From 51e105497a406c0f28e2d00ca4064f0993bdc029 Mon Sep 17 00:00:00 2001 From: Victor Baham <83256374+MasterPastures@users.noreply.github.com> Date: Wed, 25 Sep 2024 16:15:16 -0400 Subject: [PATCH 1/6] Added new secret to generate-current-manifests.yml to help generate new manifests when GitHub Actions are initiated --- .github/workflows/generate-current-manifests.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/generate-current-manifests.yml b/.github/workflows/generate-current-manifests.yml index 98ba8b5..1cd80be 100644 --- a/.github/workflows/generate-current-manifests.yml +++ b/.github/workflows/generate-current-manifests.yml @@ -28,6 +28,7 @@ jobs: with: python-version: '3.10' cache: 'pip' + token: ${{ secrets.GENERATE_MANIFESTS_ON_ACTION }} - name: Install Libraries shell: bash From 68eaa2e376fc81dc7bc1ddabdb0cd4addaef8970 Mon Sep 17 00:00:00 2001 From: MasterPastures Date: Wed, 25 Sep 2024 20:35:31 +0000 Subject: [PATCH 2/6] GitHub Action: generate latest manifests --- .../AssayAutoradMetadataTemplate.xlsx | Bin 502571 -> 502571 bytes .../AssayBisulfiteSeqMetadataTemplate.xlsx | Bin 535070 -> 535073 bytes .../AssayChIPSeqMetadataTemplate.xlsx | Bin 523741 -> 523742 bytes .../AssayHICMetadataTemplate.xlsx | Bin 529785 -> 529789 bytes .../AssayMRIMetadataTemplate.xlsx | Bin 502894 -> 502894 bytes ...AssayMethylationArrayMetadataTemplate.xlsx | Bin 506616 -> 506614 bytes .../AssayRnaArrayMetadataTemplate.xlsx | Bin 511762 -> 511762 bytes .../AssayRnaSeqMetadataTemplate.xlsx | Bin 533032 -> 533035 bytes .../AssaySTARRSeqMetadataTemplate.xlsx | Bin 555077 -> 555077 bytes .../AssayScrnaSeqMetadataTemplate.xlsx | Bin 536919 -> 536920 bytes .../AssaySnpArrayMetadataTemplate.xlsx | Bin 506460 -> 506458 bytes .../AssayTMTquantitationMetadataTemplate.xlsx | Bin 506861 -> 506857 bytes .../AssayWholeExomeSeqMetadataTemplate.xlsx | Bin 531127 -> 531127 bytes .../AssayWholeGenomeSeqMetadataTemplate.xlsx | Bin 531181 -> 531181 bytes ...BiospecimenDrosophilaMetadataTemplate.xlsx | Bin 499096 -> 499096 bytes .../BiospecimenInvitroMetadataTemplate.xlsx | Bin 511356 -> 511356 bytes .../BiospecimenMetadataTemplate.xlsx | Bin 522500 -> 522497 bytes .../FileAnnotationTemplate.xlsx | Bin 529385 -> 529487 bytes ...ividualAnimalMODEL-ADMetadataTemplate.xlsx | Bin 583565 -> 583583 bytes .../IndividualAnimalMetadataTemplate.xlsx | Bin 528247 -> 528271 bytes .../IndividualHumanMetadataTemplate.xlsx | Bin 506879 -> 507093 bytes .../NeuropathMetadataTemplate.xlsx | Bin 777167 -> 777165 bytes ...ssay16SrRNAseqMetadataTemplate.schema.json | 616 +++++----- ...D.AssayATACSeqMetadataTemplate.schema.json | 468 +++---- ...D.AssayAutoradMetadataTemplate.schema.json | 158 +-- ...ayBisulfiteSeqMetadataTemplate.schema.json | 478 ++++---- ...D.AssayChIPSeqMetadataTemplate.schema.json | 684 +++++------ .../AD.AssayHICMetadataTemplate.schema.json | 494 ++++---- .../AD.AssayMRIMetadataTemplate.schema.json | 178 +-- ...ayMetabolomicsMetadataTemplate.schema.json | 502 ++++---- ...thylationArrayMetadataTemplate.schema.json | 386 +++--- ...ssayNanostringMetadataTemplate.schema.json | 442 +++---- .../AD.AssayPETMetadataTemplate.schema.json | 152 +-- ....AssayRnaArrayMetadataTemplate.schema.json | 342 +++--- ...AD.AssayRnaSeqMetadataTemplate.schema.json | 492 ++++---- ....AssaySTARRSeqMetadataTemplate.schema.json | 514 ++++---- ....AssayScrnaSeqMetadataTemplate.schema.json | 494 ++++---- ....AssaySnpArrayMetadataTemplate.schema.json | 334 ++--- ...MTquantitationMetadataTemplate.schema.json | 374 +++--- ...yWholeExomeSeqMetadataTemplate.schema.json | 478 ++++---- ...WholeGenomeSeqMetadataTemplate.schema.json | 482 ++++---- ...imenDrosophilaMetadataTemplate.schema.json | 42 +- ...pecimenInvitroMetadataTemplate.schema.json | 416 +++---- ...AD.BiospecimenMetadataTemplate.schema.json | 600 ++++----- .../AD.FileAnnotationTemplate.schema.json | 1073 +++++++++-------- ...AnimalMODEL-ADMetadataTemplate.schema.json | 379 +++--- ...dividualAnimalMetadataTemplate.schema.json | 231 ++-- ...ndividualHumanMetadataTemplate.schema.json | 291 ++--- .../AD.NeuropathMetadataTemplate.schema.json | 360 +++--- tests/schematic-config.yml | 43 + 50 files changed, 5784 insertions(+), 5719 deletions(-) create mode 100644 tests/schematic-config.yml diff --git a/current-excel-manifests/AssayAutoradMetadataTemplate.xlsx b/current-excel-manifests/AssayAutoradMetadataTemplate.xlsx index 2432991dc17792d3ac1d95a90cac44df9ac67fa3..4cfc06a82208dc1114b50953aab8abccd624410f 100644 GIT binary patch delta 449 zcmZ2|O>XryIo<$oW)=|!4h{~6jx5WKyqrwTKzg$z(|#~xav{6O=JzZnj37}EXYzX% zfz4iQDqw-;LiYATc19p(0%B$$W&vVWAZFWM$j-j5!(q#HdzSyzJM8WE|9QGz{$9=h z;Qzlb@B6nszd1kt|A()S|NZU1|M%l=`Te);-|zqNbMbY1m;diSyYIKJ|MK?je7k?s z<0r72OWIyl{_~@Qonh5`KL!-{ZeKrv9pV(A+f=syn#f+t0&?kept#m_zm@D<)0a(S zKL--pUOt^YjTy{(FpJ#)tZcjReD>X7e{R3HkbNT9Puo)$vzvoi)8{W?e*xCewUm7( 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"proximity ligation", - "methylSeq", - "totalRNA", - "multiome", - "DNALibraryConstruction", - "rRNAdepletion", - "cellHashing", - "KapaHyperPrep", - "snIsoSeq", - "miRNAenrichment", - "polyAselection" + "pairedEnd", + "singleEnd" ] }, "readLength": { @@ -34,345 +16,363 @@ }, "minLength": 1 }, - "Component": {}, - "assayTarget": { + "libraryPrep": { "enum": [ - "DPF2", - "OLIG2", - "DEAF1", - "BHLHE41", - "YBX3", - "TCF12", - "NFIB", - "H3K4me3", - "GATAD2B", - "YBX1", - "MITF", - "ATF7", - "GATAD2A", - "NCOA2", - "BRD4", - "ZEB1", - "YY1", - "PKNOX1", - "ZNF384", - "ZKSCAN1", - "ZBTB7B", - "ZNF143", - "SREBP2", - "SATB2", - "SP1", - "ARID3A", - "TCF7L2", - "CHD4", - "input", - "NEUROD1", - "CTCF", - "FOXK2", - "SRF", - "ARID1B", - "EHMT2", - "NONO", - "Pol2", - "SIN3A", - "TRIM28", - "ARNT", - "CC2D1A", - "MAZ", - "SKIL", - "RAD21", - "ZHX1", - "KLF16", - "RB1", - "KDM4A", - "SMARCA5", - "NR3C1", - "ZEB2", - "EED", - "IE_V1-V3", - "SP4", - "ASH2L", - "IgG", - "EWSR1", - "BMI1", - "ASCL1", - "ZSCAN29", - "BRCA1", - "SIN3B", - "H3K36me3", - "H3K27ac", - "NFIC", - "CLOCK", - "ZNF207", - "EGR1", - "ZFP91", - "NR2F2", - "R-loops", - "GABPB1", - "H3K4me1", - "TBR1", - "H3K9ac", - "MEIS2", - "BHLHE40", - "REST", - "E2F1", - "SMC3", - "NRF1", - "TDP43", - "KAT2B", - "NR2F1", - "H3K9me3", - "LaminB", - "ZNF407", - "HNRNPK", - "H3K9me2", - "SOX8", - "KLF5", - "TAF1", - "CREB1", - "GATA4", - "SON", - "ZNF24", - "RELB", - "ZNF592", - "ASH1L", - "CREM", - "ZNF318", - "HCFC1", - "GMEB1", - "SIRT1", - "FOXP1", - "EZH2", - "SIX4", - "BCL11A", - "MEF2A", - "NCOR1", - "H3K27me3", - "" + "multiome", + "KapaHyperPrep", + "rRNAdepletion", + "proximity ligation", + "STARRSeq", + "amplicon", + "totalRNA", + "miRNAenrichment", + "lncRNAenrichment", + "polyAselection", + "MULTIseq", + "PCRfree", + "methylSeq", + "DNALibraryConstruction", + "snIsoSeq", + "cellHashing", + "SureCell", + "Chromium Single Cell 3'", + "EndItDNAEndRepairKit", + "SPLITseq" ] }, - "dnaBatch": {}, "platform": { "enum": [ - "Infinium Omni2.5Exome-8 v1.1", - "Olink Target 96", - "Infinium Global Diversity Array-8", - "IlluminaHumanHap300", + "llumina Infinium General Screening Array 24-Kit v3.0", "IlluminaMiSeq", + "LTQOrbitrapXL", + "Illumina_Omni2pt5M", + "Simoa HD-1 Analyzer", + "Infinium Omni2.5Exome-8 v1.5", + "IlluminaHumanHT-12_V3_0_R1", + "confocalImaging", + "time-of-flight", + "Illumina_Omni5M", + "InfiniumPsychArrayBeadChip", + "IlluminaHumanHap300", + "Illumina_Omni5-Quad", + "orbitrap", + "Q Exactive Plus", + "HiSeq4000", + "DNBSEQ", + "Orbitrap Fusion Lumos", + "HiSeq3000", + "IlluminaInfiniumGSAMD-24v2-0", + "PacBio Sequel II", + "ddSEQ Single-Cell Isolator", + "Illumina MouseWG-6 v2.0 expression beadchip", "Biocrates p180", - "Xevo G2 QTOF", + "Agilent44Karray", + "Illumina NovaSeq 6000", + "Leco Pegasus IV", + "AffymetrixU133Plus2", + "Signa Premier AIR 3T", + "IlluminaMethylationEPIC", "BGISEQ-500", - "Illumina_1M", - "PacBioRSII", - "Biograph mCT", - "llumina Infinium General Screening Array 24-Kit v3.0", - "Affy6.0", - "SequenomMultiplex", + "IlluminaNovaseq6000", + "Infinium Omni2.5Exome-8 v1.4", "NextSeq2000", - "IlluminaMethylationEPIC", + "Illumina_HumanOmni1-Quadv1.0", + "PsychChip", "Bionano Irys", + "PacBio Sequel IIe", + "Xevo G2 QTOF", + "Q Exactive HF", + "Olink Target 96", + "Infinium Omni2.5Exome-8 v1.3", + "Biograph mCT", "Perlegen300Karray", - "MiSeq", - "IlluminaHumanHap650Yv3_A", - "Xevo TQ-S", - "Infinium HumanOmniExpressExome", - "Orbitrap Exploris 240", - "triple quadrupole", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "Q Exactive HF-X", + "GAIIx", + "Affy6.0", "Affy5.0", - "confocalImaging", - "HiSeq1000", - "IlluminaInfiniumGSAMD-24v2-0", + "AffymetrixU133AB", + "IlluminaWholeGenomeDASL", + "OrbiTrap Fusion", "Affymetrix Human Gene 1.0 ST Array", + "PacBioRSII", + "triple quadrupole", + "Orbitrap Exploris 240", + "SequenomMultiplex", + "NanostringnCounter", "Illumina_Omni2.5-8_v1.1", - "Infinium Omni2.5Exome-8 v1.4", - "Orbitrap Fusion Lumos", - "Illumina_Infinium-HumanMethylation450-BeadChip", "Illumina_Omni2.5-8", + "NanostringnCounter_MouseADPanel", + "HiSeq2500", + "Xevo TQ-S", + "Infinium HumanOmniExpressExome", + "quadrupole time-of-flight", + "Illumina_h650", "HiSeqX", - "PsychChip", - "Illumina_Omni2pt5M", + "Illumina_1M", + "MiSeq", + "HiSeq2000", + "HiSeq1000", + "Q Exactive", "NextSeq500", - "PacBio Sequel II", - "Illumina_Omni5M", - "Illumina_HumanOmni1-Quadv1.0", - "Simoa HD-1 Analyzer", - "IlluminaWholeGenomeDASL", "IlluminaHumanMethylation450", - "NanostringnCounter", - "LTQOrbitrapXL", - "OrbiTrap Fusion", - "DNBSEQ", - "HiSeq2500", - "Agilent44Karray", + "Roche Cobas", + "Infinium Global Diversity Array-8", + "IlluminaHumanHap650Yv3_A", "Bruker Avance III", - "GAIIx", - "Infinium Omni2.5Exome-8 v1.5", - "HiSeq2000", - "Q Exactive", - "HiSeq4000", - "Q Exactive HF", - "Q Exactive Plus", - "Leco Pegasus IV", "Illumina_Omni2.5-8_v1.3", - "IlluminaNovaseq6000", - "Infinium Omni2.5Exome-8 v1.3", - "Illumina NovaSeq 6000", - "Q Exactive HF-X", - "Illumina_h650", - "orbitrap", - "InfiniumPsychArrayBeadChip", - "AffymetrixU133AB", - "Signa Premier AIR 3T", - "Roche Cobas", - "HiSeq3000", - "PacBio Sequel IIe", - "Illumina MouseWG-6 v2.0 expression beadchip", - "quadrupole time-of-flight", - "AffymetrixU133Plus2", - "IlluminaHumanHT-12_V3_0_R1", - "ddSEQ Single-Cell Isolator", - "Illumina_Omni5-Quad", - "time-of-flight", - "NanostringnCounter_MouseADPanel" + "Infinium Omni2.5Exome-8 v1.1" ] }, - "runType": { + "specimenID": {}, + "dnaExtractionMethod": {}, + "dnaBatch": {}, + "Component": {}, + "libraryBatch": {}, + "assayTarget": { "enum": [ - "pairedEnd", - "singleEnd" + "PKNOX1", + "ZFP91", + "ZNF318", + "TRIM28", + "NEUROD1", + "SP4", + "ZNF407", + "H3K9me2", + "H3K4me1", + "KDM4A", + "ASH1L", + "ZNF143", + "GATAD2B", + "SIRT1", + "TCF7L2", + "NRF1", + "YY1", + "BHLHE40", + "BRD4", + "ZEB1", + "SIX4", + "ARNT", + "SMC3", + "TCF12", + "FOXK2", + "BHLHE41", + "E2F1", + "OLIG2", + "TAF1", + "DEAF1", + "MEIS2", + "BMI1", + "NFIB", + "YBX3", + "CHD4", + "HCFC1", + "CTCF", + "NONO", + "GABPB1", + "SOX8", + "IgG", + "H3K9ac", + "MITF", + "SKIL", + "DPF2", + "SREBP2", + "ZHX1", + "CLOCK", + "KLF5", + "MEF2A", + "SIN3A", + "H3K9me3", + "ZNF24", + "EGR1", + "H3K4me3", + "SATB2", + "ARID3A", + "input", + "Pol2", + "ZEB2", + "ATF7", + "BRCA1", + "NR2F2", + "CC2D1A", + "H3K27ac", + "ZKSCAN1", + "IE_V1-V3", + "ZBTB7B", + "ASCL1", + "NCOR1", + "GMEB1", + "ASH2L", + "REST", + "GATAD2A", + "RAD21", + "R-loops", + "SMARCA5", + "SIN3B", + "GATA4", + "EED", + "NR3C1", + "SRF", + "CREB1", + "KLF16", + "NCOA2", + "ARID1B", + "H3K36me3", + "TBR1", + "BCL11A", + "NR2F1", + "ZNF384", + "ZNF592", + "EZH2", + "CREM", + "RB1", + "HNRNPK", + "FOXP1", + "ZSCAN29", + "MAZ", + "KAT2B", + "RELB", + "LaminB", + "YBX1", + "H3K27me3", + "SON", + "SP1", + "ZNF207", + "EHMT2", + "NFIC", + "EWSR1", + "TDP43", + "" ] }, - "specimenID": {}, "sequencingBatch": {}, - "libraryBatch": {}, - "dnaExtractionMethod": {}, "assay": { "enum": [ - "DIA", + "Vernier Caliper", + "atomicForceMicroscopy", + "Genotyping", + "locomotor activation behavior", + "ELISA", + "LTP", + "SiMoA", + "snpArray", + "MDMS-SL", + "pharmacodynamics", + "open field test", + "liquid chromatography-electrochemical detection", + "UPLC-MSMS", + "elevated plus maze test", + "high content screen", + "methylationArray", + "electrochemiluminescence", + "Wishart Catecholamines", + "Sanger sequencing", + "scwholeGenomeSeq", + "nextGenerationTargetedSequencing", + "Blood Chemistry Measurement", + "wholeGenomeSeq", + "brightfieldMicroscopy", + "ATACSeq", + "microRNAcounts", + "LC-MSMS", "10x multiome", - "UCSD Untargeted Metabolomics", - "whole-cell patch clamp", - "HiChIPseq", - "MudPIT", + "sandwich ELISA", + "16SrRNAseq", + "snrnaSeq", + "Wishart High Value Metabolites", + "novelty response behavior", "frailty assessment", - "Real Time PCR", + "mirnaArray", "UC Davis GCTOF", - "von Frey test", - "bisulfiteSeq", - "Rader Lipidomics", + "Leiden Oxylipins", "Biocrates p180", - "memory behavior", - "ELISA", - "FIA-MSMS", - "Ribo-Seq", - "CUT&Tag", - "oxBS-Seq", - "locomotor activation behavior", - "kinesthetic behavior", - "mirnaSeq", - "errBisulfiteSeq", - "photograph", - "immunohistochemistry", - "ATACSeq", + "TMT quantitation", + "contextual conditioning behavior", + "rnaSeq", + "elevated T maze apparatus method", + "lncrnaSeq", + "scCGIseq", + "in vivo bioluminescence", "FitBark", - "polymeraseChainReaction", - "mirnaArray", - "novelty response behavior", - "snpArray", - "westernBlot", - "proximity extension assay", "mRNAcounts", - "ISOSeq", - "immunofluorescence", - "Zeno Electronic Walkway", - "questionnaire", - "Biocrates Bile Acids", + "HI-C", "scATACSeq", - "rnaArray", + "exomeSeq", + "NOMe-Seq", + "Positron Emission Tomography", + "polymeraseChainReaction", + "jumpingLibrary", + "active avoidance learning behavior", + "oxBS-Seq", + "Biocrates Bile Acids", "Immunocytochemistry", - "Wishart Catecholamines", - "brightfieldMicroscopy", + "tractionForceMicroscopy", + "pharmacokinetics", + "FIA-MSMS", + "Ribo-Seq", + "STARRSeq", + "HPLC", "lentiMPRA", - "Metabolon", - "nextGenerationTargetedSequencing", - "snrnaSeq", - "high content screen", - "HPLC-MSMS", - "methylationArray", - "Positron Emission Tomography", - "MRI", - "cellViabilityAssay", - "anxiety-related behavior", - "UPLC-MSMS", - "sandwich ELISA", - "CITESeq", - "RPPA", - "lncrnaSeq", - "wheel running", - "DNA optical mapping", - "Laser Speckle Imaging", + "CUT&Tag", + "MudPIT", "rotarod performance test", + "immunohistochemistry", "LC-SRM", - "MDMS-SL", - "in vivo bioluminescence", - "contextual conditioning behavior", - "Nightingale NMR", - "atomicForceMicroscopy", - "liquid chromatography-electrochemical detection", - "scwholeGenomeSeq", - "STARRSeq", - "active avoidance learning behavior", - "Sanger sequencing", "ChIPSeq", - "wholeGenomeSeq", - "electrochemiluminescence", - "16SrRNAseq", - "rnaSeq", - "microRNAcounts", - "tractionForceMicroscopy", - "UPLC-ESI-QTOF-MS", - "Wishart High Value Metabolites", - "SiMoA", - "exomeSeq", - "scrnaSeq", - "HI-C", - "autoradiography", + "HPLC-MSMS", + "Metabolon", + "RPPA", + "MIB/MS", + "westernBlot", + "ISOSeq", "scirnaSeq", - "spontaneous alternation", - "elevated T maze apparatus method", - "pharmacodynamics", - "LC-MSMS", + "von Frey test", "long-read rnaSeq", + "immunofluorescence", + "CITESeq", + "DIA", + "Baker Lipidomics", + "spontaneous alternation", + "photograph", + "whole-cell patch clamp", + "questionnaire", + "Rader Lipidomics", + "bisulfiteSeq", + "Real Time PCR", + "DNA optical mapping", "LC-MS", - "scale", - "open field test", - "label free mass spectrometry", - "Blood Chemistry Measurement", - "LTP", - "HPLC", - "TMT quantitation", - "jumpingLibrary", - "Biocrates Q500", + "Laser Speckle Imaging", + "cellViabilityAssay", + "wheel running", "m6A-rnaSeq", + "memory behavior", + "autoradiography", + "MRI", + "UPLC-ESI-QTOF-MS", "snATACSeq", - "Vernier Caliper", - "scCGIseq", - "Baker Lipidomics", - "MIB/MS", - "NOMe-Seq", + "rnaArray", + "UCSD Untargeted Metabolomics", + "Biocrates Q500", + "Zeno Electronic Walkway", "LFP", - "pharmacokinetics", - "elevated plus maze test", - "Genotyping", - "Leiden Oxylipins" + "scrnaSeq", + "scale", + "proximity extension assay", + "Nightingale NMR", + "mirnaSeq", + "kinesthetic behavior", + "anxiety-related behavior", + "HiChIPseq", + "label free mass spectrometry", + "errBisulfiteSeq" ] } }, "required": [ - "libraryPrep", + "runType", "readLength", + "libraryPrep", "platform", - "runType", "assay" ] } \ 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 9397a98..d4eaa04 100644 --- a/current-manifest-schemas/AD.AssayATACSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayATACSeqMetadataTemplate.schema.json @@ -4,7 +4,20 @@ "title": "AssayATACSeqMetadataTemplate", "type": "object", "properties": { - "libraryBatch": {}, + "meanGCContent": {}, + "readLength": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "runType": { + "enum": [ + "pairedEnd", + "singleEnd" + ] + }, + "pcrCycles": {}, "isStranded": { "enum": [ "FALSE", @@ -12,276 +25,263 @@ "" ] }, - "runType": { + "transposaseBatch": {}, + "sequencingBatch": {}, + "meanCoverage": {}, + "libraryPreparationMethod": { "enum": [ - "singleEnd", - "pairedEnd" + "TruSeq", + "Omni-ATAC", + "SMRTbell", + "CEL-seq", + "NEBNext", + "Smart-seq4", + "Ultralow Methyl-Seq", + "Drop-Seq", + "Smart-seq2", + "NexteraXT", + "sac-seq", + "Accel-NGS Methyl-Seq", + "Illumina DNA PCR-Free Prep Kit", + "Accel-NGS 2S Plus", + "Smart-seq1", + "10x", + "" ] }, - "assay": { + "libraryID": {}, + "readStrandOrigin": { "enum": [ - "Baker Lipidomics", - "Leiden Oxylipins", - "novelty response behavior", - "Immunocytochemistry", - "snrnaSeq", - "microRNAcounts", - "scirnaSeq", - "tractionForceMicroscopy", - "LC-MS", - "locomotor activation behavior", - "CITESeq", - "pharmacokinetics", - "von Frey test", - "cellViabilityAssay", - "RPPA", - "Wishart Catecholamines", - "Laser Speckle Imaging", - "contextual conditioning behavior", - "Ribo-Seq", - "autoradiography", - "questionnaire", - "LTP", - "methylationArray", - "ChIPSeq", - "MIB/MS", - "Biocrates Bile Acids", - "wheel running", - "photograph", - "label free mass spectrometry", - "Metabolon", - "westernBlot", - "active avoidance learning behavior", - "scCGIseq", - "sandwich ELISA", - "DNA optical mapping", - "Nightingale NMR", - "CUT&Tag", - "mRNAcounts", - "elevated T maze apparatus method", - "Wishart High Value Metabolites", - "TMT quantitation", - "ISOSeq", - "MDMS-SL", - "DIA", - "Biocrates Q500", - "Positron Emission Tomography", - "rotarod performance test", - "LFP", - "FIA-MSMS", - "bisulfiteSeq", - "jumpingLibrary", - "scrnaSeq", - "scwholeGenomeSeq", - "m6A-rnaSeq", - "Biocrates p180", - "MRI", - "open field test", - "UCSD Untargeted Metabolomics", - "HiChIPseq", - "kinesthetic behavior", - "scale", - "Real Time PCR", - "SiMoA", - "Zeno Electronic Walkway", - "long-read rnaSeq", - "exomeSeq", - "Genotyping", - "mirnaArray", - "LC-SRM", - "rnaSeq", - "electrochemiluminescence", - "elevated plus maze test", - "pharmacodynamics", - "mirnaSeq", - "in vivo bioluminescence", - "LC-MSMS", - "16SrRNAseq", - "immunohistochemistry", - "Blood Chemistry Measurement", - "brightfieldMicroscopy", - "atomicForceMicroscopy", - "ELISA", - "UPLC-MSMS", - "HPLC", - "Vernier Caliper", - "liquid chromatography-electrochemical detection", - "HI-C", - "snpArray", - "Rader Lipidomics", - "frailty assessment", - "MudPIT", - "polymeraseChainReaction", - "wholeGenomeSeq", - "10x multiome", - "high content screen", - "Sanger sequencing", - "immunofluorescence", - "errBisulfiteSeq", - "lentiMPRA", - "proximity extension assay", - "UPLC-ESI-QTOF-MS", - "anxiety-related behavior", - "rnaArray", - "lncrnaSeq", - "STARRSeq", - "oxBS-Seq", - "whole-cell patch clamp", - "nextGenerationTargetedSequencing", - "HPLC-MSMS", - "FitBark", - "NOMe-Seq", - "UC Davis GCTOF", - "scATACSeq", - "ATACSeq", - "snATACSeq", - "spontaneous alternation", - "memory behavior" + "forward", + "reverse", + "" ] }, - "pcrCycles": {}, - "specimenID": {}, - "transposaseBatch": {}, - "meanCoverage": {}, - "Component": {}, - "readLength": { - "not": { - "type": "null" - }, - "minLength": 1 - }, + "libraryBatch": {}, "platform": { "enum": [ - "PsychChip", - "IlluminaMethylationEPIC", - "Infinium Omni2.5Exome-8 v1.5", "Orbitrap Fusion Lumos", - "Infinium Omni2.5Exome-8 v1.1", - "Infinium Omni2.5Exome-8 v1.4", - "MiSeq", - "orbitrap", - "quadrupole time-of-flight", - "NanostringnCounter_MouseADPanel", - "PacBio Sequel IIe", - "Xevo G2 QTOF", - "OrbiTrap Fusion", - "Illumina MouseWG-6 v2.0 expression beadchip", - "ddSEQ Single-Cell Isolator", - "AffymetrixU133Plus2", - "LTQOrbitrapXL", - "Illumina_Omni5-Quad", - "IlluminaHumanHap300", - "Q Exactive", - "Q Exactive HF-X", - "Roche Cobas", "Biograph mCT", + "SequenomMultiplex", + "HiSeq4000", "Olink Target 96", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "InfiniumPsychArrayBeadChip", - "Infinium Global Diversity Array-8", - "NextSeq2000", - "HiSeq2500", + "Affy5.0", + "Illumina_h650", + "IlluminaHumanHap300", + "Illumina_Omni5M", "IlluminaHumanHap650Yv3_A", - "Illumina_Omni2.5-8", - "Illumina_HumanOmni1-Quadv1.0", - "IlluminaHumanMethylation450", - "HiSeq4000", - "IlluminaHumanHT-12_V3_0_R1", - "Illumina_Omni2.5-8_v1.3", - "Biocrates p180", - "SequenomMultiplex", - "Leco Pegasus IV", - "HiSeq3000", - "Agilent44Karray", - "PacBioRSII", - "IlluminaInfiniumGSAMD-24v2-0", - "Bionano Irys", "Signa Premier AIR 3T", - "Q Exactive Plus", - "GAIIx", - "Illumina_Omni5M", - "confocalImaging", + "Q Exactive", + "HiSeq2000", "Infinium Omni2.5Exome-8 v1.3", - "Infinium HumanOmniExpressExome", "Simoa HD-1 Analyzer", - "triple quadrupole", - "llumina Infinium General Screening Array 24-Kit v3.0", - "Xevo TQ-S", "Illumina_Omni2.5-8_v1.1", - "time-of-flight", - "HiSeqX", - "DNBSEQ", - "HiSeq2000", + "llumina Infinium General Screening Array 24-Kit v3.0", + "orbitrap", + "IlluminaInfiniumGSAMD-24v2-0", + "Illumina_Omni2.5-8", + "NextSeq500", + "IlluminaMiSeq", + "Roche Cobas", + "Orbitrap Exploris 240", + "MiSeq", + "PacBio Sequel IIe", "HiSeq1000", + "Infinium Global Diversity Array-8", "Illumina NovaSeq 6000", - "Perlegen300Karray", - "Illumina_1M", - "IlluminaWholeGenomeDASL", - "Illumina_h650", - "Affy5.0", + "HiSeq3000", + "Infinium Omni2.5Exome-8 v1.1", + "HiSeq2500", "Affy6.0", + "IlluminaNovaseq6000", + "Illumina_HumanOmni1-Quadv1.0", + "Xevo G2 QTOF", + "IlluminaMethylationEPIC", + "Perlegen300Karray", + "Illumina MouseWG-6 v2.0 expression beadchip", + "quadrupole time-of-flight", + "Infinium HumanOmniExpressExome", + "LTQOrbitrapXL", + "PsychChip", "Illumina_Omni2pt5M", + "NanostringnCounter", + "ddSEQ Single-Cell Isolator", + "Illumina_Omni2.5-8_v1.3", + "NextSeq2000", + "IlluminaHumanMethylation450", "Q Exactive HF", - "IlluminaNovaseq6000", - "BGISEQ-500", - "Orbitrap Exploris 240", - "IlluminaMiSeq", - "Affymetrix Human Gene 1.0 ST Array", + "Xevo TQ-S", + "Leco Pegasus IV", "PacBio Sequel II", - "Bruker Avance III", + "Illumina_Omni5-Quad", + "PacBioRSII", "AffymetrixU133AB", - "NextSeq500", - "NanostringnCounter" - ] - }, - "libraryID": {}, - "meanGCContent": {}, - "libraryPreparationMethod": { - "enum": [ - "TruSeq", - "Accel-NGS Methyl-Seq", - "Smart-seq2", - "Smart-seq4", - "Drop-Seq", - "NEBNext", - "CEL-seq", - "Omni-ATAC", - "sac-seq", - "SMRTbell", - "Ultralow Methyl-Seq", - "Smart-seq1", - "Accel-NGS 2S Plus", - "10x", - "NexteraXT", - "Illumina DNA PCR-Free Prep Kit", - "" + "DNBSEQ", + "HiSeqX", + "OrbiTrap Fusion", + "Biocrates p180", + "InfiniumPsychArrayBeadChip", + "Affymetrix Human Gene 1.0 ST Array", + "confocalImaging", + "AffymetrixU133Plus2", + "Illumina_1M", + "Agilent44Karray", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "BGISEQ-500", + "Infinium Omni2.5Exome-8 v1.5", + "NanostringnCounter_MouseADPanel", + "IlluminaWholeGenomeDASL", + "IlluminaHumanHT-12_V3_0_R1", + "Q Exactive Plus", + "triple quadrupole", + "time-of-flight", + "Infinium Omni2.5Exome-8 v1.4", + "Q Exactive HF-X", + "Bruker Avance III", + "GAIIx", + "Bionano Irys" ] }, - "readStrandOrigin": { + "specimenID": {}, + "assay": { "enum": [ - "reverse", - "forward", - "" + "ATACSeq", + "Baker Lipidomics", + "MIB/MS", + "CUT&Tag", + "pharmacokinetics", + "UPLC-ESI-QTOF-MS", + "RPPA", + "Zeno Electronic Walkway", + "lentiMPRA", + "UCSD Untargeted Metabolomics", + "NOMe-Seq", + "errBisulfiteSeq", + "wholeGenomeSeq", + "TMT quantitation", + "memory behavior", + "polymeraseChainReaction", + "LC-SRM", + "Vernier Caliper", + "scirnaSeq", + "anxiety-related behavior", + "FitBark", + "microRNAcounts", + "immunohistochemistry", + "Ribo-Seq", + "open field test", + "HI-C", + "Laser Speckle Imaging", + "tractionForceMicroscopy", + "sandwich ELISA", + "Sanger sequencing", + "rnaSeq", + "scCGIseq", + "SiMoA", + "westernBlot", + "snpArray", + "whole-cell patch clamp", + "16SrRNAseq", + "liquid chromatography-electrochemical detection", + "cellViabilityAssay", + "MDMS-SL", + "scATACSeq", + "snrnaSeq", + "STARRSeq", + "photograph", + "bisulfiteSeq", + "exomeSeq", + "brightfieldMicroscopy", + "scrnaSeq", + "lncrnaSeq", + "scale", + "MudPIT", + "HPLC", + "frailty assessment", + "proximity extension assay", + "mirnaSeq", + "LC-MSMS", + "LC-MS", + "Nightingale NMR", + "mRNAcounts", + "oxBS-Seq", + "10x multiome", + "Biocrates Bile Acids", + "m6A-rnaSeq", + "atomicForceMicroscopy", + "HPLC-MSMS", + "kinesthetic behavior", + "von Frey test", + "spontaneous alternation", + "nextGenerationTargetedSequencing", + "HiChIPseq", + "Wishart Catecholamines", + "long-read rnaSeq", + "pharmacodynamics", + "novelty response behavior", + "high content screen", + "Genotyping", + "locomotor activation behavior", + "Blood Chemistry Measurement", + "elevated T maze apparatus method", + "mirnaArray", + "Positron Emission Tomography", + "ChIPSeq", + "DNA optical mapping", + "jumpingLibrary", + "electrochemiluminescence", + "Immunocytochemistry", + "Rader Lipidomics", + "elevated plus maze test", + "Wishart High Value Metabolites", + "Biocrates p180", + "immunofluorescence", + "LTP", + "UPLC-MSMS", + "snATACSeq", + "in vivo bioluminescence", + "Leiden Oxylipins", + "active avoidance learning behavior", + "contextual conditioning behavior", + "Biocrates Q500", + "scwholeGenomeSeq", + "DIA", + "CITESeq", + "methylationArray", + "MRI", + "rnaArray", + "FIA-MSMS", + "UC Davis GCTOF", + "wheel running", + "label free mass spectrometry", + "Metabolon", + "autoradiography", + "ISOSeq", + "Real Time PCR", + "LFP", + "ELISA", + "questionnaire", + "rotarod performance test" ] }, + "Component": {}, "referenceSet": { "enum": [ - "HRC", + "GRCm38", + "GRCh38", "1000 Genomes phase 3", "GRCh37", - "MMUL1.0", "dmel_r6.06", - "GRCh38", - "GRCm38", + "HRC", + "MMUL1.0", "" ] - }, - "sequencingBatch": {} + } }, "required": [ - "runType", - "assay", "readLength", - "platform" + "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 45bb2c4..ee8aa3f 100644 --- a/current-manifest-schemas/AD.AssayAutoradMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayAutoradMetadataTemplate.schema.json @@ -4,110 +4,110 @@ "title": "AssayAutoradMetadataTemplate", "type": "object", "properties": { - "scanID": {}, + "ageAssessmentUnits": { + "enum": [ + "days", + "years", + "months", + "gestational weeks", + "PCW", + "weeks", + "" + ] + }, "platform": { "enum": [ - "BGISEQ-500", - "LTQOrbitrapXL", + "Xevo TQ-S", + "Affy6.0", + "HiSeq2500", + "Illumina_1M", + "NextSeq2000", + "IlluminaHumanHT-12_V3_0_R1", "Olink Target 96", - "IlluminaMiSeq", - "PacBioRSII", - "Illumina_Omni2.5-8", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "Orbitrap Exploris 240", - "Q Exactive HF-X", - "Infinium Global Diversity Array-8", + "Xevo G2 QTOF", + "Infinium Omni2.5Exome-8 v1.1", "HiSeq4000", - "Illumina MouseWG-6 v2.0 expression beadchip", - "Illumina_Omni5-Quad", - "Perlegen300Karray", - "HiSeq3000", - "Q Exactive", - "Agilent44Karray", - "NanostringnCounter_MouseADPanel", - "orbitrap", - "Q Exactive Plus", - "Affy5.0", - "NextSeq500", - "AffymetrixU133Plus2", - "AffymetrixU133AB", - "IlluminaInfiniumGSAMD-24v2-0", + "IlluminaHumanHap300", + "Signa Premier AIR 3T", + "MiSeq", + "IlluminaWholeGenomeDASL", + "Q Exactive HF", + "Illumina_Infinium-HumanMethylation450-BeadChip", "IlluminaHumanHap650Yv3_A", - "Illumina_1M", - "OrbiTrap Fusion", "PacBio Sequel II", "HiSeq2000", - "Illumina_h650", - "Bruker Avance III", - "GAIIx", - "Bionano Irys", - "quadrupole time-of-flight", - "Infinium HumanOmniExpressExome", - "IlluminaMethylationEPIC", - "IlluminaHumanHT-12_V3_0_R1", - "Leco Pegasus IV", - "Roche Cobas", - "Orbitrap