "enum": [ - "No", + "No CVD_ART_ANY", + "Mild or Moderate or Severe", "missing or unknown", - "Yes", "" ] }, - "LEWY_ANY": { + "REAG": { "enum": [ - "Brainstem or transitional or diffuse or region unspecified group", + "High Likelihood", "missing or unknown", - "No LEWY_ANY or olfactory bulb or amygdala predominant group", - "" + "Low likelihood", + "No AD", + "Intermediate Likelihood", + "Other or Does not fulfill NIA-REAGEN criteria" ] }, - "WMRCAL": { + "INFA": { "enum": [ + "Yes", "No", "missing or unknown", - "Yes", "" ] }, - "TDP_3": { + "conservationMethod": { "enum": [ - "Hippocampus or Etorhinal", - "amygdala", - "No TDP_3", + "noConservation", + "frozen tissue only", + "fixed tissues only", "missing or unknown", - "Neocortex", - "" + "both fixed and frozen tissue" ] }, - "HEMOR": { + "HS_L": { "enum": [ - "No", + "Present Location UK", "missing or unknown", - "Yes", + "Unilateral", + "No HS_L", + "Bilateral", "" ] }, + "INT": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "brainWeight": {}, - "CVD_ATH_ANY": { + "CVD_ATH": { "enum": [ - "Mild or Moderate or Severe", + "Moderate", "missing or unknown", - "No CVD_ATH_ANY", + "No CVD_ATH", + "Mild", + "Severe", "" ] }, - "TDP_5": { + "B_SCORE": { "enum": [ - "hippocampus", - "amygdala", - "No TDP_5", + "BRAAK Stage 3-4", "missing or unknown", - "Entorhinal", - "Brainstem/Spinal Cord", - "Neocortex", - "" + "No B score", + "BRAAK Stage 5-6", + "BRAAK Stage 1-2" ] }, - "conservationMethod": { + "CVD_CAA_ANY": { "enum": [ - "frozen tissue only", - "both fixed and frozen tissue", - "fixed tissues only", + "No CVD_CAA_ANY", + "Mild or Moderate or Severe", "missing or unknown", - "noConservation" + "" ] }, "ADNC": { "enum": [ - "Intermediate", - "Low", "missing or unknown", + "Intermediate", "High", + "Low", "Not AD" ] }, - "individualID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "CERAD": { + "TDP_3": { "enum": [ - "No AD C0", - "Frequent Definite C3", + "Hippocampus or Etorhinal", "missing or unknown", - "Moderate Probable C2", - "Sparse Possible C1" + "Neocortex", + "amygdala", + "No TDP_3", + "" ] }, - "CVD_CAA_ANY": { + "alt_LEWY_full": { "enum": [ - "Mild or Moderate or Severe", "missing or unknown", - "No CVD_CAA_ANY", + "Neocortical diffuse", + "No alt_LEWY_full", + "Olfactory bulb only", + "Limbic transitional", + "Brainstem predominant", + "Amygdala only", "" ] }, - "mayoDx": { + "TDP43": { "enum": [ - "Other", - "Control", + "Yes", + "No", "missing or unknown", - "AD", "" ] }, - "REAG": { + "AMY_THAL": { "enum": [ - "Other or Does not fulfill NIA-REAGEN criteria", - "No AD", + "Phase 2", "missing or unknown", - "Low likelihood", - "High Likelihood", - "Intermediate Likelihood" + "Phase 1", + "Phase 4", + "Phase 3", + "Phase 5", + "No Thal Phase" ] }, - "CDLB": { + "LEWY_full": { "enum": [ - "Intermediate", - "High", - "Low or No clinical significance", "missing or unknown", + "Neocortical diffuse", + "Brainstem predominant", + "Limbic amygdala transitional", + "No LEWY_full", + "Olfactory bulb or Region unspecified", "" ] }, - "CVD_ART": { + "AMY_A": { "enum": [ + "Thal Phase 1 or 2", "missing or unknown", - "Severe", - "Moderate", - "Mild", - "No CVD_ART", - "" + "Thal Phase 4 or 5", + "No A Score", + "Thal Phase 3" ] }, - "MICR": { + "individualID": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "CDLB": { "enum": [ - "No", + "Low or No clinical significance", "missing or unknown", - "Yes", + "High", + "Intermediate", "" ] }, - "AMY_ANY": { + "HEMOR": { "enum": [ - "Amyloid Present", + "Yes", + "No", "missing or unknown", - "No amyloid presence", - "Some Amyloid" + "" ] }, - "HS_L": { + "CVD_CAA": { "enum": [ - "No HS_L", - "Present Location UK", - "Unilateral", + "Moderate", "missing or unknown", - "Bilateral", + "No CVD_CAA", + "Mild", + "Severe", "" ] }, - "LEWY_full": { + "alt_HS_S": { "enum": [ - "Brainstem predominant", - "Olfactory bulb or Region unspecified", - "Limbic amygdala transitional", + "Absence", + "Presence", "missing or unknown", - "Neocortical diffuse", - "No LEWY_full", "" ] }, - "pmiUnits": { + "Component": {}, + "HS_S": { "enum": [ - "minutes", - "hours" + "Yes", + "No", + "missing or unknown", + "" ] }, - "CVD_ART_ANY": { + "CVD_ATH_ANY": { "enum": [ "Mild or Moderate or Severe", "missing or unknown", - "No CVD_ART_ANY", + "No CVD_ATH_ANY", "" ] }, - "PMI": { - "not": { - "type": "null" - }, - "minLength": 1 + "mayoDx": { + "enum": [ + "AD", + "Control", + "Other", + "missing or unknown", + "" + ] }, - "TDP43": { + "WMR": { "enum": [ - "No", + "Moderate", "missing or unknown", - "Yes", + "Absent", + "Mild", + "Severe", "" ] }, "LEWY_grp": { "enum": [ + "Brainstem predominant group", "No LEWY_grp or olfactory bulb or amygdala predominant group", "Transitional or diffuse or region unspecified group", "missing or unknown", - "Brainstem predominant group", "" ] }, - "HS_S": { + "pmiUnits": { "enum": [ - "No", - "missing or unknown", - "Yes", - "" + "minutes", + "hours" ] }, - "CVD_S": { + "AMY_ANY": { "enum": [ - "Presence", + "No amyloid presence", + "Amyloid Present", "missing or unknown", - "No CVD_S", - "" + "Some Amyloid" ] }, - "WMR": { + "LEWY_ANY": { "enum": [ - "Absent", + "Brainstem or transitional or diffuse or region unspecified group", + "No LEWY_ANY or olfactory bulb or amygdala predominant group", "missing or unknown", - "Severe", - "Moderate", - "Mild", "" ] }, - "alt_HS_S": { + "Braak": { "enum": [ - "Presence", + "BRAAK Stage 3", "missing or unknown", - "Absence", - "" + "BRAAK Stage 4", + "BRAAK Stage 1", + "BRAAK Stage 5", + "BRAAK Stage 6", + "No BRAAK stage", + "BRAAK Stage 2" ] } }, "required": [ - "Braak", - "AMY_THAL", - "AMY_A", + "CERAD", + "PMI", + "REAG", + "conservationMethod", "INT", "B_SCORE", - "conservationMethod", "ADNC", + "AMY_THAL", + "AMY_A", "individualID", - "CERAD", - "REAG", - "AMY_ANY", "pmiUnits", - "PMI" + "AMY_ANY", + "Braak" ] } \ No newline at end of file