updates for CLEAR-AD needed for individual and biospecimen templates

Author: ameliakallaher

modules/biospecimen/cellType.csv

@@ -1,5 +1,5 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
-cellType,A cell type is a distinct morphological or functional form of cell.,"A549, arachnoid, astrocytes, B-lymphocytes, CD138+, CD8+ T-Cells, CNON, dopaminergic neurons, Embryonic stem cells, epithelial, epithelial-like, fibroblast, GABAergic neurons, glia, GLUtamatergic neurons, immune cell, iPSC, iPSC-derived astrocytes, iPSC-derived glia, iPSC-derived neuron, iPSC-derived neuronal progenitor cell, iPSC-derived telencephalic organoids, lymphoblast, lymphoblastoid cell line, macrophages, meningioma, microglia, monocytes, monocyte-derived microglia, NCX NES, NeuN-, NeuN+, neural progenitor cell, neuron, oligodendrocyte, peripheral blood mononuclear cell, polygonal, round, schwann, Schwann cell precusor, schwannoma, SH-SY5Y",,,False,ManifestColumn,,sage.annotations-experimentalData.cellType-0.0.9,,string,biospecimen
+cellType,A cell type is a distinct morphological or functional form of cell.,"A549, arachnoid, astrocytes, B-lymphocytes, CD138+, CD8+ T-Cells, CNON, dopaminergic neurons, Embryonic stem cells, epithelial, epithelial-like, fibroblast, GABAergic neurons, glia, GLUtamatergic neurons, immune cell, iPSC, iPSC-derived astrocytes, iPSC-derived glia, iPSC-derived neuron, iPSC-derived neuronal progenitor cell, iPSC-derived telencephalic organoids, lymphoblast, lymphoblastoid cell line, macrophages, meningioma, microglia, monocytes, monocyte-derived microglia, NCX NES, NeuN-, NeuN+, neural progenitor cell, neuron, oligodendrocyte, peripheral blood mononuclear cell, polygonal, round, schwann, Schwann cell precursor, schwannoma, SH-SY5Y",,,False,ManifestColumn,,sage.annotations-experimentalData.cellType-0.0.9,,string,biospecimen
 A549,An adenocarcinoma cell line established by D.J. Giard in 1972 from lung carcinoma tissue removed from a 58-year-old Caucasian male.,,,,,cellType,,http://www.ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C117127,,string,biospecimen
 arachnoid,An arachnoid mater is a delicate membrane that encloses the spinal cord and brain and lies between the pia mater and dura mater.,,,,,cellType,,https://www.ebi.ac.uk/ols/ontologies/bto/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_0001636,,string,biospecimen
 astrocytes,"Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with end-feet which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier.",,,,,cellType,,https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000127,,string,biospecimen
@@ -39,6 +39,6 @@ peripheral blood mononuclear cell,A leukocyte with a single non-segmented nucleu
 polygonal,"A polygonal face is a polygon bounded by a circuit of polygon edges, and includes the flat (plane) region inside the boundary.",,,,,cellType,,https://www.ebi.ac.uk/ols/ontologies/sio/terms?iri=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000503,,string,biospecimen
 round,A phenotype observation at the level of the cell shape where the cell is round,,,,,cellType,,https://www.ebi.ac.uk/ols/ontologies/cmpo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fcmpo%2FCMPO_0000118,,string,biospecimen
 schwann,Schwann cells are a variety of glial cell that keep peripheral nerve fibres (both myelinated and unmyelinated) alive.,,,,,cellType,,https://www.ebi.ac.uk/ols/ontologies/bto/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_0001220,,string,biospecimen
-Schwann cell precusor,A giioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19.,,,,,cellType,,http://purl.obolibrary.org/obo/CL_0002375,,string,biospecimen
+Schwann cell precursor,A giioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19.,,,,,cellType,,http://purl.obolibrary.org/obo/CL_0002375,,string,biospecimen
 schwannoma,"A neoplasm that arises from SCHWANN CELLS of the cranial, peripheral, and autonomic nerves.",,,,,cellType,,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0000693,,string,biospecimen
 SH-SY5Y,Human neuroblastoma clonal subline of the neuroepithelioma cell line SK-N-SH that had been established in 1970 from the bone marrow biopsy of a 4-year-old girl with metastatic neuroblastoma.,,,,,cellType,,https://www.ebi.ac.uk/ols/ontologies/bto/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_0000793,,string,biospecimen

