Merge pull request #47 from eliteportal/dictionary-update-PR46

Dictionary-update-PR46

.gitignore

@@ -20,6 +20,9 @@ data_model_creation/_logs/
 .synapseCache/*
 */schematic_service_account_creds.json
 
+# ignore local jekyll site builds
+_site/*
+
 # Allowed
 !**/old_models/*.csv
 !**/models/*.csv

_data/ManifestColumn.csv

@@ -18,7 +18,7 @@ backgroundTrait,Any background trait(s) shared by all individuals in the GWAS (e
 batchID,"ID used to identify a batch, provided by the data contributor to Sage Bionetworks. The batch identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse",,STRING,ManifestColumn,ManifestColumn
 batchLabel,Used to supply batch label information with any string value,,STRING,ManifestColumn,ManifestColumn
 captivityDuration,"The duration of captivity in months for the individuals in captivity (formatted in months, ex. 72 months).note- Applicable only to animals with captivity status captive.",,STRING,ManifestColumn,ManifestColumn
-captivityStatus,"The status of the individual with regard to captivity.note- Wild, captive, and stranded values are applicable, especially for marine mammals. Depending on life stage terminology for individual species, other values are possible. Please let the data curation team know.","Captive,Stranded,Wild",STRING,ManifestColumn,ManifestColumn
+captivityStatus,"The status of the individual with regard to captivity.note- Wild, captive, and stranded values are applicable, especially for marine mammals. Depending on life stage terminology for individual species, other values are possible. Please let the data curation team know.","Captive,Stranded,Wild, Not applicable, Not collected, Not specified, Other, Unknown",STRING,ManifestColumn,ManifestColumn
 commonName,"The biological species common name the individual belongs to (ex. ""Horned Lark""). note- As a default, the valid scientific name for the species should be indicated.",,STRING,ManifestColumn,ManifestColumn
 consentGroupID,"Indicate the consent group for the individual, provided by the data contributor's data dictionary",,STRING,ManifestColumn,ManifestColumn
 conversionRatio,The ratio or % detailing how well the bisulfite conversion worked. Provide a value or Unknown Not collected Not applicable Not specified,,STRING,ManifestColumn,ManifestColumn
@@ -68,7 +68,7 @@ libReadsSeqd,"Library reads sequenced. Total number of clones sequenced from the
 libSize,"Library size. Total number of clones in the library prepared for the project. Example - '50'Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,INTEGER,ManifestColumn,ManifestColumn
 libVector,"Library vector. Cloning vector type(s) used in the construction of libraries. Example - 'Bacteriophage P1'Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,STRING,ManifestColumn,ManifestColumn
 libraryBatchID,"Library batch identifier, provided by the data contributor to Sage Bionetworks. The batch identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,STRING,ManifestColumn,ManifestColumn
-lifeStage,The life stage of the individual.note- Other values are possible depending on life stage terminology for individual species. Please let the data curation team know.,"Adult,Juvenile,Post-Juvenile",STRING,ManifestColumn,ManifestColumn
+lifeStage,The life stage of the individual.note- Other values are possible depending on life stage terminology for individual species. Please let the data curation team know.,"Adult,Juvenile,Post-Juvenile, Not applicable, Not collected, Not specified, Other, Unknown",STRING,ManifestColumn,ManifestColumn
 measurementTechnique,"The name of the measurement technique describing the assay method. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,STRING,ManifestColumn,ManifestColumn
 mid,"Multiplex identifiers. Molecular barcodes, called Multiplex Identifiers (MIDs), are used to tag unique samples in a sequencing run specifically. Sequence should be reported in uppercase letters. Example - 'GTGAATAT'Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,STRING,ManifestColumn,ManifestColumn
 modificationParameters,"Modification parameters for a search engine run. (ex. PSI- PI http-//www.w3.org/2002/07/owl#Axiom) or used in the peptide identification database search. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,STRING,ManifestColumn,ManifestColumn

