Merge pull request #121 from adknowledgeportal/add-biocrates-mxp-quan…

…t500-xl-to-assay-csv

Added "Biocrates MxP Quant500 XL" to assay.csv

AD.model.csv

@@ -105,9 +105,10 @@ active avoidance learning behavior,Avoidance learning when the action occurs.,,,
 anxiety-related behavior,An emotional behavior related to a feeling of uneasiness or nervousness triggered by an identifiable triggering stimulus.,,,,,assay,,http://purl.obolibrary.org/obo/NBO_0000092,,string,experimentalData
 ATACSeq,Open chromatin regions measured by sequencing DNA after assay for transposase-accessible chromatin (ATAC) treatment,,,,,assay,,http://purl.obolibrary.org/obo/OBI_0002039,,string,experimentalData
 atomicForceMicroscopy,Microscopy which uses a sharp spike (known as a 'tip') mounted on the end of a cantilever to scan the surface of the specimen,,,,,assay,,http://purl.obolibrary.org/obo/CHMO_0000113,,string,experimentalData
-autoradiography, A radioactivity detection technique using X- ray film to visualize molecules or fragments of molecules that have been radioactively labeled.,,,,,assay,,http://purl.obolibrary.org/obo/ERO_0000716,,string,experimentalData
+autoradiography,A radioactivity detection technique using X- ray film to visualize molecules or fragments of molecules that have been radioactively labeled.,,,,,assay,,http://purl.obolibrary.org/obo/ERO_0000716,,string,experimentalData
 Baker Lipidomics,A comparative lipidomics approach that enables semi-quantification of approximately 400 lipid species across 22 lipid classes and subclasses. The analysis is performed by liquid chromatography tandem mass spectrometry. Stable isotope dilution (with 23 different internal standards) is used to provide quantitative data on each of the over 400 lipid species.,,,,,assay,,https://baker.edu.au/research/contract-research/metabolomics,,string,experimentalData
 Biocrates Bile Acids,"The Biocrates AbsoluteIDQ Bile Acids kit is a ready-to-use, standardized solution for the quantitation of 20 bile acids by liquid chromatography-mass spectrometry (LC-MS).",,,,,assay,,https://biocrates.com/biocrates-bile-acids-kit/,,string,experimentalData
+Biocrates MxP Quant500 XL,"The Biocrates MxP® Quant 500 XL combines quantitative metabolomics profiling of lipids and small molecules in a single kit and covers more than 1,000 metabolites from various biochemical classes.",,,,,assay,,https://biocrates.com/mxp-quant-500-xl/,,string,experimentalData
 Biocrates p180,"The Biocrates AbsoluteIDQ p180 kit is a simple and high-throughput tool for basic, clinical, and epidemiological research. The kit provides scientists with highly reproducible metabolomics data to confidently obtain detailed knowledge about the metabolic phenotypes in their studies.",,,,,assay,,https://biocrates.com/absoluteidq-p180-kit/,,string,experimentalData
 Biocrates Q500,"MxP Quant 500 extends the p180 kit and is Biocrates' most comprehensive kit for targeted metabolic profiling. With coverage of up to 630 metabolites from 26 biochemical classes, it represents an advanced and reproducible metabolomics technology.",,,,,assay,,https://biocrates.com/mxp-quant-500-kit/,,string,experimentalData
 bisulfiteSeq,Methylation data captured by sequencing of DNA treated by a bisulfite-based chemical process,,,,,assay,,http://purl.obolibrary.org/obo/OBI_0000748,,string,experimentalData
@@ -835,7 +836,7 @@ antibodyAmountUnits,Units of measure for the amount of antibody used for an assa
 apoe4Status,Presence of one or more E4 variant alleles at the human APOE gene; only use if untransformed APOE genotype is not available,"no E4, one or two E4, missing or unknown",,,False,ManifestColumn,,ADKP DCC,,string,clinical
