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Templates for Assay Data
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Genomics Assay
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+
Annotation templates are spreadsheet templates that allow contributors to annotate resources uploaded to the repository. See interactive use of these templates at our NF Data Curator App. Templates implement “minimum metadata” standards specific to the type of data/resource (hence variants exist for assay types and “raw” vs “processed” data). Templates also contain common components, e.g. many will collect core sample info associated with the data.
+Unless the template field is free-text, it is meant to be filled by the contributor using the ontology terms/controlled vocabulary defined here. For example, the “assay” property allows the contributor to use terms under Assay.
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Proteomics Assay
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Genomics Assay Templates
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Genomics Assay (Generic)
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+
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+
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Bulk RNA-Seq Assay
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+
+
+
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Single-cell RNA-Seq Assay
+
+
+
+
+
Processed Aligned Reads
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+
+
+
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Processed Variant Calls
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+
+
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Processed Expression
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+
+
+
+
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Proteomics Assay Templates
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Proteomics Assay (Generic)
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Imaging Assay Templates
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Imaging Assay (Generic)
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Other Assay Templates
Pharmacokinetics Assay
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Plate Based Reporter Assay
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Clinical Assay
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Clinical Assay Templates
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Clinical Assay (Generic)
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Other Templates
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Non-Assay Templates
Patient Timepoints
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@@ -560,10 +612,10 @@
Reserved Properties
Reserved annotation properties also describe the resource in some way, but they are not expected to be edited directly by contributors. They are computed/automated annotations set by the data platform and DCC activities.
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diff --git a/docs/templates/Behavioral_Assay_Template.csv b/docs/templates/Behavioral_Assay_Template.csv
deleted file mode 100644
index 257067d4..00000000
--- a/docs/templates/Behavioral_Assay_Template.csv
+++ /dev/null
@@ -1,12 +0,0 @@
-"Field","Description","Required","ControlledVocab","Note"
-"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
-"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
-"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of """"genomicVariants"""" might have an assay value of """"whole genome sequencing"""". ","required","#Data",""
-"assay","The technology used to generate the data in this file","required","#Assay",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
-"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
-"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
-"experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
-"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
diff --git a/docs/templates/Biospecimen_Template.csv b/docs/templates/Biospecimen_Template.csv
deleted file mode 100644
index 8bc1c162..00000000
--- a/docs/templates/Biospecimen_Template.csv
+++ /dev/null
@@ -1,4 +0,0 @@
-"Field","Description","Required","ControlledVocab","Note"
-"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
-"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
-"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
diff --git a/docs/templates/Biospecimen_Template_Normalized.csv b/docs/templates/Biospecimen_Template_Normalized.csv
deleted file mode 100644
index 1a1a4053..00000000
--- a/docs/templates/Biospecimen_Template_Normalized.csv
+++ /dev/null
@@ -1,13 +0,0 @@
-"Field","Description","Required","ControlledVocab","Note"
-"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
-"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
-"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
-"aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
-"organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
-"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
-"isCellLine","Whether or not sample source is a cell line (Yes; No)","optional","Yes, No",""
-"isPrimaryCell","Whether or not cellType is primary (Yes; No)","optional","Yes, No",""
-"cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
-"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","optional","#Tumor",""
-"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
-"modelSystemName","A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","optional","#Model_System",""
diff --git a/docs/templates/Clinical_Assay_Template.csv b/docs/templates/Clinical_Assay_Template.csv
index ddb3fb49..bd06bf84 100644
--- a/docs/templates/Clinical_Assay_Template.csv
+++ b/docs/templates/Clinical_Assay_Template.csv
@@ -1,13 +1,34 @@
"Field","Description","Required","ControlledVocab","Note"
"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
-"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of """"genomicVariants"""" might have an assay value of """"whole genome sequencing"""". ","required","#Data",""
"assay","The technology used to generate the data in this file","required","#Assay",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
-"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
-"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level",""
+"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
+"resourceType","The type of resource being stored and annotated","required","#Resource",""
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
+"cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
+"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
"experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
-"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"isCellLine","Whether or not sample source is a cell line (Yes; No)","optional","Yes, No",""
+"isPrimaryCell","Whether or not cellType is primary (Yes; No)","optional","Yes, No",""
+"modelSystemName","A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","optional","#Model_System",""
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
+"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
+"timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
+"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
+"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","optional","#Tumor",""
+"entityId",NA,NA,NA,NA
diff --git a/docs/templates/Clinical_Assay_Template_Extended.csv b/docs/templates/Clinical_Assay_Template_Extended.csv
deleted file mode 100644
index b465b9bb..00000000
--- a/docs/templates/Clinical_Assay_Template_Extended.csv
+++ /dev/null
@@ -1,15 +0,0 @@
-"Field","Description","Required","ControlledVocab","Note"
-"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
-"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
-"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of """"genomicVariants"""" might have an assay value of """"whole genome sequencing"""". ","required","#Data",""
-"assay","The technology used to generate the data in this file","required","#Assay",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
-"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
-"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
-"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
-"experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
-"compoundName","Common name for a compound, e.g. “Selumetinib” (https://pubchem.ncbi.nlm.nih.gov/compound/10127622)","optional","",""
-"compoundDose","A dose quantity for the treatment compound. To be used with compoundDoseUnit.","optional","",""
-"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
diff --git a/docs/templates/Epigenetics_Assay_Template.csv b/docs/templates/Epigenetics_Assay_Template.csv
index f2ac5400..60d2a36f 100644
--- a/docs/templates/Epigenetics_Assay_Template.csv
+++ b/docs/templates/Epigenetics_Assay_Template.csv
@@ -1,14 +1,38 @@
"Field","Description","Required","ControlledVocab","Note"
"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
-"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of """"genomicVariants"""" might have an assay value of """"whole genome sequencing"""". ","required","#Data",""
"assay","The technology used to generate the data in this file","required","#Assay",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
-"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
-"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level",""
+"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
+"resourceType","The type of resource being stored and annotated","required","#Resource",""
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
+"cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
+"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