Fusion Lumos", - "NextSeq2000", + "Infinium Omni2.5Exome-8 v1.4", "Illumina_HumanOmni1-Quadv1.0", - "NanostringnCounter", - "triple quadrupole", + "Illumina_Omni5-Quad", + "SequenomMultiplex", "Simoa HD-1 Analyzer", - "DNBSEQ", - "IlluminaWholeGenomeDASL", - "Affy6.0", - "Illumina_Omni5M", + "InfiniumPsychArrayBeadChip", + "LTQOrbitrapXL", + "Affymetrix Human Gene 1.0 ST Array", + "NanostringnCounter", + "IlluminaHumanMethylation450", + "Q Exactive", + "llumina Infinium General Screening Array 24-Kit v3.0", "ddSEQ Single-Cell Isolator", - "Xevo G2 QTOF", + "AffymetrixU133AB", + "orbitrap", + "triple quadrupole", + "Illumina NovaSeq 6000", "Infinium Omni2.5Exome-8 v1.3", - "llumina Infinium General Screening Array 24-Kit v3.0", - "MiSeq", - "HiSeq2500", - "Signa Premier AIR 3T", - "IlluminaHumanMethylation450", + "Infinium Omni2.5Exome-8 v1.5", + "OrbiTrap Fusion", + "Biocrates p180", + "Q Exactive Plus", + "quadrupole time-of-flight", + "HiSeqX", + "Bruker Avance III", + "Illumina MouseWG-6 v2.0 expression beadchip", + "PacBioRSII", + "Q Exactive HF-X", + "IlluminaInfiniumGSAMD-24v2-0", + "PacBio Sequel IIe", + "AffymetrixU133Plus2", + "Illumina_Omni5M", + "Leco Pegasus IV", + "Infinium HumanOmniExpressExome", + "GAIIx", + "Infinium Global Diversity Array-8", "PsychChip", - "SequenomMultiplex", + "BGISEQ-500", + "Agilent44Karray", + "Illumina_h650", + "time-of-flight", + "IlluminaNovaseq6000", + "DNBSEQ", + "NextSeq500", + "Roche Cobas", + "Affy5.0", + "HiSeq3000", + "IlluminaMethylationEPIC", + "HiSeq1000", + "Orbitrap Fusion Lumos", "Illumina_Omni2.5-8_v1.1", - "Infinium Omni2.5Exome-8 v1.1", "Biograph mCT", - "Illumina NovaSeq 6000", - "IlluminaHumanHap300", - "Affymetrix Human Gene 1.0 ST Array", + "NanostringnCounter_MouseADPanel", + "Orbitrap Exploris 240", "confocalImaging", + "IlluminaMiSeq", + "Illumina_Omni2.5-8", "Illumina_Omni2.5-8_v1.3", + "Perlegen300Karray", "Illumina_Omni2pt5M", - "Biocrates p180", - "time-of-flight", - "Infinium Omni2.5Exome-8 v1.4", - "PacBio Sequel IIe", - "InfiniumPsychArrayBeadChip", - "HiSeq1000", - "Xevo TQ-S", - "IlluminaNovaseq6000", - "Q Exactive HF", - "Infinium Omni2.5Exome-8 v1.5", - "HiSeqX" - ] - }, - "ageAssessmentUnits": { - "enum": [ - "gestational weeks", - "PCW", - "days", - "weeks", - "years", - "months", - "" + "Bionano Irys" ] }, - "Component": {}, "individualID": { "not": { "type": "null" }, "minLength": 1 }, - "ageAssessment": {} + "scanID": {}, + "ageAssessment": {}, + "Component": {} }, "required": [ "platform", diff --git a/current-manifest-schemas/AD.AssayBisulfiteSeqMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayBisulfiteSeqMetadataTemplate.schema.json index 5a7fa94..24c282c 100644 --- a/current-manifest-schemas/AD.AssayBisulfiteSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayBisulfiteSeqMetadataTemplate.schema.json @@ -4,253 +4,173 @@ "title": "AssayBisulfiteSeqMetadataTemplate", "type": "object", "properties": { + "specimenID": {}, + "Component": {}, + "dnaBatch": {}, "isStranded": { "enum": [ - "FALSE", "TRUE", + "FALSE", "" ] }, - "platform": { - "enum": [ - "PacBio Sequel IIe", - "PacBio Sequel II", - "HiSeq2000", - "BGISEQ-500", - "AffymetrixU133AB", - "Infinium Omni2.5Exome-8 v1.3", - "llumina Infinium General Screening Array 24-Kit v3.0", - "Leco Pegasus IV", - "Q Exactive HF-X", - "IlluminaMethylationEPIC", - "IlluminaWholeGenomeDASL", - "IlluminaHumanMethylation450", - "Illumina_Omni5-Quad", - "Illumina_Omni2pt5M", - "IlluminaMiSeq", - "ddSEQ Single-Cell Isolator", - "Signa Premier AIR 3T", - "orbitrap", - "Illumina_Omni5M", - "Bionano Irys", - "triple quadrupole", - "Illumina_Omni2.5-8_v1.1", - "LTQOrbitrapXL", - "Roche Cobas", - "NextSeq2000", - "Biograph mCT", - "Xevo TQ-S", - "Simoa HD-1 Analyzer", - "OrbiTrap Fusion", - "time-of-flight", - "DNBSEQ", - "SequenomMultiplex", - "GAIIx", - "Infinium Omni2.5Exome-8 v1.4", - "IlluminaInfiniumGSAMD-24v2-0", - "NextSeq500", - "Illumina_Omni2.5-8_v1.3", - "HiSeq1000", - "Perlegen300Karray", - "Q Exactive", - "IlluminaNovaseq6000", - "Q Exactive Plus", - "IlluminaHumanHap650Yv3_A", - "Illumina_Omni2.5-8", - "NanostringnCounter", - "Affy5.0", - "Infinium Global Diversity Array-8", - "confocalImaging", - "HiSeqX", - "AffymetrixU133Plus2", - "quadrupole time-of-flight", - "NanostringnCounter_MouseADPanel", - "Orbitrap Exploris 240", - "HiSeq3000", - "Affymetrix Human Gene 1.0 ST Array", - "Orbitrap Fusion Lumos", - "Illumina_1M", - "Xevo G2 QTOF", - "IlluminaHumanHT-12_V3_0_R1", - "Infinium Omni2.5Exome-8 v1.5", - "Bruker Avance III", - "PacBioRSII", - "Q Exactive HF", - "Infinium Omni2.5Exome-8 v1.1", - "Illumina_h650", - "PsychChip", - "Olink Target 96", - "Affy6.0", - "Illumina NovaSeq 6000", - "InfiniumPsychArrayBeadChip", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "Illumina MouseWG-6 v2.0 expression beadchip", - "Illumina_HumanOmni1-Quadv1.0", - "IlluminaHumanHap300", - "Infinium HumanOmniExpressExome", - "Biocrates p180", - "Agilent44Karray", - "HiSeq4000", - "MiSeq", - "HiSeq2500" - ] - }, - "sequencingBatch": {}, - "libraryPreparationMethod": { + "directionalBSseqLibrary": { "enum": [ - "Smart-seq2", - "TruSeq", - "Ultralow Methyl-Seq", - "10x", - "NEBNext", - "Drop-Seq", - "Accel-NGS Methyl-Seq", - "Smart-seq4", - "NexteraXT", - "Omni-ATAC", - "CEL-seq", - "sac-seq", - "SMRTbell", - "Illumina DNA PCR-Free Prep Kit", - "Smart-seq1", - "Accel-NGS 2S Plus", + "TRUE", + "FALSE", "" ] }, + "pcrCycles": {}, + "totalReads": {}, "readStrandOrigin": { "enum": [ - "forward", "reverse", - "" - ] - }, - "totalReads": {}, - "directionalBSseqLibrary": { - "enum": [ - "FALSE", - "TRUE", + "forward", "" ] }, "assay": { "enum": [ - "snpArray", - "ATACSeq", - "UC Davis GCTOF", - "spontaneous alternation", - "locomotor activation behavior", - "bisulfiteSeq", - "SiMoA", - "memory behavior", - "16SrRNAseq", - "ChIPSeq", - "mRNAcounts", - "Genotyping", - "LC-MS", + "UPLC-MSMS", "10x multiome", - "sandwich ELISA", - "NOMe-Seq", - "whole-cell patch clamp", - "Biocrates Q500", - "methylationArray", - "in vivo bioluminescence", - "STARRSeq", + "bisulfiteSeq", + "lentiMPRA", + "scale", + "Laser Speckle Imaging", + "proximity extension assay", + "jumpingLibrary", + "DIA", + "LFP", + "LTP", + "ELISA", "DNA optical mapping", - "Wishart High Value Metabolites", - "Wishart Catecholamines", - "label free mass spectrometry", - "rotarod performance test", - "snATACSeq", - "Rader Lipidomics", - "atomicForceMicroscopy", - "mirnaSeq", - "Ribo-Seq", - "TMT quantitation", - "MDMS-SL", - "Blood Chemistry Measurement", + "liquid chromatography-electrochemical detection", + "FIA-MSMS", + "active avoidance learning behavior", + "Immunocytochemistry", + "methylationArray", "FitBark", - "scATACSeq", - "CITESeq", - "open field test", - "novelty response behavior", - "MRI", + "Nightingale NMR", + "ATACSeq", + "Wishart Catecholamines", + "spontaneous alternation", + "high content screen", + "cellViabilityAssay", + "snpArray", + "Sanger sequencing", "anxiety-related behavior", - "lncrnaSeq", - "LFP", - "rnaSeq", - "tractionForceMicroscopy", - "scrnaSeq", - "Zeno Electronic Walkway", - "HiChIPseq", - "MIB/MS", - "UPLC-MSMS", - "LC-SRM", - "FIA-MSMS", + "Metabolon", + "immunohistochemistry", + "westernBlot", + "CITESeq", + "m6A-rnaSeq", + "Rader Lipidomics", + "nextGenerationTargetedSequencing", + "electrochemiluminescence", + "UCSD Untargeted Metabolomics", + "Real Time PCR", "snrnaSeq", - "Biocrates Bile Acids", + "autoradiography", + "HPLC-MSMS", "immunofluorescence", - "UCSD Untargeted Metabolomics", + "locomotor activation behavior", + "scCGIseq", + "exomeSeq", + "photograph", + "von Frey test", + "MIB/MS", + "UC Davis GCTOF", + "frailty assessment", + "pharmacodynamics", + "errBisulfiteSeq", + "scATACSeq", + "open field test", + "Vernier Caliper", + "wholeGenomeSeq", + "sandwich ELISA", + "Biocrates p180", + "contextual conditioning behavior", "RPPA", - "autoradiography", - "westernBlot", - "elevated T maze apparatus method", - "ELISA", - "microRNAcounts", - "Leiden Oxylipins", - "HI-C", - "Laser Speckle Imaging", - "proximity extension assay", - "scirnaSeq", "elevated plus maze test", - "CUT&Tag", - "Vernier Caliper", - "polymeraseChainReaction", - "scCGIseq", + "pharmacokinetics", + "Ribo-Seq", + "NOMe-Seq", + "16SrRNAseq", + "Blood Chemistry Measurement", + "rnaArray", "HPLC", - "exomeSeq", - "lentiMPRA", - "jumpingLibrary", - "m6A-rnaSeq", "long-read rnaSeq", - "Real Time PCR", - "cellViabilityAssay", - "liquid chromatography-electrochemical detection", - "errBisulfiteSeq", - "immunohistochemistry", + "Leiden Oxylipins", + "Biocrates Q500", + "rnaSeq", "ISOSeq", - "HPLC-MSMS", + "questionnaire", + "tractionForceMicroscopy", + "in vivo bioluminescence", + "scirnaSeq", + "scrnaSeq", + "microRNAcounts", + "MudPIT", + "rotarod performance test", + "atomicForceMicroscopy", + "LC-MS", + "MDMS-SL", + "elevated T maze apparatus method", + "ChIPSeq", + "LC-SRM", + "Genotyping", "oxBS-Seq", - "contextual conditioning behavior", + "mirnaSeq", "kinesthetic behavior", - "nextGenerationTargetedSequencing", + "HI-C", "Baker Lipidomics", - "active avoidance learning behavior", - "Immunocytochemistry", + "HiChIPseq", "UPLC-ESI-QTOF-MS", - "wholeGenomeSeq", - "DIA", - "MudPIT", - "electrochemiluminescence", - "pharmacodynamics", - "brightfieldMicroscopy", - "scwholeGenomeSeq", - "von Frey test", - "rnaArray", - "Sanger sequencing", - "pharmacokinetics", + "polymeraseChainReaction", + "label free mass spectrometry", + "CUT&Tag", + "STARRSeq", + "Biocrates Bile Acids", "mirnaArray", - "LC-MSMS", - "high content screen", + "brightfieldMicroscopy", + "memory behavior", "wheel running", - "scale", - "Nightingale NMR", + "Zeno Electronic Walkway", + "snATACSeq", + "novelty response behavior", + "whole-cell patch clamp", + "Wishart High Value Metabolites", + "SiMoA", "Positron Emission Tomography", - "photograph", - "Metabolon", - "Biocrates p180", - "questionnaire", - "frailty assessment", - "LTP" + "mRNAcounts", + "LC-MSMS", + "scwholeGenomeSeq", + "TMT quantitation", + "MRI", + "lncrnaSeq" + ] + }, + "meanCoverage": {}, + "libraryPreparationMethod": { + "enum": [ + "10x", + "Drop-Seq", + "Accel-NGS Methyl-Seq", + "NexteraXT", + "CEL-seq", + "Illumina DNA PCR-Free Prep Kit", + "Smart-seq4", + "TruSeq", + "Omni-ATAC", + "Smart-seq1", + "NEBNext", + "Smart-seq2", + "Ultralow Methyl-Seq", + "sac-seq", + "SMRTbell", + "Accel-NGS 2S Plus", + "" ] }, "readLength": { @@ -259,63 +179,143 @@ }, "minLength": 1 }, - "libraryID": {}, - "specimenID": {}, + "lambdaDNAconc": {}, + "sequencingBatch": {}, + "gDNAconc": {}, "libraryPrep": { "enum": [ - "miRNAenrichment", - "cellHashing", - "SPLITseq", + "lncRNAenrichment", "polyAselection", - "proximity ligation", - "Chromium Single Cell 3'", + "MULTIseq", "EndItDNAEndRepairKit", - "snIsoSeq", - "lncRNAenrichment", - "methylSeq", - "amplicon", - "rRNAdepletion", "multiome", + "SPLITseq", "STARRSeq", + "proximity ligation", + "amplicon", + "Chromium Single Cell 3'", "SureCell", - "PCRfree", - "MULTIseq", "KapaHyperPrep", + "methylSeq", + "DNALibraryConstruction", "totalRNA", - "DNALibraryConstruction" + "rRNAdepletion", + "miRNAenrichment", + "snIsoSeq", + "cellHashing", + "PCRfree" ] }, - "pcrCycles": {}, - "dnaBatch": {}, - "libraryBatch": {}, - "gDNAconc": {}, - "meanCoverage": {}, - "Component": {}, + "platform": { + "enum": [ + "Q Exactive HF", + "NanostringnCounter_MouseADPanel", + "BGISEQ-500", + "HiSeqX", + "Infinium Omni2.5Exome-8 v1.5", + "PacBioRSII", + "Affymetrix Human Gene 1.0 ST Array", + "Infinium HumanOmniExpressExome", + "AffymetrixU133AB", + "NanostringnCounter", + "IlluminaHumanHT-12_V3_0_R1", + "Bruker Avance III", + "Infinium Global Diversity Array-8", + "Illumina_Omni5-Quad", + "Illumina_h650", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "Roche Cobas", + "Simoa HD-1 Analyzer", + "Illumina NovaSeq 6000", + "HiSeq2500", + "AffymetrixU133Plus2", + "HiSeq3000", + "Xevo TQ-S", + "Orbitrap Fusion Lumos", + "IlluminaHumanHap300", + "Affy6.0", + "ddSEQ Single-Cell Isolator", + "IlluminaMiSeq", + "IlluminaWholeGenomeDASL", + "orbitrap", + "Biograph mCT", + "Illumina_Omni2pt5M", + "llumina Infinium General Screening Array 24-Kit v3.0", + "IlluminaInfiniumGSAMD-24v2-0", + "Infinium Omni2.5Exome-8 v1.3", + "quadrupole time-of-flight", + "IlluminaHumanMethylation450", + "IlluminaNovaseq6000", + "Olink Target 96", + "PsychChip", + "Signa Premier AIR 3T", + "Biocrates p180", + "Perlegen300Karray", + "Infinium Omni2.5Exome-8 v1.1", + "DNBSEQ", + "NextSeq2000", + "IlluminaHumanHap650Yv3_A", + "Bionano Irys", + "Illumina_Omni2.5-8", + "Illumina_HumanOmni1-Quadv1.0", + "NextSeq500", + "Infinium Omni2.5Exome-8 v1.4", + "PacBio Sequel II", + "Leco Pegasus IV", + "time-of-flight", + "GAIIx", + "Illumina_1M", + "Illumina_Omni2.5-8_v1.3", + "MiSeq", + "Illumina_Omni2.5-8_v1.1", + "Orbitrap Exploris 240", + "Q Exactive Plus", + "HiSeq1000", + "Illumina MouseWG-6 v2.0 expression beadchip", + "Illumina_Omni5M", + "IlluminaMethylationEPIC", + "InfiniumPsychArrayBeadChip", + "Affy5.0", + "Agilent44Karray", + "PacBio Sequel IIe", + "Q Exactive", + "confocalImaging", + "LTQOrbitrapXL", + "HiSeq2000", + "HiSeq4000", + "OrbiTrap Fusion", + "SequenomMultiplex", + "Xevo G2 QTOF", + "triple quadrupole", + "Q Exactive HF-X" + ] + }, + "libraryID": {}, "referenceSet": { "enum": [ - "HRC", - "1000 Genomes phase 3", "MMUL1.0", - "GRCh38", "dmel_r6.06", - "GRCm38", "GRCh37", + "GRCh38", + "1000 Genomes phase 3", + "GRCm38", + "HRC", "" ] }, + "libraryBatch": {}, "runType": { "enum": [ "pairedEnd", "singleEnd" ] - }, - "lambdaDNAconc": {} + } }, "required": [ - "platform", "assay", "readLength", "libraryPrep", + "platform", "runType" ] } \ 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 e9ab870..0ed6e97 100644 --- a/current-manifest-schemas/AD.AssayChIPSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayChIPSeqMetadataTemplate.schema.json @@ -4,405 +4,405 @@ "title": "AssayChIPSeqMetadataTemplate", "type": "object", "properties": { - "libraryBatch": {}, - "chromatinAmountUnits": {}, - "runType": { - "enum": [ - "pairedEnd", - "singleEnd" - ] - }, - "totalReads": {}, - "referenceSet": { - "enum": [ - "1000 Genomes phase 3", - "dmel_r6.06", - "MMUL1.0", - "HRC", - "GRCh38", - "GRCm38", - "GRCh37", - "" - ] - }, - "libraryID": {}, - "libraryPreparationMethod": { - "enum": [ - "NEBNext", - "CEL-seq", - "Smart-seq4", - "Drop-Seq", - "NexteraXT", - "SMRTbell", - "Smart-seq2", - "Illumina DNA PCR-Free Prep Kit", - "10x", - "Omni-ATAC", - "TruSeq", - "Ultralow Methyl-Seq", - "sac-seq", - "Accel-NGS Methyl-Seq", - "Smart-seq1", - "Accel-NGS 2S Plus", - "" - ] - }, "readLength": { "not": { "type": "null" }, "minLength": 1 }, - "sequencingBatch": {}, - "isStranded": { - "enum": [ - "FALSE", - "TRUE", - "" - ] - }, - "antibodyAmountUnits": {}, - "catalogNumber": {}, - "platform": { - "enum": [ - "ddSEQ Single-Cell Isolator", - "Agilent44Karray", - "BGISEQ-500", - "Illumina_Omni2.5-8_v1.3", - "Illumina_1M", - "AffymetrixU133Plus2", - "DNBSEQ", - "Xevo G2 QTOF", - "PacBio Sequel IIe", - "Biograph mCT", - "Illumina_HumanOmni1-Quadv1.0", - "IlluminaMethylationEPIC", - "Q Exactive Plus", - "SequenomMultiplex", - "Affymetrix Human Gene 1.0 ST Array", - "HiSeq4000", - "IlluminaInfiniumGSAMD-24v2-0", - "orbitrap", - "HiSeq2000", - "Bruker Avance III", - "GAIIx", - "LTQOrbitrapXL", - "PsychChip", - "Infinium Omni2.5Exome-8 v1.5", - "Biocrates p180", - "Illumina_Omni2.5-8_v1.1", - "Illumina_Omni5-Quad", - "Illumina MouseWG-6 v2.0 expression beadchip", - "Leco Pegasus IV", - "Illumina_h650", - "Illumina_Omni2.5-8", - "HiSeq3000", - "Perlegen300Karray", - "HiSeqX", - "NextSeq2000", - "Affy6.0", - "HiSeq1000", - "IlluminaHumanMethylation450", - "Olink Target 96", - "Q Exactive HF", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "NanostringnCounter", - "PacBio Sequel II", - "Affy5.0", - "Roche Cobas", - "llumina Infinium General Screening Array 24-Kit v3.0", - "MiSeq", - "Orbitrap Exploris 240", - "Illumina_Omni5M", - "Infinium Omni2.5Exome-8 v1.3", - "quadrupole time-of-flight", - "NanostringnCounter_MouseADPanel", - "IlluminaNovaseq6000", - "confocalImaging", - "IlluminaHumanHT-12_V3_0_R1", - "NextSeq500", - "Xevo TQ-S", - "Infinium Omni2.5Exome-8 v1.1", - "Infinium Omni2.5Exome-8 v1.4", - "AffymetrixU133AB", - "InfiniumPsychArrayBeadChip", - "IlluminaMiSeq", - "Orbitrap Fusion Lumos", - "IlluminaWholeGenomeDASL", - "Illumina NovaSeq 6000", - "IlluminaHumanHap650Yv3_A", - "Signa Premier AIR 3T", - "Q Exactive", - "Infinium HumanOmniExpressExome", - "Infinium Global Diversity Array-8", - "Simoa HD-1 Analyzer", - "Bionano Irys", - "time-of-flight", - "triple quadrupole", - "Illumina_Omni2pt5M", - "HiSeq2500", - "IlluminaHumanHap300", - "OrbiTrap Fusion", - "Q Exactive HF-X", - "PacBioRSII" - ] - }, - "specimenID": {}, - "lotNumber": {}, - "readStrandOrigin": { + "runType": { "enum": [ - "forward", - "reverse", - "" + "pairedEnd", + "singleEnd" ] }, - "antibodyAmount": {}, "assayTarget": { "enum": [ - "CLOCK", - "KLF5", - "IE_V1-V3", - "H3K9me2", - "SIN3B", - "LaminB", - "NFIB", + "ZNF318", + "BMI1", + "TAF1", "HNRNPK", - "EWSR1", - "ZNF407", - "H3K4me3", - "NR2F1", - "H3K27ac", - "ARID1B", - "SATB2", - "YY1", - "ZEB1", - "NR3C1", - "input", - "RAD21", - "MAZ", - "H3K27me3", + "OLIG2", + "NONO", + "E2F1", + "NR2F2", + "IE_V1-V3", + "ARID3A", + "SKIL", + "ZFP91", + "YBX3", "BRD4", "DEAF1", - "ZNF143", "ASH2L", - "IgG", - "E2F1", - "NCOA2", - "EED", + "ZNF143", + "ARID1B", + "BRCA1", "FOXP1", - "ARID3A", + "ZNF384", + "NCOA2", + "ARNT", "H3K4me1", - "ATF7", - "GABPB1", - "KLF16", + "GMEB1", "TBR1", - "NRF1", - "BRCA1", - "SON", - "ASH1L", - "CREB1", - "TDP43", - "GATAD2B", - "SIRT1", - "SOX8", - "TAF1", - "ZNF24", - "NR2F2", - "GATA4", - "ZKSCAN1", - "MITF", - "ZNF318", - "SREBP2", - "SKIL", + "BHLHE41", + "H3K9ac", + "ZEB1", + "KLF16", "SMC3", - "TRIM28", - "DPF2", + "CHD4", "EHMT2", - "RB1", - "MEF2A", + "SP1", + "SIX4", + "ZNF592", + "IgG", + "TCF7L2", "SP4", - "ZFP91", - "ZEB2", - "BMI1", - "BHLHE40", - "ARNT", - "BHLHE41", - "NFIC", + "SIN3A", + "CREB1", + "GABPB1", "ZHX1", - "SIX4", - "ASCL1", - "GATAD2A", - "RELB", - "YBX3", - "FOXK2", - "YBX1", - "NCOR1", - "KAT2B", - "H3K9me3", - "R-loops", - "H3K36me3", - "EZH2", "ZNF207", - "SIN3A", - "CHD4", - "EGR1", - "Pol2", - "TCF7L2", - "PKNOX1", - "BCL11A", - "KDM4A", - "OLIG2", - "GMEB1", - "NONO", - "ZBTB7B", - "ZNF384", + "DPF2", + "H3K4me3", + "MEF2A", + "H3K27ac", + "SMARCA5", + "R-loops", + "EWSR1", + "H3K9me2", + "BCL11A", + "CC2D1A", + "KLF5", + "MAZ", + "TDP43", + "HCFC1", + "RELB", "ZSCAN29", - "CREM", + "GATAD2A", + "LaminB", + "ASCL1", + "H3K9me3", + "FOXK2", + "NCOR1", + "GATAD2B", "REST", - "HCFC1", - "TCF12", - "SRF", - "SP1", + "SATB2", + "H3K36me3", + "ASH1L", + "SREBP2", + "YBX1", + "BHLHE40", + "SON", + "H3K27me3", + "TRIM28", "NEUROD1", - "ZNF592", - "SMARCA5", - "CTCF", + "GATA4", + "RAD21", + "SOX8", + "ZNF407", + "KDM4A", + "CLOCK", + "PKNOX1", + "NR2F1", + "EGR1", + "EED", + "EZH2", + "SIRT1", + "CREM", + "YY1", + "SRF", + "RB1", + "NR3C1", + "SIN3B", + "TCF12", + "NFIB", + "ZNF24", + "ATF7", + "KAT2B", "MEIS2", - "H3K9ac", - "CC2D1A", + "ZKSCAN1", + "CTCF", + "MITF", + "NFIC", + "input", + "ZBTB7B", + "Pol2", + "ZEB2", + "NRF1", "" ] }, - "chromatinAmount": {}, + "totalReads": {}, "Component": {}, - "vendor": {}, + "sequencingBatch": {}, "assay": { "enum": [ + "oxBS-Seq", + "scrnaSeq", + "UC Davis GCTOF", + "westernBlot", + "wheel running", + "TMT quantitation", + "Baker Lipidomics", + "LC-SRM", + "pharmacokinetics", + "snATACSeq", + "exomeSeq", + "lentiMPRA", + "tractionForceMicroscopy", "elevated T maze apparatus method", + "lncrnaSeq", + "HPLC-MSMS", + "frailty assessment", + "Positron Emission Tomography", + "16SrRNAseq", + "Wishart Catecholamines", + "Biocrates p180", + "electrochemiluminescence", + "brightfieldMicroscopy", + "LTP", + "methylationArray", "MudPIT", - "immunofluorescence", - "UPLC-ESI-QTOF-MS", - "contextual conditioning behavior", - "rnaSeq", - "Genotyping", - "ChIPSeq", - "tractionForceMicroscopy", "UPLC-MSMS", - "snATACSeq", - "Wishart High Value Metabolites", - "kinesthetic behavior", - "long-read rnaSeq", - "FIA-MSMS", + "ChIPSeq", + "in vivo bioluminescence", "liquid chromatography-electrochemical detection", - "pharmacodynamics", - "HiChIPseq", - "scrnaSeq", + "scATACSeq", + "novelty response behavior", + "LFP", + "LC-MSMS", + "mirnaArray", + "snrnaSeq", + "Genotyping", + "atomicForceMicroscopy", + "errBisulfiteSeq", + "label free mass spectrometry", + "sandwich ELISA", "ELISA", - "Immunocytochemistry", + "Leiden Oxylipins", "ATACSeq", - "HI-C", - "electrochemiluminescence", + "Real Time PCR", + "NOMe-Seq", + "DIA", + "polymeraseChainReaction", + "scale", + "immunohistochemistry", + "Rader Lipidomics", "jumpingLibrary", - "wheel running", - "Baker Lipidomics", - "scirnaSeq", - "memory behavior", - "HPLC-MSMS", - "LC-MSMS", - "pharmacokinetics", - "TMT quantitation", - "anxiety-related behavior", + "RPPA", + "UCSD Untargeted Metabolomics", + "snpArray", "whole-cell patch clamp", - "Vernier Caliper", + "spontaneous alternation", + "nextGenerationTargetedSequencing", + "Zeno Electronic Walkway", + "UPLC-ESI-QTOF-MS", + "Biocrates Bile Acids", "LC-MS", - "rotarod performance test", + "anxiety-related behavior", + "Biocrates Q500", + "HiChIPseq", + "rnaSeq", + "Immunocytochemistry", "wholeGenomeSeq", - "Laser Speckle Imaging", "locomotor activation behavior", - "Metabolon", - "LFP", - "cellViabilityAssay", - "Positron Emission Tomography", - "m6A-rnaSeq", - "Biocrates Q500", - "DNA optical mapping", - "oxBS-Seq", - "westernBlot", - "lncrnaSeq", - "Wishart Catecholamines", - "Zeno Electronic Walkway", - "methylationArray", - "Biocrates p180", + "scirnaSeq", + "rotarod performance test", + "memory behavior", "scwholeGenomeSeq", - "Leiden Oxylipins", - "label free mass spectrometry", - "mirnaSeq", + "von Frey test", + "FitBark", + "bisulfiteSeq", + "Wishart High Value Metabolites", + "questionnaire", + "MIB/MS", "Blood Chemistry Measurement", - "active avoidance learning behavior", - "high content screen", - "CUT&Tag", - "mRNAcounts", + "kinesthetic behavior", + "Sanger sequencing", + "SiMoA", + "MDMS-SL", + "DNA optical mapping", + "Laser Speckle Imaging", + "microRNAcounts", + "Vernier Caliper", + "HI-C", "HPLC", - "Real Time PCR", - "CITESeq", - "atomicForceMicroscopy", "10x multiome", - "scATACSeq", + "open field test", + 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"PacBio Sequel IIe", - "Infinium HumanOmniExpressExome", - "Q Exactive Plus", + "AffymetrixU133AB", + "Biocrates p180", "Leco Pegasus IV", + "NextSeq500", + "OrbiTrap Fusion", + "Xevo TQ-S", + "GAIIx", + "Illumina NovaSeq 6000", + "IlluminaHumanMethylation450", + "Illumina MouseWG-6 v2.0 expression beadchip", + "Olink Target 96", "Illumina_Omni5M", - "time-of-flight", - "Bruker Avance III", - "Illumina_Omni2.5-8", "Q Exactive HF", + "Q Exactive Plus", + "Q Exactive", + "Roche Cobas", + "PacBio Sequel II", + "Illumina_Omni2pt5M", + "Infinium Global Diversity Array-8", + "IlluminaWholeGenomeDASL", + "Biograph mCT", "orbitrap", - "Biocrates p180", - "InfiniumPsychArrayBeadChip", + "Orbitrap Exploris 240", "HiSeqX", - "AffymetrixU133AB", - "Illumina_1M", - "Illumina NovaSeq 6000", - "IlluminaMiSeq", + "IlluminaHumanHap650Yv3_A", + "PacBio Sequel IIe", + "Affy6.0", "BGISEQ-500", - "GAIIx", - "Illumina_Omni5-Quad", - "AffymetrixU133Plus2", "Perlegen300Karray", - "Illumina_HumanOmni1-Quadv1.0", - "Olink Target 96", - "IlluminaHumanHap300", - "SequenomMultiplex", - "Simoa HD-1 Analyzer", - "Illumina_Omni2pt5M", - "Roche Cobas", - "Signa Premier AIR 3T", - "LTQOrbitrapXL", - "Q Exactive HF-X", - "Illumina_Omni2.5-8_v1.1", - "NanostringnCounter", - "Illumina_Omni2.5-8_v1.3", - "IlluminaInfiniumGSAMD-24v2-0", - "Infinium Omni2.5Exome-8 v1.1", + "Infinium Omni2.5Exome-8 v1.3", + "HiSeq4000", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "NextSeq2000", + "Infinium Omni2.5Exome-8 v1.4", + "Illumina_Omni2.5-8", + "Bionano Irys", + "InfiniumPsychArrayBeadChip", "IlluminaNovaseq6000", - "Affy5.0", + "ddSEQ Single-Cell Isolator", "HiSeq2000", - "Illumina MouseWG-6 v2.0 expression beadchip", - "PacBioRSII", - "Bionano Irys", - "triple quadrupole", + "IlluminaInfiniumGSAMD-24v2-0", + "PsychChip", + "NanostringnCounter", + "Illumina_Omni2.5-8_v1.1", "Xevo G2 QTOF", - "DNBSEQ", - "PacBio Sequel II", - "IlluminaHumanMethylation450", + "Q Exactive HF-X", + "Affy5.0", + "Illumina_Omni5-Quad", + "PacBioRSII", + "IlluminaMiSeq", + "AffymetrixU133Plus2", + "Bruker Avance III", "confocalImaging", - "NextSeq500", - "Illumina_h650", - "Xevo TQ-S", - "HiSeq2500", - "ddSEQ Single-Cell Isolator", - "Infinium Omni2.5Exome-8 v1.4", - "Orbitrap Fusion Lumos", - "Infinium Omni2.5Exome-8 v1.3", - "HiSeq3000", - "MiSeq", - "Infinium Global Diversity Array-8", - "Orbitrap Exploris 240", - "Affy6.0", - "NanostringnCounter_MouseADPanel", - "Agilent44Karray", - "quadrupole time-of-flight", - "Infinium Omni2.5Exome-8 v1.5", + "Illumina_1M", "llumina Infinium General Screening Array 24-Kit v3.0", - "HiSeq4000", - "Biograph mCT", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "IlluminaWholeGenomeDASL", - "Q Exactive", - "IlluminaMethylationEPIC" - ] - }, - "scanID": {}, - "ageAssessmentUnits": { - "enum": [ - "gestational weeks", - "PCW", - "weeks", - "months", - "days", - "years", - "" + "Illumina_Omni2.5-8_v1.3", + "NanostringnCounter_MouseADPanel", + "Infinium Omni2.5Exome-8 v1.1" ] } }, diff --git a/current-manifest-schemas/AD.AssayMetabolomicsMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayMetabolomicsMetadataTemplate.schema.json index 83e83c7..2105ac9 100644 --- a/current-manifest-schemas/AD.AssayMetabolomicsMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayMetabolomicsMetadataTemplate.schema.json @@ -4,281 +4,285 @@ "title": "AssayMetabolomicsMetadataTemplate", "type": "object", "properties": { - "platformLocation": {}, + "softwareName": {}, "Component": {}, - "metaboliteType": { + "assay": { "enum": [ - "sugars", - "carbohydrates", - "biogenic amines", - "catecholamine", - "phosphatidylethonalamines", - "lysophosphatidylcholine", - "lysophospholipids", - "ApoA1", - "steroids", - "ketones", - "glycerides", - "triglycerides", - "sterols", - "endocannabinoids", - "ceramides", - "amino acids", - "phospholipids", - "drugs", - "cholesterol", - "peptides", - "untargeted metabolomics", - "lipoproteins", - "oxylipins", - "bile acids", - "eicosanoids", - "phosphatidylcholine", - "ApoE", - "glycerolipid", - "glycerophospholipid", - "lipids", - "TCA cycle metabolites", - "fatty acids", - "xenobiotics", - "nucleotides", - "acylcarnitines", - "cofactors and vitamins", - "sphingolipids", - "acylglycerols", - "plasmalogens", - "" + "MIB/MS", + "wholeGenomeSeq", + "Rader Lipidomics", + "von Frey test", + "wheel running", + "UPLC-ESI-QTOF-MS", + "ChIPSeq", + "scCGIseq", + "ATACSeq", + "frailty assessment", + "TMT quantitation", + "LTP", + "HPLC-MSMS", + "photograph", + "Leiden Oxylipins", + "Zeno Electronic Walkway", + "Metabolon", + "questionnaire", + "microRNAcounts", + "CUT&Tag", + "electrochemiluminescence", + "HPLC", + "Biocrates p180", + "RPPA", + "Real Time PCR", + "immunohistochemistry", + "long-read rnaSeq", + "Biocrates Q500", + "STARRSeq", + "snATACSeq", + "atomicForceMicroscopy", + "FIA-MSMS", + "autoradiography", + "kinesthetic behavior", + "10x multiome", + "pharmacokinetics", + "contextual conditioning behavior", + "sandwich ELISA", + "scirnaSeq", + "mRNAcounts", + "polymeraseChainReaction", + "active avoidance learning behavior", + "elevated T maze apparatus method", + "novelty response behavior", + "brightfieldMicroscopy", + "oxBS-Seq", + "elevated plus maze test", + "bisulfiteSeq", + "SiMoA", + "scrnaSeq", + "Ribo-Seq", + "whole-cell patch clamp", + "rnaArray", + "proximity extension assay", + "in vivo bioluminescence", + "anxiety-related behavior", + "CITESeq", + "memory behavior", + "UCSD Untargeted Metabolomics", + "errBisulfiteSeq", + "Laser Speckle Imaging", + "high content screen", + "snrnaSeq", + "cellViabilityAssay", + "MudPIT", + "scATACSeq", + "Blood Chemistry Measurement", + "scale", + "ISOSeq", + "open field test", + "Wishart Catecholamines", + "16SrRNAseq", + "Nightingale NMR", + "m6A-rnaSeq", + "tractionForceMicroscopy", + "MDMS-SL", + "LFP", + "UPLC-MSMS", + "westernBlot", + "methylationArray", + "Sanger sequencing", + "lentiMPRA", + "Wishart High Value Metabolites", + "HI-C", + "FitBark", + "jumpingLibrary", + "LC-MS", + "MRI", + "locomotor activation behavior", + "rnaSeq", + "HiChIPseq", + "exomeSeq", + "Genotyping", + "Immunocytochemistry", + "rotarod