_data/assay.csv

@@ -116,3 +116,8 @@ Key,Key Description,columnType,Source,Parent
  Wishart Catecholamines,,STRING,,ManifestColumn
  Wishart High Value Metabolites,,STRING,,ManifestColumn
  Zeno Electronic Walkway,,STRING,,ManifestColumn
+ Not collected,,STRING,,ManifestColumn
+ Not specified,,STRING,,ManifestColumn
+ Not applicable,,STRING,,ManifestColumn
+ Other,,STRING,,ManifestColumn
+ Unknown,,STRING,,ManifestColumn

_data/assay_phenotype_human_template.csv

@@ -9,5 +9,5 @@ ethnicity,Ethnicity of individual,True,STRING,,sage.annotations-demographics.eth
 race,Race of individual,True,STRING,,sage.annotations-demographics.race-0.0.2,ManifestColumn,"American Indian or Alaska Native,Asian,Black or African American,Multiracial,Native Hawaiian or Pacific Islander,Prefer not to answer,White"
 sex,The biological sex of the individual,True,STRING,,sage.annotations-experimentalData.sex-0.0.2,ManifestColumn,"Female,Male,Not applicable,Not collected,Not specified,Other,Unknown"
 age,"Age of the individual (age in years of the individual at first recorded study event (enrollment, visit, observation, sample collection, survey completion, etc.)",True,STRING,,,ManifestColumn,
-cohort,Name of the cohort the individual belongs to,True,STRING,,"http://purl.obolibrary.org/obo/NCIT_C61512,http://purl.obolibrary.org/obo/STATO_0000203",ManifestColumn,"ABC-DS, ACT, ADNI, Banner, BEB-Miller, BLSA, CHDWB, CLINCOR, DiCAD, EHBS, Emory ADRC, Framingham, HBTRC, HPGP, HUP, LBP, MARS, MAYO, MC, MCJ, MCR, MSBB, NYBB, Pitt ADRC, RADC, ROSMAP, SMRI, UK Biobank, UPBB, UPenn, UW ADRC,ABC-DS,ACT,ADNI,Banner,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,Mayo Clinic,MC,MCJ,MCR,MSBB,NYBB,Pitt ADRC,RADC,ROSMAP,SMRI,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP"
+cohort,Name of the cohort the individual belongs to,False,STRING,,"http://purl.obolibrary.org/obo/NCIT_C61512,http://purl.obolibrary.org/obo/STATO_0000203",ManifestColumn,"ABC-DS, ACT, ADNI, Banner, BEB-Miller, BLSA, CHDWB, CLINCOR, DiCAD, EHBS, Emory ADRC, Framingham, HBTRC, HPGP, HUP, LBP, MARS, MAYO, MC, MCJ, MCR, MSBB, NYBB, Pitt ADRC, RADC, ROSMAP, SMRI, UK Biobank, UPBB, UPenn, UW ADRC,ABC-DS,ACT,ADNI,Banner,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,Mayo Clinic,MC,MCJ,MCR,MSBB,NYBB,Pitt ADRC,RADC,ROSMAP,SMRI,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP"
 individualID,"Identifying string linked to the individual or animal being studied, provided by the data contributor",True,STRING,,sage.annotations-experimentalData.individualID-0.0.2,ManifestColumn,