+"dissociationMethod","Procedure by which a biological specimen is dissociated into individual cells or a cell suspension","optional","#Dissociation_Method",""
"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
"experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
+"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"isCellLine","Whether or not sample source is a cell line (Yes; No)","optional","Yes, No",""
+"isPrimaryCell","Whether or not cellType is primary (Yes; No)","optional","Yes, No",""
"libraryPrep","The general strategy by which the library was prepared","optional","#Library_Prep",""
-"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"libraryPreparationMethod","Method by which library was prepared","optional","#Library_Preparation_Method",""
+"modelSystemName","A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","optional","#Model_System",""
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","optional","#Nucleic_Acid_Source",""
+"organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
+"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
+"timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
+"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
+"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","optional","#Tumor",""
+"entityId",NA,NA,NA,NA
diff --git a/docs/templates/Genomics_Assay_Template.csv b/docs/templates/Genomics_Assay_Template.csv
index 30a3d8b4..bc0bb804 100644
--- a/docs/templates/Genomics_Assay_Template.csv
+++ b/docs/templates/Genomics_Assay_Template.csv
@@ -1,13 +1,42 @@
"Field","Description","Required","ControlledVocab","Note"
"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
-"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of """"genomicVariants"""" might have an assay value of """"whole genome sequencing"""". ","required","#Data",""
"assay","The technology used to generate the data in this file","required","#Assay",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level",""
+"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
+"readLength","Number of base pairs (bp) sequenced for a read","required","",""
+"resourceType","The type of resource being stored and annotated","required","#Resource",""
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
+"cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
+"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
+"dissociationMethod","Procedure by which a biological specimen is dissociated into individual cells or a cell suspension","optional","#Dissociation_Method",""
"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"isCellLine","Whether or not sample source is a cell line (Yes; No)","optional","Yes, No",""
+"isPrimaryCell","Whether or not cellType is primary (Yes; No)","optional","Yes, No",""
+"isStranded","Whether or not the library is stranded (Yes; No)","optional","Yes, No",""
+"libraryPrep","The general strategy by which the library was prepared","optional","#Library_Prep",""
+"libraryPreparationMethod","Method by which library was prepared","optional","#Library_Preparation_Method",""
+"modelSystemName","A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","optional","#Model_System",""
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","optional","#Nucleic_Acid_Source",""
+"organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
+"readDepth","If available, the coverage statistic as output from bedtools coverage or samtools stats.","optional","",""
+"readPair","The read of origin","optional","#Read_Pair",""
+"readPairOrientation","The relative orientation of the reads in a paired-end protocol","optional","#Read_Pair_Orientation",""
+"readStrandOrigin","The strand from which the read originates in a strand-specific protocol","optional","#Read_Strand_Origin",""
"runType","Is the sequencing run single or paired end?","optional","#Run_Type",""
-"libraryPrep","The general strategy by which the library was prepared","optional","#Library_Prep",""
-"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
+"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
+"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","optional","#Tumor",""
+"entityId",NA,NA,NA,NA
diff --git a/docs/templates/Genomics_Assay_Template_Extended.csv b/docs/templates/Genomics_Assay_Template_Extended.csv
deleted file mode 100644
index 26f47d82..00000000
--- a/docs/templates/Genomics_Assay_Template_Extended.csv
+++ /dev/null
@@ -1,16 +0,0 @@
-"Field","Description","Required","ControlledVocab","Note"
-"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
-"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
-"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of """"genomicVariants"""" might have an assay value of """"whole genome sequencing"""". ","required","#Data",""
-"assay","The technology used to generate the data in this file","required","#Assay",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
-"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
-"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
-"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
-"experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
-"runType","Is the sequencing run single or paired end?","optional","#Run_Type",""
-"libraryPrep","The general strategy by which the library was prepared","optional","#Library_Prep",""
-"genePerturbed","The HUGO gene symbol for the gene that is perturbed.","optional","",""
-"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
diff --git a/docs/templates/Genomics_Assay_Template_Normalized.csv b/docs/templates/Genomics_Assay_Template_Normalized.csv
deleted file mode 100644
index 4522eef4..00000000
--- a/docs/templates/Genomics_Assay_Template_Normalized.csv
+++ /dev/null
@@ -1,13 +0,0 @@
-"Field","Description","Required","ControlledVocab","Note"
-"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
-"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
-"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of """"genomicVariants"""" might have an assay value of """"whole genome sequencing"""". ","required","#Data",""
-"assay","The technology used to generate the data in this file","required","#Assay",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
-"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
-"aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
-"runType","Is the sequencing run single or paired end?","optional","#Run_Type",""
-"libraryPrep","The general strategy by which the library was prepared","optional","#Library_Prep",""
-"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
diff --git a/docs/templates/Imaging_Assay_Template.csv b/docs/templates/Imaging_Assay_Template.csv
index c784c248..287db22a 100644
--- a/docs/templates/Imaging_Assay_Template.csv
+++ b/docs/templates/Imaging_Assay_Template.csv
@@ -1,13 +1,32 @@
"Field","Description","Required","ControlledVocab","Note"
"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
-"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of """"genomicVariants"""" might have an assay value of """"whole genome sequencing"""". ","required","#Data",""
-"assay","The technology used to generate the data in this file","required","#Assay",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
"assay","The technology used to generate the data in this file","required","#Assay",""
-"platformTarget",NA,NA,NA,NA
+"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level",""
+"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
+"resourceType","The type of resource being stored and annotated","required","#Resource",""
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
+"cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
+"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"isCellLine","Whether or not sample source is a cell line (Yes; No)","optional","Yes, No",""
+"isPrimaryCell","Whether or not cellType is primary (Yes; No)","optional","Yes, No",""
+"modelSystemName","A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","optional","#Model_System",""
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
-"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
+"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
+"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","optional","#Tumor",""
+"entityId",NA,NA,NA,NA
+"platformTarget",NA,NA,NA,NA
diff --git a/docs/templates/Imaging_Assay_Template_Extended.csv b/docs/templates/Imaging_Assay_Template_Extended.csv
deleted file mode 100644
index 9946b1ce..00000000
--- a/docs/templates/Imaging_Assay_Template_Extended.csv
+++ /dev/null
@@ -1,16 +0,0 @@
-"Field","Description","Required","ControlledVocab","Note"
-"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
-"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
-"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of """"genomicVariants"""" might have an assay value of """"whole genome sequencing"""". ","required","#Data",""
-"assay","The technology used to generate the data in this file","required","#Assay",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
-"assay","The technology used to generate the data in this file","required","#Assay",""
-"platformTarget",NA,NA,NA,NA
-"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
-"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
-"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
-"experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
-"genePerturbed","The HUGO gene symbol for the gene that is perturbed.","optional","",""
-"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
diff --git a/docs/templates/Individual_Template.csv b/docs/templates/Individual_Template.csv
deleted file mode 100644
index af4c5dfb..00000000
--- a/docs/templates/Individual_Template.csv
+++ /dev/null
@@ -1,10 +0,0 @@
-"Field","Description","Required","ControlledVocab","Note"