 apoeGenotype,Apolipoprotein E genotype,"22, 23, 24, 33, 34, 44",,,False,ManifestColumn,,sage.annotations-clinical.apoeGenotype-0.0.2,,string,clinical
 arrayBatch,The hybridization batch the sample was in,,,,False,ManifestColumn,,sage.annotations-batch.arrayBatch-0.0.2,,string,batch
-assay,The technology used to generate the data in this file,"10x multiome, 16SrRNAseq, active avoidance learning behavior, anxiety-related behavior, ATACSeq, atomicForceMicroscopy, autoradiography, Baker Lipidomics, Biocrates Bile Acids, Biocrates p180, Biocrates Q500, bisulfiteSeq, Blood Chemistry Measurement, brightfieldMicroscopy, cellViabilityAssay, ChIPSeq, CITESeq, contextual conditioning behavior, CUT&Tag, DIA, DNA optical mapping, electrochemiluminescence, elevated plus maze test, elevated T maze apparatus method, ELISA, errBisulfiteSeq, exomeSeq, FIA-MSMS, FitBark, frailty assessment, Genotyping, HI-C, HiChIPseq, high content screen, HPLC, HPLC-MSMS, Immunocytochemistry, immunofluorescence, immunohistochemistry, in vivo bioluminescence, ISOSeq, jumpingLibrary, kinesthetic behavior, label free mass spectrometry, Laser Speckle Imaging, LC-MS, LC-MSMS, LC-SRM, Leiden Oxylipins, lentiMPRA, LFP, liquid chromatography-electrochemical detection, lncrnaSeq, locomotor activation behavior, long-read rnaSeq, LTP, MDMS-SL, memory behavior, Metabolon, methylationArray, MIB/MS, microRNAcounts, mirnaArray, mirnaSeq, MRI, mRNAcounts, MudPIT, m6A-rnaSeq, nextGenerationTargetedSequencing, Nightingale NMR, NOMe-Seq, novelty response behavior, open field test, oxBS-Seq, pharmacodynamics, pharmacokinetics, photograph, polymeraseChainReaction, Positron Emission Tomography, proximity extension assay, questionnaire, Rader Lipidomics, Real Time PCR, Ribo-Seq, rotarod performance test, rnaArray, rnaSeq, RPPA, sandwich ELISA, Sanger sequencing, scale, scATACSeq, scCGIseq, scirnaSeq, scrnaSeq, scwholeGenomeSeq, SiMoA, snpArray, snATACSeq, snrnaSeq, spontaneous alternation, STARRSeq, TMT quantitation, tractionForceMicroscopy, UPLC-MSMS, UPLC-ESI-QTOF-MS, UC Davis GCTOF, UCSD Untargeted Metabolomics, Vernier Caliper, von Frey test, westernBlot, wheel running, whole-cell patch clamp, wholeGenomeSeq, Wishart Catecholamines, Wishart High Value Metabolites, Zeno Electronic Walkway",,,True,ManifestColumn,,sage.annotations-experimentalData.assay-0.0.26,,string,experimentalData
+assay,The technology used to generate the data in this file,"10x multiome, 16SrRNAseq, active avoidance learning behavior, anxiety-related behavior, ATACSeq, atomicForceMicroscopy, autoradiography, Baker Lipidomics, Biocrates Bile Acids, Biocrates MxP Quant500 XL, Biocrates p180, Biocrates Q500, bisulfiteSeq, Blood Chemistry Measurement, brightfieldMicroscopy, cellViabilityAssay, ChIPSeq, CITESeq, contextual conditioning behavior, CUT&Tag, DIA, DNA optical mapping, electrochemiluminescence, elevated plus maze test, elevated T maze apparatus method, ELISA, errBisulfiteSeq, exomeSeq, FIA-MSMS, FitBark, frailty assessment, Genotyping, HI-C, HiChIPseq, high content screen, HPLC, HPLC-MSMS, Immunocytochemistry, immunofluorescence, immunohistochemistry, in vivo bioluminescence, ISOSeq, jumpingLibrary, kinesthetic behavior, label free mass spectrometry, Laser Speckle Imaging, LC-MS, LC-MSMS, LC-SRM, Leiden Oxylipins, lentiMPRA, LFP, liquid chromatography-electrochemical detection, lncrnaSeq, locomotor activation behavior, long-read rnaSeq, LTP, MDMS-SL, memory behavior, Metabolon, methylationArray, MIB/MS, microRNAcounts, mirnaArray, mirnaSeq, MRI, mRNAcounts, MudPIT, m6A-rnaSeq, nextGenerationTargetedSequencing, Nightingale