performance test", + "Vernier Caliper", + "immunofluorescence", + "mirnaSeq", + "NOMe-Seq", + "Biocrates Bile Acids", + "Baker Lipidomics", + "nextGenerationTargetedSequencing", + "label free mass spectrometry", + "Positron Emission Tomography", + "liquid chromatography-electrochemical detection", + "mirnaArray", + "lncrnaSeq", + "ELISA", + "scwholeGenomeSeq", + "DNA optical mapping", + "snpArray", + "LC-MSMS", + "pharmacodynamics", + "DIA", + "UC Davis GCTOF", + "spontaneous alternation", + "LC-SRM" ] }, + "ionMode": {}, + "specimenID": {}, "spectrometerFrequency": {}, + "controlType": { + "enum": [ + "study pool", + "blank injection", + "water plus Baker ISTD", + "NIST SRM 1950", + "AIBL pool", + "Replicate", + "GIS", + "GoldenWest", + "qc mix", + "Baker pool", + "" + ] + }, + "platformLocation": {}, "batch": {}, - "ionMode": {}, + "batchSize": {}, + "metaboliteType": { + "type": "array", + "items": { + "enum": [ + "TCA cycle metabolites", + "cholesterol", + "glycerides", + "ApoA1", + "ceramides", + "phosphatidylcholine", + "glycerophospholipid", + "steroids", + "drugs", + "lysophospholipids", + "glycerolipid", + "lysophosphatidylcholine", + "ApoE", + "lipids", + "biogenic amines", + "sugars", + "fatty acids", + "plasmalogens", + "acylcarnitines", + "phosphatidylethonalamines", + "acylglycerols", + "oxylipins", + "catecholamine", + "eicosanoids", + "sterols", + "endocannabinoids", + "nucleotides", + "ketones", + "peptides", + "cofactors and vitamins", + "untargeted metabolomics", + "amino acids", + "carbohydrates", + "bile acids", + "lipoproteins", + "phospholipids", + "triglycerides", + "sphingolipids", + "xenobiotics", + "" + ] + }, + "maxItems": 39 + }, "platform": { "enum": [ - "PsychChip", - "IlluminaHumanMethylation450", - "Illumina_HumanOmni1-Quadv1.0", - "llumina Infinium General Screening Array 24-Kit v3.0", - "Agilent44Karray", - "Illumina_Omni2.5-8_v1.3", + "IlluminaMiSeq", + "IlluminaHumanHap300", + "AffymetrixU133AB", + "PacBio Sequel II", + "Q Exactive HF", + "DNBSEQ", + "HiSeq3000", + "IlluminaHumanHT-12_V3_0_R1", "Illumina NovaSeq 6000", - "NextSeq500", - "NextSeq2000", + "Biocrates p180", + "orbitrap", + "IlluminaHumanMethylation450", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "Illumina_h650", + "Illumina MouseWG-6 v2.0 expression beadchip", "Infinium Global Diversity Array-8", - "HiSeq4000", + "Infinium HumanOmniExpressExome", + "Q Exactive", + "Biograph mCT", + "Signa Premier AIR 3T", + "Orbitrap Fusion Lumos", + "PsychChip", + "Roche Cobas", + "Xevo G2 QTOF", + "IlluminaNovaseq6000", "BGISEQ-500", + "IlluminaInfiniumGSAMD-24v2-0", "NanostringnCounter", - "Infinium Omni2.5Exome-8 v1.3", - "Affymetrix Human Gene 1.0 ST Array", + "SequenomMultiplex", + "Illumina_Omni5M", + "MiSeq", + "AffymetrixU133Plus2", + "Illumina_1M", + "Olink Target 96", + "Infinium Omni2.5Exome-8 v1.1", + "HiSeq2000", + "Illumina_Omni2.5-8_v1.3", + "IlluminaMethylationEPIC", + "confocalImaging", "ddSEQ Single-Cell Isolator", - "Infinium HumanOmniExpressExome", - "IlluminaHumanHap650Yv3_A", - "quadrupole time-of-flight", - "IlluminaHumanHT-12_V3_0_R1", - "Illumina MouseWG-6 v2.0 expression beadchip", + "GAIIx", + "llumina Infinium General Screening Array 24-Kit v3.0", + "Infinium Omni2.5Exome-8 v1.4", "Perlegen300Karray", + "NextSeq500", + "Illumina_HumanOmni1-Quadv1.0", + "quadrupole time-of-flight", + "Orbitrap Exploris 240", + "Illumina_Omni5-Quad", + "PacBio Sequel IIe", "time-of-flight", - "Biocrates p180", - "Infinium Omni2.5Exome-8 v1.4", - "HiSeq2500", - "Q Exactive Plus", - "HiSeq1000", - "LTQOrbitrapXL", - "Olink Target 96", - "Infinium Omni2.5Exome-8 v1.1", + "Q Exactive HF-X", "Affy5.0", - "InfiniumPsychArrayBeadChip", + "HiSeq1000", + "IlluminaWholeGenomeDASL", "PacBioRSII", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "Q Exactive", - "triple quadrupole", - "IlluminaHumanHap300", - "IlluminaNovaseq6000", - "AffymetrixU133Plus2", "HiSeqX", - "MiSeq", - "Q Exactive HF-X", - "Affy6.0", - "NanostringnCounter_MouseADPanel", - "OrbiTrap Fusion", - "Simoa HD-1 Analyzer", - "Orbitrap Fusion Lumos", - "Q Exactive HF", - "SequenomMultiplex", - "orbitrap", - "PacBio Sequel II", - "DNBSEQ", - "confocalImaging", - "Illumina_h650", - "PacBio Sequel IIe", + "InfiniumPsychArrayBeadChip", + "NextSeq2000", + "triple quadrupole", + "Affymetrix Human Gene 1.0 ST Array", "Bionano Irys", - "Biograph mCT", - "HiSeq2000", - "IlluminaMethylationEPIC", - "Orbitrap Exploris 240", - "Illumina_Omni2.5-8_v1.1", - "Illumina_Omni5-Quad", - "IlluminaInfiniumGSAMD-24v2-0", - "Illumina_Omni2.5-8", - "IlluminaMiSeq", - "Xevo G2 QTOF", - "Illumina_1M", - "Bruker Avance III", + "HiSeq4000", + "Infinium Omni2.5Exome-8 v1.3", "Xevo TQ-S", + "Q Exactive Plus", + "LTQOrbitrapXL", + "OrbiTrap Fusion", + "Affy6.0", + "Simoa HD-1 Analyzer", "Leco Pegasus IV", - "Signa Premier AIR 3T", - "GAIIx", - "AffymetrixU133AB", - "HiSeq3000", - "Roche Cobas", + "Illumina_Omni2.5-8_v1.1", + "NanostringnCounter_MouseADPanel", + "IlluminaHumanHap650Yv3_A", "Infinium Omni2.5Exome-8 v1.5", - "Illumina_Omni5M", "Illumina_Omni2pt5M", - "IlluminaWholeGenomeDASL" - ] - }, - "softwareName": {}, - "controlType": { - "enum": [ - "Baker pool", - "NIST SRM 1950", - "AIBL pool", - "Replicate", - "GIS", - "study pool", - "blank injection", - "water plus Baker ISTD", - "qc mix", - "GoldenWest", - "" - ] - }, - "specimenID": {}, - "batchSize": {}, - "assay": { - "enum": [ - "snATACSeq", - "Laser Speckle Imaging", - "16SrRNAseq", - "rnaSeq", - "Leiden Oxylipins", - "memory behavior", - "mirnaSeq", - "rnaArray", - "mRNAcounts", - "scale", - "Real Time PCR", - "pharmacokinetics", - "polymeraseChainReaction", - "Biocrates Bile Acids", - "HPLC", - "RPPA", - "elevated plus maze test", - "anxiety-related behavior", - "westernBlot", - "10x multiome", - "brightfieldMicroscopy", - "snpArray", - "UPLC-MSMS", - "cellViabilityAssay", - "Rader Lipidomics", - "active avoidance learning behavior", - "exomeSeq", - "DNA optical mapping", - "high content screen", - "NOMe-Seq", - "methylationArray", - "LFP", - "oxBS-Seq", - "Ribo-Seq", - "FitBark", - "m6A-rnaSeq", - "HPLC-MSMS", - "LTP", - "MudPIT", - "proximity extension assay", - "UCSD Untargeted Metabolomics", - "von Frey test", - "kinesthetic behavior", - "rotarod performance test", - "Biocrates p180", - "snrnaSeq", - "elevated T maze apparatus method", - "Nightingale NMR", - "UPLC-ESI-QTOF-MS", - "wheel running", - "wholeGenomeSeq", - "immunofluorescence", - "in vivo bioluminescence", - "LC-MS", - "Sanger sequencing", - "immunohistochemistry", - "SiMoA", - "nextGenerationTargetedSequencing", - "Zeno Electronic Walkway", - "spontaneous alternation", - "frailty assessment", - "bisulfiteSeq", - "scwholeGenomeSeq", - "electrochemiluminescence", - "LC-MSMS", - "questionnaire", - "mirnaArray", - "locomotor activation behavior", - "Immunocytochemistry", - "scirnaSeq", - "lncrnaSeq", - "scrnaSeq", - "Wishart High Value Metabolites", - "LC-SRM", - "Metabolon", - "Wishart Catecholamines", - "CITESeq", - "CUT&Tag", - "DIA", - "MDMS-SL", - "lentiMPRA", - "microRNAcounts", - "MIB/MS", - "open field test", - "Positron Emission Tomography", - "sandwich ELISA", - "ISOSeq", - "atomicForceMicroscopy", - "Biocrates Q500", - "ChIPSeq", - "contextual conditioning behavior", - "tractionForceMicroscopy", - "scCGIseq", - "HI-C", - "ELISA", - "Vernier Caliper", - "long-read rnaSeq", - "scATACSeq", - "UC Davis GCTOF", - "MRI", - "Genotyping", - "photograph", - "errBisulfiteSeq", - "TMT quantitation", - "ATACSeq", - "label free mass spectrometry", - "Blood Chemistry Measurement", - "pharmacodynamics", - "whole-cell patch clamp", - "autoradiography", - "STARRSeq", - "Baker Lipidomics", - "HiChIPseq", - "liquid chromatography-electrochemical detection", - "FIA-MSMS", - "jumpingLibrary", - "novelty response behavior" + "Agilent44Karray", + "Illumina_Omni2.5-8", + "HiSeq2500", + "Bruker Avance III" ] } }, "required": [ - "platform", - "assay" + "assay", + "platform" ] } \ 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 196203d..2f00114 100644 --- a/current-manifest-schemas/AD.AssayMethylationArrayMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayMethylationArrayMetadataTemplate.schema.json @@ -4,223 +4,223 @@ "title": "AssayMethylationArrayMetadataTemplate", "type": "object", "properties": { - "Component": {}, - "SentrixID": {}, - "dnaBatch": {}, - "GQN": {}, + "SentrixRowColumn": {}, + "arrayBatch": {}, + "ratio260over230": {}, "specimenID": {}, - "platform": { - "enum": [ - "InfiniumPsychArrayBeadChip", - "HiSeq4000", - "IlluminaHumanMethylation450", - "time-of-flight", - "Illumina_Omni5M", - "IlluminaHumanHap650Yv3_A", - "Simoa HD-1 Analyzer", - "Illumina_HumanOmni1-Quadv1.0", - "Infinium Omni2.5Exome-8 v1.3", - "BGISEQ-500", - "HiSeq3000", - "Olink Target 96", - "NextSeq2000", - "AffymetrixU133Plus2", - "NanostringnCounter_MouseADPanel", - "Roche Cobas", - "IlluminaWholeGenomeDASL", - "GAIIx", - "Xevo TQ-S", - "Illumina_Omni2.5-8_v1.1", - "HiSeq2500", - "Infinium Omni2.5Exome-8 v1.4", - "SequenomMultiplex", - "Signa Premier AIR 3T", - "Orbitrap Exploris 240", - "confocalImaging", - "MiSeq", - "PsychChip", - "Leco Pegasus IV", - "Perlegen300Karray", - "triple quadrupole", - "IlluminaInfiniumGSAMD-24v2-0", - "Affy6.0", - "Orbitrap Fusion Lumos", - "PacBioRSII", - "Q Exactive Plus", - "HiSeq2000", - "IlluminaNovaseq6000", - "Illumina NovaSeq 6000", - "Infinium Global Diversity Array-8", - "LTQOrbitrapXL", - "Illumina_1M", - "Infinium Omni2.5Exome-8 v1.5", - "AffymetrixU133AB", - "IlluminaHumanHap300", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "Q Exactive HF", - "IlluminaMiSeq", - "Biocrates p180", - "Illumina_Omni5-Quad", - "Biograph mCT", - "HiSeq1000", - "Infinium Omni2.5Exome-8 v1.1", - "DNBSEQ", - "Q Exactive", - "NanostringnCounter", - "Illumina_Omni2pt5M", - "Bruker Avance III", - "orbitrap", - "Infinium HumanOmniExpressExome", - "Affymetrix Human Gene 1.0 ST Array", - "IlluminaHumanHT-12_V3_0_R1", - "Q Exactive HF-X", - "Illumina_h650", - "PacBio Sequel II", - "IlluminaMethylationEPIC", - "Xevo G2 QTOF", - "OrbiTrap Fusion", - "Illumina MouseWG-6 v2.0 expression beadchip", - "Illumina_Omni2.5-8_v1.3", - "Bionano Irys", - "NextSeq500", - "ddSEQ Single-Cell Isolator", - "Agilent44Karray", - "llumina Infinium General Screening Array 24-Kit v3.0", - "Illumina_Omni2.5-8", - "quadrupole time-of-flight", - "HiSeqX", - "PacBio Sequel IIe", - "Affy5.0" - ] - }, "ratio260over280": {}, + "dnaBatch": {}, "assay": { "enum": [ - "elevated plus maze test", - "16SrRNAseq", - "LC-MSMS", - "frailty assessment", - "Ribo-Seq", + "FitBark", + "DNA optical mapping", + "proximity extension assay", + "Biocrates p180", + "anxiety-related behavior", "RPPA", + "bisulfiteSeq", + "pharmacodynamics", + "LC-MS", + "CUT&Tag", + "scale", + "tractionForceMicroscopy", + "Laser Speckle Imaging", + "von Frey test", + "pharmacokinetics", + "scCGIseq", + "wholeGenomeSeq", + "ChIPSeq", + "DIA", + "ELISA", + "open field test", + "Immunocytochemistry", + "ATACSeq", + "LC-SRM", + "UPLC-MSMS", + "oxBS-Seq", + "HiChIPseq", + "contextual conditioning behavior", + "Rader Lipidomics", + "Biocrates Q500", + "snpArray", "scwholeGenomeSeq", - "FitBark", - "scATACSeq", - "Biocrates Bile Acids", "10x multiome", + "scrnaSeq", + "frailty assessment", + "STARRSeq", "photograph", - "MIB/MS", + "LFP", "polymeraseChainReaction", - "ELISA", - "Metabolon", - "MudPIT", - "STARRSeq", - "ChIPSeq", - "atomicForceMicroscopy", - "LTP", - "oxBS-Seq", - "pharmacokinetics", - "LC-MS", - "tractionForceMicroscopy", - "Blood Chemistry Measurement", + "Wishart High Value Metabolites", + "cellViabilityAssay", + "mirnaArray", + "rnaSeq", + "kinesthetic behavior", + "lentiMPRA", "methylationArray", - "pharmacodynamics", - "contextual conditioning behavior", + "LTP", + "electrochemiluminescence", + "Metabolon", + "westernBlot", + "questionnaire", + "HPLC-MSMS", + "immunohistochemistry", + "elevated T maze apparatus method", + "Vernier Caliper", + "NOMe-Seq", "memory behavior", - "snATACSeq", - "HI-C", - "FIA-MSMS", "in vivo bioluminescence", - "scale", - "brightfieldMicroscopy", - "HiChIPseq", - "whole-cell patch clamp", - "Sanger sequencing", - "snpArray", - "UPLC-MSMS", - "Biocrates Q500", - "rotarod performance test", - "mirnaSeq", - "immunohistochemistry", - "microRNAcounts", - "Real Time PCR", - "rnaArray", - "rnaSeq", - "LC-SRM", - "UCSD Untargeted Metabolomics", + "Baker Lipidomics", + "high content screen", + "sandwich ELISA", + "UPLC-ESI-QTOF-MS", + "novelty response behavior", + "immunofluorescence", "spontaneous alternation", - "ATACSeq", + "scirnaSeq", + "Real Time PCR", "autoradiography", - "Positron Emission Tomography", - "MRI", - "exomeSeq", - "DNA optical mapping", - "von Frey test", - "liquid chromatography-electrochemical detection", - "TMT quantitation", - "CUT&Tag", + "errBisulfiteSeq", "active avoidance learning behavior", - "wholeGenomeSeq", + "Leiden Oxylipins", + "long-read rnaSeq", + "UCSD Untargeted Metabolomics", + "HI-C", + "label free mass spectrometry", + "MudPIT", + "Zeno Electronic Walkway", + "16SrRNAseq", + "m6A-rnaSeq", + "TMT quantitation", + "exomeSeq", + "LC-MSMS", + "CITESeq", + "Wishart Catecholamines", + "lncrnaSeq", + "MDMS-SL", + "Positron Emission Tomography", + "rnaArray", "mRNAcounts", + "microRNAcounts", + "UC Davis GCTOF", + "nextGenerationTargetedSequencing", + "liquid chromatography-electrochemical detection", + "snATACSeq", + "atomicForceMicroscopy", + "MRI", + "mirnaSeq", + "HPLC", + "Genotyping", + "Biocrates Bile Acids", + "Sanger sequencing", + "rotarod performance test", "ISOSeq", + "brightfieldMicroscopy", + "Ribo-Seq", + "elevated plus maze test", + "Blood Chemistry Measurement", + "wheel running", "SiMoA", - "HPLC", - "immunofluorescence", - "Vernier Caliper", - "Baker Lipidomics", - "open field test", + "whole-cell patch clamp", + "FIA-MSMS", "snrnaSeq", - "Immunocytochemistry", - "lentiMPRA", - "UC Davis GCTOF", - "bisulfiteSeq", - "scCGIseq", - "Wishart Catecholamines", - "HPLC-MSMS", - "cellViabilityAssay", - "Wishart High Value Metabolites", - "Biocrates p180", - "m6A-rnaSeq", - "Rader Lipidomics", - "mirnaArray", - "long-read rnaSeq", - "kinesthetic behavior", "Nightingale NMR", - "proximity extension assay", - "sandwich ELISA", - "novelty response behavior", - "electrochemiluminescence", - "Zeno Electronic Walkway", "locomotor activation behavior", - "DIA", - "elevated T maze apparatus method", - "Genotyping", - "scirnaSeq", - "questionnaire", - "LFP", - "wheel running", - "NOMe-Seq", - "Laser Speckle Imaging", - "scrnaSeq", - "anxiety-related behavior", - "nextGenerationTargetedSequencing", - "MDMS-SL", - "Leiden Oxylipins", - "lncrnaSeq", - "westernBlot", - "errBisulfiteSeq", - "CITESeq", - "UPLC-ESI-QTOF-MS", - "label free mass spectrometry", - "high content screen", - "jumpingLibrary" + "jumpingLibrary", + "scATACSeq", + "MIB/MS" ] }, - "SentrixRowColumn": {}, - "ratio260over230": {}, - "arrayBatch": {} + "Component": {}, + "SentrixID": {}, + "platform": { + "enum": [ + "NanostringnCounter_MouseADPanel", + "HiSeqX", + "Biocrates p180", + "GAIIx", + "Affymetrix Human Gene 1.0 ST Array", + "Signa Premier AIR 3T", + "HiSeq1000", + "IlluminaMethylationEPIC", + "NanostringnCounter", + "IlluminaMiSeq", + "AffymetrixU133Plus2", + "BGISEQ-500", + "PacBio Sequel IIe", + "confocalImaging", + "SequenomMultiplex", + "DNBSEQ", + "Illumina_h650", + "IlluminaHumanHap300", + "Biograph mCT", + "Affy5.0", + "PacBio Sequel II", + "Bruker Avance III", + "Illumina_Omni2.5-8_v1.3", + "Affy6.0", + "NextSeq2000", + "Q Exactive", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "Roche Cobas", + "Infinium Omni2.5Exome-8 v1.5", + "Simoa HD-1 Analyzer", + "Illumina_HumanOmni1-Quadv1.0", + "Bionano Irys", + "HiSeq4000", + "IlluminaHumanHT-12_V3_0_R1", + "ddSEQ Single-Cell Isolator", + "IlluminaInfiniumGSAMD-24v2-0", + "Illumina_Omni5-Quad", + "MiSeq", + "PacBioRSII", + "IlluminaHumanHap650Yv3_A", + "PsychChip", + "Agilent44Karray", + "IlluminaHumanMethylation450", + "Illumina_Omni2.5-8", + "Q Exactive Plus", + "Olink Target 96", + "LTQOrbitrapXL", + "Illumina_Omni5M", + "Illumina MouseWG-6 v2.0 expression beadchip", + "Infinium Global Diversity Array-8", + "IlluminaNovaseq6000", + "Infinium Omni2.5Exome-8 v1.4", + "Infinium HumanOmniExpressExome", + "HiSeq3000", + "Illumina_Omni2pt5M", + "triple quadrupole", + "Xevo TQ-S", + "Infinium Omni2.5Exome-8 v1.3", + "Illumina_Omni2.5-8_v1.1", + "Leco Pegasus IV", + "AffymetrixU133AB", + "InfiniumPsychArrayBeadChip", + "Q Exactive HF-X", + "Illumina NovaSeq 6000", + "HiSeq2000", + "Xevo G2 QTOF", + "HiSeq2500", + "Illumina_1M", + "Orbitrap Fusion Lumos", + "orbitrap", + "NextSeq500", + "time-of-flight", + "quadrupole time-of-flight", + "Infinium Omni2.5Exome-8 v1.1", + "Q Exactive HF", + "IlluminaWholeGenomeDASL", + "Perlegen300Karray", + "Orbitrap Exploris 240", + "llumina Infinium General Screening Array 24-Kit v3.0", + "OrbiTrap Fusion" + ] + }, + "GQN": {} }, "required": [ - "platform", - "assay" + "assay", + "platform" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.AssayNanostringMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayNanostringMetadataTemplate.schema.json index 4074730..995e721 100644 --- a/current-manifest-schemas/AD.AssayNanostringMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayNanostringMetadataTemplate.schema.json @@ -4,268 +4,268 @@ "title": "AssayNanostringMetadataTemplate", "type": "object", "properties": { - "libraryPrep": { + "assay": { "enum": [ - "polyAselection", - "snIsoSeq", - "PCRfree", - "rRNAdepletion", - "proximity ligation", + "lentiMPRA", + "lncrnaSeq", + "scATACSeq", + "scwholeGenomeSeq", + "Zeno Electronic Walkway", + "tractionForceMicroscopy", + "nextGenerationTargetedSequencing", + "RPPA", + "HiChIPseq", + "questionnaire", + "von Frey test", + "novelty response behavior", + "in vivo bioluminescence", + "Laser Speckle Imaging", + "scCGIseq", + "westernBlot", + "high content screen", + "ATACSeq", + "electrochemiluminescence", + "Nightingale NMR", + "ChIPSeq", + "cellViabilityAssay", + "jumpingLibrary", + "exomeSeq", + "Ribo-Seq", + "snrnaSeq", + "long-read rnaSeq", + "Biocrates p180", + "scirnaSeq", + "proximity extension assay", + "memory behavior", + "UPLC-MSMS", + "Sanger sequencing", + "LTP", + "ELISA", + "LFP", + "DIA", + "Leiden Oxylipins", + "MudPIT", + "bisulfiteSeq", + "locomotor activation behavior", + "mirnaArray", + "CUT&Tag", + "MRI", + "frailty assessment", + "photograph", + "errBisulfiteSeq", + "Rader Lipidomics", + "pharmacokinetics", + "kinesthetic behavior", + "wholeGenomeSeq", + "Genotyping", + "Real Time PCR", + "SiMoA", + "contextual conditioning behavior", + "elevated T maze apparatus method", + "TMT quantitation", + "pharmacodynamics", + "microRNAcounts", + "whole-cell patch clamp", + "LC-SRM", + "sandwich ELISA", + "HPLC", + "UC Davis GCTOF", + "immunohistochemistry", + "active avoidance learning behavior", + "m6A-rnaSeq", + "UPLC-ESI-QTOF-MS", + "atomicForceMicroscopy", + "wheel running", + "MIB/MS", + "LC-MSMS", + "Biocrates Bile Acids", + "LC-MS", + "polymeraseChainReaction", + "label free mass spectrometry", + "rnaSeq", + "DNA optical mapping", + "Positron Emission Tomography", + "MDMS-SL", + "snpArray", + "Wishart High Value Metabolites", + "oxBS-Seq", + "brightfieldMicroscopy", + "HPLC-MSMS", + "anxiety-related behavior", + "FIA-MSMS", + "Baker Lipidomics", + "NOMe-Seq", + "snATACSeq", + "HI-C", + "16SrRNAseq", + "Biocrates Q500", + "mirnaSeq", + "CITESeq", + "spontaneous alternation", + "Metabolon", + "elevated plus maze test", + "Blood Chemistry Measurement", + "rnaArray", + "methylationArray", + "10x multiome", + "FitBark", + "immunofluorescence", + "liquid chromatography-electrochemical detection", "STARRSeq", - "SPLITseq", - "methylSeq", - "amplicon", - "cellHashing", - "MULTIseq", - "DNALibraryConstruction", - "EndItDNAEndRepairKit", - "KapaHyperPrep", - "totalRNA", - "lncRNAenrichment", - "Chromium Single Cell 3'", - "multiome", - "miRNAenrichment", - "SureCell" + "mRNAcounts", + "ISOSeq", + "scale", + "Immunocytochemistry", + "Wishart Catecholamines", + "scrnaSeq", + "Vernier Caliper", + "open field test", + "UCSD Untargeted Metabolomics", + "rotarod performance test", + "autoradiography" ] }, "platform": { "enum": [ - "Illumina_HumanOmni1-Quadv1.0", - "Simoa HD-1 Analyzer", - "HiSeq3000", - "NextSeq2000", - "Illumina MouseWG-6 v2.0 expression beadchip", - "Bionano Irys", - "llumina Infinium General Screening Array 24-Kit v3.0", - "Illumina_Omni2.5-8_v1.1", + "Illumina_Omni2pt5M", + "Perlegen300Karray", + "Infinium HumanOmniExpressExome", + "IlluminaHumanMethylation450", + "PacBioRSII", + "BGISEQ-500", + "ddSEQ Single-Cell Isolator", "Orbitrap Fusion Lumos", - "Leco Pegasus IV", - "quadrupole time-of-flight", - "InfiniumPsychArrayBeadChip", - "PacBio Sequel IIe", - "HiSeqX", - "OrbiTrap Fusion", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "NanostringnCounter_MouseADPanel", "SequenomMultiplex", - "HiSeq2500", - "Illumina_Omni5-Quad", + "Leco Pegasus IV", "time-of-flight", - "IlluminaWholeGenomeDASL", - "HiSeq4000", + "Infinium Omni2.5Exome-8 v1.4", "Illumina_h650", - "IlluminaHumanHap650Yv3_A", - "Perlegen300Karray", - "Infinium Global Diversity Array-8", "Agilent44Karray", - "PacBio Sequel II", - "IlluminaNovaseq6000", - "PacBioRSII", - "Illumina_Infinium-HumanMethylation450-BeadChip", - 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NovaSeq 6000", - "BGISEQ-500", + "Xevo G2 QTOF", "Bruker Avance III", + "Illumina_1M", + "Infinium Omni2.5Exome-8 v1.3", + "AffymetrixU133Plus2", "Orbitrap Exploris 240", - "Xevo G2 QTOF", - "ddSEQ Single-Cell Isolator", - "IlluminaInfiniumGSAMD-24v2-0", - "orbitrap", - "Biograph mCT", + "Q Exactive", + "InfiniumPsychArrayBeadChip", + "Q Exactive Plus", + "Infinium Omni2.5Exome-8 v1.5", + "IlluminaNovaseq6000", + "LTQOrbitrapXL", + "Illumina_Omni2.5-8_v1.1", + "NanostringnCounter", + "PacBio Sequel IIe", "Illumina_Omni2.5-8_v1.3", - "AffymetrixU133Plus2", + "IlluminaMethylationEPIC", + "orbitrap", + "IlluminaMiSeq", + "llumina Infinium General Screening Array 24-Kit v3.0", + "Simoa HD-1 Analyzer", + "triple quadrupole", + "NextSeq500", + "Illumina_Omni5M", + "Signa Premier AIR 3T", + "HiSeq4000", + "Illumina_Omni2.5-8", "PsychChip", + "Illumina_HumanOmni1-Quadv1.0", + "IlluminaHumanHap300", + "Infinium Global Diversity Array-8", + "Bionano Irys", + "confocalImaging", + "HiSeq3000", + "HiSeqX", + "Q Exactive HF", + "DNBSEQ", + "Biograph mCT", + "Q Exactive HF-X", + "OrbiTrap Fusion", + "PacBio Sequel II", + "HiSeq2500", + "quadrupole time-of-flight", + "HiSeq2000", "HiSeq1000", - "confocalImaging" + "Illumina NovaSeq 6000", + "Illumina MouseWG-6 v2.0 expression beadchip", + "IlluminaWholeGenomeDASL", + "NextSeq2000", + "IlluminaHumanHap650Yv3_A", + "Illumina_Omni5-Quad" ] }, + "RIN": {}, "specimenID": {}, - "Component": {}, - "geneRLF": {}, - "nanostringBatch": {}, - "bindingDensity": {}, "libraryBatch": {}, - "RIN": {}, "rnaBatch": {}, - "assay": { - "enum": [ - "ATACSeq", - "LC-SRM", - "Genotyping", - "sandwich ELISA", - "questionnaire", - "immunofluorescence", - "photograph", - "memory behavior", - "HI-C", - "long-read rnaSeq", - "novelty response behavior", - "16SrRNAseq", - "MIB/MS", - "methylationArray", - "LFP", - "ChIPSeq", - "pharmacokinetics", - "HiChIPseq", - "CUT&Tag", - "high content screen", - "CITESeq", - "UPLC-ESI-QTOF-MS", - "scirnaSeq", - "atomicForceMicroscopy", - "TMT quantitation", - "MudPIT", - "Sanger sequencing", - "ELISA", - "wheel running", - "Wishart Catecholamines", - "UPLC-MSMS", - "RPPA", - "jumpingLibrary", - "snpArray", - "von Frey test", - "scwholeGenomeSeq", - "in vivo bioluminescence", - "10x multiome", - "kinesthetic behavior", - "HPLC", - "elevated plus maze test", - "Biocrates Bile Acids", - "Leiden Oxylipins", - "Biocrates Q500", - "FitBark", - "cellViabilityAssay", - "lncrnaSeq", - "snrnaSeq", - "Baker Lipidomics", - "DIA", - "spontaneous alternation", - "ISOSeq", - "FIA-MSMS", - "Metabolon", - "errBisulfiteSeq", - "Blood Chemistry Measurement", - "scATACSeq", - "label free mass spectrometry", - "anxiety-related behavior", - "Wishart High Value Metabolites", - "lentiMPRA", - "Rader Lipidomics", - "pharmacodynamics", - "STARRSeq", - "rnaArray", - "liquid chromatography-electrochemical detection", - "MRI", - "locomotor activation behavior", - "proximity extension assay", - "mirnaSeq", - "Nightingale NMR", - "NOMe-Seq", - "bisulfiteSeq", - "scale", - "m6A-rnaSeq", - "immunohistochemistry", - "Ribo-Seq", - "rotarod performance test", - "LTP", - "westernBlot", - "open field test", - "tractionForceMicroscopy", - "frailty assessment", - "wholeGenomeSeq", - "Biocrates p180", - "DNA optical mapping", - "oxBS-Seq", - "whole-cell patch clamp", - "Laser Speckle Imaging", - "MDMS-SL", - "nextGenerationTargetedSequencing", - "microRNAcounts", - "Zeno Electronic Walkway", - "exomeSeq", - "scrnaSeq", - "brightfieldMicroscopy", - "mirnaArray", - "Real Time PCR", - "UCSD Untargeted Metabolomics", - "LC-MSMS", - "mRNAcounts", - "Positron Emission Tomography", - "autoradiography", - "active avoidance learning behavior", - "Immunocytochemistry", - "rnaSeq", - "scCGIseq", - "snATACSeq", - "contextual conditioning behavior", - "UC Davis GCTOF", - "Vernier Caliper", - "polymeraseChainReaction", - "elevated T maze apparatus method", - "HPLC-MSMS", - "LC-MS", - "electrochemiluminescence", - "SiMoA" - ] - }, + "nanostringBatch": {}, + "Component": {}, + "geneRLF": {}, "libraryPreparationMethod": { "enum": [ + "Accel-NGS Methyl-Seq", + "Omni-ATAC", + "Smart-seq1", "Smart-seq4", - "Drop-Seq", "Illumina DNA PCR-Free Prep Kit", + "Drop-Seq", "NEBNext", - "Smart-seq2", - "Accel-NGS 2S Plus", - "CEL-seq", "NexteraXT", - "Omni-ATAC", "TruSeq", "sac-seq", "Ultralow Methyl-Seq", - "Smart-seq1", - "SMRTbell", - "Accel-NGS Methyl-Seq", + "Accel-NGS 2S Plus", + "CEL-seq", "10x", + "SMRTbell", + "Smart-seq2", "" ] - } + }, + "libraryPrep": { + "enum": [ + "EndItDNAEndRepairKit", + "rRNAdepletion", + "polyAselection", + "cellHashing", + "lncRNAenrichment", + "proximity ligation", + "STARRSeq", + "SureCell", + "multiome", + "totalRNA", + "PCRfree", + "KapaHyperPrep", + "Chromium Single Cell 3'", + "methylSeq", + "SPLITseq", + "DNALibraryConstruction", + "amplicon", + "snIsoSeq", + "miRNAenrichment", + "MULTIseq" + ] + }, + "bindingDensity": {} }, "required": [ - "libraryPrep", + "assay", "platform", - "assay" + "libraryPrep" ] } \ 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 c382283..bea9f62 100644 --- a/current-manifest-schemas/AD.AssayPETMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayPETMetadataTemplate.schema.json @@ -6,109 +6,109 @@ "properties": { "platform": { "enum": [ - "Perlegen300Karray", - "NextSeq2000", - "Illumina_Omni2.5-8_v1.1", - "DNBSEQ", + "Infinium Omni2.5Exome-8 v1.4", "MiSeq", + "Illumina NovaSeq 6000", + "Infinium Omni2.5Exome-8 v1.1", + "confocalImaging", + "HiSeq2000", + "Q Exactive", + "IlluminaHumanHT-12_V3_0_R1", + "Signa Premier AIR 3T", "llumina Infinium General Screening Array 24-Kit v3.0", - "Illumina MouseWG-6 v2.0 expression beadchip", - "HiSeq1000", - "Bruker Avance III", - "Agilent44Karray", - "IlluminaInfiniumGSAMD-24v2-0", - "Biocrates p180", - "NanostringnCounter", - "SequenomMultiplex", - "IlluminaHumanHap650Yv3_A", - "quadrupole time-of-flight", + "Simoa HD-1 Analyzer", "PsychChip", - "Roche Cobas", - "HiSeq3000", - "Infinium Omni2.5Exome-8 v1.3", - "Illumina_1M", - "Q Exactive", + "Illumina_Omni5-Quad", "Illumina_Infinium-HumanMethylation450-BeadChip", - "OrbiTrap Fusion", - "Infinium HumanOmniExpressExome", - "Q Exactive HF", + "Illumina_HumanOmni1-Quadv1.0", + "IlluminaHumanHap300", + "ddSEQ Single-Cell Isolator", "AffymetrixU133Plus2", - "AffymetrixU133AB", - "PacBio Sequel IIe", + "quadrupole time-of-flight", + "HiSeq3000", + "Bruker Avance III", + "time-of-flight", + "Illumina_Omni5M", + "Perlegen300Karray", + "Q Exactive HF", + "HiSeq4000", + "Infinium Omni2.5Exome-8 v1.3", + "BGISEQ-500", + "SequenomMultiplex", + "Illumina_Omni2pt5M", "Biograph mCT", - "HiSeq2000", - "triple quadrupole", - "Illumina_Omni5-Quad", - "LTQOrbitrapXL", - "Bionano Irys", - "confocalImaging", "NextSeq500", - "Orbitrap Fusion Lumos", - "GAIIx", - "Infinium Omni2.5Exome-8 v1.4", - "Illumina_Omni2pt5M", "Q Exactive Plus", - "HiSeq4000", - "HiSeqX", - "IlluminaWholeGenomeDASL", - "InfiniumPsychArrayBeadChip", - "Infinium Omni2.5Exome-8 v1.1", "Affy6.0", + "IlluminaWholeGenomeDASL", + "GAIIx", + "Illumina_Omni2.5-8", + "IlluminaHumanMethylation450", + "Illumina_Omni2.5-8_v1.1", + "LTQOrbitrapXL", + "Orbitrap