-"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
-"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
-"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
-"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
-"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
-"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
-"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
-"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
-"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
diff --git a/docs/templates/MRI_Assay_Template.csv b/docs/templates/MRI_Assay_Template.csv
index c60e0933..e5f38f78 100644
--- a/docs/templates/MRI_Assay_Template.csv
+++ b/docs/templates/MRI_Assay_Template.csv
@@ -1,14 +1,35 @@
"Field","Description","Required","ControlledVocab","Note"
"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
-"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of """"genomicVariants"""" might have an assay value of """"whole genome sequencing"""". ","required","#Data",""
"assay","The technology used to generate the data in this file","required","#Assay",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
-"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
-"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
-"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
-"experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
+"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level",""
+"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
+"resourceType","The type of resource being stored and annotated","required","#Resource",""
"MRISequence","The scanning sequence/modality that is used for a conventional MRI scan.","optional","T1-weighted,T2-weighted,PD-weighted,Short Tau Inversion Recovery",""
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
+"cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
+"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
+"experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
+"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"isCellLine","Whether or not sample source is a cell line (Yes; No)","optional","Yes, No",""
+"isPrimaryCell","Whether or not cellType is primary (Yes; No)","optional","Yes, No",""
+"modelSystemName","A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","optional","#Model_System",""
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
+"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
+"timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
+"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
+"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","optional","#Tumor",""
+"entityId",NA,NA,NA,NA
diff --git a/docs/templates/PDX_Genomics_Assay_Template.csv b/docs/templates/PDX_Genomics_Assay_Template.csv
deleted file mode 100644
index 773ca237..00000000
--- a/docs/templates/PDX_Genomics_Assay_Template.csv
+++ /dev/null
@@ -1,17 +0,0 @@
-"Field","Description","Required","ControlledVocab","Note"
-"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
-"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
-"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of """"genomicVariants"""" might have an assay value of """"whole genome sequencing"""". ","required","#Data",""
-"assay","The technology used to generate the data in this file","required","#Assay",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
-"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
-"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
-"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
-"experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
-"transplantationType","Type of transplantation involved in the experiment, derived from MESH","optional","allograft, xenograft, autograft, isograft",""
-"genePerturbed","The HUGO gene symbol for the gene that is perturbed.","optional","",""
-"runType","Is the sequencing run single or paired end?","optional","#Run_Type",""
-"libraryPrep","The general strategy by which the library was prepared","optional","#Library_Prep",""
-"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
diff --git a/docs/templates/Patient_Timepoints_Template.csv b/docs/templates/Patient_Timepoints_Template.csv
index 58744d5b..336a6605 100644
--- a/docs/templates/Patient_Timepoints_Template.csv
+++ b/docs/templates/Patient_Timepoints_Template.csv
@@ -1,4 +1,12 @@
"Field","Description","Required","ControlledVocab","Note"
"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
-"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
"experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
+"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
diff --git a/docs/templates/Pharmacokinetics_Assay_Template.csv b/docs/templates/Pharmacokinetics_Assay_Template.csv
index 9946b1ce..6088e0a8 100644
--- a/docs/templates/Pharmacokinetics_Assay_Template.csv
+++ b/docs/templates/Pharmacokinetics_Assay_Template.csv
@@ -1,16 +1,38 @@
"Field","Description","Required","ControlledVocab","Note"
"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
-"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of """"genomicVariants"""" might have an assay value of """"whole genome sequencing"""". ","required","#Data",""
-"assay","The technology used to generate the data in this file","required","#Assay",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
"assay","The technology used to generate the data in this file","required","#Assay",""
-"platformTarget",NA,NA,NA,NA
-"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
-"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level",""
+"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
+"resourceType","The type of resource being stored and annotated","required","#Resource",""
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
+"cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
+"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
"experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
+"genePerturbationTechnology","Technology used to perform gene perturbation","optional","#Gene_Perturbation_Technology",""
+"genePerturbationType","Specific way in which a single gene was perturbed in a sample","optional","#Gene_Perturbation",""
"genePerturbed","The HUGO gene symbol for the gene that is perturbed.","optional","",""
-"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"isCellLine","Whether or not sample source is a cell line (Yes; No)","optional","Yes, No",""
+"isPrimaryCell","Whether or not cellType is primary (Yes; No)","optional","Yes, No",""
+"modelSystemName","A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","optional","#Model_System",""
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
+"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
+"timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
+"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
+"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","optional","#Tumor",""
+"entityId",NA,NA,NA,NA
+"platformTarget",NA,NA,NA,NA
diff --git a/docs/templates/Plate_Based_Reporter_Assay_Template.csv b/docs/templates/Plate_Based_Reporter_Assay_Template.csv
index ba435e78..89940165 100644
--- a/docs/templates/Plate_Based_Reporter_Assay_Template.csv
+++ b/docs/templates/Plate_Based_Reporter_Assay_Template.csv
@@ -1,17 +1,37 @@
"Field","Description","Required","ControlledVocab","Note"
"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
-"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of """"genomicVariants"""" might have an assay value of """"whole genome sequencing"""". ","required","#Data",""
-"assay","The technology used to generate the data in this file","required","#Assay",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
"assay","The technology used to generate the data in this file","required","#Assay",""
-"platformTarget",NA,NA,NA,NA
-"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
-"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level",""
+"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
+"resourceType","The type of resource being stored and annotated","required","#Resource",""
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
+"cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
+"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
"experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
+"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"isCellLine","Whether or not sample source is a cell line (Yes; No)","optional","Yes, No",""
+"isPrimaryCell","Whether or not cellType is primary (Yes; No)","optional","Yes, No",""
+"modelSystemName","A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","optional","#Model_System",""
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
+"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
"reporterGene","A biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.","optional","",""
"reporterSubstance","A gene which produces an easily assayed phenotype. Often used for expression studies of heterologous promoters.","optional","",""
-"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
+"timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
+"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
+"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","optional","#Tumor",""
+"entityId",NA,NA,NA,NA
+"platformTarget",NA,NA,NA,NA
diff --git a/docs/templates/Processed_Aligned_Reads_Template.csv b/docs/templates/Processed_Aligned_Reads_Template.csv
new file mode 100644
index 00000000..e7f38918
--- /dev/null
+++ b/docs/templates/Processed_Aligned_Reads_Template.csv
@@ -0,0 +1,45 @@
+"Field","Description","Required","ControlledVocab","Note"
+"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
+"Filename","The name of the file.","required","","Automatically filled when using the curator app."