NMR, NOMe-Seq, novelty response behavior, open field test, oxBS-Seq, pharmacodynamics, pharmacokinetics, photograph, polymeraseChainReaction, Positron Emission Tomography, proximity extension assay, questionnaire, Rader Lipidomics, Real Time PCR, Ribo-Seq, rotarod performance test, rnaArray, rnaSeq, RPPA, sandwich ELISA, Sanger sequencing, scale, scATACSeq, scCGIseq, scirnaSeq, scrnaSeq, scwholeGenomeSeq, SiMoA, snpArray, snATACSeq, snrnaSeq, spontaneous alternation, STARRSeq, TMT quantitation, tractionForceMicroscopy, UPLC-MSMS, UPLC-ESI-QTOF-MS, UC Davis GCTOF, UCSD Untargeted Metabolomics, Vernier Caliper, von Frey test, westernBlot, wheel running, whole-cell patch clamp, wholeGenomeSeq, Wishart Catecholamines, Wishart High Value Metabolites, Zeno Electronic Walkway",,,True,ManifestColumn,,sage.annotations-experimentalData.assay-0.0.26,,string,experimentalData
 assayTarget,,"ARID1B, ARID3A, ARNT, ASCL1, ASH1L, ASH2L, ATF7, BCL11A, BHLHE40, BHLHE41, BMI1, BRCA1, BRD4, CC2D1A, CHD4, CLOCK, CREB1, CREM, CTCF, DEAF1, DPF2, EED, EGR1, EHMT2, E2F1, EWSR1, EZH2, FOXK2, FOXP1, GABPB1, GATA4, GATAD2A, GATAD2B, GMEB1, H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9ac, H3K9me2, H3K9me3, HCFC1, HNRNPK, IE_V1-V3, IgG, input, KAT2B, KDM4A, KLF16, KLF5, LaminB, MAZ, MEF2A, MEIS2, MITF, NCOA2, NCOR1, NEUROD1, NFIB, NFIC, NONO, NR2F1, NRF1, NR2F2, NR3C1, OLIG2, PKNOX1, Pol2, R-loops, RAD21, RB1, RELB, REST, SATB2, SIN3A, SIN3B, SIRT1, SIX4, SKIL, SMARCA5, SMC3, SON, SOX8, SP1, SP4, SRF, SREBP2, TAF1, TBR1, TCF12, TCF7L2, TDP43, TRIM28, YBX1, YBX3, YY1, ZBTB7B, ZEB1, ZEB2, ZFP91, ZHX1, ZKSCAN1, ZNF143, ZNF207, ZNF24, ZNF318, ZNF384, ZNF407, ZNF592, ZSCAN29",,,False,ManifestColumn,,sage.annotations-experimentalData.assayTarget-0.0.6,,string,demographics
 B_SCORE,B score,"No B score, BRAAK Stage 1-2, BRAAK Stage 3-4, BRAAK Stage 5-6, missing or unknown",,,True,ManifestColumn,,sage-annotations-clinical.B_SCORE-0.0.2,string,,clinical
 batch,Batch specimen was processed in,,,,False,ManifestColumn,,sage.annotations-batch.batch-0.0.2,,string,batch

AD.model.jsonld

@@ -2433,6 +2433,9 @@
                 {
                     "@id": "bts:BiocratesBileAcids"
                 },
+                {
+                    "@id": "bts:BiocratesMxPQuant500XL"
+                },
                 {
                     "@id": "bts:Biocratesp180"
                 },
@@ -2898,6 +2901,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:BiocratesMxPQuant500XL",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "The Biocrates MxP® Quant 500 XL combines quantitative metabolomics profiling of lipids and small molecules in a single kit and covers more than 1,000 metabolites from various biochemical classes.",
+            "rdfs:label": "BiocratesMxPQuant500XL",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Biocrates MxP Quant500 XL",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Biocratesp180",
             "@type": "rdfs:Class",

modules/experimentalData/assay.csv

@@ -1,14 +1,15 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