Exploris 240", + "Illumina MouseWG-6 v2.0 expression beadchip", + "NanostringnCounter", + "Xevo TQ-S", + "IlluminaInfiniumGSAMD-24v2-0", + "HiSeq1000", + "Illumina_Omni2.5-8_v1.3", "Infinium Global Diversity Array-8", + "Xevo G2 QTOF", + "triple quadrupole", "HiSeq2500", - "IlluminaMiSeq", - "IlluminaHumanHap300", - "ddSEQ Single-Cell Isolator", + "InfiniumPsychArrayBeadChip", + "NextSeq2000", "Illumina_h650", - "IlluminaMethylationEPIC", + "IlluminaHumanHap650Yv3_A", + "Bionano Irys", + "Biocrates p180", + "Roche Cobas", "IlluminaNovaseq6000", - "Affy5.0", - "Illumina_Omni2.5-8_v1.3", - "IlluminaHumanMethylation450", - "time-of-flight", - "PacBioRSII", - "Infinium Omni2.5Exome-8 v1.5", - "BGISEQ-500", - "Olink Target 96", + "Infinium HumanOmniExpressExome", + "HiSeqX", "NanostringnCounter_MouseADPanel", - "PacBio Sequel II", - "IlluminaHumanHT-12_V3_0_R1", + "IlluminaMethylationEPIC", + "AffymetrixU133AB", + "Olink Target 96", "orbitrap", - "Orbitrap Exploris 240", - "Illumina_Omni2.5-8", - "Xevo G2 QTOF", - "Leco Pegasus IV", - "Xevo TQ-S", - "Illumina NovaSeq 6000", - "Simoa HD-1 Analyzer", - "Illumina_Omni5M", - "Signa Premier AIR 3T", + "Agilent44Karray", "Affymetrix Human Gene 1.0 ST Array", - "Illumina_HumanOmni1-Quadv1.0", - "Q Exactive HF-X" + "Illumina_1M", + "Orbitrap Fusion Lumos", + "DNBSEQ", + "PacBio Sequel IIe", + "PacBioRSII", + "Affy5.0", + "Leco Pegasus IV", + "PacBio Sequel II", + "IlluminaMiSeq", + "OrbiTrap Fusion", + "Q Exactive HF-X", + "Infinium Omni2.5Exome-8 v1.5" ] }, - "individualID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "scanID": {}, "ageAssessmentUnits": { "enum": [ - "days", - "gestational weeks", "months", + "gestational weeks", "PCW", - "weeks", "years", + "days", + "weeks", "" ] }, - "ageAssessment": {}, "Component": {}, - "ligand": {} + "individualID": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "ageAssessment": {}, + "ligand": {}, + "scanID": {} }, "required": [ "platform", diff --git a/current-manifest-schemas/AD.AssayRnaArrayMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayRnaArrayMetadataTemplate.schema.json index 24a11af..ae4fd26 100644 --- a/current-manifest-schemas/AD.AssayRnaArrayMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayRnaArrayMetadataTemplate.schema.json @@ -4,216 +4,216 @@ "title": "AssayRnaArrayMetadataTemplate", "type": "object", "properties": { - "rnaBatch": {}, + "RIN": {}, + "specimenID": {}, "platform": { "enum": [ - "AffymetrixU133Plus2", - "Olink Target 96", - "Infinium Omni2.5Exome-8 v1.4", - "Infinium Omni2.5Exome-8 v1.5", + "OrbiTrap Fusion", + "Illumina_h650", "Illumina 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"wholeGenomeSeq", + "16SrRNAseq", + "autoradiography", + "errBisulfiteSeq", + "HI-C", + "lncrnaSeq", + "novelty response behavior", + "elevated plus maze test", + "Baker Lipidomics", + "bisulfiteSeq", "Metabolon", - "whole-cell patch clamp", - "UPLC-MSMS", - "LC-MS", - "ATACSeq", - "m6A-rnaSeq", - "HiChIPseq", - "LC-MSMS", - "Immunocytochemistry", - "scirnaSeq", - "ELISA", - "cellViabilityAssay", - "Rader Lipidomics", - "rnaArray", - "ISOSeq", "immunofluorescence", - "snATACSeq", - "scATACSeq", - "wholeGenomeSeq", - "FitBark", - "open field test", - "von Frey test", - "nextGenerationTargetedSequencing", - "brightfieldMicroscopy", - "liquid chromatography-electrochemical detection", - "MIB/MS", + "CUT&Tag", + "westernBlot", "MudPIT", - "jumpingLibrary", - "polymeraseChainReaction", - "10x multiome", + "UPLC-MSMS", + "mirnaSeq", "tractionForceMicroscopy", - "microRNAcounts", - "HI-C", - "Biocrates p180", - "Leiden Oxylipins", - "sandwich ELISA", - "frailty assessment", - "Nightingale NMR", - "scale", - "UC Davis GCTOF", - "STARRSeq", - "electrochemiluminescence", + "von Frey test", + "Vernier Caliper", "locomotor activation behavior", + "HPLC-MSMS", + "MIB/MS", + "Leiden Oxylipins", + "Positron Emission Tomography", + "scwholeGenomeSeq", + "FitBark", + "UCSD Untargeted Metabolomics", + "m6A-rnaSeq", + "polymeraseChainReaction", + "open field test", + "brightfieldMicroscopy", "elevated T maze apparatus method", - "FIA-MSMS", + "long-read rnaSeq", + "nextGenerationTargetedSequencing", + "HPLC", + "scATACSeq", + "jumpingLibrary", + "Rader Lipidomics", "memory behavior", - "errBisulfiteSeq", + "Immunocytochemistry", + "whole-cell patch clamp", + "methylationArray", + "atomicForceMicroscopy", "questionnaire", + "frailty assessment", + "scrnaSeq", + "Wishart Catecholamines", + "Ribo-Seq", + "high content screen", + "rnaSeq", + "ATACSeq", + "anxiety-related behavior", + "LTP", + "LFP", + "Sanger sequencing", + "DIA", "MDMS-SL", - "Real Time PCR", - "MRI", - "immunohistochemistry", + "ISOSeq", + "CITESeq", + "proximity extension assay", + "10x multiome", + "electrochemiluminescence", + "LC-MSMS", + "Laser Speckle Imaging", + "Biocrates Q500", + "Blood Chemistry Measurement", + "ELISA", "active avoidance learning behavior", - "exomeSeq", - "LFP", - "Biocrates Bile Acids", + "TMT quantitation", + "photograph", + "scCGIseq", + "Biocrates p180", + "LC-SRM", + "FIA-MSMS", + "ChIPSeq", + "Nightingale NMR", + "contextual conditioning behavior", + "UPLC-ESI-QTOF-MS", + "scale", "mirnaArray", - "HPLC", - "westernBlot", - "autoradiography", - "mirnaSeq", + "STARRSeq", + "snpArray", + "UC Davis GCTOF", + "Genotyping", + "LC-MS", "in vivo bioluminescence", - "UPLC-ESI-QTOF-MS", - "anxiety-related behavior", - "Positron Emission Tomography", - "long-read rnaSeq", - "ChIPSeq", - "TMT quantitation", - "HPLC-MSMS", - "snrnaSeq", - "mRNAcounts", - "LTP", + "liquid chromatography-electrochemical detection", + "Zeno Electronic Walkway", + "Biocrates Bile Acids", + "snATACSeq", "wheel running", - "lncrnaSeq", - "proximity extension assay", - "16SrRNAseq", + "oxBS-Seq", + "mRNAcounts", + "Real Time PCR", + "SiMoA", + "snrnaSeq", + "NOMe-Seq", + "label free mass spectrometry", + "microRNAcounts", "Wishart High Value Metabolites", - "Wishart Catecholamines", - "rnaSeq", - "lentiMPRA", - "spontaneous alternation", - "Ribo-Seq", - "Sanger sequencing", - "contextual conditioning behavior", - "atomicForceMicroscopy", - "photograph", - "DNA optical mapping", - "Zeno Electronic Walkway", - "CITESeq", - "UCSD Untargeted Metabolomics", - "Genotyping", - "kinesthetic behavior" + "immunohistochemistry", + "scirnaSeq", + "kinesthetic behavior", + "rotarod performance test", + "sandwich ELISA" ] }, - "arrayBatch": {}, - "RIN": {}, - "Component": {}, - "specimenID": {} + "arrayBatch": {} }, "required": [ "platform", diff --git a/current-manifest-schemas/AD.AssayRnaSeqMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayRnaSeqMetadataTemplate.schema.json index d4f3c5a..13d69b9 100644 --- a/current-manifest-schemas/AD.AssayRnaSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayRnaSeqMetadataTemplate.schema.json @@ -5,310 +5,310 @@ "type": "object", "properties": { "libraryVersion": {}, - "Component": {}, + "sequencingBatch": {}, + "libraryPreparationMethod": { + "enum": [ + "Accel-NGS Methyl-Seq", + "Illumina DNA PCR-Free Prep Kit", + "CEL-seq", + "Smart-seq2", + "TruSeq", + "Smart-seq4", + "Ultralow Methyl-Seq", + "Omni-ATAC", + "Drop-Seq", + "Accel-NGS 2S Plus", + "NexteraXT", + "Smart-seq1", + "SMRTbell", + "sac-seq", + "10x", + "NEBNext", + "" + ] + }, + "totalReads": {}, + "validBarcodeReads": {}, + "DV200": {}, "rnaBatch": {}, "runType": { "enum": [ - "pairedEnd", - "singleEnd" + "singleEnd", + "pairedEnd" ] }, - "libraryBatch": {}, - "readLength": { - "not": { - "type": "null" - }, - "minLength": 1 + "libraryID": {}, + "platform": { + "enum": [ + "IlluminaInfiniumGSAMD-24v2-0", + "ddSEQ Single-Cell Isolator", + "OrbiTrap Fusion", + "DNBSEQ", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "SequenomMultiplex", + "HiSeq3000", + "Q Exactive HF", + "NanostringnCounter", + "NanostringnCounter_MouseADPanel", + "orbitrap", + "Infinium Omni2.5Exome-8 v1.5", + "Illumina_Omni2.5-8", + "confocalImaging", + "HiSeq4000", + "quadrupole time-of-flight", + "PacBio Sequel IIe", + "IlluminaHumanHT-12_V3_0_R1", + "Infinium Omni2.5Exome-8 v1.4", + "Bruker Avance III", + "IlluminaHumanHap650Yv3_A", + "Infinium Omni2.5Exome-8 v1.1", + "IlluminaHumanHap300", + "Affy6.0", + "HiSeqX", + "IlluminaMiSeq", + "Biograph mCT", + "Infinium HumanOmniExpressExome", + "Q Exactive Plus", + "Illumina_1M", + "Affy5.0", + "Simoa HD-1 Analyzer", + "NextSeq500", + "InfiniumPsychArrayBeadChip", + "Illumina_HumanOmni1-Quadv1.0", + "Signa Premier AIR 3T", + "Illumina_Omni5-Quad", + "IlluminaWholeGenomeDASL", + "Perlegen300Karray", + "Infinium Omni2.5Exome-8 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+ ] + }, + "readStrandOrigin": { + "enum": [ + "reverse", + "forward", "" ] }, "libraryPrep": { "enum": [ - "STARRSeq", - "KapaHyperPrep", - "PCRfree", - "proximity ligation", - "amplicon", - "SPLITseq", "multiome", "DNALibraryConstruction", - "SureCell", - "EndItDNAEndRepairKit", - "snIsoSeq", - "miRNAenrichment", - "lncRNAenrichment", - "Chromium Single Cell 3'", + "proximity ligation", "methylSeq", - "totalRNA", + "MULTIseq", "cellHashing", + "Chromium Single Cell 3'", + "rRNAdepletion", + "amplicon", + "miRNAenrichment", + "snIsoSeq", + "KapaHyperPrep", "polyAselection", - "MULTIseq", - "rRNAdepletion" - ] - }, - "libraryID": {}, - "specimenID": {}, - "libraryPreparationMethod": { - "enum": [ - "10x", - "TruSeq", - "Omni-ATAC", - "Illumina DNA PCR-Free Prep Kit", - "NexteraXT", - "SMRTbell", - "Smart-seq1", - "Drop-Seq", - "sac-seq", - "Ultralow Methyl-Seq", - "Accel-NGS Methyl-Seq", - "Accel-NGS 2S Plus", - "Smart-seq2", - "Smart-seq4", - "CEL-seq", - "NEBNext", - "" + "totalRNA", 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"platform", "libraryPrep", "assay", - "platform" + "readLength" ] } \ 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 5c998bc..37b9d02 100644 --- a/current-manifest-schemas/AD.AssaySTARRSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssaySTARRSeqMetadataTemplate.schema.json @@ -4,60 +4,177 @@ "title": "AssaySTARRSeqMetadataTemplate", "type": "object", "properties": { + "dnaBatch": {}, + "runType": { + "enum": [ + "pairedEnd", + "singleEnd" + ] + }, + "rnaBatch": {}, + "libraryID": {}, + "sequencingBatch": {}, + "referenceSet": { + "enum": [ + "GRCh38", + "GRCh37", + "GRCm38", + "MMUL1.0", + "HRC", + "dmel_r6.06", + "1000 Genomes phase 3", + "" + ] + }, + "libraryVersion": {}, + "Component": {}, + "numberCells": {}, "libraryPrep": { "enum": [ - "EndItDNAEndRepairKit", - "MULTIseq", - "amplicon", + "Chromium Single Cell 3'", "SureCell", "snIsoSeq", + "STARRSeq", "polyAselection", "lncRNAenrichment", - "methylSeq", + "multiome", + "miRNAenrichment", + "KapaHyperPrep", "totalRNA", + "EndItDNAEndRepairKit", + "cellHashing", "PCRfree", "SPLITseq", - "miRNAenrichment", - "Chromium Single Cell 3'", - "cellHashing", "rRNAdepletion", - "KapaHyperPrep", - "DNALibraryConstruction", + "amplicon", "proximity ligation", - "multiome", - "STARRSeq" + "DNALibraryConstruction", + "methylSeq", + "MULTIseq" ] }, - "readLength": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "libraryPreparationMethod": { + "validBarcodeReads": {}, + "assay": { "enum": [ - "Accel-NGS 2S Plus", - "SMRTbell", - "Illumina DNA PCR-Free Prep Kit", - "NexteraXT", - "Smart-seq4", - "Accel-NGS Methyl-Seq", - "10x", - "Smart-seq1", - "Ultralow Methyl-Seq", - "sac-seq", - "Drop-Seq", - "Omni-ATAC", - "NEBNext", - "TruSeq", - "CEL-seq", - "Smart-seq2", - "" + "Immunocytochemistry", + "Leiden Oxylipins", + "nextGenerationTargetedSequencing", + "HPLC-MSMS", + "SiMoA", + "kinesthetic behavior", + "STARRSeq", + "HI-C", + "ISOSeq", + "electrochemiluminescence", + "tractionForceMicroscopy", + "Biocrates p180", + "UC Davis GCTOF", + "LC-SRM", + "photograph", + "scwholeGenomeSeq", + "Wishart High Value Metabolites", + "LC-MS", + "autoradiography", + "label free mass spectrometry", + "DIA", + "snATACSeq", + "microRNAcounts", + "wholeGenomeSeq", + "10x multiome", + "LTP", + "questionnaire", + "Real Time PCR", + "HPLC", + "immunofluorescence", + "in vivo bioluminescence", + "m6A-rnaSeq", + "Laser Speckle Imaging", + "elevated plus maze test", + "lncrnaSeq", + "elevated T maze apparatus method", + "brightfieldMicroscopy", + "locomotor activation behavior", + "immunohistochemistry", + "Metabolon", + "mirnaSeq", + "MRI", + "rotarod performance test", + "TMT quantitation", + "Nightingale NMR", + "LC-MSMS", + "jumpingLibrary", + "CITESeq", + "NOMe-Seq", + "scrnaSeq", + "active avoidance learning behavior", + "Zeno Electronic Walkway", + "UPLC-MSMS", + "whole-cell patch clamp", + "contextual conditioning behavior", + "scATACSeq", + "Sanger sequencing", + "ATACSeq", + "Genotyping", + "Positron Emission Tomography", + "oxBS-Seq", + "RPPA", + "FIA-MSMS", + "Baker Lipidomics", + "Blood Chemistry Measurement", + "methylationArray", + "polymeraseChainReaction", + "mirnaArray", + "long-read rnaSeq", + "Vernier Caliper", + "errBisulfiteSeq", + "CUT&Tag", + "Biocrates Q500", + "MIB/MS", + "LFP", + "memory behavior", + "Wishart Catecholamines", + "ChIPSeq", + "Biocrates Bile Acids", + "16SrRNAseq", + "UCSD Untargeted Metabolomics", + "mRNAcounts", + "scCGIseq", + "lentiMPRA", + "scirnaSeq", + "liquid chromatography-electrochemical detection", + "HiChIPseq", + "westernBlot", + "rnaArray", + "spontaneous alternation", + "Rader Lipidomics", + "DNA optical mapping", + "anxiety-related behavior", + "pharmacodynamics", + "cellViabilityAssay", + "exomeSeq", + "proximity extension assay", + "von Frey test", + "scale", + "novelty response behavior", + "high content screen", + "atomicForceMicroscopy", + "ELISA", + "sandwich ELISA", + "Ribo-Seq", + "rnaSeq", + "FitBark", + "snpArray", + "open field test", + "frailty assessment", + "MudPIT", + "snrnaSeq", + "UPLC-ESI-QTOF-MS", + "pharmacokinetics", + "bisulfiteSeq", + "wheel running", + "MDMS-SL" ] }, - "medianGenes": {}, - "ratio260over280": {}, - "dnaBatch": {}, "isStranded": { "enum": [ "FALSE", @@ -65,104 +182,122 @@ "" ] }, - "numberCells": {}, - "runType": { + "libraryPreparationMethod": { "enum": [ - "singleEnd", - "pairedEnd" + "TruSeq", + "Drop-Seq", + "Illumina DNA PCR-Free Prep Kit", + "Smart-seq4", + "CEL-seq", + "sac-seq", + "SMRTbell", + "Smart-seq2", + "NEBNext", + "Ultralow Methyl-Seq", + "10x", + "NexteraXT", + "Accel-NGS Methyl-Seq", + "Omni-ATAC", + "Smart-seq1", + "Accel-NGS 2S Plus", + "" ] }, - "specimenID": {}, - "sequencingBatch": {}, - "medianUMIs": {}, "libraryBatch": {}, - "rnaBatch": {}, + "medianUMIs": {}, + "totalReads": {}, + "RIN": {}, + "ratio260over280": {}, + "readLength": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "platform": { "enum": [ + "IlluminaHumanMethylation450", + "Infinium HumanOmniExpressExome", + "Illumina_1M", + "Biograph mCT", + "InfiniumPsychArrayBeadChip", "PsychChip", - "HiSeq4000", - "IlluminaHumanHap650Yv3_A", - "HiSeq2000", - "triple quadrupole", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "Orbitrap Exploris 240", - "Signa Premier AIR 3T", - "Affymetrix Human Gene 1.0 ST Array", - "DNBSEQ", - "time-of-flight", - "HiSeq2500", - "IlluminaNovaseq6000", - "HiSeqX", - "Illumina MouseWG-6 v2.0 expression beadchip", - "PacBio Sequel IIe", - "Illumina_Omni2.5-8_v1.3", - "Bionano Irys", - "LTQOrbitrapXL", - "IlluminaMiSeq", - "quadrupole time-of-flight", - "Illumina_Omni5M", - "Q Exactive HF-X", - "Orbitrap Fusion Lumos", - "IlluminaWholeGenomeDASL", - "Illumina_HumanOmni1-Quadv1.0", - "Leco Pegasus IV", + "Q Exactive Plus", + "HiSeq3000", + "Biocrates p180", + "NextSeq500", + "PacBio Sequel II", "Affy6.0", - "Q Exactive HF", - "MiSeq", - "Illumina_Omni5-Quad", - "NanostringnCounter", - "NanostringnCounter_MouseADPanel", "IlluminaMethylationEPIC", - "confocalImaging", - "AffymetrixU133AB", - "BGISEQ-500", - "Infinium Omni2.5Exome-8 v1.3", - "PacBio Sequel II", - "Simoa HD-1 Analyzer", - "Perlegen300Karray", + "Illumina_h650", "IlluminaHumanHap300", - "Biograph mCT", - "Roche Cobas", - "Q Exactive Plus", - "Illumina NovaSeq 6000", - "InfiniumPsychArrayBeadChip", - "IlluminaInfiniumGSAMD-24v2-0", - "HiSeq3000", - "Infinium Omni2.5Exome-8 v1.1", - "Infinium Global Diversity Array-8", + "Bruker Avance III", + "GAIIx", + "Illumina MouseWG-6 v2.0 expression beadchip", + "Q Exactive HF", + "Xevo G2 QTOF", + "IlluminaWholeGenomeDASL", "Illumina_Omni2pt5M", - "NextSeq500", - "IlluminaHumanMethylation450", + "time-of-flight", + "Signa Premier AIR 3T", + "IlluminaNovaseq6000", + "HiSeq2000", + "IlluminaInfiniumGSAMD-24v2-0", + "SequenomMultiplex", + "Roche Cobas", + "confocalImaging", + "Infinium Omni2.5Exome-8 v1.3", + "NanostringnCounter_MouseADPanel", + "orbitrap", + "triple quadrupole", + "Illumina_Omni2.5-8_v1.3", + "Olink Target 96", + "HiSeq4000", + "llumina Infinium General Screening Array 24-Kit v3.0", "PacBioRSII", - "IlluminaHumanHT-12_V3_0_R1", + "Leco Pegasus IV", + "LTQOrbitrapXL", + "MiSeq", + "HiSeq1000", + "OrbiTrap Fusion", "Illumina_Omni2.5-8", - "Xevo G2 QTOF", - "GAIIx", + "Illumina NovaSeq 6000", + "Affy5.0", + "DNBSEQ", "Agilent44Karray", - "orbitrap", "ddSEQ Single-Cell Isolator", - "Q Exactive", - "Xevo TQ-S", + "AffymetrixU133AB", "Infinium Omni2.5Exome-8 v1.5", - "Olink Target 96", - "OrbiTrap Fusion", - "SequenomMultiplex", - "Illumina_h650", - "llumina Infinium General Screening Array 24-Kit v3.0", - "Illumina_1M", + "NanostringnCounter", + "Simoa HD-1 Analyzer", + "IlluminaHumanHap650Yv3_A", + "HiSeqX", + "quadrupole time-of-flight", + "Infinium Global Diversity Array-8", "Illumina_Omni2.5-8_v1.1", - "HiSeq1000", - "Affy5.0", - "Biocrates p180", - "Bruker Avance III", - "Infinium HumanOmniExpressExome", - "NextSeq2000", + "Perlegen300Karray", + "AffymetrixU133Plus2", + "Q Exactive", + "Affymetrix Human Gene 1.0 ST Array", + "Illumina_Omni5M", + "IlluminaMiSeq", + "Illumina_Omni5-Quad", "Infinium Omni2.5Exome-8 v1.4", - "AffymetrixU133Plus2" + "BGISEQ-500", + "Illumina_HumanOmni1-Quadv1.0", + "PacBio Sequel IIe", + "IlluminaHumanHT-12_V3_0_R1", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "Bionano Irys", + "NextSeq2000", + "Xevo TQ-S", + "Q Exactive HF-X", + "Orbitrap Exploris 240", + "HiSeq2500", + "Infinium Omni2.5Exome-8 v1.1", + "Orbitrap Fusion Lumos" ] }, - "libraryVersion": {}, - "ratio260over230": {}, "readStrandOrigin": { "enum": [ "reverse", @@ -170,151 +305,16 @@ "" ] }, - "assay": { - "enum": [ - "anxiety-related behavior", - "kinesthetic behavior", - "Blood Chemistry Measurement", - "scirnaSeq", - "pharmacodynamics", - "SiMoA", - "FitBark", - "Genotyping", - "immunohistochemistry", - "CITESeq", - "MIB/MS", - "atomicForceMicroscopy", - "MudPIT", - "rnaArray", - "DNA optical mapping", - "ISOSeq", - "proximity extension assay", - "sandwich ELISA", - "scale", - "electrochemiluminescence", - "locomotor activation behavior", - "methylationArray", - "LFP", - "jumpingLibrary", - "Biocrates Q500", - "STARRSeq", - "rotarod performance test", - "rnaSeq", - "UPLC-MSMS", - "TMT quantitation", - "pharmacokinetics", - "high content screen", - "scATACSeq", - "questionnaire", - "LTP", - "cellViabilityAssay", - "lentiMPRA", - "Laser Speckle Imaging", - "Metabolon", - "ELISA", - "snATACSeq", - "tractionForceMicroscopy", - "HPLC-MSMS", - "FIA-MSMS", - "LC-SRM", - "mRNAcounts", - "novelty response behavior", - "polymeraseChainReaction", - "ATACSeq", - "LC-MS", - "Leiden Oxylipins", - "label free mass spectrometry", - "von Frey test", - "errBisulfiteSeq", - "UPLC-ESI-QTOF-MS", - "elevated plus maze test", - "Wishart High Value Metabolites", - "DIA", - "scrnaSeq", - "mirnaArray", - "Vernier Caliper", - "Nightingale NMR", - "snrnaSeq", - "CUT&Tag", - "long-read rnaSeq", - "open field test", - "frailty assessment", - "NOMe-Seq", - "16SrRNAseq", - "brightfieldMicroscopy", - "HI-C", - "HPLC", - "mirnaSeq", - "autoradiography", - "MDMS-SL", - "MRI", - "immunofluorescence", - "ChIPSeq", - "Positron Emission Tomography", - "wheel running", - "lncrnaSeq", - "Ribo-Seq", - "Baker Lipidomics", - "UCSD Untargeted Metabolomics", - "active avoidance learning behavior", - "elevated T maze apparatus method", - "whole-cell patch clamp", - "Biocrates Bile Acids", - "bisulfiteSeq", - "microRNAcounts", - "m6A-rnaSeq", - "liquid chromatography-electrochemical detection", - "LC-MSMS", - "Immunocytochemistry", - "Real Time PCR", - "snpArray", - "wholeGenomeSeq", - "UC Davis GCTOF", - "spontaneous alternation", - "Wishart Catecholamines", - "scCGIseq", - "contextual conditioning behavior", - "RPPA", - "Rader Lipidomics", - "memory behavior", - "photograph", - "Biocrates p180", - "Zeno Electronic Walkway", - "10x multiome", - "westernBlot", - "exomeSeq", - "Sanger sequencing", - "in vivo bioluminescence", - "nextGenerationTargetedSequencing", - "oxBS-Seq", - "scwholeGenomeSeq", - "HiChIPseq" - ] - }, - "Component": {}, - "RIN": {}, - "validBarcodeReads": {}, - "totalReads": {}, + "ratio260over230": {}, + "specimenID": {}, "GQN": {}, - "libraryID": {}, - "referenceSet": { - "enum": [ - "GRCh38", - "MMUL1.0", - "GRCh37", - "HRC", - "dmel_r6.06", - "1000 Genomes phase 3", - "GRCm38", - "" - ] - } + "medianGenes": {} }, "required": [ + "runType", "libraryPrep", + "assay", "readLength", - "runType", - "platform", - "assay" + "platform" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.AssayScrnaSeqMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayScrnaSeqMetadataTemplate.schema.json index 99c58ef..feaa534 100644 --- a/current-manifest-schemas/AD.AssayScrnaSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayScrnaSeqMetadataTemplate.schema.json @@ -4,270 +4,276 @@ "title": "AssayScrnaSeqMetadataTemplate", "type": "object", "properties": { - "readLength": { - "not": { - "type": "null" - }, - "minLength": 1 + "libraryType": { + "enum": [ + "ADT", + "LMO", + "cDNA", + "HTO", + "CMO", + "plasmid DNA", + "" + ] + }, + "sampleBarcode": {}, + "RIN": {}, + "libraryPreparationMethod": { + "enum": [ + "Smart-seq4", + "Accel-NGS 2S Plus", + "Omni-ATAC", + "sac-seq", + "NexteraXT", + "Smart-seq2", + "Accel-NGS Methyl-Seq", + "10x", + "Illumina DNA PCR-Free Prep Kit", + "Smart-seq1", + "CEL-seq", + "NEBNext", + "Ultralow Methyl-Seq", + "Drop-Seq", + "TruSeq", + "SMRTbell", + "" + ] }, "assay": { "enum": [ - "electrochemiluminescence", - "HiChIPseq", - "memory behavior", - "CUT&Tag", - "SiMoA", - "exomeSeq", - "Blood Chemistry Measurement", - "MIB/MS", - "anxiety-related behavior", - "MudPIT", - "CITESeq", - "active avoidance learning behavior", - "von Frey test", - "wheel running", - "LC-MS", - "mirnaSeq", - "scirnaSeq", - "FIA-MSMS", - "label free mass spectrometry", - "mRNAcounts", - "in vivo bioluminescence", - "snATACSeq", - "oxBS-Seq", - "locomotor activation behavior", - "FitBark", - "LFP", - "atomicForceMicroscopy", + "rnaArray", + "16SrRNAseq", + "westernBlot", "LC-SRM", - "rotarod performance test", - "Baker Lipidomics", - "novelty response behavior", - "Rader Lipidomics", - "m6A-rnaSeq", - "MDMS-SL", - "polymeraseChainReaction", + "lentiMPRA", + "scirnaSeq", + "Genotyping", + "Immunocytochemistry", + "whole-cell patch clamp", + "10x multiome", "snpArray", - "Ribo-Seq", - "tractionForceMicroscopy", - "westernBlot", - "autoradiography", + "CITESeq", + "Wishart High Value Metabolites", + "pharmacodynamics", "ELISA", - "Leiden Oxylipins", - "MRI", + "high content screen", + "elevated plus maze test", + "snrnaSeq", + "Vernier Caliper", + "Zeno Electronic Walkway", + "Biocrates Q500", + "Ribo-Seq", "scale", - "elevated T maze apparatus method", - "rnaArray", - "Sanger sequencing", - "sandwich ELISA", + "photograph", + "locomotor activation behavior", + "polymeraseChainReaction", + "scATACSeq", "liquid chromatography-electrochemical detection", - "DIA", - "scwholeGenomeSeq", + "DNA optical mapping", + "pharmacokinetics", + "UC Davis GCTOF", + "electrochemiluminescence", "immunohistochemistry", + "von Frey test", + "bisulfiteSeq", + "Biocrates p180", "ISOSeq", - "HPLC", - "microRNAcounts", + "atomicForceMicroscopy", "errBisulfiteSeq", - "Wishart High Value Metabolites", - "ATACSeq", - "16SrRNAseq", - "Zeno Electronic Walkway", - "ChIPSeq", - "LTP", - "pharmacodynamics", - "Metabolon", - "Laser Speckle Imaging", - "bisulfiteSeq", - "STARRSeq", - "lncrnaSeq", + "LFP", + "UPLC-ESI-QTOF-MS", + "scwholeGenomeSeq", + "brightfieldMicroscopy", + "autoradiography", + "snATACSeq", + "kinesthetic behavior", "wholeGenomeSeq", - "Genotyping", - "methylationArray", - "UC Davis GCTOF", + "ATACSeq", + "HPLC-MSMS", + "active avoidance learning behavior", + "Blood Chemistry Measurement", + "MDMS-SL", "frailty assessment", - "Biocrates Bile Acids", - "photograph", + "MIB/MS", + "UPLC-MSMS", + "microRNAcounts", + "methylationArray", + "CUT&Tag", "Positron Emission Tomography", - "scATACSeq", - "Vernier Caliper", - "open field test", - "proximity extension assay", - "rnaSeq", - "NOMe-Seq", + "Rader Lipidomics", + "anxiety-related behavior", + "FitBark", + "LC-MS", + "Wishart Catecholamines", "immunofluorescence", - "DNA optical mapping", - "scCGIseq", - "brightfieldMicroscopy", - "whole-cell patch clamp", - "scrnaSeq", - "kinesthetic behavior", - "contextual conditioning behavior", - "jumpingLibrary", + "STARRSeq", + "LC-MSMS", + "mRNAcounts", + "Laser Speckle Imaging", + "Sanger sequencing", + "memory behavior", + "Leiden Oxylipins", + "in vivo bioluminescence", + "TMT quantitation", + "exomeSeq", "mirnaArray", - "UPLC-MSMS", - "elevated plus maze test", - "UCSD Untargeted Metabolomics", + "long-read rnaSeq", + "HI-C", "nextGenerationTargetedSequencing", - "10x multiome", - "HPLC-MSMS", + "proximity extension assay", + "SiMoA", + "Baker Lipidomics", + "label free mass spectrometry", + "Biocrates Bile Acids", "questionnaire", - "Biocrates Q500", - "lentiMPRA", - "UPLC-ESI-QTOF-MS", - "pharmacokinetics", - "RPPA", - "spontaneous alternation", - "Wishart Catecholamines", + "UCSD Untargeted Metabolomics", + "LTP", + "sandwich ELISA", "Nightingale NMR", - "Biocrates p180", - "TMT quantitation", - "Immunocytochemistry", + "wheel running", + "MRI", + "open field test", + "ChIPSeq", + "DIA", + "jumpingLibrary", + "HiChIPseq", + "mirnaSeq", + "scrnaSeq", + "oxBS-Seq", + "spontaneous alternation", + "m6A-rnaSeq", + "FIA-MSMS", "cellViabilityAssay", - "HI-C", - "long-read rnaSeq", + "HPLC", "Real Time PCR", - "snrnaSeq", - "LC-MSMS", - "high content screen" + "Metabolon", + "rnaSeq", + "rotarod performance test", + "NOMe-Seq", + "scCGIseq", + "MudPIT", + "lncrnaSeq", + "tractionForceMicroscopy", + "elevated T maze apparatus method", + "contextual conditioning behavior", + "RPPA", + "novelty response behavior" ] }, - "libraryBatch": {}, - "numberCells": {}, - "totalReads": {}, "specimenID": {}, - "runType": { + "rnaBatch": {}, + "libraryVersion": {}, + "isStranded": { "enum": [ - "singleEnd", - "pairedEnd" + "TRUE", + "FALSE", + "" ] }, + "numberCells": {}, + "readLength": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "libraryID": {}, "platform": { "enum": [ - "AffymetrixU133AB", - "HiSeq3000", - "Illumina_Omni2.5-8_v1.1", - "LTQOrbitrapXL", + "PacBio Sequel II", + "Xevo TQ-S", + "Orbitrap Fusion Lumos", + "Q Exactive Plus", + "Biograph mCT", + "Illumina_Omni2.5-8", + "NanostringnCounter_MouseADPanel", "llumina Infinium General Screening Array 24-Kit v3.0", - "Infinium Omni2.5Exome-8 v1.4", - "HiSeq2500", + "Bionano Irys", + "Illumina_Infinium-HumanMethylation450-BeadChip", "confocalImaging", - "AffymetrixU133Plus2", "Orbitrap Exploris 240", - "PacBio Sequel II", - "Illumina_Omni2.5-8_v1.3", - "Illumina_Omni5M", + "IlluminaHumanHap650Yv3_A", + "OrbiTrap Fusion", + "Roche Cobas", "Illumina_Omni5-Quad", - "HiSeq4000", - "Illumina_1M", - "PacBioRSII", - "Q Exactive", - "IlluminaHumanHap300", + "LTQOrbitrapXL", + "Affy5.0", + "HiSeq3000", + "GAIIx", + "Illumina_HumanOmni1-Quadv1.0", + "Illumina NovaSeq 6000", + "AffymetrixU133AB", + "IlluminaNovaseq6000", + "Infinium Omni2.5Exome-8 v1.1", + "Biocrates p180", + "Infinium Global Diversity Array-8", + "time-of-flight", "quadrupole time-of-flight", + "Q Exactive HF-X", + "AffymetrixU133Plus2", + "HiSeq4000", + "triple quadrupole", + "orbitrap", "MiSeq", - "Agilent44Karray", - "HiSeq2000", - "IlluminaWholeGenomeDASL", - "IlluminaMiSeq", - "Xevo G2 QTOF", + "NextSeq500", + "Illumina_1M", + "DNBSEQ", "InfiniumPsychArrayBeadChip", - "GAIIx", + "IlluminaMethylationEPIC", + "IlluminaMiSeq", + "PsychChip", + "IlluminaWholeGenomeDASL", "Leco Pegasus IV", - "orbitrap", - "NextSeq500", - 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HumanOmniExpressExome", - "HiSeq1000", + "PacBio Sequel IIe", + "NextSeq2000", "Signa Premier AIR 3T", + "Infinium HumanOmniExpressExome", "IlluminaInfiniumGSAMD-24v2-0", - "OrbiTrap