+"assay","The technology used to generate the data in this file","required","#Assay",""
+"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level",""
+"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
+"resourceType","The type of resource being stored and annotated","required","#Resource",""
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
+"averageBaseQuality","Average base quality collected from samtools","optional","",""
+"averageInsertSize","Average insert size as reported by samtools","optional","",""
+"averageReadLength","Average read length collected from samtools","optional","",""
+"cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
+"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
+"genomicReference","Version of genome reference used for alignment in processing workflow","optional","",""
+"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"isCellLine","Whether or not sample source is a cell line (Yes; No)","optional","Yes, No",""
+"isPrimaryCell","Whether or not cellType is primary (Yes; No)","optional","Yes, No",""
+"meanCoverage","Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard Tools","optional","",""
+"modelSystemName","A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","optional","#Model_System",""
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
+"pairsOnDifferentChr","Pairs on different chromosomes collected from samtools","optional","",""
+"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
+"proportionCoverage10x","Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools","optional","",""
+"proportionCoverage30x","Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools","optional","",""
+"readDepth","If available, the coverage statistic as output from bedtools coverage or samtools stats.","optional","",""
+"readsDuplicatedPercent","Percent of duplicated reads collected from samtools","optional","",""
+"readsMappedPercent","Percent of mapped reads collected from samtools","optional","",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
+"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
+"totalReads","If available, the total number of reads collected from samtools.","optional","",""
+"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","optional","#Tumor",""
+"workflow","Name and version of the workflow used to generate/analyze the data","optional","",""
+"workflowLink","Workflow URL reference","optional","",""
+"entityId",NA,NA,NA,NA
diff --git a/docs/templates/Processed_Expression_Template.csv b/docs/templates/Processed_Expression_Template.csv
new file mode 100644
index 00000000..32d34d14
--- /dev/null
+++ b/docs/templates/Processed_Expression_Template.csv
@@ -0,0 +1,23 @@
+"Field","Description","Required","ControlledVocab","Note"
+"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
+"Filename","The name of the file.","required","","Automatically filled when using the curator app."
+"assay","The technology used to generate the data in this file","required","#Assay",""
+"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level",""
+"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
+"expressionUnit","Measure used for transcript expression quantification","required","TPM,RPKM,FPKM,Counts,Other",""
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
+"resourceType","The type of resource being stored and annotated","required","#Resource",""
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
+"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"workflow","Name and version of the workflow used to generate/analyze the data","optional","",""
+"workflowLink","Workflow URL reference","optional","",""
+"entityId",NA,NA,NA,NA
diff --git a/docs/templates/Processed_Variant_Calls_Template.csv b/docs/templates/Processed_Variant_Calls_Template.csv
new file mode 100644
index 00000000..12ed2260
--- /dev/null
+++ b/docs/templates/Processed_Variant_Calls_Template.csv
@@ -0,0 +1,22 @@
+"Field","Description","Required","ControlledVocab","Note"
+"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
+"Filename","The name of the file.","required","","Automatically filled when using the curator app."
+"assay","The technology used to generate the data in this file","required","#Assay",""
+"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level",""
+"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
+"resourceType","The type of resource being stored and annotated","required","#Resource",""
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
+"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"workflow","Name and version of the workflow used to generate/analyze the data","optional","",""
+"workflowLink","Workflow URL reference","optional","",""
+"entityId",NA,NA,NA,NA
diff --git a/docs/templates/Proteomics_Assay_Template.csv b/docs/templates/Proteomics_Assay_Template.csv
index ba2950c4..45e4c65d 100644
--- a/docs/templates/Proteomics_Assay_Template.csv
+++ b/docs/templates/Proteomics_Assay_Template.csv
@@ -1,14 +1,35 @@
"Field","Description","Required","ControlledVocab","Note"
"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
-"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of """"genomicVariants"""" might have an assay value of """"whole genome sequencing"""". ","required","#Data",""
"assay","The technology used to generate the data in this file","required","#Assay",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
-"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
-"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level",""
+"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
+"proteinExtractSource","Source of the extracted protein used in the experiment","required","cell lysate, nuclei, mitochondria, cytoplasm",""
+"resourceType","The type of resource being stored and annotated","required","#Resource",""
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
+"cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
+"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
"experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
-"proteinExtractSource","Source of the extracted protein used in the experiment","required","cell lysate, nuclei, mitochondria, cytoplasm",""
-"comments ",NA,NA,NA,NA
+"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"isCellLine","Whether or not sample source is a cell line (Yes; No)","optional","Yes, No",""
+"isPrimaryCell","Whether or not cellType is primary (Yes; No)","optional","Yes, No",""
+"modelSystemName","A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","optional","#Model_System",""
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
+"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
+"timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
+"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
+"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","optional","#Tumor",""
+"entityId",NA,NA,NA,NA
diff --git a/docs/templates/Protocol_Template.csv b/docs/templates/Protocol_Template.csv
deleted file mode 100644
index d0d8c33c..00000000
--- a/docs/templates/Protocol_Template.csv
+++ /dev/null
@@ -1,8 +0,0 @@
-"Field","Description","Required","ControlledVocab","Note"
-"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
-"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"author","The author of the resource; preferably use an ORCID ID, GitHub profile link, etc., if available and a text name if not.","optional","",""
-"citation",NA,NA,NA,NA
-"license","Link to a license or name of license applicable for the resource.",NA,"",""
-"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
diff --git a/docs/templates/RNASeq_Template.csv b/docs/templates/RNASeq_Template.csv
new file mode 100644
index 00000000..f1011f1d
--- /dev/null
+++ b/docs/templates/RNASeq_Template.csv
@@ -0,0 +1,43 @@
+"Field","Description","Required","ControlledVocab","Note"
+"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
+"Filename","The name of the file.","required","","Automatically filled when using the curator app."