-assay,The technology used to generate the data in this file,"10x multiome, 16SrRNAseq, active avoidance learning behavior, anxiety-related behavior, ATACSeq, atomicForceMicroscopy, autoradiography, Baker Lipidomics, Biocrates Bile Acids, Biocrates p180, Biocrates Q500, bisulfiteSeq, Blood Chemistry Measurement, brightfieldMicroscopy, cellViabilityAssay, ChIPSeq, CITESeq, contextual conditioning behavior, CUT&Tag, DIA, DNA optical mapping, electrochemiluminescence, elevated plus maze test, elevated T maze apparatus method, ELISA, errBisulfiteSeq, exomeSeq, FIA-MSMS, FitBark, frailty assessment, Genotyping, HI-C, HiChIPseq, high content screen, HPLC, HPLC-MSMS, Immunocytochemistry, immunofluorescence, immunohistochemistry, in vivo bioluminescence, ISOSeq, jumpingLibrary, kinesthetic behavior, label free mass spectrometry, Laser Speckle Imaging, LC-MS, LC-MSMS, LC-SRM, Leiden Oxylipins, lentiMPRA, LFP, liquid chromatography-electrochemical detection, lncrnaSeq, locomotor activation behavior, long-read rnaSeq, LTP, MDMS-SL, memory behavior, Metabolon, methylationArray, MIB/MS, microRNAcounts, mirnaArray, mirnaSeq, MRI, mRNAcounts, MudPIT, m6A-rnaSeq, nextGenerationTargetedSequencing, Nightingale NMR, NOMe-Seq, novelty response behavior, open field test, oxBS-Seq, pharmacodynamics, pharmacokinetics, photograph, polymeraseChainReaction, Positron Emission Tomography, proximity extension assay, questionnaire, Rader Lipidomics, Real Time PCR, Ribo-Seq, rotarod performance test, rnaArray, rnaSeq, RPPA, sandwich ELISA, Sanger sequencing, scale, scATACSeq, scCGIseq, scirnaSeq, scrnaSeq, scwholeGenomeSeq, SiMoA, snpArray, snATACSeq, snrnaSeq, spontaneous alternation, STARRSeq, TMT quantitation, tractionForceMicroscopy, UPLC-MSMS, UPLC-ESI-QTOF-MS, UC Davis GCTOF, UCSD Untargeted Metabolomics, Vernier Caliper, von Frey test, westernBlot, wheel running, whole-cell patch clamp, wholeGenomeSeq, Wishart Catecholamines, Wishart High Value Metabolites, Zeno Electronic Walkway",,,True,ManifestColumn,,sage.annotations-experimentalData.assay-0.0.26,,string,experimentalData
+assay,The technology used to generate the data in this file,"10x multiome, 16SrRNAseq, active avoidance learning behavior, anxiety-related behavior, ATACSeq, atomicForceMicroscopy, autoradiography, Baker Lipidomics, Biocrates Bile Acids, Biocrates MxP Quant500 XL, Biocrates p180, Biocrates Q500, bisulfiteSeq, Blood Chemistry Measurement, brightfieldMicroscopy, cellViabilityAssay, ChIPSeq, CITESeq, contextual conditioning behavior, CUT&Tag, DIA, DNA optical mapping, electrochemiluminescence, elevated plus maze test, elevated T maze apparatus method, ELISA, errBisulfiteSeq, exomeSeq, FIA-MSMS, FitBark, frailty assessment, Genotyping, HI-C, HiChIPseq, high content screen, HPLC, HPLC-MSMS, Immunocytochemistry, immunofluorescence, immunohistochemistry, in vivo bioluminescence, ISOSeq, jumpingLibrary, kinesthetic behavior, label free mass spectrometry, Laser Speckle Imaging, LC-MS, LC-MSMS, LC-SRM, Leiden Oxylipins, lentiMPRA, LFP, liquid chromatography-electrochemical detection, lncrnaSeq, locomotor activation behavior, long-read rnaSeq, LTP, MDMS-SL, memory behavior, Metabolon, methylationArray, MIB/MS, microRNAcounts, mirnaArray, mirnaSeq, MRI, mRNAcounts, MudPIT, m6A-rnaSeq, nextGenerationTargetedSequencing, Nightingale NMR, NOMe-Seq, novelty response behavior, open field test, oxBS-Seq, pharmacodynamics, pharmacokinetics, photograph, polymeraseChainReaction, Positron Emission Tomography, proximity extension assay, questionnaire, Rader Lipidomics, Real Time PCR, Ribo-Seq, rotarod performance test, rnaArray, rnaSeq, RPPA, sandwich ELISA, Sanger sequencing, scale, scATACSeq, scCGIseq, scirnaSeq, scrnaSeq, scwholeGenomeSeq, SiMoA, snpArray, snATACSeq, snrnaSeq, spontaneous alternation, STARRSeq, TMT quantitation, tractionForceMicroscopy, UPLC-MSMS, UPLC-ESI-QTOF-MS, UC Davis GCTOF, UCSD Untargeted Metabolomics, Vernier Caliper, von Frey test, westernBlot, wheel running, whole-cell patch clamp, wholeGenomeSeq, Wishart Catecholamines, Wishart High Value Metabolites, Zeno Electronic Walkway",,,True,ManifestColumn,,sage.annotations-experimentalData.assay-0.0.26,,string,experimentalData