Fusion", - "IlluminaHumanHap650Yv3_A", - "HiSeqX", - "Affy5.0", - "Bionano Irys", - "Illumina_Omni2pt5M", - "Infinium Omni2.5Exome-8 v1.3", - "Perlegen300Karray", - "NanostringnCounter", - "DNBSEQ", - "Orbitrap Fusion Lumos", - "Biocrates p180", - "Q Exactive HF-X", - "Infinium Omni2.5Exome-8 v1.1", - "Illumina_h650", - "triple quadrupole", + "HiSeq2500", + "Illumina MouseWG-6 v2.0 expression beadchip", + "Simoa HD-1 Analyzer", + "Affymetrix Human Gene 1.0 ST Array", + "HiSeq2000", + "Bruker Avance III", + "IlluminaHumanHap300", "BGISEQ-500", - "PacBio Sequel IIe", - "Biograph mCT" + "IlluminaHumanHT-12_V3_0_R1", + "Perlegen300Karray", + "Illumina_Omni2.5-8_v1.1", + "Agilent44Karray", + "PacBioRSII", + "Infinium Omni2.5Exome-8 v1.5", + "Olink Target 96", + "IlluminaHumanMethylation450", + "HiSeq1000" ] }, "referenceSet": { "enum": [ + "GRCm38", "1000 Genomes phase 3", + "HRC", "MMUL1.0", "GRCh38", - "HRC", "GRCh37", "dmel_r6.06", - "GRCm38", "" ] }, - "libraryID": {}, - "libraryVersion": {}, - "RIN": {}, - "libraryPrep": { - "enum": [ - "amplicon", - "multiome", - "rRNAdepletion", - "STARRSeq", - "proximity ligation", - "SureCell", - "KapaHyperPrep", - "DNALibraryConstruction", - "methylSeq", - "cellHashing", - "snIsoSeq", - "totalRNA", - "EndItDNAEndRepairKit", - "SPLITseq", - "PCRfree", - "polyAselection", - "Chromium Single Cell 3'", - "lncRNAenrichment", - "MULTIseq", - "miRNAenrichment" - ] - }, - "sampleBarcode": {}, - "medianGenes": {}, - "medianUMIs": {}, - "validBarcodeReads": {}, + "sequencingBatch": {}, "readStrandOrigin": { "enum": [ "reverse", @@ -275,54 +281,48 @@ "" ] }, - "isStranded": { + "medianGenes": {}, + "runType": { "enum": [ - "FALSE", - "TRUE", - "" + "singleEnd", + "pairedEnd" ] }, - "libraryPreparationMethod": { + "medianUMIs": {}, + "libraryPrep": { "enum": [ - "Smart-seq4", - "CEL-seq", - "Illumina DNA PCR-Free Prep Kit", - "Ultralow Methyl-Seq", - "Accel-NGS 2S Plus", - "NexteraXT", - "SMRTbell", - "10x", - "sac-seq", - "TruSeq", - "Omni-ATAC", - "Smart-seq2", - "NEBNext", - "Drop-Seq", - "Smart-seq1", - "Accel-NGS Methyl-Seq", - "" + "SPLITseq", + "KapaHyperPrep", + "PCRfree", + "MULTIseq", + "DNALibraryConstruction", + "Chromium Single Cell 3'", + "miRNAenrichment", + "proximity ligation", + "amplicon", + "multiome", + "cellHashing", + "EndItDNAEndRepairKit", + "STARRSeq", + "methylSeq", + "SureCell", + "rRNAdepletion", + "totalRNA", + "polyAselection", + "lncRNAenrichment", + "snIsoSeq" ] }, "Component": {}, - "libraryType": { - "enum": [ - "ADT", - "LMO", - "CMO", - "HTO", - "plasmid DNA", - "cDNA", - "" - ] - }, - "rnaBatch": {}, - "sequencingBatch": {} + "validBarcodeReads": {}, + "libraryBatch": {}, + "totalReads": {} }, "required": [ - "readLength", "assay", - "runType", + "readLength", "platform", + "runType", "libraryPrep" ] } \ 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 7f31e96..c135e43 100644 --- a/current-manifest-schemas/AD.AssaySnpArrayMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssaySnpArrayMetadataTemplate.schema.json @@ -4,217 +4,217 @@ "title": "AssaySnpArrayMetadataTemplate", "type": "object", "properties": { - "arrayBatch": {}, - "ratio260over230": {}, - "ratio260over280": {}, - "Component": {}, "assay": { "enum": [ - "bisulfiteSeq", - "scATACSeq", - "jumpingLibrary", - "Zeno Electronic Walkway", - "HI-C", - "in vivo bioluminescence", - "nextGenerationTargetedSequencing", - "HPLC", - "atomicForceMicroscopy", - "Wishart High Value Metabolites", - "liquid chromatography-electrochemical detection", - "microRNAcounts", + "label free mass spectrometry", + "rotarod performance test", + "FitBark", + "Genotyping", + "LC-SRM", + "ATACSeq", "Blood Chemistry Measurement", + "scirnaSeq", + "Wishart Catecholamines", + "liquid chromatography-electrochemical detection", "immunohistochemistry", - "autoradiography", - "brightfieldMicroscopy", - "memory behavior", + "mirnaArray", + "frailty assessment", + "pharmacodynamics", "sandwich ELISA", - "scirnaSeq", + "ISOSeq", + "10x multiome", + "LTP", + "methylationArray", + "rnaSeq", "long-read rnaSeq", - "STARRSeq", - "scale", + "TMT quantitation", "whole-cell patch clamp", - "MRI", - "Real Time PCR", - "UCSD Untargeted Metabolomics", + "westernBlot", + "LC-MSMS", + "rnaArray", + "electrochemiluminescence", + "scATACSeq", + "Positron Emission Tomography", + "open field test", + "CITESeq", + "nextGenerationTargetedSequencing", + "Wishart High Value Metabolites", + "Nightingale NMR", + "atomicForceMicroscopy", + "Zeno Electronic Walkway", "16SrRNAseq", - "high content screen", - "exomeSeq", - "Immunocytochemistry", + "Biocrates p180", + "novelty response behavior", + "polymeraseChainReaction", + "autoradiography", "MIB/MS", - "FIA-MSMS", - "Metabolon", - "rotarod performance test", - "Sanger sequencing", - "proximity extension assay", - "open field test", - "methylationArray", - "Wishart Catecholamines", + "tractionForceMicroscopy", + "Ribo-Seq", + "brightfieldMicroscopy", "errBisulfiteSeq", + "elevated T maze apparatus method", + "lncrnaSeq", + "active avoidance learning behavior", + "photograph", + "UPLC-ESI-QTOF-MS", + "high content screen", + "elevated plus maze test", + "Sanger sequencing", + "UC Davis GCTOF", "von Frey test", - "LC-SRM", - "mRNAcounts", - "CITESeq", - "rnaArray", - "Rader Lipidomics", - "ISOSeq", - "cellViabilityAssay", - "Nightingale NMR", + "MRI", "NOMe-Seq", - "wheel running", - "active avoidance learning behavior", - "lncrnaSeq", + "locomotor activation behavior", + "Leiden Oxylipins", + "Metabolon", + "ELISA", + "Rader Lipidomics", + "HPLC", + "scale", + "SiMoA", + "bisulfiteSeq", + "lentiMPRA", + "Laser Speckle Imaging", "UPLC-MSMS", - "rnaSeq", - "MudPIT", - "mirnaSeq", - "Ribo-Seq", + "STARRSeq", + "pharmacokinetics", + "FIA-MSMS", + "immunofluorescence", + "wheel running", "m6A-rnaSeq", - "scwholeGenomeSeq", - "snATACSeq", - "UC Davis GCTOF", - "Laser Speckle Imaging", - "Biocrates p180", - "LC-MS", - "pharmacodynamics", - "scCGIseq", - "ELISA", + "anxiety-related behavior", + "questionnaire", + "Immunocytochemistry", + "mRNAcounts", + "HiChIPseq", + "CUT&Tag", + "LFP", + "UCSD Untargeted Metabolomics", + "MudPIT", "spontaneous alternation", - "elevated plus maze test", - "mirnaArray", - "UPLC-ESI-QTOF-MS", - "kinesthetic behavior", - "lentiMPRA", - "DIA", - "locomotor activation behavior", + "Real Time PCR", "Biocrates Q500", - "novelty response behavior", - "label free mass spectrometry", - "LFP", - "Biocrates Bile Acids", - "HiChIPseq", - "immunofluorescence", - "photograph", - "Vernier Caliper", - "contextual conditioning behavior", + "memory behavior", + "snpArray", + "cellViabilityAssay", + "in vivo bioluminescence", "MDMS-SL", - "tractionForceMicroscopy", - "HPLC-MSMS", + "scCGIseq", + "exomeSeq", + "mirnaSeq", + "DNA optical mapping", + "kinesthetic behavior", "wholeGenomeSeq", + "Vernier Caliper", + "jumpingLibrary", + "contextual conditioning behavior", + "HI-C", + "LC-MS", + "proximity extension assay", "ChIPSeq", - "scrnaSeq", - "Baker Lipidomics", - "LC-MSMS", - "DNA optical mapping", - "LTP", - "questionnaire", - "electrochemiluminescence", - "elevated T maze apparatus method", - "frailty assessment", - "10x multiome", - "polymeraseChainReaction", - "TMT quantitation", - "westernBlot", - "FitBark", + "HPLC-MSMS", + "scwholeGenomeSeq", + "Biocrates Bile Acids", + "DIA", "oxBS-Seq", - "pharmacokinetics", - "Genotyping", - "anxiety-related behavior", - "Positron Emission Tomography", - "ATACSeq", - "Leiden Oxylipins", - "CUT&Tag", + "scrnaSeq", + "snATACSeq", "RPPA", - "snpArray", - "snrnaSeq", - "SiMoA" + "microRNAcounts", + "Baker Lipidomics", + "snrnaSeq" ] }, + "Component": {}, "dnaBatch": {}, + "ratio260over280": {}, "platform": { "enum": [ - "Q Exactive", - "IlluminaHumanHT-12_V3_0_R1", - "Infinium Omni2.5Exome-8 v1.4", - "llumina Infinium General Screening Array 24-Kit v3.0", - "NanostringnCounter", "Bruker Avance III", - "Perlegen300Karray", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "Xevo TQ-S", - "quadrupole time-of-flight", - "IlluminaMethylationEPIC", - "Illumina_1M", + "Q Exactive", "HiSeq1000", - "HiSeq3000", - "IlluminaWholeGenomeDASL", - "Q Exactive HF", - "Affy5.0", - "Biograph mCT", - "PacBio Sequel IIe", - "Illumina_Omni5-Quad", - "Bionano Irys", - "Orbitrap Fusion Lumos", - "triple quadrupole", + "Agilent44Karray", + "PacBio Sequel II", + "AffymetrixU133Plus2", "Illumina_Omni2pt5M", - "NextSeq500", - "orbitrap", - "LTQOrbitrapXL", - "IlluminaHumanHap650Yv3_A", - "confocalImaging", - "Illumina MouseWG-6 v2.0 expression beadchip", + "HiSeq2000", + "IlluminaInfiniumGSAMD-24v2-0", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "NanostringnCounter", + "Illumina_Omni2.5-8_v1.1", + "Illumina_Omni5-Quad", "Illumina_Omni2.5-8", - "Orbitrap Exploris 240", - "Illumina_Omni5M", + "Q Exactive HF", + "IlluminaMethylationEPIC", "Infinium HumanOmniExpressExome", - "Xevo G2 QTOF", - "IlluminaMiSeq", - "BGISEQ-500", - "Affy6.0", - "GAIIx", + "Illumina NovaSeq 6000", + "Affymetrix Human Gene 1.0 ST Array", + "llumina Infinium General Screening Array 24-Kit v3.0", + "HiSeq2500", + "Leco Pegasus IV", + "IlluminaHumanHap300", + "IlluminaHumanHT-12_V3_0_R1", + "Infinium Global Diversity Array-8", + "Orbitrap Exploris 240", + "NextSeq500", "OrbiTrap Fusion", "Signa Premier AIR 3T", - "MiSeq", - "Illumina_h650", - "InfiniumPsychArrayBeadChip", - "Simoa HD-1 Analyzer", - "HiSeq2000", - "Roche Cobas", - "ddSEQ Single-Cell Isolator", - "DNBSEQ", "time-of-flight", - "Leco Pegasus IV", - "Infinium Global Diversity Array-8", - "Biocrates p180", - "NanostringnCounter_MouseADPanel", - "NextSeq2000", - "PsychChip", - "HiSeq2500", - "Illumina NovaSeq 6000", - "AffymetrixU133Plus2", - "Infinium Omni2.5Exome-8 v1.3", - "IlluminaHumanMethylation450", - "Illumina_Omni2.5-8_v1.1", - "Affymetrix Human Gene 1.0 ST Array", - "IlluminaInfiniumGSAMD-24v2-0", - "Q Exactive HF-X", - "AffymetrixU133AB", - "Infinium Omni2.5Exome-8 v1.5", "Infinium Omni2.5Exome-8 v1.1", + "Biocrates p180", "IlluminaNovaseq6000", - "HiSeqX", + "Perlegen300Karray", + "IlluminaHumanHap650Yv3_A", + "IlluminaHumanMethylation450", "PacBioRSII", - "SequenomMultiplex", - "Agilent44Karray", - "PacBio Sequel II", + "Simoa HD-1 Analyzer", + "Affy5.0", + "IlluminaWholeGenomeDASL", "Illumina_HumanOmni1-Quadv1.0", + "Q Exactive HF-X", + "BGISEQ-500", "Illumina_Omni2.5-8_v1.3", "HiSeq4000", - "IlluminaHumanHap300", + "Bionano Irys", + "Infinium Omni2.5Exome-8 v1.3", + "Xevo G2 QTOF", + "triple quadrupole", + "PacBio Sequel IIe", + "IlluminaMiSeq", + "HiSeq3000", + "Illumina_Omni5M", + "Orbitrap Fusion Lumos", + "Q Exactive Plus", + "Infinium Omni2.5Exome-8 v1.4", + "orbitrap", + "Roche Cobas", + "AffymetrixU133AB", + "GAIIx", + "Illumina_1M", + "DNBSEQ", "Olink Target 96", - "Q Exactive Plus" + "LTQOrbitrapXL", + "Illumina_h650", + "Biograph mCT", + "HiSeqX", + "SequenomMultiplex", + "ddSEQ Single-Cell Isolator", + "InfiniumPsychArrayBeadChip", + "MiSeq", + "Illumina MouseWG-6 v2.0 expression beadchip", + "Xevo TQ-S", + "Infinium Omni2.5Exome-8 v1.5", + "Affy6.0", + "PsychChip", + "NanostringnCounter_MouseADPanel", + "confocalImaging", + "NextSeq2000", + "quadrupole time-of-flight" ] }, + "ratio260over230": {}, "specimenID": {}, + "arrayBatch": {}, "GQN": {} }, "required": [ diff --git a/current-manifest-schemas/AD.AssayTMTquantitationMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayTMTquantitationMetadataTemplate.schema.json index 7a81b6f..9e0c9af 100644 --- a/current-manifest-schemas/AD.AssayTMTquantitationMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayTMTquantitationMetadataTemplate.schema.json @@ -4,234 +4,234 @@ "title": "AssayTMTquantitationMetadataTemplate", "type": "object", "properties": { + "specimenID": {}, + "batch": {}, + "controlType": { + "enum": [ + "NIST SRM 1950", + "qc mix", + "GIS", + "blank injection", + "GoldenWest", + "Replicate", + "Baker pool", + "study pool", + "AIBL pool", + "water plus Baker ISTD", + "" + ] + }, + "Component": {}, "assay": { "enum": [ - "jumpingLibrary", - "mirnaArray", - "Vernier Caliper", - "DIA", - "m6A-rnaSeq", - "Blood Chemistry Measurement", - "pharmacodynamics", - "HPLC", - "open field test", + "brightfieldMicroscopy", + "Wishart Catecholamines", + "Immunocytochemistry", "Sanger sequencing", - "lncrnaSeq", - "electrochemiluminescence", - "HI-C", - "rotarod performance test", - "UC Davis GCTOF", - "Nightingale NMR", + "microRNAcounts", + "Biocrates Bile Acids", + "snATACSeq", + "Positron Emission Tomography", + "scirnaSeq", + "DNA optical mapping", + "UPLC-ESI-QTOF-MS", + "wholeGenomeSeq", + "immunohistochemistry", + "Zeno Electronic Walkway", + "HPLC", + "lentiMPRA", + "NOMe-Seq", + "anxiety-related behavior", + "MDMS-SL", + "mRNAcounts", + "Blood Chemistry Measurement", "locomotor activation behavior", - "exomeSeq", - "liquid chromatography-electrochemical detection", - "rnaSeq", - "MIB/MS", - "novelty response behavior", - "tractionForceMicroscopy", - "Metabolon", - "methylationArray", + "10x multiome", + "mirnaArray", "MRI", - "elevated T maze apparatus method", - "lentiMPRA", - "scrnaSeq", - "Positron Emission Tomography", - "FitBark", - "rnaArray", - "brightfieldMicroscopy", - "in vivo bioluminescence", - "UPLC-MSMS", - "Real Time PCR", + "contextual conditioning behavior", "ISOSeq", - "FIA-MSMS", - "16SrRNAseq", - "RPPA", - "mRNAcounts", - "LC-SRM", - "CUT&Tag", - "scCGIseq", - "memory behavior", "Laser Speckle Imaging", - "Rader Lipidomics", - "westernBlot", + "FIA-MSMS", + "whole-cell patch clamp", + "novelty response behavior", + "Ribo-Seq", + "immunofluorescence", "active avoidance learning behavior", - "NOMe-Seq", - "10x multiome", "atomicForceMicroscopy", - "contextual conditioning behavior", - "immunohistochemistry", - "questionnaire", - "HPLC-MSMS", - "ATACSeq", - "LC-MSMS", - "scATACSeq", - "ChIPSeq", + "nextGenerationTargetedSequencing", + "memory behavior", + "Biocrates p180", "polymeraseChainReaction", - "scale", + "DIA", + "pharmacokinetics", + "westernBlot", + "Rader Lipidomics", + "ChIPSeq", "TMT quantitation", - "von Frey test", - "immunofluorescence", - "oxBS-Seq", - "ELISA", - "bisulfiteSeq", - "frailty assessment", - "scwholeGenomeSeq", - "high content screen", - "CITESeq", - "mirnaSeq", - "errBisulfiteSeq", - "snATACSeq", - "microRNAcounts", - "MDMS-SL", - "snpArray", + "kinesthetic behavior", "Wishart High Value Metabolites", - "Genotyping", - "cellViabilityAssay", - "Ribo-Seq", - "elevated plus maze test", - "LTP", - "autoradiography", - "MudPIT", - "Immunocytochemistry", - "pharmacokinetics", - "wheel running", - "label free mass spectrometry", - "LC-MS", - "nextGenerationTargetedSequencing", - "photograph", - "Biocrates Q500", - "LFP", - "anxiety-related behavior", + "scale", + "CITESeq", + "STARRSeq", "sandwich ELISA", + "Leiden Oxylipins", + "in vivo bioluminescence", + "scCGIseq", + "high content screen", + "elevated plus maze test", + "HiChIPseq", + "scwholeGenomeSeq", "SiMoA", - "UPLC-ESI-QTOF-MS", - "whole-cell patch clamp", + "CUT&Tag", + "Metabolon", + "jumpingLibrary", + "LFP", "Baker Lipidomics", - "Wishart Catecholamines", - "proximity extension assay", - "wholeGenomeSeq", - "Biocrates Bile Acids", - "STARRSeq", + "HI-C", + "rnaArray", + "cellViabilityAssay", + "liquid chromatography-electrochemical detection", + "ATACSeq", + "bisulfiteSeq", + "frailty assessment", + "rotarod performance test", + "LTP", + "von Frey test", + "FitBark", + "methylationArray", + "UC Davis GCTOF", + "scATACSeq", + "MudPIT", + "Vernier Caliper", + "exomeSeq", "UCSD Untargeted Metabolomics", - "DNA optical mapping", - "Leiden Oxylipins", - "scirnaSeq", + "scrnaSeq", + "LC-MS", + "UPLC-MSMS", "snrnaSeq", - "Zeno Electronic Walkway", - "Biocrates p180", + "16SrRNAseq", + "questionnaire", "spontaneous alternation", + "RPPA", + "m6A-rnaSeq", + "Nightingale NMR", + "open field test", + "LC-SRM", + "ELISA", + "photograph", + "errBisulfiteSeq", + "tractionForceMicroscopy", + "HPLC-MSMS", + "pharmacodynamics", + "wheel running", "long-read rnaSeq", - "HiChIPseq", - "kinesthetic behavior" - ] - }, - "multiconsensusStudyFileID": {}, - "TMTType": {}, - "Component": {}, - "batchChannel": {}, - "controlType": { - "enum": [ - "Replicate", - "water plus Baker ISTD", - "qc mix", - "NIST SRM 1950", - "study pool", - "GIS", - "GoldenWest", - "AIBL pool", - "blank injection", - "Baker pool", - "" + "proximity extension assay", + "label free mass spectrometry", + "mirnaSeq", + "electrochemiluminescence", + "Genotyping", + "oxBS-Seq", + "snpArray", + "LC-MSMS", + "rnaSeq", + "lncrnaSeq", + "MIB/MS", + "Biocrates Q500", + "Real Time PCR", + "autoradiography", + "elevated T maze apparatus method" ] }, - "specimenID": {}, "fragmentation": {}, + "TMTType": {}, + "multiconsensusStudyFileID": {}, "resolution": {}, "platform": { "enum": [ - "Orbitrap Fusion Lumos", + "IlluminaWholeGenomeDASL", + "Infinium Omni2.5Exome-8 v1.4", + "HiSeq1000", + "triple quadrupole", + "Affymetrix Human Gene 1.0 ST Array", + "HiSeq4000", + "Infinium Omni2.5Exome-8 v1.1", + "IlluminaHumanMethylation450", + "Perlegen300Karray", "Illumina_Omni2pt5M", + "Illumina_Omni2.5-8_v1.3", + "OrbiTrap Fusion", + "Bionano Irys", + "Affy5.0", + "Illumina_Omni5-Quad", + "Illumina_HumanOmni1-Quadv1.0", + "Affy6.0", + "NextSeq2000", + "Q Exactive Plus", + "Biograph mCT", + "GAIIx", + "Orbitrap Fusion Lumos", + "Biocrates p180", + "IlluminaHumanHT-12_V3_0_R1", + "Xevo G2 QTOF", + "PacBioRSII", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "NextSeq500", "confocalImaging", - "PacBio Sequel II", - "InfiniumPsychArrayBeadChip", + "Infinium HumanOmniExpressExome", + "IlluminaMethylationEPIC", "Simoa HD-1 Analyzer", - "Q Exactive", - "Illumina_1M", - "PacBio Sequel IIe", - "IlluminaInfiniumGSAMD-24v2-0", - "Q Exactive HF-X", "Illumina_h650", - "NextSeq500", - "Xevo TQ-S", - "HiSeq2500", - "Signa Premier AIR 3T", - "Leco Pegasus IV", - "Q Exactive Plus", - "Illumina_Omni2.5-8_v1.3", - "llumina Infinium General Screening Array 24-Kit v3.0", - "NanostringnCounter_MouseADPanel", - "HiSeq2000", - "LTQOrbitrapXL", - "Q Exactive HF", - "NextSeq2000", - "SequenomMultiplex", - "triple quadrupole", - "IlluminaHumanHap300", - "HiSeq3000", "HiSeqX", - "Illumina_Omni5-Quad", - "Illumina_Omni2.5-8", "Agilent44Karray", - "Xevo G2 QTOF", - "IlluminaHumanMethylation450", - "IlluminaMethylationEPIC", + "time-of-flight", + "Q Exactive HF-X", + "LTQOrbitrapXL", + "Illumina_Omni2.5-8_v1.1", + "IlluminaHumanHap650Yv3_A", + "NanostringnCounter_MouseADPanel", + "Q Exactive", + "InfiniumPsychArrayBeadChip", + "IlluminaNovaseq6000", + "IlluminaInfiniumGSAMD-24v2-0", + "HiSeq2500", + "quadrupole time-of-flight", + "Bruker Avance III", + "AffymetrixU133AB", + "Infinium Omni2.5Exome-8 v1.5", + "AffymetrixU133Plus2", + "Xevo TQ-S", "BGISEQ-500", + "NanostringnCounter", "Illumina MouseWG-6 v2.0 expression beadchip", - "HiSeq1000", - "DNBSEQ", - "AffymetrixU133AB", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "Affymetrix Human Gene 1.0 ST Array", + "HiSeq2000", + "orbitrap", + "Illumina_1M", "Illumina_Omni5M", - "IlluminaMiSeq", - "Bruker Avance III", + "HiSeq3000", + "Signa Premier AIR 3T", + "PacBio Sequel IIe", + "llumina Infinium General Screening Array 24-Kit v3.0", + "DNBSEQ", + "Illumina_Omni2.5-8", + "Leco Pegasus IV", + "ddSEQ Single-Cell Isolator", + "PacBio Sequel II", + "Illumina NovaSeq 6000", + "MiSeq", + "SequenomMultiplex", "PsychChip", - "Bionano Irys", - "IlluminaHumanHT-12_V3_0_R1", - "Affy6.0", - "AffymetrixU133Plus2", + "Roche Cobas", "Olink Target 96", - "HiSeq4000", - "IlluminaWholeGenomeDASL", "Orbitrap Exploris 240", - "orbitrap", - "Infinium HumanOmniExpressExome", - "Roche Cobas", - "OrbiTrap Fusion", - "Illumina NovaSeq 6000", - "GAIIx", - "Infinium Omni2.5Exome-8 v1.1", - "Infinium Omni2.5Exome-8 v1.4", - "MiSeq", - "Biograph mCT", - "PacBioRSII", - "Illumina_HumanOmni1-Quadv1.0", - "time-of-flight", + "Q Exactive HF", + "IlluminaMiSeq", "Infinium Omni2.5Exome-8 v1.3", "Infinium Global Diversity Array-8", - "NanostringnCounter", - "quadrupole time-of-flight", - "Affy5.0", - "Biocrates p180", - "Infinium Omni2.5Exome-8 v1.5", - "IlluminaNovaseq6000", - "ddSEQ Single-Cell Isolator", - "IlluminaHumanHap650Yv3_A", - "Perlegen300Karray", - "Illumina_Omni2.5-8_v1.1" + "IlluminaHumanHap300" ] }, - "batch": {} + "batchChannel": {} }, "required": [ "assay", diff --git a/current-manifest-schemas/AD.AssayWholeExomeSeqMetadataTemplate.schema.json b/current-manifest-schemas/AD.AssayWholeExomeSeqMetadataTemplate.schema.json index a0687c4..c290c64 100644 --- a/current-manifest-schemas/AD.AssayWholeExomeSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayWholeExomeSeqMetadataTemplate.schema.json @@ -4,295 +4,295 @@ "title": "AssayWholeExomeSeqMetadataTemplate", "type": "object", "properties": { - "sequencingBatch": {}, "ratio260over280": {}, + "Component": {}, + "dnaBatch": {}, "runType": { "enum": [ "singleEnd", "pairedEnd" ] }, - "libraryPreparationMethod": { - "enum": [ - "NEBNext", - "NexteraXT", - "TruSeq", - "CEL-seq", - "sac-seq", - "Smart-seq2", - "Illumina DNA PCR-Free Prep Kit", - "Smart-seq4", - "Ultralow Methyl-Seq", - "Omni-ATAC", - "Smart-seq1", - "SMRTbell", - "10x", - "Accel-NGS 2S Plus", - "Drop-Seq", - "Accel-NGS Methyl-Seq", - "" - ] - }, - "dnaBatch": {}, "libraryID": {}, - "assay": { - "enum": [ - "westernBlot", - "LTP", - "open field test", - "HI-C", - "lentiMPRA", - "methylationArray", - "contextual conditioning behavior", - "MRI", - "CITESeq", - "Vernier Caliper", - "autoradiography", - "LFP", - "scATACSeq", - "Biocrates Bile Acids", - "brightfieldMicroscopy", - "ATACSeq", - "frailty assessment", - "Leiden Oxylipins", - "Sanger sequencing", - "elevated plus maze test", - "LC-MS", - "memory behavior", - "CUT&Tag", - "m6A-rnaSeq", - "pharmacokinetics", - "anxiety-related behavior", - "pharmacodynamics", - "Biocrates Q500", - "long-read rnaSeq", - "in vivo bioluminescence", - "locomotor activation behavior", - "wholeGenomeSeq", - "scrnaSeq", - "snpArray", - "immunohistochemistry", - "Metabolon", - "UCSD Untargeted Metabolomics", - "kinesthetic behavior", - "snrnaSeq", - "RPPA", - "snATACSeq", - "von Frey test", - "ISOSeq", - "scale", - "UC Davis GCTOF", - "DNA optical mapping", - "ChIPSeq", - "photograph", - "exomeSeq", - "Positron Emission Tomography", - "LC-MSMS", - "mRNAcounts", - "UPLC-MSMS", - "elevated T maze apparatus method", - "electrochemiluminescence", - "rnaSeq", - "Biocrates p180", - "STARRSeq", - "active avoidance learning behavior", - "Ribo-Seq", - "rotarod performance test", - "sandwich ELISA", - "Baker Lipidomics", - "liquid chromatography-electrochemical detection", - "oxBS-Seq", - "HPLC-MSMS", - "10x multiome", - "Laser Speckle Imaging", - "wheel running", - "cellViabilityAssay", - "immunofluorescence", - "scwholeGenomeSeq", - "novelty response behavior", - "Nightingale NMR", - "FIA-MSMS", - "atomicForceMicroscopy", - "Wishart Catecholamines", - "microRNAcounts", - "rnaArray", - "DIA", - "Genotyping", - "MIB/MS", - "spontaneous alternation", - "HiChIPseq", - "lncrnaSeq", - "label free mass spectrometry", - "UPLC-ESI-QTOF-MS", - "16SrRNAseq", - "questionnaire", - "scCGIseq", - "nextGenerationTargetedSequencing", - "high content screen", - "whole-cell patch clamp", - "FitBark", - "mirnaArray", - "ELISA", - "scirnaSeq", - "Immunocytochemistry", - "Blood Chemistry Measurement", - "errBisulfiteSeq", - "Zeno Electronic Walkway", - "LC-SRM", - "mirnaSeq", - "SiMoA", - "proximity extension assay", - "MDMS-SL", - "TMT quantitation", - "polymeraseChainReaction", - "MudPIT", - "bisulfiteSeq", - "NOMe-Seq", - "HPLC", - "tractionForceMicroscopy", - "Real Time PCR", - "jumpingLibrary", - "Rader Lipidomics", - "Wishart High Value Metabolites" - ] - }, "libraryPrep": { "enum": [ - "STARRSeq", "proximity ligation", + "SureCell", + "STARRSeq", + "MULTIseq", + "KapaHyperPrep", "snIsoSeq", - "DNALibraryConstruction", + "EndItDNAEndRepairKit", + "totalRNA", "PCRfree", - "MULTIseq", - "Chromium Single Cell 3'", + "DNALibraryConstruction", "cellHashing", + "methylSeq", + "rRNAdepletion", + "miRNAenrichment", "amplicon", "lncRNAenrichment", - "SureCell", - "SPLITseq", - "miRNAenrichment", - "KapaHyperPrep", + "Chromium Single Cell 3'", "multiome", - "EndItDNAEndRepairKit", - "rRNAdepletion", - "methylSeq", - "polyAselection", - "totalRNA" + "SPLITseq", + "polyAselection" ] }, "referenceSet": { "enum": [ - "GRCh37", - "1000 Genomes phase 3", "MMUL1.0", - "GRCm38", + "GRCh37", "GRCh38", + "GRCm38", "dmel_r6.06", + "1000 Genomes phase 3", "HRC", "" ] }, - "specimenID": {}, - "ratio260over230": {}, - "totalReads": {}, - "GQN": {}, - "Component": {}, - "readLength": { - "not": { - "type": "null" - }, - "minLength": 1 - }, "platform": { "enum": [ - "LTQOrbitrapXL", "Orbitrap Fusion Lumos", - "PacBio Sequel II", - "Roche Cobas", - "Infinium Omni2.5Exome-8 v1.1", - "HiSeq3000", + "NanostringnCounter_MouseADPanel", + "Illumina NovaSeq 6000", + "IlluminaHumanMethylation450", + "triple quadrupole", + "Simoa HD-1 Analyzer", + "Illumina_HumanOmni1-Quadv1.0", + "BGISEQ-500", + "Q Exactive", + "Q Exactive HF-X", + "HiSeq2000", + "PsychChip", + "Biograph mCT", + "Illumina_Omni2pt5M", + "Q Exactive HF", + "Illumina_Omni5M", + "GAIIx", + "Infinium Global Diversity Array-8", + "DNBSEQ", + "IlluminaNovaseq6000", "Infinium HumanOmniExpressExome", + "InfiniumPsychArrayBeadChip", + "Roche Cobas", + "Signa Premier AIR 3T", + "IlluminaHumanHT-12_V3_0_R1", + "HiSeq1000", + "Leco Pegasus IV", + "ddSEQ Single-Cell Isolator", + "LTQOrbitrapXL", + "Illumina MouseWG-6 v2.0 expression beadchip", "HiSeq2500", + "Illumina_Omni2.5-8_v1.1", + "quadrupole time-of-flight", "Bionano Irys", - "Illumina_Omni2.5-8_v1.3", - "Olink Target 96", - "PacBio Sequel IIe", - "Leco Pegasus IV", - "IlluminaHumanHap650Yv3_A", - "Infinium Omni2.5Exome-8 v1.3", - "Q Exactive", - "Orbitrap Exploris 240", + "Affy6.0", + "IlluminaInfiniumGSAMD-24v2-0", + "Illumina_h650", + "Infinium Omni2.5Exome-8 v1.4", + "Xevo TQ-S", + "Agilent44Karray", + "Infinium Omni2.5Exome-8 v1.5", + "HiSeq3000", "IlluminaWholeGenomeDASL", - "Bruker Avance III", - "IlluminaMiSeq", - "MiSeq", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "ddSEQ Single-Cell Isolator", - "IlluminaNovaseq6000", + "Illumina_1M", "orbitrap", - "GAIIx", - "Q Exactive HF-X", - "Biograph mCT", - "OrbiTrap Fusion", - "IlluminaMethylationEPIC", "SequenomMultiplex", - "Illumina_Omni2.5-8", "NextSeq2000", - "Illumina_1M", - "PsychChip", + "time-of-flight", + "llumina Infinium General Screening Array 24-Kit v3.0", + "HiSeqX", + "PacBio Sequel II", "Biocrates p180", - "Xevo G2 QTOF", - "Affy5.0", - "IlluminaInfiniumGSAMD-24v2-0", - "Simoa HD-1 Analyzer", - "Illumina_h650", - "Illumina MouseWG-6 v2.0 expression beadchip", "IlluminaHumanHap300", - "HiSeq4000", - "Illumina_HumanOmni1-Quadv1.0", - "Affy6.0", - "NanostringnCounter", - "Xevo TQ-S", "NextSeq500", - "time-of-flight", - "Illumina NovaSeq 6000", - "confocalImaging", + "IlluminaHumanHap650Yv3_A", + "Infinium Omni2.5Exome-8 v1.1", + "Infinium Omni2.5Exome-8 v1.3", + "Olink Target 96", + "Illumina_Infinium-HumanMethylation450-BeadChip", + "Affymetrix Human Gene 1.0 ST Array", + "Affy5.0", "Illumina_Omni5-Quad", + "confocalImaging", + "Illumina_Omni2.5-8_v1.3", + "PacBioRSII", + "AffymetrixU133Plus2", + "IlluminaMethylationEPIC", + "PacBio Sequel IIe", "Perlegen300Karray", - "HiSeq2000", - "triple quadrupole", - "IlluminaHumanMethylation450", - "llumina Infinium General Screening Array 24-Kit v3.0", - "NanostringnCounter_MouseADPanel", - "Illumina_Omni2pt5M", - "Signa Premier AIR 3T", - "Illumina_Omni5M", - "HiSeqX", - "Illumina_Omni2.5-8_v1.1", - "Infinium Global Diversity Array-8", "Q Exactive Plus", - "Agilent44Karray", + "Orbitrap Exploris 240", + "IlluminaMiSeq", + "Xevo G2 QTOF", + "OrbiTrap Fusion", + "NanostringnCounter", "AffymetrixU133AB", - "BGISEQ-500", - "Infinium Omni2.5Exome-8 v1.5", - "Affymetrix Human Gene 1.0 ST Array", - "InfiniumPsychArrayBeadChip", - "DNBSEQ", - "Q Exactive HF", - "HiSeq1000", - "AffymetrixU133Plus2", - "PacBioRSII", - "Infinium Omni2.5Exome-8 v1.4", - "IlluminaHumanHT-12_V3_0_R1", - "quadrupole time-of-flight" + "HiSeq4000", + "Bruker Avance III", + "Illumina_Omni2.5-8", + "MiSeq" + ] + }, + "sequencingBatch": {}, + "ratio260over230": {}, + "specimenID": {}, + "libraryPreparationMethod": { + "enum": [ + "NexteraXT", + "10x", + "Omni-ATAC", + "sac-seq", + "Smart-seq2", + "Accel-NGS Methyl-Seq", + "Smart-seq4", + "SMRTbell", + "TruSeq", + "Drop-Seq", + "NEBNext", + "Smart-seq1", + "Ultralow Methyl-Seq", + "CEL-seq", + "Accel-NGS 2S Plus", + "Illumina DNA PCR-Free Prep Kit", + "" ] + }, + "totalReads": {}, + "assay": { + "enum": [ + "bisulfiteSeq", + "Rader Lipidomics", + "sandwich ELISA", + "methylationArray", + "LC-SRM", + "Nightingale NMR", + "Baker Lipidomics", + "photograph", + "ATACSeq", + "Biocrates Q500", + "spontaneous alternation", + "novelty response behavior", + "MIB/MS", + "scATACSeq", + "immunofluorescence", + "RPPA", + "westernBlot", + "frailty assessment", + "autoradiography", + "tractionForceMicroscopy", + "jumpingLibrary", + "exomeSeq", + "ISOSeq", + "m6A-rnaSeq", + "UC Davis GCTOF", + "lncrnaSeq", + "Wishart Catecholamines", + "scale", + "Ribo-Seq", + "MRI", + "lentiMPRA", + "STARRSeq", + "Real Time PCR", + "memory behavior", + "in vivo bioluminescence", + "MudPIT", + "pharmacokinetics", + "16SrRNAseq", + "FitBark", + "Leiden Oxylipins", + "liquid chromatography-electrochemical detection", + "mRNAcounts", + "Laser Speckle Imaging", + "immunohistochemistry", + "proximity extension assay", + "anxiety-related behavior", + "von Frey test", + "CUT&Tag", + "Blood Chemistry Measurement", + "Sanger sequencing", + "UPLC-ESI-QTOF-MS", + "wholeGenomeSeq", + "electrochemiluminescence", + "atomicForceMicroscopy", + "LC-MS", + "LTP", + "MDMS-SL", + "rnaSeq", + "scrnaSeq", + "brightfieldMicroscopy", + "DNA optical mapping", + "active avoidance learning behavior", + "CITESeq", + "locomotor activation behavior", + "polymeraseChainReaction", + "elevated T maze apparatus method", + "NOMe-Seq", + "whole-cell patch clamp", + "Vernier Caliper", + "label free mass spectrometry", + "HPLC-MSMS", + "Biocrates p180", + "cellViabilityAssay", + "Genotyping", + "mirnaSeq", + "high content screen", + "scirnaSeq", + "Positron Emission Tomography", + "DIA", + "LFP", + "scwholeGenomeSeq", + "nextGenerationTargetedSequencing", + "HPLC", + "scCGIseq", + "kinesthetic behavior", + "snATACSeq", + "rnaArray", + "rotarod performance test", + "microRNAcounts", + "errBisulfiteSeq", + "Biocrates Bile Acids", + "long-read rnaSeq", + "contextual conditioning behavior", + "snpArray", + "snrnaSeq", + "TMT quantitation", + "mirnaArray", + "oxBS-Seq", + "Metabolon", + "Zeno Electronic Walkway", + "questionnaire", + "elevated plus maze test", + "Wishart High Value Metabolites", + "UCSD Untargeted Metabolomics", + "UPLC-MSMS", + "ELISA", + "HI-C", + "HiChIPseq", + "ChIPSeq", + "SiMoA", + "open field test", + "FIA-MSMS", + "10x multiome", + "LC-MSMS", + "wheel running", + "Immunocytochemistry", + "pharmacodynamics" + ] + }, + "GQN": {}, + "readLength": { + "not": { + "type": "null" + }, + "minLength": 1 } }, "required": [ "runType", - "assay", "libraryPrep", - "readLength", - "platform" + "platform", + "assay", + "readLength" ] } \ 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 a7d103d..b3b35e7 100644 --- a/current-manifest-schemas/AD.AssayWholeGenomeSeqMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.AssayWholeGenomeSeqMetadataTemplate.schema.json @@ -4,296 +4,296 @@ "title": "AssayWholeGenomeSeqMetadataTemplate", "type": "object", "properties": { - "libraryPreparationMethod": { - "enum": [ - "SMRTbell", - "Smart-seq1", - "TruSeq", - "10x", - "NexteraXT", - "Drop-Seq", - "NEBNext", - "Accel-NGS 2S Plus", - "Smart-seq4", - "Omni-ATAC", - "sac-seq", - "CEL-seq", - "Smart-seq2", - "Illumina DNA PCR-Free Prep Kit", - "Accel-NGS Methyl-Seq", - "Ultralow Methyl-Seq", - "" - ] - }, - "readLength": { - "not": { - "type": "null" - }, - "minLength": 1 - }, "platform": { "enum": [ + "Simoa HD-1 Analyzer", + "Illumina NovaSeq 6000", + "Xevo TQ-S", "IlluminaMethylationEPIC", - "IlluminaHumanHT-12_V3_0_R1", - "Signa Premier AIR 3T", - "Olink Target 96", - "InfiniumPsychArrayBeadChip", + "PsychChip", + "Perlegen300Karray", + "PacBioRSII", + "Infinium Global Diversity Array-8", + "MiSeq", + "IlluminaInfiniumGSAMD-24v2-0", "Q Exactive", - "HiSeq2500", - "Orbitrap Exploris 240", "Affy5.0", - "Q Exactive HF", - "Bruker Avance III", - "Affymetrix Human Gene 1.0 ST Array", - "SequenomMultiplex", - "AffymetrixU133AB", - "Perlegen300Karray", - "LTQOrbitrapXL", - "Illumina_1M", - "Roche Cobas", - "Q Exactive Plus", "Affy6.0", - "DNBSEQ", - "IlluminaWholeGenomeDASL", - "NanostringnCounter_MouseADPanel", - "Infinium Global Diversity Array-8", - "HiSeq1000", - "PacBio Sequel IIe", - "AffymetrixU133Plus2", - "IlluminaMiSeq", - "Bionano Irys", - "IlluminaNovaseq6000", + "Biocrates p180", + "IlluminaHumanMethylation450", + "Orbitrap Fusion Lumos", + "Agilent44Karray", + "Infinium HumanOmniExpressExome", "quadrupole time-of-flight", + "triple quadrupole", + "Olink Target 96", + "IlluminaHumanHap300", + "Q Exactive HF", + "IlluminaNovaseq6000", + "Bionano Irys", + "NextSeq2000", + "Illumina_HumanOmni1-Quadv1.0", "ddSEQ Single-Cell Isolator", + "confocalImaging", + "PacBio Sequel IIe", + "AffymetrixU133Plus2", + "HiSeqX", "Leco Pegasus IV", - "orbitrap", - "MiSeq", - "IlluminaHumanHap650Yv3_A", - "Infinium HumanOmniExpressExome", "Infinium Omni2.5Exome-8 v1.5", - "IlluminaHumanHap300", - "Infinium Omni2.5Exome-8 v1.4", - "Xevo TQ-S", - "Illumina MouseWG-6 v2.0 expression beadchip", + "Illumina_Omni5-Quad", + "Illumina_1M", + "HiSeq1000", + "NextSeq500", + "DNBSEQ", "Biograph mCT", - "Illumina_Omni2.5-8_v1.3", + "Orbitrap Exploris 240", + "Q Exactive HF-X", + "IlluminaMiSeq", + "Illumina MouseWG-6 v2.0 expression beadchip", "HiSeq4000", + "Illumina_Omni2.5-8", + "BGISEQ-500", + "AffymetrixU133AB", + "HiSeq3000", + "Affymetrix Human Gene 1.0 ST Array", + "Q Exactive Plus", + "Infinium Omni2.5Exome-8 v1.4", + "OrbiTrap Fusion", + "PacBio Sequel II", + "IlluminaHumanHT-12_V3_0_R1", + "IlluminaWholeGenomeDASL", + "Illumina_Omni2.5-8_v1.3", + "HiSeq2500", "time-of-flight", + "SequenomMultiplex", + "Infinium Omni2.5Exome-8 v1.1", "Xevo G2 QTOF", - "HiSeqX", - "Illumina_Omni5-Quad", - "Biocrates p180", + "Illumina_Omni2pt5M", + "Signa Premier AIR 3T", + "NanostringnCounter_MouseADPanel", + "NanostringnCounter", + "Illumina_h650", "GAIIx", - "Orbitrap Fusion Lumos", - "PacBioRSII", + "InfiniumPsychArrayBeadChip", "Illumina_Omni2.5-8_v1.1", - "Infinium Omni2.5Exome-8 v1.1", + "Illumina_Infinium-HumanMethylation450-BeadChip", "Infinium Omni2.5Exome-8 v1.3", - "BGISEQ-500", - "PsychChip", - "Q Exactive HF-X", - "Illumina_Omni2.5-8", - "triple quadrupole", - "PacBio Sequel II", + "IlluminaHumanHap650Yv3_A", + "llumina Infinium General Screening Array 24-Kit v3.0", + "Bruker Avance III", "Illumina_Omni5M", - "OrbiTrap Fusion", + "orbitrap", + "Roche Cobas", "HiSeq2000", - "Illumina_HumanOmni1-Quadv1.0", - "Illumina_Infinium-HumanMethylation450-BeadChip", - "NanostringnCounter", - "confocalImaging", - "NextSeq500", - "HiSeq3000", - "IlluminaInfiniumGSAMD-24v2-0", - "Illumina_h650", - "llumina Infinium General Screening Array 24-Kit v3.0", - "Simoa HD-1 Analyzer", - "Agilent44Karray", - "NextSeq2000", - "IlluminaHumanMethylation450", - "Illumina_Omni2pt5M", - "Illumina NovaSeq 6000" + "LTQOrbitrapXL" ] }, - "referenceSet": { - "enum": [ - "GRCm38", - "GRCh38", - "MMUL1.0", - "1000 Genomes phase 3", - "GRCh37", - "HRC", - "dmel_r6.06", - "" - ] - }, - "libraryPrep": { - "enum": [ - "STARRSeq", - "EndItDNAEndRepairKit", - "multiome", - "SPLITseq", - "snIsoSeq", - "methylSeq", - "KapaHyperPrep", - "PCRfree", - "DNALibraryConstruction", - "MULTIseq", - "proximity ligation", - "polyAselection", - "amplicon", - "rRNAdepletion", - "lncRNAenrichment", - "SureCell", - "Chromium Single Cell 3'", - "miRNAenrichment", - "cellHashing", - "totalRNA" - ] - }, - "Component": {}, "libraryID": {}, - "runType": { + "ratio260over230": {}, + "dnaBatch": {}, + "ratio260over280": {}, + "specimenID": {}, + "libraryPreparationMethod": { "enum": [ - "singleEnd", - "pairedEnd" + "NEBNext", + "Drop-Seq", + "Ultralow Methyl-Seq", + "SMRTbell", + "Accel-NGS 2S Plus", + "CEL-seq", + "Illumina DNA PCR-Free Prep Kit", + "NexteraXT", + "Smart-seq2", + "Smart-seq4", + "Smart-seq1", + "sac-seq", + "TruSeq", + "10x", + "Accel-NGS Methyl-Seq", + "Omni-ATAC", + "" ] }, - "sequencingBatch": {}, - "specimenID": {}, - "totalReads": {}, - "numberCells": {}, - "dnaBatch": {}, - "ratio260over230": {}, "assay": { "enum": [ - "westernBlot", - "methylationArray", - "LC-MS", - "exomeSeq", - "UPLC-MSMS", - "Real Time PCR", - "SiMoA", - "FIA-MSMS", - "DIA", - "mirnaSeq", - "ELISA", - "Wishart Catecholamines", - "wholeGenomeSeq", - "contextual conditioning behavior", - "Positron Emission Tomography", - "autoradiography", - "high content screen", - "m6A-rnaSeq", - "von Frey test", + "rotarod performance test", + "Nightingale NMR", + "immunohistochemistry", + "novelty response behavior", "bisulfiteSeq", - "scirnaSeq", - "tractionForceMicroscopy", - "snATACSeq", - "Leiden Oxylipins", - "CUT&Tag", + "HPLC", "Wishart High Value Metabolites", - "scATACSeq", - "whole-cell patch clamp", - "elevated T maze apparatus method", - "Ribo-Seq", - "Sanger sequencing", - "rnaSeq", - "label free mass spectrometry", - "RPPA", - "long-read rnaSeq", - "active avoidance learning behavior", - "snrnaSeq", - "in vivo bioluminescence", - "kinesthetic behavior", + "Biocrates Q500", + "scirnaSeq", + "contextual conditioning behavior", "lncrnaSeq", - "polymeraseChainReaction", - "Genotyping", - "anxiety-related behavior", + "immunofluorescence", + "scale", + "FIA-MSMS", "microRNAcounts", - "MudPIT", - "LC-SRM", - "10x multiome", - "pharmacokinetics", - "Metabolon", - "Nightingale NMR", - "NOMe-Seq", + "Genotyping", + "Vernier Caliper", + "HPLC-MSMS", + "SiMoA", + "Biocrates p180", "memory behavior", - "proximity extension assay", - "nextGenerationTargetedSequencing", - "oxBS-Seq", - "sandwich ELISA", - "snpArray", - "FitBark", - "questionnaire", - "rotarod performance test", - "16SrRNAseq", + "LTP", + "RPPA", + "STARRSeq", + "MDMS-SL", + "snrnaSeq", "electrochemiluminescence", - "HI-C", - "photograph", - "Biocrates Q500", - "immunohistochemistry", + "rnaArray", + "rnaSeq", + "pharmacokinetics", + "FitBark", "lentiMPRA", - "UPLC-ESI-QTOF-MS", - "Biocrates Bile Acids", - "ChIPSeq", - "HiChIPseq", - "Biocrates p180", - "UCSD Untargeted Metabolomics", - "wheel running", - "immunofluorescence", - "liquid chromatography-electrochemical detection", - "ISOSeq", - "MDMS-SL", - "mRNAcounts", - "Rader Lipidomics", - "brightfieldMicroscopy", - "LC-MSMS", - "scale", - "ATACSeq", - "scwholeGenomeSeq", + "LFP", + "UPLC-MSMS", + "scCGIseq", + "UC Davis GCTOF", + "ELISA", + "10x multiome", "elevated plus maze test", - "LTP", + "NOMe-Seq", + "LC-MSMS", + "photograph", + "Blood Chemistry Measurement", + "von Frey test", + "MudPIT", + "scrnaSeq", "spontaneous alternation", + "mRNAcounts", + "scATACSeq", + "polymeraseChainReaction", + "LC-SRM", + "whole-cell patch clamp", + "westernBlot", + "high content screen", + "CUT&Tag", + "nextGenerationTargetedSequencing", + "DNA optical mapping", + "wheel running", + "brightfieldMicroscopy", + "errBisulfiteSeq", + "questionnaire", + "wholeGenomeSeq", + "elevated T maze apparatus method", + "Rader Lipidomics", "pharmacodynamics", - "STARRSeq", "cellViabilityAssay", - "atomicForceMicroscopy", - "rnaArray", + "CITESeq", + "m6A-rnaSeq", + "tractionForceMicroscopy", + "long-read rnaSeq", "mirnaArray", - "UC Davis GCTOF", - "errBisulfiteSeq", - "LFP", - "scrnaSeq", - "Blood Chemistry Measurement", + "in vivo bioluminescence", + "sandwich ELISA", + "UCSD Untargeted Metabolomics", + "Laser Speckle Imaging", + "liquid chromatography-electrochemical detection", + "ATACSeq", + "label free mass spectrometry", + "methylationArray", + "ChIPSeq", + "DIA", + "snpArray", + "snATACSeq", + "Wishart Catecholamines", + "Baker Lipidomics", + "Ribo-Seq", + "anxiety-related behavior", "jumpingLibrary", - "CITESeq", + "UPLC-ESI-QTOF-MS", + "HiChIPseq", + "locomotor activation behavior", + "frailty assessment", + "scwholeGenomeSeq", "Zeno Electronic Walkway", - "Baker Lipidomics", - "DNA optical mapping", - "HPLC-MSMS", - "Laser Speckle Imaging", - "Vernier Caliper", - "HPLC", + "Metabolon", + "Sanger sequencing", + "autoradiography", + "active avoidance learning behavior", + "MRI", + "Real Time PCR", + "mirnaSeq", + "16SrRNAseq", + "exomeSeq", + "kinesthetic behavior", + "atomicForceMicroscopy", + "HI-C", + "proximity extension assay", "open field test", - "scCGIseq", - "frailty assessment", - "locomotor activation behavior", + "LC-MS", + "Leiden Oxylipins", + "ISOSeq", "TMT quantitation", + "Biocrates Bile Acids", + "Positron Emission Tomography", + "oxBS-Seq", "MIB/MS", - "MRI", - "Immunocytochemistry", - "novelty response behavior" + "Immunocytochemistry" ] }, - "ratio260over280": {}, - "GQN": {} + "totalReads": {}, + "Component": {}, + "readLength": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "GQN": {}, + "libraryPrep": { + "enum": [ + "EndItDNAEndRepairKit", + "lncRNAenrichment", + "multiome", + "proximity ligation", + "polyAselection", + "totalRNA", + "snIsoSeq", + "cellHashing", + "rRNAdepletion", + "SureCell", + "miRNAenrichment", + "MULTIseq", + "DNALibraryConstruction", + "PCRfree", + "KapaHyperPrep", + "STARRSeq", + "amplicon", + "Chromium Single Cell 3'", + "SPLITseq", + "methylSeq" + ] + }, + "sequencingBatch": {}, + "referenceSet": { + "enum": [ + "GRCh38", + "GRCh37", + "MMUL1.0", + "HRC", + "1000 Genomes phase 3", + "dmel_r6.06", + "GRCm38", + "" + ] + }, + "runType": { + "enum": [ + "singleEnd", + "pairedEnd" + ] + }, + "numberCells": {} }, "required": [ - "readLength", "platform", + "assay", + "readLength", "libraryPrep", - "runType", - "assay" + "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 3cd8729..f4597a6 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": { + "tissueWeight": {}, + "ageDays": {}, + "nMale": {}, + "genotype": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "nucleicAcidSource": { "enum": [ - "not applicable", - "single cell", + "sorted nuclei", + "mitochondria", + "cfDNA", + "bulk cell", "bulk nuclei", + "single cell", "sorted cells", + "not applicable", "single nucleus", - "mitochondria", - "bulk cell", - "cfDNA", - "sorted nuclei", "" ] }, - "ageDays": {}, - "specimenID": {}, - "tissueWeight": {}, - "Component": {}, - "nIndividuals": {}, - "nFemale": {}, - "genotype": { - "not": { - "type": "null" - }, - "minLength": 1 - }, "temperature": {}, - "nMale": {}, "bodyPart": { "enum": [ - "brain", "head", + "brain", "" ] - } + }, + "nIndividuals": {}, + "nFemale": {}, + "specimenID": {}, + "Component": {} }, "required": [ "genotype" diff --git a/current-manifest-schemas/AD.BiospecimenInvitroMetadataTemplate.schema.json b/current-manifest-schemas/AD.BiospecimenInvitroMetadataTemplate.schema.json index 8849333..d904426 100644 --- a/current-manifest-schemas/AD.BiospecimenInvitroMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.BiospecimenInvitroMetadataTemplate.schema.json @@ -4,222 +4,101 @@ "title": "BiospecimenInvitroMetadataTemplate", "type": "object", "properties": { - "sourceCell": { + "terminalDifferentiationPoint": {}, + "treatmentType": { "enum": [ - "lymphoblast", - "fibroblast", - "astrocytes", - "cord blood stem cells", - "peripheral blood mononuclear cell", - "B-lymphocytes", - "embryonic stem cells", - "iPSC", + "cuprizone", + "clozapine", + "levetiracetam", + "verubecestat", + "haloperidol", + "Control", + "Abeta42 oligomer", + "Abeta42 fibril", + "placebo", "" ] }, - "specimenIdSource": {}, - "assay": { - "enum": [ - "MRI", - "snpArray", - "label free mass spectrometry", - "10x multiome", - "liquid chromatography-electrochemical detection", - "Biocrates p180", - "Leiden Oxylipins", - "methylationArray", - "scwholeGenomeSeq", - "proximity extension assay", - "frailty assessment", - "novelty response behavior", - "TMT quantitation", - "ELISA", - "snATACSeq", - "errBisulfiteSeq", - "immunofluorescence", - "16SrRNAseq", - "rnaSeq", - "pharmacodynamics", - "photograph", - "von Frey test", - "immunohistochemistry", - "cellViabilityAssay", - "Nightingale NMR", - "high content screen", - "westernBlot", - "rotarod performance test", - "ISOSeq", - "UPLC-ESI-QTOF-MS", - "LC-MS", - "nextGenerationTargetedSequencing", - "scrnaSeq", - "microRNAcounts", - "ChIPSeq", - "DNA optical mapping", - "brightfieldMicroscopy", - "spontaneous alternation", - "Positron Emission Tomography", - "jumpingLibrary", - "MIB/MS", - "wholeGenomeSeq", - "Zeno Electronic Walkway", - "MDMS-SL", - "HiChIPseq", - "Biocrates Bile Acids", - "open field test", - "Sanger sequencing", - "lncrnaSeq", - "elevated T maze apparatus method", - "scCGIseq", - "in vivo bioluminescence", - "Wishart Catecholamines", - "autoradiography", - "Genotyping", - "Biocrates Q500", - "LFP", - "pharmacokinetics", - "sandwich ELISA", - "LTP", - "NOMe-Seq", - "HPLC", - "HI-C", - "whole-cell patch clamp", - "FIA-MSMS", - "atomicForceMicroscopy", - "DIA", - "questionnaire", - "Blood Chemistry Measurement", - "elevated plus maze test", - "wheel running", - "CITESeq", - "LC-MSMS", - "locomotor activation behavior", - "Vernier Caliper", - "anxiety-related behavior", - "CUT&Tag", - "m6A-rnaSeq", - "SiMoA", - "ATACSeq", - "Laser Speckle Imaging", - "LC-SRM", - "lentiMPRA", - "Rader Lipidomics", - "Ribo-Seq", - "Wishart High Value Metabolites", - "Immunocytochemistry", - "UPLC-MSMS", - "FitBark", - "scale", - "bisulfiteSeq", - "active avoidance learning behavior", - "Metabolon", - "exomeSeq", - "HPLC-MSMS", - "UCSD Untargeted Metabolomics", - "scATACSeq", - "MudPIT", - "mirnaArray", - "electrochemiluminescence", - "kinesthetic behavior", - "snrnaSeq", - "oxBS-Seq", - "long-read rnaSeq", - "mirnaSeq", - "scirnaSeq", - "polymeraseChainReaction", - "STARRSeq", - "mRNAcounts", - "tractionForceMicroscopy", - "UC Davis GCTOF", - "memory behavior", - "rnaArray", - "contextual conditioning behavior", - "Real Time PCR", - "RPPA", - "Baker Lipidomics" - ] - }, "nucleicAcidSource": { "enum": [ - "single nucleus", "single cell", "sorted cells", "not applicable", - "bulk cell", - "bulk nuclei", - "cfDNA", - "sorted nuclei", + "single nucleus", "mitochondria", + "sorted nuclei", + "cfDNA", + "bulk nuclei", + "bulk cell", + "" + ] + }, + "differentiationMethod": { + "enum": [ + "directed differentiation", + "Ngn2 induction", "" ] }, "cellType": { "enum": [ - "polygonal", - "round", - "arachnoid", - "lymphoblast", - "meningioma", - "fibroblast", - "astrocytes", - "NCX NES", - "iPSC-derived neuronal progenitor cell", - "SH-SY5Y", - "iPSC-derived astrocytes", - "iPSC", + "CNON", + "iPSC-derived neuron", + "neural progenitor cell", + "monocyte-derived microglia", + "NeuN+", + "B-lymphocytes", "oligodendrocyte", "iPSC-derived glia", - "macrophages", - "microglia", - "monocytes", - "glia", - "dopaminergic neurons", - "schwannoma", - "GABAergic neurons", - "A549", - "iPSC-derived telencephalic organoids", - "lymphoblastoid cell line", - "neural progenitor cell", - "NeuN-", + "NCX NES", + "SH-SY5Y", "CD8+ T-Cells", - "peripheral blood mononuclear cell", - "CD138+", - "B-lymphocytes", - "immune cell", "GLUtamatergic neurons", + "lymphoblast", + "immune cell", + "lymphoblastoid cell line", + "macrophages", + "dopaminergic neurons", "schwann", - "CNON", - "monocyte-derived microglia", - "Schwann cell precusor", - "iPSC-derived neuron", + "embryonic stem cells", + "polygonal", + "fibroblast", + "iPSC-derived astrocytes", + "peripheral blood mononuclear cell", + "epithelial", "epithelial-like", + "arachnoid", + "meningioma", + "GABAergic neurons", + "microglia", + "CD138+", + "NeuN-", + "iPSC-derived neuronal progenitor cell", "neuron", - "epithelial", - "NeuN+", - "embryonic stem cells", - "" - ] - }, - "modelSystemType": { - "enum": [ - "immortalized cell line", - "organoid", - "primary cell culture", - "cerebral organoid", - "animal", + "A549", + "astrocytes", + "monocytes", "iPSC", + "Schwann cell precusor", + "round", + "schwannoma", + "glia", + "iPSC-derived telencephalic organoids", "" ] }, - "terminalDifferentiationPoint": {}, - "differentiationMethod": { + "samplingAgeUnits": { "enum": [ - "directed differentiation", - "Ngn2 induction", + "years", + "PCW", + "days", + "months", + "weeks", + "gestational weeks", "" ] }, - "Component": {}, + "specimenID": {}, "reprogrammingMethod": { "enum": [ "Sendai virus", @@ -228,43 +107,164 @@ "" ] }, - "passage": {}, - "samplingAge": {}, "individualID": { "not": { "type": "null" }, "minLength": 1 }, - "treatmentType": { + "specimenIdSource": {}, + "samplingAge": {}, + "Component": {}, + "assay": { "enum": [ - "Abeta42 fibril", - "haloperidol", - "Control", - "placebo", - "clozapine", - "levetiracetam", - "cuprizone", - "Abeta42 oligomer", - "verubecestat", + "rnaArray", + "Biocrates p180", + "rotarod performance test", + "nextGenerationTargetedSequencing", + "FitBark", + "LFP", + "Biocrates Q500", + "methylationArray", + "immunofluorescence", + "active avoidance learning behavior", + "MRI", + "LC-MS", + "spontaneous alternation", + "ATACSeq", + "MIB/MS", + "HPLC", + "immunohistochemistry", + "Wishart Catecholamines", + "Nightingale NMR", + "frailty assessment", + "LC-SRM", + "locomotor activation behavior", + "mirnaSeq", + "DNA optical mapping", + "CITESeq", + "polymeraseChainReaction", + "scrnaSeq", + "jumpingLibrary", + "MDMS-SL", + "UC Davis GCTOF", + "in vivo bioluminescence", + "rnaSeq", + "whole-cell patch clamp", + "HPLC-MSMS", + "tractionForceMicroscopy", + "errBisulfiteSeq", + "mRNAcounts", + "HI-C", + "lentiMPRA", + "Metabolon", + "anxiety-related behavior", + "high content screen", + "Vernier Caliper", + "kinesthetic behavior", + "Genotyping", + "sandwich ELISA", + "bisulfiteSeq", + "microRNAcounts", + "wholeGenomeSeq", + "Baker Lipidomics", + "scATACSeq", + "label free mass spectrometry", + "Zeno Electronic Walkway", + "Ribo-Seq", + "Real Time PCR", + "CUT&Tag", + "lncrnaSeq", + "MudPIT", + "Biocrates Bile Acids", + "LC-MSMS", + "Rader Lipidomics", + "elevated plus maze test", + "UPLC-MSMS", + "UCSD Untargeted Metabolomics", + "brightfieldMicroscopy", + "questionnaire", + "Sanger sequencing", + "snrnaSeq", + "16SrRNAseq", + "mirnaArray", + "scwholeGenomeSeq", + "HiChIPseq", + "Blood Chemistry Measurement", + "elevated T maze apparatus method", + "STARRSeq", + "snpArray", + "electrochemiluminescence", + "contextual conditioning behavior", + "ISOSeq", + "TMT quantitation", + "Leiden Oxylipins", + "Immunocytochemistry", + "proximity extension assay", + "10x multiome", + "open field test", + "cellViabilityAssay", + "wheel running", + "memory behavior", + "RPPA", + "SiMoA", + "m6A-rnaSeq", + "UPLC-ESI-QTOF-MS", + "Wishart High Value Metabolites", + "scale", + "atomicForceMicroscopy", + "snATACSeq", + "DIA", + "pharmacokinetics", + "ChIPSeq", + "ELISA", + "scCGIseq", + "Positron Emission Tomography", + "exomeSeq", + "long-read rnaSeq", + "Laser Speckle Imaging", + "von Frey test", + "LTP", + "novelty response behavior", + "autoradiography", + "FIA-MSMS", + "oxBS-Seq", + "scirnaSeq", + "pharmacodynamics", + "photograph", + "NOMe-Seq", + "liquid chromatography-electrochemical detection", + "westernBlot" + ] + }, + "modelSystemType": { + "enum": [ + "organoid", + "cerebral organoid", + "animal", + "immortalized cell line", + "primary cell culture", + "iPSC", "" ] }, - "samplingAgeUnits": { + "sourceCell": { "enum": [ - "days", - "gestational weeks", - "PCW", - "months", - "years", - "weeks", + "embryonic stem cells", + "fibroblast", + "peripheral blood mononuclear cell", + "cord blood stem cells", + "astrocytes", + "iPSC", + "lymphoblast", + "B-lymphocytes", "" ] }, - "specimenID": {} + "passage": {} }, "required": [ - "assay", - "individualID" + "individualID", + "assay" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.BiospecimenMetadataTemplate.schema.json b/current-manifest-schemas/AD.BiospecimenMetadataTemplate.schema.json index 0854587..901de59 100644 --- a/current-manifest-schemas/AD.BiospecimenMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.BiospecimenMetadataTemplate.schema.json @@ -4,32 +4,28 @@ "title": "BiospecimenMetadataTemplate", "type": "object", "properties": { - "BrodmannArea": {}, - "isPostMortem": { - "enum": [ - "FALSE", - "TRUE", - "" - ] - }, "treatmentType": { "enum": [ - "Control", - "placebo", - "Abeta42 fibril", - "Abeta42 oligomer", - "clozapine", - "levetiracetam", "cuprizone", "verubecestat", + "Abeta42 oligomer", + "placebo", + "Control", + "Abeta42 fibril", "haloperidol", + "levetiracetam", + "clozapine", "" ] }, - "fastingState": { + "samplingAgeUnits": { "enum": [ - "FALSE", - "TRUE", + "weeks", + "years", + "months", + "PCW", + "days", + "gestational weeks", "" ] }, @@ -39,336 +35,340 @@ }, "minLength": 1 }, - "nucleicAcidSource": { + "cellType": { "enum": [ - "single nucleus", - "mitochondria", - "sorted cells", - "bulk cell", - "sorted nuclei", - "not applicable", - "bulk nuclei", - "cfDNA", - "single cell", + "GABAergic neurons", + "iPSC-derived neuronal progenitor cell", + "embryonic stem cells", + "epithelial", + "iPSC-derived neuron", + "fibroblast", + "NeuN-", + "oligodendrocyte", + "NeuN+", + "peripheral blood mononuclear cell", + "iPSC-derived glia", + "meningioma", + "astrocytes", + "schwann", + "Schwann cell precusor", + "macrophages", + "CD8+ T-Cells", + "CNON", + "A549", + "epithelial-like", + "lymphoblastoid cell line", + "monocyte-derived microglia", + "iPSC-derived telencephalic organoids", + "microglia", + "CD138+", + "iPSC", + "lymphoblast", + "round", + "schwannoma", + "glia", + "dopaminergic neurons", + "NCX NES", + "iPSC-derived astrocytes", + "monocytes", + "arachnoid", + "GLUtamatergic neurons", + "neuron", + "SH-SY5Y", + "immune cell", + "neural progenitor cell", + "B-lymphocytes", + "polygonal", "" ] }, - "specimenIdSource": {}, - "samplingAge": {}, + "fastingState": { + "enum": [ + "TRUE", + "FALSE", + "" + ] + }, + "visitNumber": {}, "treatmentDose": {}, + "samplingAge": {}, + "organ": { + "enum": [ + "nerves", + "large intestine", + "brain", + "prostate", + "mammary gland", + "blood", + "nose", + "cerebrospinal fluid", + "pancreas", + "Bursa Of Fabricius", + "lung", + "liver", + "ovary", + "spleen", + "lymph node", + "bone marrow", + "breast", + "colon", + "skin", + "kidney" + ] + }, "Component": {}, - "samplingAgeUnits": { + "sampleStatus": { "enum": [ - "months", - "gestational weeks", - "PCW", - "days", - "years", - "weeks", + "fresh", + "formalin-fixed", + "paxgene", + "frozen", "" ] }, "specimenID": {}, - "tissue": { + "isPostMortem": { "enum": [ - "right cerebral hemisphere", - "precentral gyrus", - "nerve tissue", - "superior temporal gyrus", - "inferior frontal gyrus", - "serum", - "dorsal anterior cingulate cortex", - "parietal cortex", - "cerebellum", - "parahippocampal gyrus", - "cecum derived fecal material", - "inferolateral temporal cortex", - "liver", - "fecal material", - "amygdaloid complex", - "forebrain", - "frontal pole", - "blood", - "parietal lobe", - "Dorsal Root Ganglion", - "lateral entorhinal cortex", - "middle frontal gyrus", - "medial frontal cortex", - "prefrontal cortex", - "primary tumor", - "plasma", - "nucleus accumbens", - "posterior inferior parietal cortex", - "subgenual cingulate cortex", - "VZ/SVZ", - "cerebral cortex", - "occipital visual cortex", - "embryonic tissue", - "superior parietal lobe", - "subgenual anterior cingulate cortex", - "inferior temporal gyrus", - "head of caudate nucleus", - "medial ganglionic eminence", - "primary motor cortex", - "cerebellar cortex", - "meninges", - "occipital lobe", - "medial dorsal nucleus of thalamus", - "temporal lobe", - "bone marrow", - "insula", - "dorsal pallium", - "anterior cingulate cortex", - "entorhinal cortex", - "posterior cingulate cortex", - "whole brain", - "ventrolateral prefrontal cortex", - "striatum", - "midbrain", - "middle temporal gyrus", - "olfactory neuroepithelium", - "thalamus", - "fusiform gyrus", - "medial prefrontal cortex", - "primary somatosensory cortex", - "temporal cortex", - "posterior superior temporal cortex", - "frontal cortex", - "Not Applicable", - "frontal lobe", - "unspecified", - "dorsolateral prefrontal cortex", - "putamen", - "dorsomedial prefrontal cortex", - "insular cortex", - "posteroinferior parietal cortex", - "ventricular zone", - "orbitofrontal cortex", - "angular gyrus", - "temporal pole", - "cortical plate", - "caudate nucleus", - "Buccal Mucosa", - "primary visual cortex", - "Buffy Coat", - "hippocampus", - "left cerebral hemisphere", - "primary auditory cortex", - "mammillary body", - "amygdala", - "inferior temporal cortex", - "medial entorhinal cortex", - "splenocyte", - "medial orbital frontal cortex" + "TRUE", + "FALSE", + "" ] }, + "specimenIdSource": {}, "assay": { "enum": [ - "MDMS-SL", - "Positron Emission Tomography", - "westernBlot", - "exomeSeq", - "Biocrates Q500", - "LC-MS", - "immunohistochemistry", - "Genotyping", - "LTP", - "Ribo-Seq", - "errBisulfiteSeq", - "cellViabilityAssay", - "rotarod