+"assay","The technology used to generate the data in this file","required","#Assay",""
+"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level",""
+"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
+"readLength","Number of base pairs (bp) sequenced for a read","required","",""
+"resourceType","The type of resource being stored and annotated","required","#Resource",""
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
+"cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
+"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
+"dissociationMethod","Procedure by which a biological specimen is dissociated into individual cells or a cell suspension","optional","#Dissociation_Method",""
+"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"isCellLine","Whether or not sample source is a cell line (Yes; No)","optional","Yes, No",""
+"isPrimaryCell","Whether or not cellType is primary (Yes; No)","optional","Yes, No",""
+"isStranded","Whether or not the library is stranded (Yes; No)","optional","Yes, No",""
+"libraryPrep","The general strategy by which the library was prepared","optional","#Library_Prep",""
+"libraryPreparationMethod","Method by which library was prepared","optional","#Library_Preparation_Method",""
+"modelSystemName","A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","optional","#Model_System",""
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","optional","#Nucleic_Acid_Source",""
+"organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
+"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
+"readDepth","If available, the coverage statistic as output from bedtools coverage or samtools stats.","optional","",""
+"readPair","The read of origin","optional","#Read_Pair",""
+"readPairOrientation","The relative orientation of the reads in a paired-end protocol","optional","#Read_Pair_Orientation",""
+"readStrandOrigin","The strand from which the read originates in a strand-specific protocol","optional","#Read_Strand_Origin",""
+"runType","Is the sequencing run single or paired end?","optional","#Run_Type",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
+"targetDepth","The targeted read depth prior to sequencing.","optional","",""
+"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
+"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","optional","#Tumor",""
+"entityId",NA,NA,NA,NA
diff --git a/docs/templates/ScRNASeq_Template.csv b/docs/templates/ScRNASeq_Template.csv
new file mode 100644
index 00000000..bc0bb804
--- /dev/null
+++ b/docs/templates/ScRNASeq_Template.csv
@@ -0,0 +1,42 @@
+"Field","Description","Required","ControlledVocab","Note"
+"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
+"Filename","The name of the file.","required","","Automatically filled when using the curator app."
+"assay","The technology used to generate the data in this file","required","#Assay",""
+"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level",""
+"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
+"readLength","Number of base pairs (bp) sequenced for a read","required","",""
+"resourceType","The type of resource being stored and annotated","required","#Resource",""
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
+"cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
+"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
+"dissociationMethod","Procedure by which a biological specimen is dissociated into individual cells or a cell suspension","optional","#Dissociation_Method",""
+"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"isCellLine","Whether or not sample source is a cell line (Yes; No)","optional","Yes, No",""
+"isPrimaryCell","Whether or not cellType is primary (Yes; No)","optional","Yes, No",""
+"isStranded","Whether or not the library is stranded (Yes; No)","optional","Yes, No",""
+"libraryPrep","The general strategy by which the library was prepared","optional","#Library_Prep",""
+"libraryPreparationMethod","Method by which library was prepared","optional","#Library_Preparation_Method",""
+"modelSystemName","A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","optional","#Model_System",""
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","optional","#Nucleic_Acid_Source",""
+"organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
+"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
+"readDepth","If available, the coverage statistic as output from bedtools coverage or samtools stats.","optional","",""
+"readPair","The read of origin","optional","#Read_Pair",""
+"readPairOrientation","The relative orientation of the reads in a paired-end protocol","optional","#Read_Pair_Orientation",""
+"readStrandOrigin","The strand from which the read originates in a strand-specific protocol","optional","#Read_Strand_Origin",""
+"runType","Is the sequencing run single or paired end?","optional","#Run_Type",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
+"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
+"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","optional","#Tumor",""
+"entityId",NA,NA,NA,NA
diff --git a/docs/templates/Source_Code_Template.csv b/docs/templates/Source_Code_Template.csv
index d76b5da6..af1609ac 100644
--- a/docs/templates/Source_Code_Template.csv
+++ b/docs/templates/Source_Code_Template.csv
@@ -1,8 +1,10 @@
"Field","Description","Required","ControlledVocab","Note"
"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
"Filename","The name of the file.","required","","Automatically filled when using the curator app."
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"programmingLanguage","A computer programming language","optional","Python, R, MATLAB, Java, C, C++, C#, Javascript, bash",""
+"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
"documentation","URL to any documentation describing the resource and its use.","optional","",""
+"programmingLanguage","A computer programming language","optional","Python, R, MATLAB, Java, C, C++, C#, Javascript, bash",""
"runtimePlatform","Runtime platform or script interpreter dependencies (e.g. Java v1, Python 2.3).","optional","",""
-"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"entityId",NA,NA,NA,NA
diff --git a/docs/templates/Update_Milestone_Report.csv b/docs/templates/Update_Milestone_Report.csv
deleted file mode 100644
index ab02359f..00000000
--- a/docs/templates/Update_Milestone_Report.csv
+++ /dev/null
@@ -1,5 +0,0 @@
-"Field","Description","Required","ControlledVocab","Note"
-"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
-"Filename","The name of the file.","required","","Automatically filled when using the curator app."