_data/biospecimen.csv

@@ -1,9 +1,9 @@
 Key,Key Description,Valid Values,columnType,Parent,module
-cellType,Indicate the cell type.,"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",STRING,ManifestColumn,biospecimen
+cellType,Indicate the cell type.,"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, Not collected, Not specified, Not applicable, Other, Unknown",STRING,ManifestColumn,biospecimen
 fastingState,Was individual fasting when the sample was taken (true/false)?,"FALSE,Not applicable,Not collected,Not specified,TRUE,Unknown",STRING,ManifestColumn,biospecimen
 isPostMortem,Was the sample taken after death (true/false)?,"TRUE, FALSE",STRING,ManifestColumn,biospecimen
 nucleicAcidSource,"Specifies the type of nucleic acid (DNA, RNA, Pooled, etc.) found in a sample.","bulk cell,bulk nuclei,mitochondria,Not applicable,Not collected,Not specified,single cell,single nucleus,sorted cells,sorted nuclei,Unknown",STRING,ManifestColumn,biospecimen
-organ,Indicate the organ the specimen is from,"blood, bone marrow, brain, breast, Bursa Of Fabricius, cerebrospinal fluid, colon, kidney, large intestine, liver, lung, lymph node, mammary gland, nerves, nose, ovary, pancreas, prostate, skin, spleen",STRING,ManifestColumn,biospecimen
+organ,Indicate the organ the specimen is from,"blood, bone marrow, brain, breast, Bursa Of Fabricius, cerebrospinal fluid, colon, kidney, large intestine, liver, lung, lymph node, mammary gland, nerves, nose, ovary, pancreas, prostate, skin, spleen, Not collected, Not specified, Not applicable, Other, Unknown",STRING,ManifestColumn,biospecimen
 samplingAge,"The calculated age of the sample, measurement is determined or coded by the data contributor.Other,Unknown, Not collected, Not applicable",,STRING,ManifestColumn,biospecimen
 specimenID,"Identifying string linked to a particular sample or specimen, provide by the data contributor",,STRING,ManifestColumn,biospecimen
 tissue,Indicate the tissue the specimen is from,"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",STRING,ManifestColumn,biospecimen

_data/biospecimen_human_template.csv

@@ -6,11 +6,11 @@ specimenType,Type of biological material comprising the Specimen,True,STRING,,,M
 tissueVolume,The volume of the tissue sample. Measured in microliters.,True,STRING,,,ManifestColumn,
 Component,,False,,,,,
 Filename,,False,,,,,
-cellType,Indicate the cell type.,True,STRING,,sage.annotations-experimentalData.cellType-0.0.9,ManifestColumn,"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"
+cellType,Indicate the cell type.,True,STRING,,sage.annotations-experimentalData.cellType-0.0.9,ManifestColumn,"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, Not collected, Not specified, Not applicable, Other, Unknown"
 fastingState,Was individual fasting when the sample was taken (true/false)?,True,STRING,,sage.annotations-experimentalData.fastingState-0.0.2,ManifestColumn,"FALSE,Not applicable,Not collected,Not specified,TRUE,Unknown"
 isPostMortem,Was the sample taken after death (true/false)?,True,STRING,,sage.annotations-experimentalData.isPostMortem-0.0.2,ManifestColumn,"TRUE, FALSE"
 nucleicAcidSource,"Specifies the type of nucleic acid (DNA, RNA, Pooled, etc.) found in a sample.",True,STRING,,sage.annotations-ngs.nucleicAcidSource-0.0.3,ManifestColumn,"bulk cell,bulk nuclei,mitochondria,Not applicable,Not collected,Not specified,single cell,single nucleus,sorted cells,sorted nuclei,Unknown"
-organ,Indicate the organ the specimen is from,True,STRING,,sage.annotations-experimentalData.organ-0.0.4,ManifestColumn,"blood, bone marrow, brain, breast, Bursa Of Fabricius, cerebrospinal fluid, colon, kidney, large intestine, liver, lung, lymph node, mammary gland, nerves, nose, ovary, pancreas, prostate, skin, spleen"
+organ,Indicate the organ the specimen is from,True,STRING,,sage.annotations-experimentalData.organ-0.0.4,ManifestColumn,"blood, bone marrow, brain, breast, Bursa Of Fabricius, cerebrospinal fluid, colon, kidney, large intestine, liver, lung, lymph node, mammary gland, nerves, nose, ovary, pancreas, prostate, skin, spleen, Not collected, Not specified, Not applicable, Other, Unknown"
 samplingAge,"The calculated age of the sample, measurement is determined or coded by the data contributor.Other,Unknown, Not collected, Not applicable",True,STRING,,sage.annotations-experimentalData.samplingAge-0.0.2,ManifestColumn,
 specimenID,"Identifying string linked to a particular sample or specimen, provide by the data contributor",True,STRING,,sage.annotations-experimentalData.specimenID-0.0.2,ManifestColumn,
 tissue,Indicate the tissue the specimen is from,True,STRING,,sage.annotations-experimentalData.tissue-0.0.11,ManifestColumn,"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"