 10x multiome,Simultaneous profiling of gene expression and open chromatin from the same cell.,,,,,assay,,http://www.ebi.ac.uk/efo/EFO_0030059,,string,experimentalData
 16SrRNAseq,An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample.,,,,,assay,,http://www.ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0002763,,string,experimentalData
 active avoidance learning behavior,Avoidance learning when the action occurs.,,,,,assay,,http://purl.obolibrary.org/obo/NBO_0000217,,string,experimentalData
 anxiety-related behavior,An emotional behavior related to a feeling of uneasiness or nervousness triggered by an identifiable triggering stimulus.,,,,,assay,,http://purl.obolibrary.org/obo/NBO_0000092,,string,experimentalData
 ATACSeq,Open chromatin regions measured by sequencing DNA after assay for transposase-accessible chromatin (ATAC) treatment,,,,,assay,,http://purl.obolibrary.org/obo/OBI_0002039,,string,experimentalData
 atomicForceMicroscopy,Microscopy which uses a sharp spike (known as a 'tip') mounted on the end of a cantilever to scan the surface of the specimen,,,,,assay,,http://purl.obolibrary.org/obo/CHMO_0000113,,string,experimentalData
-autoradiography, A radioactivity detection technique using X- ray film to visualize molecules or fragments of molecules that have been radioactively labeled.,,,,,assay,,http://purl.obolibrary.org/obo/ERO_0000716,,string,experimentalData
+autoradiography,A radioactivity detection technique using X- ray film to visualize molecules or fragments of molecules that have been radioactively labeled.,,,,,assay,,http://purl.obolibrary.org/obo/ERO_0000716,,string,experimentalData
 Baker Lipidomics,A comparative lipidomics approach that enables semi-quantification of approximately 400 lipid species across 22 lipid classes and subclasses. The analysis is performed by liquid chromatography tandem mass spectrometry. Stable isotope dilution (with 23 different internal standards) is used to provide quantitative data on each of the over 400 lipid species.,,,,,assay,,https://baker.edu.au/research/contract-research/metabolomics,,string,experimentalData
 Biocrates Bile Acids,"The Biocrates AbsoluteIDQ Bile Acids kit is a ready-to-use, standardized solution for the quantitation of 20 bile acids by liquid chromatography-mass spectrometry (LC-MS).",,,,,assay,,https://biocrates.com/biocrates-bile-acids-kit/,,string,experimentalData
+Biocrates MxP Quant500 XL,"The Biocrates MxP® Quant 500 XL combines quantitative metabolomics profiling of lipids and small molecules in a single kit and covers more than 1,000 metabolites from various biochemical classes.",,,,,assay,,https://biocrates.com/mxp-quant-500-xl/,,string,experimentalData
 Biocrates p180,"The Biocrates AbsoluteIDQ p180 kit is a simple and high-throughput tool for basic, clinical, and epidemiological research. The kit provides scientists with highly reproducible metabolomics data to confidently obtain detailed knowledge about the metabolic phenotypes in their studies.",,,,,assay,,https://biocrates.com/absoluteidq-p180-kit/,,string,experimentalData
 Biocrates Q500,"MxP Quant 500 extends the p180 kit and is Biocrates' most comprehensive kit for targeted metabolic profiling. With coverage of up to 630 metabolites from 26 biochemical classes, it represents an advanced and reproducible metabolomics technology.",,,,,assay,,https://biocrates.com/mxp-quant-500-kit/,,string,experimentalData
 bisulfiteSeq,Methylation data captured by sequencing of DNA treated by a bisulfite-based chemical process,,,,,assay,,http://purl.obolibrary.org/obo/OBI_0000748,,string,experimentalData