performance test", - "ISOSeq", - "wholeGenomeSeq", - "methylationArray", - "novelty response behavior", - "kinesthetic behavior", - "16SrRNAseq", - "ELISA", - "elevated plus maze test", - "nextGenerationTargetedSequencing", - "rnaArray", - "mirnaArray", - "Laser Speckle Imaging", - "UPLC-MSMS", - "mirnaSeq", - "m6A-rnaSeq", - "brightfieldMicroscopy", - "STARRSeq", - "atomicForceMicroscopy", - "DNA optical mapping", - "ChIPSeq", - "active avoidance learning behavior", + "high content screen", "HI-C", - "immunofluorescence", - "memory behavior", - "UPLC-ESI-QTOF-MS", - "pharmacokinetics", - "UC Davis GCTOF", - "Baker Lipidomics", - "polymeraseChainReaction", - "Sanger sequencing", - "locomotor activation behavior", - "FIA-MSMS", - "Biocrates Bile Acids", - "ATACSeq", - "HiChIPseq", - "whole-cell patch clamp", + "elevated T maze apparatus method", + "anxiety-related behavior", + "microRNAcounts", + "ISOSeq", + "MIB/MS", "NOMe-Seq", - "lncrnaSeq", - "UCSD Untargeted Metabolomics", - "10x multiome", + "SiMoA", + "Biocrates p180", + "scCGIseq", "CITESeq", + "spontaneous alternation", + "Blood Chemistry Measurement", + "Sanger sequencing", + "RPPA", + "LC-MSMS", + "pharmacokinetics", + "scwholeGenomeSeq", + "m6A-rnaSeq", + "active avoidance learning behavior", + "sandwich ELISA", + "TMT quantitation", + "16SrRNAseq", "Leiden Oxylipins", - "oxBS-Seq", - "autoradiography", - "von Frey test", + "Wishart Catecholamines", + "Laser Speckle Imaging", + "10x multiome", + "atomicForceMicroscopy", + "Metabolon", + "MudPIT", "liquid chromatography-electrochemical detection", - "SiMoA", - "questionnaire", - "lentiMPRA", - "sandwich ELISA", - "snATACSeq", - "bisulfiteSeq", - "RPPA", - "spontaneous alternation", "open field test", + "ATACSeq", + "memory behavior", + "kinesthetic behavior", "scale", - "Rader Lipidomics", - "LC-MSMS", - "contextual conditioning behavior", - "elevated T maze apparatus method", - "in vivo bioluminescence", - "frailty assessment", + "long-read rnaSeq", + "exomeSeq", + "STARRSeq", + "bisulfiteSeq", + "snpArray", + "mirnaSeq", + "whole-cell patch clamp", "wheel running", - "Metabolon", - "scwholeGenomeSeq", - "Immunocytochemistry", - "Nightingale NMR", - "Vernier Caliper", + "UC Davis GCTOF", "scrnaSeq", - "Zeno Electronic Walkway", - "HPLC-MSMS", - "Blood Chemistry Measurement", - "scCGIseq", - "tractionForceMicroscopy", "rnaSeq", - "HPLC", - "FitBark", - "anxiety-related behavior", + "CUT&Tag", + "autoradiography", + "rnaArray", + "Baker Lipidomics", + "LC-SRM", + "MDMS-SL", "label free mass spectrometry", - "scirnaSeq", + "Genotyping", + "HiChIPseq", + "LC-MS", + "contextual conditioning behavior", "pharmacodynamics", + "FIA-MSMS", + "LTP", + "westernBlot", + "Zeno Electronic Walkway", + "elevated plus maze test", + "scATACSeq", "photograph", - "Wishart Catecholamines", + "errBisulfiteSeq", + "UCSD Untargeted Metabolomics", + "ELISA", + "HPLC", "LFP", - "long-read rnaSeq", - "mRNAcounts", - "MudPIT", - "TMT quantitation", - "MRI", - "electrochemiluminescence", - "microRNAcounts", - "jumpingLibrary", - "proximity extension assay", - "CUT&Tag", - "snpArray", - "scATACSeq", - "high content screen", "Real Time PCR", - "Biocrates p180", + "rotarod performance test", + "cellViabilityAssay", + "lentiMPRA", + "immunofluorescence", + "novelty response behavior", + "immunohistochemistry", "snrnaSeq", + "brightfieldMicroscopy", + "in vivo bioluminescence", + "questionnaire", + "methylationArray", + "oxBS-Seq", + "mirnaArray", + "MRI", + "nextGenerationTargetedSequencing", + "Immunocytochemistry", + "HPLC-MSMS", + "Rader Lipidomics", + "Positron Emission Tomography", + "scirnaSeq", + "jumpingLibrary", "Wishart High Value Metabolites", + "wholeGenomeSeq", + "locomotor activation behavior", + "electrochemiluminescence", + "FitBark", + "UPLC-ESI-QTOF-MS", + "snATACSeq", + "UPLC-MSMS", + "frailty assessment", + "polymeraseChainReaction", + "von Frey test", "DIA", - "MIB/MS", - "LC-SRM" - ] - }, - "sampleStatus": { - "enum": [ - "fresh", - "paxgene", - "formalin-fixed", - "frozen", - "" + "proximity extension assay", + "Ribo-Seq", + "Biocrates Bile Acids", + "lncrnaSeq", + "Vernier Caliper", + "Nightingale NMR", + "DNA optical mapping", + "ChIPSeq", + "tractionForceMicroscopy", + "Biocrates Q500", + "mRNAcounts" ] }, - "cellType": { + "BrodmannArea": {}, + "nucleicAcidSource": { "enum": [ - "lymphoblast", - "astrocytes", - "Schwann cell precusor", - "NCX NES", - "immune cell", - "neural progenitor cell", - "A549", - "monocytes", - "arachnoid", - "peripheral blood mononuclear cell", - "macrophages", - "iPSC", - "iPSC-derived telencephalic organoids", - "embryonic stem cells", - "meningioma", - "SH-SY5Y", - "epithelial-like", - "microglia", - "dopaminergic neurons", - "epithelial", - "CD8+ T-Cells", - "CD138+", - "NeuN+", - "NeuN-", - "B-lymphocytes", - "polygonal", - "fibroblast", - "schwannoma", - "neuron", - "CNON", - "schwann", - "iPSC-derived neuronal progenitor cell", - "GLUtamatergic neurons", - "monocyte-derived microglia", - "GABAergic neurons", - "round", - "iPSC-derived glia", - "iPSC-derived neuron", - "glia", - "lymphoblastoid cell line", - "oligodendrocyte", - "iPSC-derived astrocytes", + "bulk cell", + "not applicable", + "sorted cells", + "single nucleus", + "mitochondria", + "cfDNA", + "sorted nuclei", + "bulk nuclei", + "single cell", "" ] }, - "organ": { + "tissue": { "enum": [ - "bone marrow", - "skin", - "cerebrospinal fluid", - "ovary", - "lymph node", - "kidney", - "Bursa Of Fabricius", - "breast", - "spleen", - "prostate", - "brain", - "mammary gland", - "lung", + "lateral entorhinal cortex", + "medial ganglionic eminence", + "VZ/SVZ", + "mammillary body", + "occipital lobe", + "inferior frontal gyrus", + "amygdaloid complex", + "frontal cortex", + "plasma", + "midbrain", + "anterior cingulate cortex", + "parahippocampal gyrus", + "embryonic tissue", + "inferior temporal gyrus", + "primary auditory cortex", + "cerebral cortex", + "meninges", + "temporal pole", + "primary somatosensory cortex", + "forebrain", + "occipital visual cortex", "liver", - "pancreas", - "large intestine", - "colon", - "nose", + "hippocampus", + "primary motor cortex", + "cerebellum", + "inferior temporal cortex", + "fusiform gyrus", + "thalamus", + "dorsal pallium", + "temporal lobe", + "ventricular zone", + "cerebellar cortex", + "cecum derived fecal material", + "insular cortex", + "frontal lobe", + "cortical plate", + "amygdala", + "entorhinal cortex", + "superior parietal lobe", + "inferolateral temporal cortex", + "dorsomedial prefrontal cortex", + "angular gyrus", + "right cerebral hemisphere", + "bone marrow", + "fecal material", + "insula", + "posterior superior temporal cortex", + "middle frontal gyrus", + "precentral gyrus", + "primary tumor", + "superior temporal gyrus", + "frontal pole", "blood", - "nerves" + "whole brain", + "medial prefrontal cortex", + "subgenual cingulate cortex", + "putamen", + "nucleus accumbens", + "middle temporal gyrus", + "striatum", + "nerve tissue", + "posterior inferior parietal cortex", + "caudate nucleus", + "temporal cortex", + "Buffy Coat", + "posteroinferior parietal cortex", + "head of caudate nucleus", + "prefrontal cortex", + "Not Applicable", + "Buccal Mucosa", + "serum", + "splenocyte", + "left cerebral hemisphere", + "primary visual cortex", + "dorsolateral prefrontal cortex", + "parietal cortex", + "olfactory neuroepithelium", + "medial dorsal nucleus of thalamus", + "medial entorhinal cortex", + "subgenual anterior cingulate cortex", + "orbitofrontal cortex", + "posterior cingulate cortex", + "medial orbital frontal cortex", + "unspecified", + "parietal lobe", + "dorsal anterior cingulate cortex", + "medial frontal cortex", + "ventrolateral prefrontal cortex", + "Dorsal Root Ganglion" ] - }, - "visitNumber": {} + } }, "required": [ "individualID", - "tissue", + "organ", "assay", - "organ" + "tissue" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.FileAnnotationTemplate.schema.json b/current-manifest-schemas/AD.FileAnnotationTemplate.schema.json index 3742e55..0a52448 100644 --- a/current-manifest-schemas/AD.FileAnnotationTemplate.schema.json +++ b/current-manifest-schemas/AD.FileAnnotationTemplate.schema.json @@ -6,44 +6,67 @@ "properties": { "metadataType": { "enum": [ - "data dictionary", - "analytical covariates", - "ID mapping", "manifest", + "individual", + "data dictionary", "assay metadata", - "biospecimen", + "ID mapping", "protocol", - "individual", + "analytical covariates", + "biospecimen", "" ] }, + "Component": {}, + "isModelSystem": { + "enum": [ + "TRUE", + "FALSE" + ] + }, + "Filename": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "resourceType": { + "enum": [ + "experimentalData", + "report", + "curatedData", + "analysis", + "metadata", + "tool" + ] + }, "chromosome": { "enum": [ - "7", - "9", - "11", + "20", + "8", "mitochondrial", - "12", - "10", + "17", "22", + "5", + "2", + "10", + "21", + "12", + "11", "16", - "14", - "1", - "X", + "15", + "6", + "7", "Y", - "21", + "19", "3", - "8", - "6", "13", + "9", + "14", "18", - "20", - "5", - "19", + "X", "4", - "15", - "2", - "17", + "1", "" ] }, @@ -53,32 +76,25 @@ }, "minLength": 1 }, - "dataType": { + "specimenID": {}, + "consortium": { "enum": [ - "kinomics", - "isoformExpression", - "metagenomics", - "image", - "immunoassay", - "cellularPhysiology", - "proteomics", - "electrophysiology", - "clinical", - "Volume", - "Weight", - "network", - "genomicVariants", - "pharmacology", - "surveyData", - "geneExpression", - "Pharmacokinetic Study", - "epigenetics", - "metabolomics", - "chromatinActivity", - "behavior process", - "drugScreen", - "drugCombinationScreen", - "" + "ELITE", + "AMP-AD", + "BSMN", + "CDCP", + "PEC", + "M2OVE-AD", + "DHART SPORE", + "GENIE", + "PSON", + "CMC", + "Psych-AD", + "CSBC", + "MODEL-AD", + "Resilience-AD", + "Synodos", + "Not Applicable" ] }, "isMultiSpecimen": { @@ -87,535 +103,520 @@ "FALSE" ] }, + "fileFormat": { + "enum": [ + "json", + "RData", + "sqlite", + "bim", + "sf3", + "idx", + "bam", + "png", + "tbi", + "cram", + "hdf", + "idat", + "cel", + "tab", + "mtx", + "recal", + "csv", + "powerpoint", + "saf", + "pdstudy", + "md", + "zip", + "pdview", + "bed gappedPeak", + "fig", + "tranches", + "bsc", + "fastq", + "pdresult", + "chp", + "tif", + "abf", + "maf", + "sav", + "svs", + "raw", + "R script", + "vcf", + "bed narrowPeak", + "Synapse Table", + "RLF", + "gct", + "tar", + "txt", + "bcf", + "plink", + "Sentrix descriptor file", + "rmd", + "bgzip", + "doc", + "DICOM", + "mov", + "bed", + "fasta", + "7z", + "czi", + "sam", + "RCC", + "yaml", + "fam", + "mp4", + "dup", + "tagAlign", + "mat", + "excel", + "html", + "gtf", + "sif", + "bpm", + "seg", + "bed broadPeak", + "flagstat", + "gzip", + "pzfx", + "xml", + "Python script", + "bai", + "jpg", + "msf", + "locs", + "ab1", + "dat", + "hyperlink", + "bash script", + "hic", + "wiggle", + "nirs", + "bedgraph", + "bigwig", + "tsv", + "sra", + "avi", + "pdf", + "sdf", + "svg", + "gff3" + ] + }, + "dataSubtype": { + "enum": [ + "dataMatrix", + "raw", + "processed", + "metadata", + "residualized", + "normalized", + "" + ] + }, + "individualID": {}, "assay": { "enum": [ - "Baker Lipidomics", - "Biocrates Bile Acids", - "spontaneous alternation", - "in vivo bioluminescence", - "anxiety-related behavior", - "Real Time PCR", - "questionnaire", - "atomicForceMicroscopy", - "Ribo-Seq", + "oxBS-Seq", + "HiChIPseq", "lncrnaSeq", - "frailty assessment", - "autoradiography", - "Wishart High Value Metabolites", - "TMT quantitation", - "polymeraseChainReaction", - "DNA optical mapping", - "sandwich ELISA", - "Blood Chemistry Measurement", - "LC-SRM", - "immunohistochemistry", - "MRI", + "MDMS-SL", + "scCGIseq", "memory behavior", - "CITESeq", - "elevated plus maze test", - "microRNAcounts", - "HPLC-MSMS", + "frailty assessment", + "m6A-rnaSeq", + "UCSD Untargeted Metabolomics", + "westernBlot", + "Immunocytochemistry", + "LTP", + "mirnaSeq", + "Rader Lipidomics", + "Biocrates Bile Acids", + "exomeSeq", + "Genotyping", + "jumpingLibrary", "Positron Emission Tomography", - "open field test", - "Biocrates p180", - "Zeno Electronic Walkway", - "ISOSeq", - "UC Davis GCTOF", - "Wishart Catecholamines", - "SiMoA", - "kinesthetic behavior", + "scale", + "MRI", + "snrnaSeq", + "pharmacokinetics", + "Sanger sequencing", + "long-read rnaSeq", + "atomicForceMicroscopy", "LC-MSMS", - "nextGenerationTargetedSequencing", - "lentiMPRA", - "oxBS-Seq", + "LC-SRM", + "label free mass spectrometry", + "wheel running", "16SrRNAseq", - "NOMe-Seq", - "mirnaSeq", - "jumpingLibrary", - "whole-cell patch clamp", + "MIB/MS", + "pharmacodynamics", "rnaSeq", - "errBisulfiteSeq", + "in vivo bioluminescence", + "HI-C", + "lentiMPRA", + "mRNAcounts", + "UPLC-MSMS", + "brightfieldMicroscopy", + "questionnaire", + "MudPIT", "liquid chromatography-electrochemical detection", - "FIA-MSMS", - "tractionForceMicroscopy", - "ATACSeq", - "immunofluorescence", - "proximity extension assay", - "long-read rnaSeq", + "cellViabilityAssay", "RPPA", - "scCGIseq", - "scwholeGenomeSeq", - "brightfieldMicroscopy", - "elevated T maze apparatus method", + "FitBark", + "Blood Chemistry Measurement", + "immunofluorescence", + "ISOSeq", "ELISA", - "photograph", - "LC-MS", - "LFP", - "locomotor activation behavior", - "HI-C", + "CUT&Tag", + "DNA optical mapping", + "bisulfiteSeq", + "ATACSeq", + "SiMoA", + "immunohistochemistry", + "Metabolon", + "UC Davis GCTOF", + "von Frey test", + "contextual conditioning behavior", + "autoradiography", "wholeGenomeSeq", - "MudPIT", "rotarod performance test", - "snATACSeq", "HPLC", - "electrochemiluminescence", - "scrnaSeq", - "pharmacodynamics", - "mRNAcounts", - "Immunocytochemistry", - "scale", - "UPLC-ESI-QTOF-MS", - "active avoidance learning behavior", - "exomeSeq", - "high content screen", - "Rader Lipidomics", - "pharmacokinetics", - "label free mass spectrometry", - "Laser Speckle Imaging", - "scirnaSeq", - "Genotyping", + "errBisulfiteSeq", "methylationArray", + "elevated plus maze test", + "microRNAcounts", + "photograph", + "scwholeGenomeSeq", "rnaArray", - "HiChIPseq", - "novelty response behavior", - "FitBark", - "MDMS-SL", - "Biocrates Q500", - "STARRSeq", - "snpArray", - "Nightingale NMR", - "m6A-rnaSeq", - "snrnaSeq", - "cellViabilityAssay", - "MIB/MS", - "UCSD Untargeted Metabolomics", - "ChIPSeq", - "wheel running", - "von Frey test", - "mirnaArray", - "CUT&Tag", - "westernBlot", + "10x multiome", + "snATACSeq", + "LC-MS", + "scrnaSeq", + "high content screen", "Leiden Oxylipins", - "LTP", - "Sanger sequencing", - "bisulfiteSeq", - "scATACSeq", - "UPLC-MSMS", - "Metabolon", + "Zeno Electronic Walkway", "Vernier Caliper", + "scATACSeq", + "Wishart High Value Metabolites", + "spontaneous alternation", + "elevated T maze apparatus method", + "FIA-MSMS", + "novelty response behavior", + "tractionForceMicroscopy", + "Ribo-Seq", + "ChIPSeq", + "electrochemiluminescence", "DIA", - "contextual conditioning behavior", - "10x multiome" + "active avoidance learning behavior", + "Nightingale NMR", + "Baker Lipidomics", + "NOMe-Seq", + "HPLC-MSMS", + "LFP", + "anxiety-related behavior", + "TMT quantitation", + "Wishart Catecholamines", + "locomotor activation behavior", + "mirnaArray", + "open field test", + "polymeraseChainReaction", + "scirnaSeq", + "kinesthetic behavior", + "CITESeq", + "proximity extension assay", + "snpArray", + "STARRSeq", + "Real Time PCR", + "UPLC-ESI-QTOF-MS", + "Biocrates p180", + "nextGenerationTargetedSequencing", + "Biocrates Q500", + "whole-cell patch clamp", + "Laser Speckle Imaging", + "sandwich ELISA" ] }, - "analysisType": { + "dataType": { "enum": [ - "Copy number estimation", - "correlation", - "assessment", - "DNA methylation imputation", - "somatic mutation calling", - "ANOVA", - "Gene expression comparison", - "principal component analysis", - "hidden confounder detection", - "genotype imputation", - "search engine output files", - "differential methylation", - "protein quantitative trait loci detection", - "chromatin accessible quantitative trait loci detection", - "Supervised Machine Learning", - "de-novo assembly", - "genotypeAncestry", - "network analysis", - "transcript quantification", - 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"metabolomics", + "chromatinActivity", + "pharmacology", + "Weight", + "kinomics", + "Volume", + "cellularPhysiology", + "image", + "immunoassay", + "epigenetics", + "drugScreen", + "behavior process", "" ] }, - "study": { - "enum": [ - "UCI_BIN1", - "UFLOR_ABI3_GNGT2", - "MODEL-AD_APOE4_Trem2", - "ADMC_UPenn", - "LBP", - "UCI_Multiomics", - "MSMM", - "diseasePseudotime", - "OFMM", - "APOE-TR", - "VirusResilience_iPSC", - "CMC-PEC", - "U1-70_PrimaryCellCulture", - "Jax.IU.Pitt_Verubecestat_5XFAD", - "NHP-Macaque", - "Banner", - "VMC", - "ADAtlas_Archive", - "BrainGVEX", - "MRGWAS", - "AD_ADRD_Exposome", - "ROSMAP", - "ROSMAP_Lipidomics_Emory", - "MayoRNAseq", - "SUNYStrokeModel", - "MIT_ROSMAP_Multiomics", - "iNiAstshRNA", - "TyrobpKO", - "VirusResilience_Banner", - "APOEPSC", - "MODEL-AD_APOE4_KI", - "scRNAseq_microglia_wild_ADmice", - "SY5Y_Emory", - "rnaSeqReprocessing", - "ADMC_ADNI_NightingaleNMR", - "TauD35", - "MSBB_ArrayTissuePanel", - "UCI_3xTg-AD", - "BPSD_AD_AnimalStudy_NU", - "ADMC_ADNI2-GO", - "eQTLmetaAnalysis", - "Jax.IU.Pitt_LOAD2.PrimaryScreen", - "HumanFC", - "ADAMTS7", - "TS-RNAseq", - "UCI_PrimaryScreen", - "ROSMAP_CellTypeSpecificHA", - "UCI_StrainValidation", - "DukeAD_PTSD", - "VirusResilience_Mayo.MSBB.ROSMAP", - "MOA-PAD", - "BroadiPSC", - "SEA-AD", - "LLFS", - "RNAseq_Harmonization", - "MayoeGWAS", - "ELPSCRNA", - "MODEL-AD_Trem2_R47H", - "ROSMAP_nucleus_hashing", - "BCM-DMAS", - "3Dchromatin", - "LillyMicroglia", - "iPSC-HiC", - "BLSA", - "miR155", - "UAB_ADRC", - "Aging-PheWAS", - "UCI_Microbiome", - "iPSCAstrocytes", - "DiCAD", - "IntegrativePathwayAnalysis", - "Jax.IU.Pitt_APOE4.Trem2.R47H", - "SV_xQTL", - "MSSMiPSC", - "TASTPM", - "SWS", - "APOE4_Myelination", - "HDAC1-cKOBrain", - "RADEL", - "ROSMAP_MammillaryBody", - "MayoPilotRNAseq", - "MODEL-AD_hAbeta_KI", - "lncRNA Pilot", - "Jax.IU.Pitt.Proteomics_Metabolomics_Pilot", - "Organoid_scRNAseq", - "Abeta_microglia", - "UCSF_MAC", - "CNON", - "HBTRC", - "UCI_ABCA7", - "MC-CAA", - 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"ABC-DS", - "MC-BrAD", - "MSBB", - "IL10_APPmouse", - "MEF2_Resilience", - "MODEL-AD_Ceacam_KO_APOE4_Trem2", - "BroadMDMi", - "NAPS", - "ADMC_ADNI_BakerLipidomics", - "EpiGABA", - "MindPhenomeKB", - "MODEL-AD_Mthfr_APOE4_Trem2", - "rnaSeqSampleSwap", - "SY5Y_REST", - "TyrobpKO_AppPs1", - "Yale-ASD", - "BipSeq", - "ROSMAP-IA", - "BroadAstrom109", - "UCI_Apoe-Ch", - "UCI_Trem2_Cuprizone", - "iPSC", - "NPS-AD", - "WGS_Harmonization", - "ROSMAP_bsSeq", - "Jax.IU.Pitt_PrimaryScreen", - "mtDNA_AD", - "ADMC_ADNI_UHawaiiGutMetabolites", - "SuperAgerEpiMap" - ] - }, - "resourceType": { - "enum": [ - "analysis", - "experimentalData", - "metadata", - "report", - "tool", - "curatedData" - ] - }, - "isModelSystem": { - "enum": [ - "TRUE", - "FALSE" - ] - }, - "fileFormat": { - "enum": [ - "ab1", - "pdstudy", - "fig", - "czi", - "sif", - "cel", - "Sentrix descriptor file", - "tagAlign", - "Python script", - "zip", - "fasta", - "sf3", - "bash script", - "csv", - "locs", - "svs", - "RCC", - "bim", - 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- "Resilience-AD", - "CDCP", - "M2OVE-AD", - "ELITE" - ] - }, - "individualID": {}, - "Component": {}, - "Filename": { - "not": { - "type": "null" - }, - "minLength": 1 + "study": { + "enum": [ + "MayoHippocampus", + "Banner", + "TASTPM", + "MODEL-AD_Abca7_APOE4_Trem2", + "MindPhenomeKB", + "HBTRC", + "MSBB", + "SuperAgerEpiMap", + "SY5Y_REST", + "ROSMAP_bsSeq", + "BipSeq", + "AMP-AD_DiverseCohorts", + "NAPS", + "ADAMTS7", + "TWAS", + "MODEL-AD_Rat_F344", + "snRNAseqAD_TREM2", + "LBP", + "LLFS", + "UCI_ABCA7", + "StJude_BannerSun", + "SMIB-AD", + "VirusResilience_iPSC", + "ROSMAP_MammillaryBody", + "NHP-Chimpanzee", + "MSDM", + "APOE4_Myelination", + "MODEL-AD_5XFAD", + "NPS-AD", + "VirusResilience_Banner", + "MODEL-AD_Mthfr_APOE4_Trem2", + "ADMC_ADNI_BakerLipidomics", + "UCI_Trem2-R47H_NSS", + "MODEL-AD_APOE4_KI", + "UCI_Apoe-Ch", + "ADAtlas_Archive", + "BrainGVEX", + "LillyMicroglia", + "ROSMAP_CellTypeSpecificHA", + "MC_snRNA", + "UAB_ADRC", + "UCI_3xTg-AD", + "HumanFC", + "BroadMDMi", + "rnaSeqSampleSwap", + "U1-70_PrimaryCellCulture", + "MayoRNAseq", + "MayoLOADGWAS", + "MODEL-AD_hTau_Trem2", + "ROSMAP_CognitiveResilience", + "EmoryDrosophilaTau", + "Abeta_microglia", + "SWS", + "MSBB_ArrayTissuePanel", + "MODEL-AD_Ceacam_KO_APOE4_Trem2", + "MSSMiPSC", + "ADMC_ADNI_Biocrates_MxP_Q500", + "MayoeGWAS", + "Jax.IU.Pitt.Proteomics_Metabolomics_Pilot", + "APOEPSC", + "MODEL-AD_hAbeta_KI", + "MRGWAS", + "ADMC_ADNI1", + "UCI_BIN1", + "TAUAPPms", + "IntegrativePathwayAnalysis", + "TyrobpKO_AppPs1", + "iPSC", + "MSMM", + "rnaSeqReprocessing", + "ABC-DS", + "MIT_ROSMAP_Multiomics", + "Jax.IU.Pitt_StrainValidation", + "Trisomy21iN", + "Jax.IU.Pitt_MicrobiomePilot", + "MC-CAA", + "UCSF_MAC", + "CMC_HBCC", + "VirusResilience_LCL", + "MayoPilotRNAseq", + "Jax.IU.Pitt_Levetiracetam-5XFAD", + "HBI_scRNAseq", + "ROSMAP_Lipidomics_Emory", + "BLSA", + "iNiAstshRNA", + "RADEL", + "VirusResilience_Mayo.MSBB.ROSMAP", + "UFLOR_ABI3_GNGT2", + "Jax.IU.Pitt_PrimaryScreen", + "ADMC_UPenn", + "DiCAD", + "SUNYStrokeModel", + "VMC", + "MODEL-AD_Harmonization", + "MOA-PAD", + "CMC-PEC", + "Jax.IU.Pitt_LOAD2.PrimaryScreen", + "Aging-PheWAS", + "NHP-Macaque", + "SY5Y_Emory", + "lncRNA Pilot", + "RNAseq_Harmonization", + "WGS_Harmonization", + "UCLA-ASD", + "CMC", + "eQTLmetaAnalysis", + "Yale-ASD", + "APOE-TR", + "IL10_APPmouse", + "MARS WISCONSIN", + "SEA-AD", + "BCM-DMAS", + "Jax.IU.Pitt_APP.PS1", + "RR_APOE4", + "mtDNA_AD", + "MODEL-AD_Il1rapKO_APOE4_Trem2_exon2KO", + "UCI_PrimaryScreen", + "ROSMAP-IA", + "Jax.IU.Pitt_APOE4.Trem2.R47H", + "iPSCAstrocytes", + "MEF2_Resilience", + "EpiGABA", + "UCI_CCLines", + "ACOM", + "MouseHAL", + "ADMC_ADNI_UHawaiiGutMetabolites", + "BroadiPSC", + "iPSC-HiC", + "MODEL-AD_Trem2_R47H", + "ADMC_ADNI2-GO", + "TauD35", + "scRNAseq_microglia_wild_ADmice", + "MC-BrAD", + "UCI_Microbiome", + "OFMM", + "Organoid_scRNAseq", + "UCI_Trem2_Cuprizone", + "UCI_Multiomics", + "HDAC1-cKOBrain", + "UPenn", + "miR155", + "CHDWB", + "CNON", + "3Dchromatin", + "iPSCMicroglia", + "SV_xQTL", + "ADMC_ADNI_NightingaleNMR", + "Plxnb1_KO", + "EpiMap", + "ROSMAP_nucleus_hashing", + "Emory_ADRC", + "BroadAstrom109", + "ACT", + "TS-RNAseq", + "omicsADDS", + "WallOfTargets", + "MCMPS", + "MODEL-AD_APOE4_Trem2", + "ELPSCRNA", + "AD-BXD", + "ROSMAP-IN", + "TyrobpKO", + "MODEL-AD_hCR1_KI_on_APOE4_Trem2", + "ROSMAP", + "AD_ADRD_Exposome", + "Jax.IU.Pitt_Verubecestat_5XFAD", + "FreshMicro", + "DukeAD_PTSD", + "WGBS Pilot", + "UCI_StrainValidation", + "diseasePseudotime", + "BPSD_AD_AnimalStudy_NU" + ] }, - "dataSubtype": { + "analysisType": { "enum": [ - "normalized", - "metadata", - "processed", - "residualized", - "dataMatrix", - "raw", + "genotypeAncestry", + "correlation", + "Supervised Machine Learning", + "outlier detection", + "Mendelian randomization analysis", + "methylation quantitative trait loci detection", + "differential network analysis", + "network driver detection", + "differential methylation", + "manifold learning", + "search engine output files", + "network analysis", + "visualization", + "assessment", + "peak calling", + "protein quantitative trait loci detection", + "variancePartition", + "expression quantitative trait loci detection", + "Genome-Wide Association", + "chromatin accessible quantitative trait loci detection", + "principal component analysis", + "differential expression", + "statistical network reconstruction", + "Enrichment analysis", + "de-novo assembly", + "Variant calling", + "comparison", + "DNA methylation imputation", + "somatic mutation calling", + "genotype imputation", + "Copy number estimation", + "Gene expression comparison", + "quality control", + "dose response study", + "EWAS", + "structural variation detection", + "hidden confounder detection", + "genome-wide pleiotropy", + "purity", + "Sequence alignment", + "Polygenic Risk Scores", + "batch effect correction", + "transcript quantification", + "data mining", + "covariate specification", + "data normalization", + "Clustering", + "ANOVA", "" ] }, - "specimenID": {}, "species": { "enum": [ - "Drosophila melanogaster", - "Human", "Rhesus macaque", + "Rat", "Sus scrofa", + "Pan troglodytes", "Gallus gallus", + "Human", "Mouse", - "Rat", - "Pan troglodytes", + "Drosophila melanogaster", "" ] } }, "required": [ + "isModelSystem", + "Filename", + "resourceType", "grant", + "consortium", "isMultiSpecimen", - "assay", - "study", - "resourceType", - "isModelSystem", "fileFormat", - "consortium", - "Filename" + "assay", + "study" ], "allOf": [ { @@ -635,14 +636,14 @@ "properties": { "species": { "enum": [ - "Drosophila melanogaster", - "Human", "Rhesus macaque", + "Rat", "Sus scrofa", + "Pan troglodytes", "Gallus gallus", + "Human", "Mouse", - "Rat", - "Pan troglodytes" + "Drosophila melanogaster" ] } }, diff --git a/current-manifest-schemas/AD.IndividualAnimalMODEL-ADMetadataTemplate.schema.json b/current-manifest-schemas/AD.IndividualAnimalMODEL-ADMetadataTemplate.schema.json index 6a6dec3..d0a7039 100644 --- a/current-manifest-schemas/AD.IndividualAnimalMODEL-ADMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.IndividualAnimalMODEL-ADMetadataTemplate.schema.json @@ -4,127 +4,179 @@ "title": "IndividualAnimalMODEL-ADMetadataTemplate", "type": "object", "properties": { - "Component": {}, - "brainWeight": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "generation": {}, - "rodentDiet": { - "enum": [ - "6% standard", - "4% standard", - "5W80 western diet", - "45% high-fat diet", - "7% standard" - ] - }, - "bedding": { + "strainOfficialName": {}, + "sex": { "enum": [ - "Alpha-dri", - "corn cob", - "aspen", - "pine", - "sanichip", - "aspen sanichip" + "missing or unknown", + "female", + "male" ] }, - "genotypeBackground": { + "stockNumber": {}, + "individualID": { "not": { "type": "null" }, "minLength": 1 }, + "treatmentDose": {}, + "Component": {}, "genotype": { "not": { "type": "null" }, "minLength": 1 }, - "species": { - "enum": [ - "Human", - "Rat", - "Pan troglodytes", - "Gallus gallus", - "Rhesus macaque", - "Mouse", - "Sus scrofa", - "Drosophila melanogaster" - ] - }, - "sex": { - "enum": [ - "male", - "female" - ] - }, - "microchipID": {}, - "materialOrigin": { - "enum": [ - "UCI_TMF", - "IU", - "Pitt", - "JAX" - ] - }, - "ageDeath": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "room": {}, "individualIdSource": { "enum": [ - "Mayo Clinic", - "XCell Science", - "TAA", - "IU", - "UCSF", - "Pritzker", + "ADNI", + "JAX", "UW-CDL", - "Emory", - "NDRI", - "NIMH-HBCC", - "Pitt", - "DongLab", - "StemExpress", + "SMRI", + "ABN", + "UCSF", + "IU", + "MayoBrainBank", + "UM-BTB", + "Vaccarino", + "BEB_Miller", "MSSM", - "PGP", - "ADNI", - "LIBD", - "Clotomics_PAIKEA_MSSM", + "NYBB", + "DongLab", "Oxford", "BannerSun", + "Emory", + "LivingBrainProject_MSSM", "Yale", - "Einstein", - "NYBB", - "BEB_Miller", - "Penn", - "MayoBrainBank", - "Novogenix", - "HBTRC", + "Pritzker", "Rush", - "Vaccarino", - "NICHD", - "JAX", - "LivingBrainProject_MSSM", - "SMRI", - "Sestan", - "UM-BTB", "UCI_TMF", + "Penn", "Newcastle", + "AIBS", "Geschwind", + "Sestan", "HBSFRC", - "ABN", + "Clotomics_PAIKEA_MSSM", + "NIMH-HBCC", + "PGP", + "HBTRC", + "StemExpress", + "Pitt", + "TAA", + "Mayo Clinic", + "NICHD", + "XCell Science", + "Novogenix", + "NDRI", + "LIBD", "ABR", - "AIBS" + "Einstein" ] }, - "climbID": { + "room": {}, + "matingID": {}, + "modelSystemName": { + "enum": [ + "Abca7A1527GAPOE4Trem2R47H", + "APOE3KI", + "AppKOAPOE4Trem2R47H", + "APPE693Q", + "BRI2-AB42", + "Mtmr4V297GSNP", + "B6.Gfap-APOE4", + "rTg4510", + "TYROBP_KO.KO", + "C57BL6J", + "TAUPS19_Plexin-B1-KO", + "Abi3S209F_Aduci", + "Plexin-B1-KO", + "TAUPS19", + "APOE2KI", + "Spi1rs1377416", + "TREM2", + "APOE4Trem2R47H", + "Trem2R47H", + "Abca7KO", + "CRND8", + "hTauTrem2", + "TYROBP_WT", + "PicalmH458R", + "Sorl1A528TSNP", + "APPKM670-671NL-PSEN1deltaexon9", + "Plcg2KO", + "Bin1K358R_Aduci", + "Trem2Y38C", + "TYROBP_WT.KO", + "Kif21bT82TSNP", + "APPPS1", + "Bin1.B6", + "Clasp2L163PSNP", + "Trem2flox", + "Trem2KO", + "3xTg-AD", + "AB42", + "ApoEKO", + "Plcg2M28LSNP", + "hTau", + "Trem2R47H_NSS", + "APOE4KI", + "Snx1D465NSNP", + "Cd2ap.B6", + "TYROBP", + "APPS1_Plexin-B1-KO", + "B6.Clu", + "APPKM650", + "MAPT-P301K", + "hAPPAPOE4Trem2R47H", + "APPKM670", + "Abca7V1599M_rs117187003", + "Il1rapKO", + "hCR1KIAPOE4Trem2", + "Meox2KOHET", + "hAbetaKI", + "MthfrC677TSNP", + "Ceacam1KO", + "5XFAD" + ] + }, + "treatmentType": { + "enum": [ + "haloperidol", + "verubecestat", + "Abeta42 oligomer", + "Control", + "placebo", + "levetiracetam", + "cuprizone", + "clozapine", + "Abeta42 fibril", + "" + ] + }, + "rodentDiet": { + "enum": [ + "7% standard", + "4% standard", + "45% high-fat diet", + "6% standard", + "5W80 western diet" + ] + }, + "generation": {}, + "species": { + "enum": [ + "Rhesus macaque", + "Gallus gallus", + "Mouse", + "Drosophila melanogaster", + "Pan troglodytes", + "Human", + "Rat", + "Sus scrofa" + ] + }, + "genotypeBackground": { "not": { "type": "null" }, @@ -132,127 +184,76 @@ }, "ageDeathUnits": { "enum": [ - "PCW", "months", + "gestational weeks", "years", - "weeks", + "PCW", "days", - "gestational weeks" + "weeks" ] }, - "dateBirth": { + "microchipID": {}, + "rodentWeight": {}, + "materialOrigin": { + "enum": [ + "UCI_TMF", + "Pitt", + "IU", + "JAX" + ] + }, + "bedding": { + "enum": [ + "pine", + "corn cob", + "sanichip", + "aspen", + "aspen sanichip", + "Alpha-dri" + ] + }, + "climbID": { "not": { "type": "null" }, "minLength": 1 }, - "treatmentDose": {}, + "waterpH": {}, "birthID": {}, - "matingID": {}, - "individualID": { + "brainWeight": { "not": { "type": "null" }, "minLength": 1 }, - "treatmentType": { - "enum": [ - "Abeta42 fibril", - "clozapine", - "Control", - "levetiracetam", - "cuprizone", - "placebo", - "verubecestat", - "Abeta42 oligomer", - "haloperidol", - "" - ] + "dateBirth": { + "not": { + "type": "null" + }, + "minLength": 1 }, - "strainOfficialName": {}, - "rodentWeight": {}, - "waterpH": {}, - "stockNumber": {}, - "modelSystemName": { - "enum": [ - "Il1rapKO", - "TAUPS19", - "APPS1_Plexin-B1-KO", - "APOE4Trem2R47H", - "PicalmH458R", - "Clasp2L163PSNP", - "5XFAD", - "Ceacam1KO", - "Trem2flox", - "APPKM670-671NL-PSEN1deltaexon9", - "Abca7KO", - "Plcg2M28LSNP", - "ApoEKO", - "Bin1.B6", - "B6.Clu", - "hCR1KIAPOE4Trem2", - "TYROBP_KO.KO", - "Sorl1A528TSNP", - "Plcg2KO", - "Abi3S209F_Aduci", - "Trem2R47H", - "CRND8", - "MthfrC677TSNP", - "BRI2-AB42", - "AppKOAPOE4Trem2R47H", - "hAbetaKI", - "hTauTrem2", - "Plexin-B1-KO", - "rTg4510", - "Spi1rs1377416", - "Trem2R47H_NSS", - "3xTg-AD", - "Cd2ap.B6", - "Abca7A1527GAPOE4Trem2R47H", - "Trem2Y38C", - "AB42", - "MAPT-P301K", - "APPKM670", - "TYROBP_WT.KO", - "APPPS1", - "APPKM650", - "hAPPAPOE4Trem2R47H", - "Snx1D465NSNP", - "TYROBP", - "APOE3KI", - "APOE4KI", - "B6.Gfap-APOE4", - "C57BL6J", - "Meox2KOHET", - "Mtmr4V297GSNP", - "APPE693Q", - "hTau", - "Abca7V1599M_rs117187003", - "Bin1K358R_Aduci", - "TREM2", - "Kif21bT82TSNP", - "TYROBP_WT", - "APOE2KI", - "TAUPS19_Plexin-B1-KO", - "Trem2KO" - ] + "ageDeath": { + "not": { + "type": "null" + }, + "minLength": 1 } }, "required": [ - "brainWeight", - "rodentDiet", - "bedding", - "genotypeBackground", + "sex", + "individualID", "genotype", + "individualIdSource", + "modelSystemName", + "rodentDiet", "species", - "sex", + "genotypeBackground", + "ageDeathUnits", "materialOrigin", - "ageDeath", - "individualIdSource", + "bedding", "climbID", - "ageDeathUnits", + "brainWeight", "dateBirth", - "individualID", - "modelSystemName" + "ageDeath" ] } \ 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 5db43f5..1388c99 100644 --- a/current-manifest-schemas/AD.IndividualAnimalMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.IndividualAnimalMetadataTemplate.schema.json @@ -4,175 +4,176 @@ "title": "IndividualAnimalMetadataTemplate", "type": "object", "properties": { + "genotypeBackground": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "individualID": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "room": {}, + "genotype": { + "not": { + "type": "null" + }, + "minLength": 1 + }, "Component": {}, "modelSystemName": { "enum": [ - "Plcg2KO", - "Abi3S209F_Aduci", - "TYROBP_WT.KO", - "APPPS1", "Cd2ap.B6", "PicalmH458R", - "APPS1_Plexin-B1-KO", + "Bin1.B6", + "TAUPS19_Plexin-B1-KO", + "Trem2KO", + "Abi3S209F_Aduci", + "Bin1K358R_Aduci", + "Spi1rs1377416", + "APPKM670", + "TREM2", "MthfrC677TSNP", - "ApoEKO", - "Plcg2M28LSNP", - "APOE4KI", - "Trem2R47H_NSS", + "Abca7V1599M_rs117187003", + "APOE3KI", + "hTau", + "B6.Gfap-APOE4", "Trem2R47H", - "Il1rapKO", - "Spi1rs1377416", - "hAPPAPOE4Trem2R47H", - "MAPT-P301K", "Abca7KO", - "Abca7V1599M_rs117187003", - "Mtmr4V297GSNP", + "Meox2KOHET", + "Trem2R47H_NSS", + "APPKM650", + "MAPT-P301K", + "ApoEKO", "Kif21bT82TSNP", - "APOE4Trem2R47H", - "Trem2flox", - "Bin1.B6", + "TYROBP_WT.KO", "TYROBP", - "Snx1D465NSNP", - "Sorl1A528TSNP", + "APOE2KI", + "Clasp2L163PSNP", "hAbetaKI", - "B6.Clu", - "hTau", - "Trem2KO", - "APPKM670", - "TREM2", - "Trem2Y38C", - "Bin1K358R_Aduci", "Abca7A1527GAPOE4Trem2R47H", - "APPKM670-671NL-PSEN1deltaexon9", - "B6.Gfap-APOE4", - "Clasp2L163PSNP", - "C57BL6J", - "Meox2KOHET", - "AppKOAPOE4Trem2R47H", - "3xTg-AD", "5XFAD", - "BRI2-AB42", - "AB42", "Ceacam1KO", - "TAUPS19", - "APOE2KI", + "Trem2Y38C", + "hAPPAPOE4Trem2R47H", "rTg4510", - "TAUPS19_Plexin-B1-KO", + "Snx1D465NSNP", + "Mtmr4V297GSNP", "TYROBP_KO.KO", - "CRND8", + "AppKOAPOE4Trem2R47H", + "APPKM670-671NL-PSEN1deltaexon9", + "B6.Clu", + "Sorl1A528TSNP", + "C57BL6J", + "TAUPS19", "TYROBP_WT", + "3xTg-AD", "APPE693Q", - "hTauTrem2", - "APOE3KI", "Plexin-B1-KO", + "hTauTrem2", + "AB42", + "APOE4Trem2R47H", + "APPS1_Plexin-B1-KO", + "BRI2-AB42", + "APOE4KI", + "CRND8", "hCR1KIAPOE4Trem2", - "APPKM650" + "Plcg2M28LSNP", + "Il1rapKO", + "APPPS1", + "Plcg2KO", + "Trem2flox" ] }, "litter": {}, - "treatmentDose": {}, - "genotypeBackground": { + "dateBirth": { "not": { "type": "null" }, "minLength": 1 }, - "room": {}, - "dateDeath": {}, + "sexChromosome": {}, + "sex": { + "enum": [ + "female", + "male", + "missing or unknown" + ] + }, "individualIdSource": { "enum": [ - "Newcastle", - "Penn", + "MSSM", + "Oxford", + "Pritzker", + "TAA", "NICHD", + "MayoBrainBank", + "Novogenix", + "SMRI", + "BannerSun", + "ABR", + "LIBD", "AIBS", - "Einstein", + "NIMH-HBCC", "StemExpress", - "UCSF", - "LivingBrainProject_MSSM", + "BEB_Miller", "Mayo Clinic", - "LIBD", - "UM-BTB", - "Oxford", - "Rush", - "XCell Science", - "NIMH-HBCC", "NYBB", - "Clotomics_PAIKEA_MSSM", - "DongLab", - "HBSFRC", - "HBTRC", - "MayoBrainBank", - "Vaccarino", - "BEB_Miller", + "JAX", + "UM-BTB", + "UW-CDL", + "Emory", "ADNI", - "BannerSun", - "UCI_TMF", - "Novogenix", "Yale", "IU", - "UW-CDL", - "Emory", - "Pritzker", - "TAA", - "ABR", - "Geschwind", - "JAX", - "PGP", "ABN", - "Sestan", - "MSSM", + "Penn", + "Rush", + "HBSFRC", + "Newcastle", + "DongLab", + "Clotomics_PAIKEA_MSSM", + "PGP", + "Einstein", + "Vaccarino", + "UCI_TMF", "NDRI", - "SMRI", - "Pitt" + "HBTRC", + "Sestan", + "Pitt", + "UCSF", + "Geschwind", + "LivingBrainProject_MSSM", + "XCell Science" ] }, - "genotype": { - "not": { - "type": "null" - }, - "minLength": 1 - }, + "dateDeath": {}, "species": { "enum": [ - "Human", + "Mouse", "Sus scrofa", - "Pan troglodytes", + "Drosophila melanogaster", "Rhesus macaque", "Rat", - "Mouse", "Gallus gallus", - "Drosophila melanogaster" - ] - }, - "matingID": {}, - "sex": { - "enum": [ - "female", - "male" + "Pan troglodytes", + "Human" ] }, - "individualID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "dateBirth": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "sexChromosome": {} + "treatmentDose": {}, + "matingID": {} }, "required": [ - "modelSystemName", "genotypeBackground", - "individualIdSource", + "individualID", "genotype", - "species", + "modelSystemName", + "dateBirth", "sex", - "individualID", - "dateBirth" + "individualIdSource", + "species" ] } \ 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 4e577a8..e79b3ab 100644 --- a/current-manifest-schemas/AD.IndividualHumanMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.IndividualHumanMetadataTemplate.schema.json @@ -4,214 +4,229 @@ "title": "IndividualHumanMetadataTemplate", "type": "object", "properties": { - "PMI": {}, - "ethnicity": {}, - "pH": {}, "Braak": { "enum": [ - "BRAAK Stage 3", - "BRAAK Stage 5", "No BRAAK stage", - "BRAAK Stage 1", + "BRAAK Stage 5", + "BRAAK Stage 3", "missing or unknown", "BRAAK Stage 4", "BRAAK Stage 2", + "BRAAK Stage 1", "BRAAK Stage 6", "" ] }, + "apoe4Status": { + "enum": [ + "missing or unknown", + "one or two E4", + "no E4", + "" + ] + }, + "species": { + "enum": [ + "Drosophila melanogaster", + "Rat", + "Rhesus macaque", + "Pan troglodytes", + "Sus scrofa", + "Mouse", + "Human", + "Gallus gallus" + ] + }, + "ethnicity": {}, + "CERAD": { + "enum": [ + "Frequent Definite C3", + "No AD C0", + "missing or unknown", + "Moderate Probable C2", + "Sparse Possible C1", + "" + ] + }, "diagnosis": { "enum": [ - "Colon Cancer", - "Neurofibromatosis 2", - "Skin Cancer", - "progressive supranuclear palsy", - "Fibrocystic Breast Disease", - "Pancreatic Cancer", - "Brain Cancer", - "Juvenile Myelomonocytic Leukemia", - "anxiety", - "Tourette Syndrome", - "multiple system atrophy", - "Neurofibromatosis 1", - "Cervical Cancer", - "no cognitive impairment", - "CS-DS", - "traumatic brain injury", - "Prostate Cancer", - "Substance Related Disorder", + "Bipolar Disorder", + "dementia", + "essential tremor", "frontotemporal dementia", - "Autism Spectrum Disorder", + "Major Depressive Disorder", "MCI-DS", + "Parkinson's disease", + "Substance Related Disorder", + "Bladder Cancer", + "CS-DS", + "progressive supranuclear palsy", + "Leukemia", "Ovary Cancer", - "vascular dementia", + "Lung Cancer", + "corticobasal degeneration disorder", "Williams Syndrome", - "dystonia", - "amyotrophic lateral sclerosis", - "Bipolar Disorder", - "Leukemia", - "Parkinson's disease", - "obsessive compulsive disorder", + "Breast Cancer", "pathological aging", + "amyotrophic lateral sclerosis", + "Fibrocystic Breast Disease", "type 2 diabetes mellitus", - "Lung Cancer", - "corticobasal degeneration disorder", + "Affective Disorder", + "Skin Cancer", + "vascular dementia", + "Not Applicable", + "no cognitive impairment", + "obsessive compulsive disorder", + "obesity", + "Lewy body disease", "hypoxia", - "Major Depressive Disorder", - "Bladder Cancer", + "Neurofibromatosis 2", + "dystonia", + "Brain Cancer", + "Tourette Syndrome", + "anxiety", + "Cervical Cancer", + "mild cognitive impairment", "Control", + "Schizophrenia", "Alzheimer Disease", - "essential tremor", - "Lewy body disease", + "Pancreatic Cancer", + "Neurofibromatosis 1", "Alzheimer disease with psychosis", - "obesity", - "Affective Disorder", - "gliosis", - "Not Applicable", - "dementia", - "Breast Cancer", - "mild cognitive impairment", "AD-DS", - "Schizophrenia", + "multiple system atrophy", + "Colon Cancer", + "Prostate Cancer", + "gliosis", + "traumatic brain injury", + "Autism Spectrum Disorder", + "Juvenile Myelomonocytic Leukemia", + "" + ] + }, + "pmiUnits": { + "enum": [ + "minutes", + "hours", "" ] }, + "Component": {}, "individualID": { "not": { "type": "null" }, "minLength": 1 }, - "CERAD": { + "causeDeath": {}, + "sex": { "enum": [ "missing or unknown", - "Moderate Probable C2", - "Sparse Possible C1", - "No AD C0", - "Frequent Definite C3", - "" + "male", + "female" ] }, "race": { "enum": [ + "American Indian or Alaska Native", + "Native Hawaiian or Other Pacific Islander", "Asian", "White", "Black or African American", - "Native Hawaiian or Other Pacific Islander", - "American Indian or Alaska Native", "" ] }, - "brainWeight": {}, - "cohort": { - "enum": [ - "Banner", - "UPenn", - "ADNI", - "UW ADRC", - "RADC", - "Columbia ADRC", - "ACT", - "HBCC", - "DiCAD", - "MCR", - "CLINCOR", - "HUP", - "WHICAP", - "EFIGA", - "MSBB", - "HPGP", - "LBP", - "CHDWB", - "BLSA", - "NYBB", - "BEB-Miller", - "SMRI", - "UK Biobank", - "UFL", - "HBTRC", - "Pitt ADRC", - "MCJ", - "MC", - "FBS", - "UPBB", - "Biggs Institute Brain Bank", - "EHBS", - "Emory_ADRC", - "Framingham", - "MARS", - "Mayo Clinic", - "ABC-DS", - "ROSMAP", - "" - ] - }, - "yearsEducation": {}, - "Component": {}, + "pH": {}, "apoeGenotype": { "enum": [ "22", - "24", "34", - "33", + "24", "44", "23", + "33", "" ] }, - "ageDeathUnits": { - "enum": [ - "months", - "weeks", - "PCW", - "days", - "gestational weeks", - "years", - "" - ] - }, - "species": { - "enum": [ - "Mouse", - "Sus scrofa", - "Drosophila melanogaster", - "Pan troglodytes", - "Gallus gallus", - "Rat", - "Rhesus macaque", - "Human" - ] - }, - "ageDeath": {}, "mannerDeath": { "enum": [ "suicide", - "accident", - "homicide", "undetermined", + "homicide", "natural causes", + "accident", "" ] }, - "causeDeath": {}, - "pmiUnits": { + "cohort": { "enum": [ - "minutes", - "hours", + "CHDWB", + "EFIGA", + "MIND", + "UFL", + "Framingham", + "POINTER", + "ADNI", + "Columbia ADRC", + "Biggs Institute Brain Bank", + "ABC-DS", + "Banner", + "HBCC", + "Pitt ADRC", + "Tulsa LIBR-1000", + "BLSA", + "HBTRC", + "Emory_ADRC", + "MARS-WI", + "UK Biobank", + "NYBB", + "EHBS", + "MARS", + "ADRC", + "FBS", + "SMRI", + "UW ADRC", + "UPenn", + "HPGP", + "BEB-Miller", + "MCJ", + "UPBB", + "MC", + "HUP", + "BEAM", + "ROSMAP", + "MSBB", + "ACT", + "WHICAP", + "RADC", + "Mayo Clinic", + "DiCAD", + "MCR", + "CLINCOR", + "LBP", "" ] }, - "sex": { + "ageDeath": {}, + "yearsEducation": {}, + "PMI": {}, + "diagnosisCriteria": {}, + "brainWeight": {}, + "ageDeathUnits": { "enum": [ - "male", - "female" + "PCW", + "years", + "months", + "days", + "gestational weeks", + "weeks", + "" ] - }, - "diagnosisCriteria": {} + } }, "required": [ - "individualID", "species", + "individualID", "sex" ] } \ No newline at end of file diff --git a/current-manifest-schemas/AD.NeuropathMetadataTemplate.schema.json b/current-manifest-schemas/AD.NeuropathMetadataTemplate.schema.json index 4a55837..2e846af 100644 --- a/current-manifest-schemas/AD.NeuropathMetadataTemplate.schema.json +++ b/current-manifest-schemas/AD.NeuropathMetadataTemplate.schema.json @@ -4,364 +4,364 @@ "title": "NeuropathMetadataTemplate", "type": "object", "properties": { - "pmiUnits": { + "Braak": { "enum": [ - "minutes", - "hours" + "missing or unknown", + "No BRAAK stage", + "BRAAK Stage 6", + "BRAAK Stage 1", + "BRAAK Stage 4", + "BRAAK Stage 3", + "BRAAK Stage 5", + "BRAAK Stage 2" ] }, - "CVD_ART": { + "REAG": { + "enum": [ + "missing or unknown", + "Other or Does not fulfill NIA-REAGEN criteria", + "No AD", + "High Likelihood", + "Low likelihood", + "Intermediate Likelihood" + ] + }, + "CVD_CAA": { "enum": [ - "Moderate", - "Severe", "missing or unknown", "Mild", - "No CVD_ART", + "Severe", + "No CVD_CAA", + "Moderate", "" ] }, "mayoDx": { "enum": [ - "missing or unknown", - "Other", "AD", "Control", + "missing or unknown", + "Other", "" ] }, - "alt_HS_S": { + "INFA": { "enum": [ + "Yes", + "No", "missing or unknown", - "Presence", - "Absence", "" ] }, - "CVD_CAA_ANY": { + "CVD_ART": { "enum": [ - "Mild or Moderate or Severe", "missing or unknown", - "No CVD_CAA_ANY", + "Mild", + "Severe", + "No CVD_ART", + "Moderate", "" ] }, - "CVD_ATH_ANY": { + "CVD_ART_ANY": { "enum": [ "Mild or Moderate or Severe", + "No CVD_ART_ANY", "missing or unknown", - "No CVD_ATH_ANY", "" ] }, - "CVD_CAA": { + "conservationMethod": { "enum": [ - "No CVD_CAA", - "Moderate", - "Severe", + "both fixed and frozen tissue", + "fixed tissues only", "missing or unknown", - "Mild", - "" + "frozen tissue only", + "noConservation" ] }, - "TDP_3": { + "AMY_THAL": { "enum": [ - "Hippocampus or Etorhinal", - "No TDP_3", "missing or unknown", - "amygdala", - "Neocortex", - "" + "Phase 4", + "Phase 3", + "Phase 2", + "Phase 1", + "No Thal Phase", + "Phase 5" ] }, - "TDP43": { + "alt_HS_S": { "enum": [ - "No", + "Absence", + "Presence", "missing or unknown", - "Yes", "" ] }, - "LEWY_full": { + "CERAD": { "enum": [ - "No LEWY_full", - "Limbic amygdala transitional", + "Frequent Definite C3", "missing or unknown", - "Olfactory bulb or Region unspecified", - "Neocortical diffuse", - "Brainstem predominant", - "" + "Sparse Possible C1", + "No AD C0", + "Moderate Probable C2" ] }, - "PMI": { + "INT": { "not": { "type": "null" }, "minLength": 1 }, - "CVD_S": { + "HS_L": { "enum": [ + "Unilateral", "missing or unknown", - "No CVD_S", - "Presence", + "Bilateral", + "No HS_L", + "Present Location UK", "" ] }, - "HEMOR": { + "TDP_5": { "enum": [ - "No", "missing or unknown", - "Yes", + "No TDP_5", + "amygdala", + "Neocortex", + "hippocampus", + "Entorhinal", + "Brainstem/Spinal Cord", "" ] }, - "WMRCAL": { + "alt_LEWY_full": { "enum": [ - "No", + "Brainstem predominant", + "No alt_LEWY_full", "missing or unknown", - "Yes", + "Limbic transitional", + "Amygdala only", + "Olfactory bulb only", + "Neocortical diffuse", "" ] }, - "CVD_ART_ANY": { + "CVD_ATH": { "enum": [ - "Mild or Moderate or Severe", "missing or unknown", - "No CVD_ART_ANY", + "Mild", + "Severe", + "No CVD_ATH", + "Moderate", "" ] }, - "WMR": { + "TDP_3": { "enum": [ - "Moderate", - "Absent", - "Severe", "missing or unknown", - "Mild", + "amygdala", + "Neocortex", + "No TDP_3", + "Hippocampus or Etorhinal", "" ] }, - "INT": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "B_SCORE": { + "Component": {}, + "HEMOR": { "enum": [ - "BRAAK Stage 3-4", - "No B score", + "Yes", + "No", "missing or unknown", - "BRAAK Stage 1-2", - "BRAAK Stage 5-6" + "" ] }, - "HS_L": { + "CVD_ATH_ANY": { "enum": [ - "Present Location UK", - "Unilateral", - "No HS_L", - "Bilateral", + "Mild or Moderate or Severe", "missing or unknown", + "No CVD_ATH_ANY", "" ] }, - "individualID": { - "not": { - "type": "null" - }, - "minLength": 1 - }, - "ADNC": { + "TDP43": { "enum": [ - "Not AD", - "Low", - "Intermediate", + "Yes", + "No", "missing or unknown", - "High" + "" ] }, - "Component": {}, - "REAG": { + "WMRCAL": { "enum": [ - "High Likelihood", - "Other or Does not fulfill NIA-REAGEN criteria", - "No AD", - "Low likelihood", + "Yes", + "No", "missing or unknown", - "Intermediate Likelihood" + "" ] }, - "TDP_5": { + "LEWY_grp": { "enum": [ - "Entorhinal", + "No LEWY_grp or olfactory bulb or amygdala predominant group", + "Transitional or diffuse or region unspecified group", "missing or unknown", - "No TDP_5", - "amygdala", - "hippocampus", - "Neocortex", - "Brainstem/Spinal Cord", + "Brainstem predominant group", "" ] }, - "AMY_A": { + "AMY_ANY": { "enum": [ - "Thal Phase 3", - "No A Score", + "No amyloid presence", + "Amyloid Present", "missing or unknown", - "Thal Phase 1 or 2", - "Thal Phase 4 or 5" + "Some Amyloid" ] }, - "AMY_THAL": { + "CVD_CAA_ANY": { "enum": [ - "Phase 3", - "Phase 5", - "Phase 2", + "Mild or Moderate or Severe", + "No CVD_CAA_ANY", "missing or unknown", - "Phase 4", - "Phase 1", - "No Thal Phase" + "" ] }, - "LEWY_grp": { + "AMY_A": { "enum": [ - "No LEWY_grp or olfactory bulb or amygdala predominant group", - "Brainstem predominant group", "missing or unknown", - "Transitional or diffuse or region unspecified group", - "" + "No A Score", + "Thal Phase 1 or 2", + "Thal Phase 3", + "Thal Phase 4 or 5" ] }, - "INFA": { + "WMR": { "enum": [ - "No", "missing or unknown", - "Yes", + "Mild", + "Severe", + "Absent", + "Moderate", "" ] }, - "conservationMethod": { + "CVD_S": { "enum": [ - "frozen tissue only", - "both fixed and frozen tissue", + "No CVD_S", + "Presence", "missing or unknown", - "fixed tissues only", - "noConservation" + "" ] }, - "CVD_ATH": { + "ADNC": { "enum": [ - "Moderate", - "Severe", + "Not AD", "missing or unknown", - "Mild", - "No CVD_ATH", - "" + "Intermediate", + "Low", + "High" ] }, - "LEWY_ANY": { + "pmiUnits": { "enum": [ - "Brainstem or transitional or diffuse or region unspecified group", - "missing or unknown", - "No LEWY_ANY or olfactory bulb or amygdala predominant group", - "" + "hours", + "minutes" ] }, - "alt_LEWY_full": { + "LEWY_full": { "enum": [ - "Amygdala only", - "No alt_LEWY_full", - "Limbic transitional", + "Brainstem predominant", "missing or unknown", + "Olfactory bulb or Region unspecified", "Neocortical diffuse", - "Brainstem predominant", - "Olfactory bulb only", + "Limbic amygdala transitional", + "No LEWY_full", "" ] }, - "CERAD": { - "enum": [ - "Frequent Definite C3", - "missing or unknown", - "Sparse Possible C1", - "No AD C0", - "Moderate Probable C2" - ] + "brainWeight": { + "not": { + "type": "null" + }, + "minLength": 1 }, - "Braak": { + "CDLB": { "enum": [ - "BRAAK Stage 2", - "BRAAK Stage 5", - "BRAAK Stage 4", - "BRAAK Stage 6", - "No BRAAK stage", "missing or unknown", - "BRAAK Stage 3", - "BRAAK Stage 1" + "Intermediate", + "High", + "Low or No clinical significance", + "" ] }, "MICR": { "enum": [ + "Yes", "No", "missing or unknown", - "Yes", "" ] }, - "AMY_ANY": { + "individualID": { + "not": { + "type": "null" + }, + "minLength": 1 + }, + "B_SCORE": { "enum": [ "missing or unknown", - "Amyloid Present", - "Some Amyloid", - "No amyloid presence" + "BRAAK Stage 5-6", + "No B score", + "BRAAK Stage 3-4", + "BRAAK Stage 1-2" ] }, - "CDLB": { + "HS_S": { "enum": [ - "Intermediate", + "Yes", + "No", "missing or unknown", - "Low or No clinical significance", - "High", "" ] }, "WBVD": { "enum": [ + "Yes", "No", "missing or unknown", - "Yes", "" ] }, - "brainWeight": { + "PMI": { "not": { "type": "null" }, "minLength": 1 }, - "HS_S": { + "LEWY_ANY": { "enum": [ - "No", + "Brainstem or transitional or diffuse or region unspecified group", "missing or unknown", - "Yes", + "No LEWY_ANY or olfactory bulb or amygdala predominant group", "" ] } }, "required": [ - "pmiUnits", - "PMI", - "INT", - "B_SCORE", - "individualID", - "ADNC", + "Braak", "REAG", - "AMY_A", - "AMY_THAL", "conservationMethod", + "AMY_THAL", "CERAD", - "Braak", + "INT", "AMY_ANY", - "brainWeight" + "AMY_A", + "ADNC", + "pmiUnits", + "brainWeight", + "individualID", + "B_SCORE", + "PMI" ] } \ No newline at end of file diff --git a/tests/schematic-config.yml b/tests/schematic-config.yml new file mode 100644 index 0000000..e98de43 --- /dev/null +++ b/tests/schematic-config.yml @@ -0,0 +1,43 @@ +# This is an example config for Schematic. +# All listed values are those that are the default if a config is not used. +# Save this as config.yml, this will be gitignored. +# Remove any fields in the config you don't want to change +# If you remove all fields from a section, the entire section should be removed including the header. +# Change the values of any fields you do want to change + + +# This describes where assets such as manifests are stored +asset_store: + # This is when assets are stored in a synapse project + synapse: + # Synapse ID of the file view listing all project data assets. + master_fileview_id: "syn51324810" #AD Portal backend internal project - DCA Asset View + # Path to the synapse config file, either absolute or relative to this file + config: ".synapseConfig" + # Base name that manifest files will be saved as + manifest_basename: "synapse_storage_manifest" + +# This describes information about manifests as it relates to generation and validation +manifest: + # Location where manifests will saved to + manifest_folder: "manifests" + # Title or title prefix given to generated manifest(s) + title: "AD_" + # Data types of manifests to be generated or data type (singular) to validate manifest against + data_type: + - "Biospecimen" + - "Patient" + +# Describes the location of your schema +model: + # Location of your schema jsonld, it must be a path relative to this file or absolute + location: "AD.model.jsonld" + +# This section is for using google sheets with Schematic +google_sheets: + # Path to the synapse config file, either absolute or relative to this file + service_acct_creds: "schematic_service_account_creds.json" + # When doing google sheet validation (regex match) with the validation rules. + # true is alerting the user and not allowing entry of bad values. + # false is warning but allowing the entry on to the sheet. + strict_validation: true From 5d309fa535944f5ab50fce8fd90536c49a5c1347 Mon Sep 17 00:00:00 2001 From: Victor Baham <83256374+MasterPastures@users.noreply.github.com> Date: Wed, 25 Sep 2024 16:49:44 -0400 Subject: [PATCH 3/6] Added explanatory inline comment to generate-current-manifests.yml To describe how the token secrets.GENERATE_MANIFESTS_ON_ACTION was generated --- .github/workflows/generate-current-manifests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/generate-current-manifests.yml b/.github/workflows/generate-current-manifests.yml index 1cd80be..f27b259 100644 --- a/.github/workflows/generate-current-manifests.yml +++ b/.github/workflows/generate-current-manifests.yml @@ -28,7 +28,7 @@ jobs: with: python-version: '3.10' cache: 'pip' - token: ${{ secrets.GENERATE_MANIFESTS_ON_ACTION }} + token: ${{ secrets.GENERATE_MANIFESTS_ON_ACTION }} # this PAT was generated w/ "Read and Write access to actions" and the default "Read access to metadata" Repo permissions - name: Install Libraries shell: bash From 4abeed13c858fff35de357ac475148e6a3bf9b6e Mon Sep 17 00:00:00 2001 From: Victor Baham <83256374+MasterPastures@users.noreply.github.com> Date: Wed, 25 Sep 2024 16:53:24 -0400 Subject: [PATCH 4/6] Lengthened inline comment to explain new PAT in generate-current-manifests.yml also added why it was generated --- .github/workflows/generate-current-manifests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/generate-current-manifests.yml b/.github/workflows/generate-current-manifests.yml index f27b259..d1c1b9b 100644 --- a/.github/workflows/generate-current-manifests.yml +++ b/.github/workflows/generate-current-manifests.yml @@ -28,7 +28,7 @@ jobs: with: python-version: '3.10' cache: 'pip' - token: ${{ secrets.GENERATE_MANIFESTS_ON_ACTION }} # this PAT was generated w/ "Read and Write access to actions" and the default "Read access to metadata" Repo permissions + token: ${{ secrets.GENERATE_MANIFESTS_ON_ACTION }} # this Fine-grained PAT was generated to circumvent the issue with the manifest generation action hitting branch protection, has "Read and Write access to actions" and the default "Read access to metadata" Repo permissions, the resource owner is the adknowledgeportal org, it has access to the data-models repo - name: Install Libraries shell: bash From 7e2b0d432382872580ced7b51ebc64f13614b366 Mon Sep 17 00:00:00 2001 From: Victor Baham <83256374+MasterPastures@users.noreply.github.com> Date: Wed, 25 Sep 2024 16:59:44 -0400 Subject: [PATCH 5/6] Update README.md with description of new secret GENERATE_MANIFESTS_ON_ACTION --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 243549f..391c917 100644 --- a/README.md +++ b/README.md @@ -93,6 +93,7 @@ If you want to make changes to the data model and test them out by generating ma Codespace secrets: - SYNAPSE_PAT: scoped to view and download permissions on the sysbio-dcc-tasks-01 Synapse service account - SERVICE_ACCOUNT_CREDS: these are creds for using the Google sheets api with schematic +- GENERATE_MANIFESTS_ON_ACTION: this fine-grained PAT lets manifests be successfully generated despite branch protection, has read/write access to actions, and has repo access to adknowledgeportal/data-models ## Legacy data models: Previous versions of the data model live in the `legacy-data-models/` folder. This include the Diverse Cohorts pilot model and the intial "legacy" model representing the AD Portal Synapse project metadata dictionary and metadata templates from August 2023. These are not being used by DCA. From 421a31e1a5824f41be25119aaae435aeed046de0 Mon Sep 17 00:00:00 2001 From: Victor Baham <83256374+MasterPastures@users.noreply.github.com> Date: Wed, 25 Sep 2024 17:01:33 -0400 Subject: [PATCH 6/6] Rewrote inline comment in generate-current-manifests.yml to remove redundancy --- .github/workflows/generate-current-manifests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/generate-current-manifests.yml b/.github/workflows/generate-current-manifests.yml index d1c1b9b..fd02165 100644 --- a/.github/workflows/generate-current-manifests.yml +++ b/.github/workflows/generate-current-manifests.yml @@ -28,7 +28,7 @@ jobs: with: python-version: '3.10' cache: 'pip' - token: ${{ secrets.GENERATE_MANIFESTS_ON_ACTION }} # this Fine-grained PAT was generated to circumvent the issue with the manifest generation action hitting branch protection, has "Read and Write access to actions" and the default "Read access to metadata" Repo permissions, the resource owner is the adknowledgeportal org, it has access to the data-models repo + token: ${{ secrets.GENERATE_MANIFESTS_ON_ACTION }} # this Fine-grained PAT was generated to generate manifests despite branch protection, was granted "Read and Write access to actions" permissions, and has access to the adknowledgeportal/data-models repo (resource owner is adknowledgeportal) - name: Install Libraries shell: bash