Merge pull request #147 from adknowledgeportal/add-deleteme-assay-to-test-workflow

Update assay.csv with trivial value "DELETEME"

Author: MasterPastures

AD.model.csv

@@ -119,6 +119,7 @@ ChIPSeq,Chromatin immuno-precipitation followed by sequencing,,,,,assay,,http://
 CITESeq,CITE-seq is a method that combines highly multiplexed antibody-based detection of protein markers together with unbiased transcriptome profiling for thousands of single cells in parallel.,,,,,assay,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5669064/,,string,experimentalData
 contextual conditioning behavior,,,,,,assay,,http://purl.obolibrary.org/obo/NBO_0000223,,string,experimentalData
 CUT&Tag,"In CUT&Tag, a chromatin protein is bound in situ by a specific antibody, which then tethers a protein A-Tn5 transposase fusion protein. Activation of the transposase efficiently generates fragment libraries with high resolution and exceptionally low background.",,,,,assay,,https://www.nature.com/articles/s41467-019-09982-5,,string,experimentalData
+DELETEME,,,,,,assay,,https://www.google.com,,string,experimentalData
 DIA,Data-independent acquisition (DIA) is a method for collecting tandem mass spectrometry data where the m/z values for all the ions are fragmented and analyzed during the second stage of spectrometry.,,,,,assay,,http://purl.obolibrary.org/obo/NCIT_C161786,,string,experimentalData
 DNA optical mapping,Fluorescent imaging of linearly extended DNA molecules to probe information patterns along the molecules,,,,,assay,,https://doi.org/10.1016/j.copbio.2013.01.009,,string,experimentalData
 electrochemiluminescence,"A method in which electromagnetic radiation, in the form of light emission, is generated from an electrochemical reaction in a solution.",,,,,assay,,http://purl.obolibrary.org/obo/NCIT_C111193,,string,experimentalData
@@ -854,7 +855,7 @@ 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 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, TotalRNAseq,mRNAseq,RRBS,Illumina EPIC Array",,,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, DELETEME, 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, TotalRNAseq,mRNAseq,RRBS,Illumina EPIC Array",,,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

@@ -2466,6 +2466,9 @@
                 {
                     "@id": "bts:CUT&Tag"
                 },
+                {
+                    "@id": "bts:DELETEME"
+                },
                 {
                     "@id": "bts:DIA"
                 },
@@ -3362,6 +3365,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:DELETEME",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "DELETEME",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "DELETEME",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:DIA",
             "@type": "rdfs:Class",

modules/experimentalData/assay.csv

@@ -1,5 +1,5 @@
 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 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, TotalRNAseq,mRNAseq,RRBS,Illumina EPIC Array",,,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, DELETEME, 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, TotalRNAseq,mRNAseq,RRBS,Illumina EPIC Array",,,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
@@ -20,6 +20,7 @@ ChIPSeq,Chromatin immuno-precipitation followed by sequencing,,,,,assay,,http://
 CITESeq,CITE-seq is a method that combines highly multiplexed antibody-based detection of protein markers together with unbiased transcriptome profiling for thousands of single cells in parallel.,,,,,assay,,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5669064/,,string,experimentalData
 contextual conditioning behavior,,,,,,assay,,http://purl.obolibrary.org/obo/NBO_0000223,,string,experimentalData
 CUT&Tag,"In CUT&Tag, a chromatin protein is bound in situ by a specific antibody, which then tethers a protein A-Tn5 transposase fusion protein. Activation of the transposase efficiently generates fragment libraries with high resolution and exceptionally low background.",,,,,assay,,https://www.nature.com/articles/s41467-019-09982-5,,string,experimentalData
+DELETEME,,,,,,assay,,https://www.google.com,,string,experimentalData
 DIA,Data-independent acquisition (DIA) is a method for collecting tandem mass spectrometry data where the m/z values for all the ions are fragmented and analyzed during the second stage of spectrometry.,,,,,assay,,http://purl.obolibrary.org/obo/NCIT_C161786,,string,experimentalData
 DNA optical mapping,Fluorescent imaging of linearly extended DNA molecules to probe information patterns along the molecules,,,,,assay,,https://doi.org/10.1016/j.copbio.2013.01.009,,string,experimentalData
 electrochemiluminescence,"A method in which electromagnetic radiation, in the form of light emission, is generated from an electrochemical reaction in a solution.",,,,,assay,,http://purl.obolibrary.org/obo/NCIT_C111193,,string,experimentalData