modules/biospecimen/tissue.csv

@@ -1,5 +1,5 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
-tissue,A tissue is a mereologically maximal collection of cells that together perform physiological function.,"amygdala, amygdaloid complex, anterior cingulate cortex, angular gyrus, blood, bone marrow, Buccal Mucosa, Buffy Coat, caudate nucleus, cecum derived fecal material, cerebellar cortex, cerebellum, cerebral cortex, cortical plate, dorsal anterior cingulate cortex, dorsal pallium, Dorsal Root Ganglion, dorsolateral prefrontal cortex, dorsomedial prefrontal cortex, embryonic tissue, entorhinal cortex, fecal material, forebrain, frontal cortex, frontal lobe, frontal pole, fusiform gyrus, hippocampus, head of caudate nucleus, inferior frontal gyrus, inferior temporal cortex, inferior temporal gyrus, inferolateral temporal cortex, insula, insular cortex, lateral entorhinal cortex, left cerebral hemisphere, liver, mammillary body, medial dorsal nucleus of thalamus, medial entorhinal cortex, medial frontal cortex, medial ganglionic eminence, medial orbital frontal cortex, medial prefrontal cortex, meninges, midbrain, middle frontal gyrus, middle temporal gyrus, nerve tissue, Not Applicable, nucleus accumbens, occipital lobe, occipital visual cortex, olfactory neuroepithelium, orbitofrontal cortex, parahippocampal gyrus, parietal cortex, parietal lobe, plasma, posterior cingulate cortex, posteroinferior parietal cortex, posterior inferior parietal cortex, posterior superior temporal cortex, precentral gyrus, prefrontal cortex, primary auditory cortex, primary motor cortex, primary somatosensory cortex, primary tumor, primary visual cortex, putamen, right cerebral hemisphere, serum, splenocyte, striatum, subgenual anterior cingulate cortex, subgenual cingulate cortex, superior parietal lobe, superior temporal gyrus, temporal cortex, temporal lobe, temporal pole, thalamus, unspecified, ventricular zone, ventrolateral prefrontal cortex, VZ/SVZ, whole brain",,,True,ManifestColumn,,sage.annotations-experimentalData.tissue-0.0.11,,string,biospecimen
+tissue,A tissue is a mereologically maximal collection of cells that together perform physiological function.,"amygdala, amygdaloid complex, anterior cingulate cortex, angular gyrus, blood, bone marrow, Buccal Mucosa, Buffy Coat, caudate nucleus, cecum derived fecal material, cerebellar cortex, cerebellum, cerebral cortex, cortical plate, dorsal anterior cingulate cortex, dorsal pallium, Dorsal Root Ganglion, dorsolateral prefrontal cortex, dorsomedial prefrontal cortex, embryonic tissue, entorhinal cortex, fecal material, forebrain, frontal cortex, frontal lobe, frontal pole, fusiform gyrus, hippocampus, head of caudate nucleus, inferior frontal gyrus, inferior temporal cortex, inferior temporal gyrus, inferolateral temporal cortex, insula, insular cortex, lateral entorhinal cortex, left cerebral hemisphere, liver, mammillary body, medial dorsal nucleus of thalamus, medial entorhinal cortex, medial frontal cortex, medial ganglionic eminence, medial orbital frontal cortex, medial prefrontal cortex, meninges, midbrain, middle frontal gyrus, middle temporal gyrus, nerve tissue, Not Applicable, nucleus accumbens, occipital lobe, occipital visual cortex, olfactory neuroepithelium, orbitofrontal cortex, parahippocampal gyrus, parietal cortex, parietal lobe, plasma, posterior cingulate cortex, posteroinferior parietal cortex, posterior inferior parietal cortex, posterior superior temporal cortex, precentral gyrus, prefrontal cortex, primary auditory cortex, primary motor cortex, primary somatosensory cortex, primary tumor, primary visual cortex, putamen, right cerebral hemisphere, serum, splenocyte, striatum, subgenual anterior cingulate cortex, subgenual cingulate cortex, superior parietal lobe, superior temporal gyrus, temporal cortex, temporal lobe, temporal pole, thalamus, unspecified, ventricular zone, ventrolateral prefrontal cortex, VZ/SVZ, whole brain, Cerebellar Hemisphere, inferior Parietal Gyrus,occipital pole, Transentorhinal Cortex",,,True,ManifestColumn,,sage.annotations-experimentalData.tissue-0.0.11,,string,biospecimen
 amygdala,The one of the four basal ganglia in each cerebral hemisphere that is part of the limbic system and consists of an almond-shaped mass of gray matter in the anterior extremity of the temporal lobe.,,,,,tissue,,https://www.ebi.ac.uk/ols/ontologies/bto/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_0001042,,string,biospecimen
 amygdaloid complex,,,,,,tissue,,Sage Bionetworks,,string,biospecimen
 angular gyrus,Part of inferior parietal lobule formed by the cortex surrounding the upturned end of the superior temporal sulcus.,,,,,tissue,,http://purl.obolibrary.org/obo/UBERON_0002686,,string,biospecimen