-"resourceType","The type of resource being stored and annotated","required","#Resource",""
-"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
diff --git a/docs/templates/WES_Template.csv b/docs/templates/WES_Template.csv
new file mode 100644
index 00000000..e7ef0015
--- /dev/null
+++ b/docs/templates/WES_Template.csv
@@ -0,0 +1,43 @@
+"Field","Description","Required","ControlledVocab","Note"
+"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
+"Filename","The name of the file.","required","","Automatically filled when using the curator app."
+"assay","The technology used to generate the data in this file","required","#Assay",""
+"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level",""
+"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
+"readLength","Number of base pairs (bp) sequenced for a read","required","",""
+"resourceType","The type of resource being stored and annotated","required","#Resource",""
+"targetCaptureKitID","A unique identifier for the kit used to construct a genomic library using target capture-based techniques, which should be composed of the vendor name, kit name and kit version.","required","","For WES processing, the target BED used could be provided based on the target capture kit."
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
+"cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
+"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
+"dissociationMethod","Procedure by which a biological specimen is dissociated into individual cells or a cell suspension","optional","#Dissociation_Method",""
+"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"isCellLine","Whether or not sample source is a cell line (Yes; No)","optional","Yes, No",""
+"isPrimaryCell","Whether or not cellType is primary (Yes; No)","optional","Yes, No",""
+"isStranded","Whether or not the library is stranded (Yes; No)","optional","Yes, No",""
+"libraryPrep","The general strategy by which the library was prepared","optional","#Library_Prep",""
+"libraryPreparationMethod","Method by which library was prepared","optional","#Library_Preparation_Method",""
+"modelSystemName","A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","optional","#Model_System",""
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","optional","#Nucleic_Acid_Source",""
+"organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
+"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
+"readDepth","If available, the coverage statistic as output from bedtools coverage or samtools stats.","optional","",""
+"readPair","The read of origin","optional","#Read_Pair",""
+"readPairOrientation","The relative orientation of the reads in a paired-end protocol","optional","#Read_Pair_Orientation",""
+"readStrandOrigin","The strand from which the read originates in a strand-specific protocol","optional","#Read_Strand_Origin",""
+"runType","Is the sequencing run single or paired end?","optional","#Run_Type",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
+"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
+"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","optional","#Tumor",""
+"entityId",NA,NA,NA,NA
diff --git a/docs/templates/WGS_Template.csv b/docs/templates/WGS_Template.csv
new file mode 100644
index 00000000..bc0bb804
--- /dev/null
+++ b/docs/templates/WGS_Template.csv
@@ -0,0 +1,42 @@
+"Field","Description","Required","ControlledVocab","Note"
+"Component","Category of metadata manifest; provide the same one for all items/rows.","required","",""
+"Filename","The name of the file.","required","","Automatically filled when using the curator app."
+"assay","The technology used to generate the data in this file","required","#Assay",""
+"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level",""
+"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
+"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
+"readLength","Number of base pairs (bp) sequenced for a read","required","",""
+"resourceType","The type of resource being stored and annotated","required","#Resource",""
+"age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
+"ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
+"aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
+"cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
+"comments","Brief free-text comments that may also be important to understanding the resource.","optional","",""
+"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
+"dissociationMethod","Procedure by which a biological specimen is dissociated into individual cells or a cell suspension","optional","#Dissociation_Method",""
+"individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort."
+"isCellLine","Whether or not sample source is a cell line (Yes; No)","optional","Yes, No",""
+"isPrimaryCell","Whether or not cellType is primary (Yes; No)","optional","Yes, No",""
+"isStranded","Whether or not the library is stranded (Yes; No)","optional","Yes, No",""
+"libraryPrep","The general strategy by which the library was prepared","optional","#Library_Prep",""
+"libraryPreparationMethod","Method by which library was prepared","optional","#Library_Preparation_Method",""
+"modelSystemName","A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","optional","#Model_System",""
+"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
+"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","optional","#Nucleic_Acid_Source",""
+"organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
+"parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"progressReportNumber","Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
+"readDepth","If available, the coverage statistic as output from bedtools coverage or samtools stats.","optional","",""
+"readPair","The read of origin","optional","#Read_Pair",""
+"readPairOrientation","The relative orientation of the reads in a paired-end protocol","optional","#Read_Pair_Orientation",""
+"readStrandOrigin","The strand from which the read originates in a strand-specific protocol","optional","#Read_Strand_Origin",""
+"runType","Is the sequencing run single or paired end?","optional","#Run_Type",""
+"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
+"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
+"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","optional","#Tumor",""
+"entityId",NA,NA,NA,NA
diff --git a/modules/Assay/annotationProperty.csv b/modules/Assay/annotationProperty.csv
index 03278372..6c9fefc1 100644
--- a/modules/Assay/annotationProperty.csv