modules/clinical/cohort.csv

@@ -1,5 +1,5 @@
 Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
-cohort,A study group population where the members are human beings who meet inclusion criteria.,"ABC-DS,ACT,ADNI,ADRC,Banner,BEAM,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,MARS-WI,Mayo Clinic ADRC (Mayo ADRC),MC,MCJ,MCR,MIND,MSBB,NYBB,Pitt ADRC,POINTER,RADC,ROSMAP,SMRI,Tulsa LIBR-1000,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP",,,False,ManifestColumn,,http://purl.obolibrary.org/obo/STATO_0000203,,string,clinical
+cohort,A study group population where the members are human beings who meet inclusion criteria.,"ABC-DS,ACT,ADNI,ADRC,Banner,BEAM,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,MARS-WI,Mayo Clinic ADRC (Mayo ADRC),MC,MCJ,MCR,MIND,MSBB,NYBB,Pitt ADRC,POINTER,RADC,ROSMAP,SMRI,Tulsa LIBR-1000,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP, Mayo Clinic Study of Aging (MCSA),Mayo Clinic Brain Bank (MCBB),Michigan ADRC (MADC),Knight ADRC, 1Florida ADRC (1FL ADRC),Emory ADRC, Indiana ADRC (IADRC)",,,False,ManifestColumn,,http://purl.obolibrary.org/obo/STATO_0000203,,string,clinical
 ABC-DS,Alzheimer's Biomarkers Consortium - Down Syndrome,,,,False,cohort,,https://www.abcds.pitt.edu/,,string,clinical
 ACT,Adult Changes in Thought - Kaiser Permanente Washington Health Research Institute,,,,False,cohort,,https://actagingresearch.org/about,,string,clinical
 ADNI,Alzheimer's Disease Neuroimaging Initative,,,,False,cohort,,https://adni.loni.usc.edu/,,string,clinical

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",,,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, 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

modules/experimentalData/collectionMethod.csv

@@ -0,0 +1,2 @@
+Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
+collectionMethod,For CLEAR-AD.Blood samples that are collected in heparin tubes will be sent directly to NCRAD for them to extract and store PBMCs for eventual generation of iPSCs.,"PAXgene Blood Tube, EDTA Purple Top Tube, Heparin (NaHep) Green Top Tubes,other, not collected",,,False,ManifestColumn,,sage.annotations-experimentalData.collectionMethod-0.0.11,,string,biospecimen

modules/experimentalData/freezeThawCycles.csv

@@ -0,0 +1,2 @@
+Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
+freezeThawCycles,The number of freeze thaw cycles of fluid samples as multiple freeze thaw cycles may compromise sample integrity,,,,False,ManifestColumn,,sage.annotations-experimentalData.freezeThawCycles-0.0.11,,string,biospecimen