+++ b/modules/Assay/annotationProperty.csv
@@ -2,6 +2,7 @@ Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,D
drugScreenType,String describing general class of drug screen,"singleMolecule, smallMoleculeLibraryScreen, combinationLibraryScreen, combinationScreen",,FALSE,,compoundScreen,,,,drugScreenType,Property,Assay,annotationProperty,,,,
assay,The technology used to generate the data in this file,"elevated plus maze test, open field test, rotarod performance test, mRNAcounts, high content screen, Immunocytochemistry, immunofluorescence, autoradiography, electrochemiluminescence, Real Time PCR, in vivo tumor growth, scale, Blood Chemistry Measurement, in vivo bioluminescence, immunohistochemistry, NOMe-Seq, FIA-MSMS, UPLC-MSMS, HPLC-MSMS, liquid chromatography-electrochemical detection, rnaSeq, mirnaSeq, LC-MSMS, LC-MS, lncrnaSeq, Whole Exome Sequencing, Sanger sequencing, ChIPSeq, rnaArray, snpArray, methylationArray, mirnaArray, bisulfiteSeq, ATACSeq, HI-C, errBisulfiteSeq, ISOSeq, westernBlot, wholeGenomeSeq, polymeraseChainReaction, cellViabilityAssay, atomicForceMicroscopy, brightfieldMicroscopy, tractionForceMicroscopy, nextGenerationTargetedSequencing, jumpingLibrary, MIB/MS, scCGIseq, MudPIT, questionnaire, DNA optical mapping, oxBS-Seq, Ribo-Seq, Positron Emission Tomography, RPPA, ELISA, LTP, LFP, whole-cell patch clamp, sandwich ELISA, Laser Speckle Imaging, Genotyping, TMT quantitation, label free mass spectrometry, cell count, reporter gene assay, Single Cell RNA Sequencing, spatial transcriptomics, Conventional MRI, Functional MRI, Magnetic Resonance Spectroscopy, 2D Incucyte, 2D CellTiter-Glo, 3D microtissue viability, in vivo PDX viability, 2D AlamarBlue fluorescence, 2D AlamarBlue absorbance, rheometry, FTIR Spectroscopy, differential scanning calorimetry, Gel filtration chromatography, Massively Parallel Reporter Assay,Riccardi and Ablon scales,Spatial Frequency Domain Imaging,Optical Coherence Tomography",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one,
platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","HiSeq3000, HiSeq2500, HiSeq4000, NextSeq500, HiSeq2000, MiSeq, Zeiss LSM 980, Affy5.0, Affy6.0, PacBioRSII, GAIIx, Illumina_HumanOmni1-Quadv1.0, Illumina_1M, Illumina_h650, Illumina_Omni2pt5M, Illumina_Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen300Karray, Agilent44Karray, IlluminaWholeGenomeDASL, IlluminaHumanHap300, NanostringnCounter, LTQOrbitrapXL, IlluminaHumanMethylation450, Illumina Infinium MethylationEPIC BeadChip, AffymetrixU133AB, Affymetrix Human Gene 1.0 ST Array, AffymetrixU133Plus2, HiSeqX, Bionano Irys, Infinium HumanOmniExpressExome, NextSeq 550, NextSeq 1000, NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, NanostringGeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader,Vectra H1 3D Imaging System,Vevo 3100 Imaging System,10x Visium Spatial Gene Expression",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,,
+targetCaptureKitID,"A unique identifier for the kit used to construct a genomic library using target capture-based techniques, which should be composed of the vendor name, kit name and kit version.",,,TRUE,http://purl.obolibrary.org/obo/NCIT_C177583,experimentalData,,,,targetCaptureKitID,Property,Assay,annotationProperty,,,,"For WES processing, the target BED used could be provided based on the target capture kit."
libraryID,,,,TRUE,,experimentalData,,,,libraryID,Property,Assay,annotationProperty,,,,
assayTarget,The HUGO gene symbol that represents the target analyte assayed.,,,FALSE,Sage Bionetworks,experimentalData,,,,assayTarget,Property,Assay,annotationProperty,,,,
proteinExtractSource,Source of the extracted protein used in the experiment,"cell lysate, nuclei, mitochondria, cytoplasm",,TRUE,http://purl.obolibrary.org/obo/OBI_0000894,experimentalData,,,,proteinExtractSource,Property,Assay,annotationProperty,,,,
@@ -17,6 +18,8 @@ libraryPrep,The general strategy by which the library was prepared,"rRNAdepletio
libraryPreparationMethod,Method by which library was prepared,"10x, CEL-seq, Drop-Seq, Smart-seq2, TruSeq, Smart-seq4, Omni-ATAC, NEBNext mRNA Library Prep Reagent Set for Illumina, IDT xGen Exome Research Panel, TruSeq standard total RNA library kit, Illumina TruSeq DNA Nano, KAPA HyperPrep Kit PCR-free,KAPA RNA HyperPrep Kit with RiboErase (HMR),GTAC@WUSTL in-house prep",,FALSE,,ngs,,,,libraryPreparationMethod,Property,Assay,annotationProperty,ngsParameter,Library_Preparation_Method,,
nucleicAcidSource,Source of the extracted nucleic acid used in the experiment,"bulk cell, single cell, bulk nuclei, single nucleus, mitochondria",,FALSE,Sage Bionetworks,ngs,,,,nucleicAcidSource,Property,Assay,annotationProperty,ngsParameter,Nucleic_Acid_Source,,
dissociationMethod,Procedure by which a biological specimen is dissociated into individual cells or a cell suspension,"10x_v2, FACS, Fluidigm C1, drop-seq, inDrop, mouth pipette, bulk, enzymatic, mechanical, none",,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0009088,ngs,,,,dissociationMethod,Property,Assay,annotationProperty,ngsParameter,Dissociation_Method,,
-readLength,Number of base pairs (bp) sequenced for a read,,,FALSE,,ngs,,,,readLength,DataProperty,Assay,annotationProperty,ngsParameter,,,
-readDepth,"If available, coverage statistic as output from bedtools coverage or samtools stats.",,,FALSE,Sage Bionetworks,ngs,,,,readDepth,DataProperty,Assay,annotationProperty,ngsParameter,,,
-isPairedEnd,"(Legacy/deprecated annotation) Whether or not is paired-end sequencing (Yes; No). Note that this can be inferred as 'Yes' when runType=pairedEnd; current templates actually use runType to capture this info.","Yes, No",,FALSE,,ngs,,,,isPairedEnd,DataProperty,Assay,annotationProperty,ngsParameter,,,
+readLength,Number of base pairs (bp) sequenced for a read,,,TRUE,,ngs,,,,readLength,DataProperty,Assay,annotationProperty,ngsParameter,,,
+readDepth,"If available, the coverage statistic as output from bedtools coverage or samtools stats.",,,FALSE,Sage Bionetworks,ngs,,,,readDepth,DataProperty,Assay,annotationProperty,ngsParameter,,,
+isPairedEnd,(Legacy/deprecated annotation) Whether or not is paired-end sequencing (Yes; No). Note that this can be inferred as 'Yes' when runType=pairedEnd; current templates actually use runType to capture this info.,"Yes, No",,FALSE,,ngs,,,,isPairedEnd,DataProperty,Assay,annotationProperty,ngsParameter,,,
+totalReads,"If available, the total number of reads collected from samtools.",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=total_reads,ngs,,,,totalReads,DataProperty,Assay,annotationProperty,ngsParameter,,,
+targetDepth,"The targeted read depth prior to sequencing.",,,FALSE,https://data.humantumoratlas.org/standards/bulkrnaseq#TargetDepth,ngs,,,,targetDepth,DataProperty,Assay,annotationProperty,ngsParameter,,,
diff --git a/modules/Data/Data_Class.csv b/modules/Data/Data_Class.csv
index 8564538c..f962a126 100644
--- a/modules/Data/Data_Class.csv
+++ b/modules/Data/Data_Class.csv
@@ -3,8 +3,13 @@ raw counts,The number or amount of something.,"",assay,FALSE,http://purl.obolibr
Volume,The amount of three dimensional space occupied by an object or the capacity of a space or container.,"",assay,FALSE,http://purl.obolibrary.org/obo/NCIT_C25335,dataType,,"","",Volume,Class,Data,Data_Class,"","","",""
Weight,The vertical force exerted by a mass as a result of gravity.,"",assay,FALSE,http://purl.obolibrary.org/obo/NCIT_C25208,dataType,,"","",Weight,Class,Data,Data_Class,"","","",""
Pharmacokinetic Study,"A study of the process by which a drug is absorbed, distributed, metabolized, and eliminated by the body.","",assay,FALSE,http://purl.obolibrary.org/obo/NCIT_C49663,dataType,,"","",Pharmacokinetic_Study,Class,Data,Data_Class,"","","",""
-genomicVariants,"Genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence.","",assay,FALSE,https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Foperation_3227,dataType,,"","",Genomic_Variants,Class,Data,Data_Class,"","","",""
-behavior process,"The action, reaction, or performance of an organism in response to external or internal stimuli.","",assay,FALSE,http://purl.obolibrary.org/obo/NBO_0000313,dataType,,"","",Behavior_Process,Class,Data,Data_Class,"","","",""
+genomicVariants,"Genomic alterations, including single nucleotide polymorphisms, short indels and structural variants. Use more specific term if possible, esp. if data is only of one specific subset.","",assay,FALSE,https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Foperation_3227,dataType,,"","",Genomic_Variants,Class,Data,Data_Class,"","","",""
+AlignedReads,"Aligned reads output from alignment workflows","",assay,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads,dataType,,"","",Aligned_Reads,Class,Data,Data_Class,"","","",""
+SomaticVariants,"Specifically genomic variants data that includes somatic variants and excludes germline variants","",assay,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=simple_somatic_mutation,dataType,,"","",Somatic_Variants,Class,Data,Data_Class,"",,"",""
+AnnotatedSomaticVariants,"Specifically genomic variants data that includes somatic variants with annotations added from some annotation workflow","",assay,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=annotated_somatic_mutation,dataType,,"","",Annotated_Somatic_Variants,Class,Data,Data_Class,"","","",""
+GermlineVariants,"Specifically genomic variants data that includes called germline variants","",assay,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=simple_germline_variation,dataType,,"","",Germline_Variants,Class,Data,Data_Class,"","","",""
+StructuralVariants,"Specifically genomic variants data classified as structural variants, which may be derived from specialized variant calling workflows","",assay,FALSE,,dataType,,"","",Structural_Variants,Class,Data,Data_Class,"","","",""
+behavior process,"The action, reaction, or performance of an organism in response to external or internal stimuli.","",assay,FALSE,hhttps://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=structural_variation,dataType,,"","",Behavior_Process,Class,Data,Data_Class,"","","",""
metabolomics,"The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism.","",assay,FALSE,http://edamontology.org/topic_3172,dataType,,"","",Metabolomics,Class,Data,Data_Class,"","","",""
image,Biological or biomedical data that has been rendered into an image.,"",assay,FALSE,https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_2968,dataType,,"","",Image,Class,Data,Data_Class,"","","",""
geneExpression,The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data.,"",assay,FALSE,https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Ftopic_0203,dataType,,"","",Gene_Expression,Class,Data,Data_Class,"","","",""
diff --git a/modules/Data/annotationProperty.csv b/modules/Data/annotationProperty.csv
index e86cea5a..b1221613 100644
--- a/modules/Data/annotationProperty.csv
+++ b/modules/Data/annotationProperty.csv
@@ -2,9 +2,10 @@ Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,D
curatedDataType,The type of information being curated.,"reference sequence, gene symbol, clinical data, gene function, chemical descriptor",,TRUE,,curatedData,,,,curatedDataType,Property,Data,annotationProperty,,,,
referenceSet,"A set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data.","GRCh38, GRCh37, MMUL1.0, HRC",,TRUE,,curatedData,,,,referenceSet,Property,Data,annotationProperty,,,,
reference sequence,Syntactic sequences that has a role as reference of an annotation.,,,FALSE,http://rdf.biosemantics.org/ontologies/rsa#ReferenceSequence,curatedDataType,,,,referenceSequence,Property,Data,annotationProperty,,,,
-dataSubtype,"Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","normalized, dataMatrix, raw, processed, metadata, representative",,TRUE,,experimentalData,,,,dataSubtype,Property,Data,annotationProperty,,Data,one,
+dataSubtype,"Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","normalized, dataMatrix, raw, processed, metadata, representative",,TRUE,,experimentalData,,,,dataSubtype,Property,Data,annotationProperty,,Data_Level,one,
metadataType,"For files of dataSubtype: metadata, a description of the type of metadata in the file.","individual, biospecimen, assay, data dictionary, manifest, protocol",,FALSE,,experimentalData,,,,metadataType,Property,Data,annotationProperty,,,,
-dataType,"A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of """"genomicVariants"""" might have an assay value of """"whole genome sequencing"""". ","Volume, Weight, Pharmacokinetic Study, genomicVariants, behavior process, metabolomics, image, geneExpression, isoformExpression, proteomics, kinomics, drugScreen, drugCombinationScreen, cellularPhysiology, chromatinActivity, surveyData, network, clinical, immunoassay, electrophysiology, raw counts, mask image",dataSubtype,TRUE,,experimentalData,,,,dataType,Property,Data,annotationProperty,,Data,one,
+dataType,"A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","Volume, Weight, Pharmacokinetic Study, genomicVariants,behavior process, metabolomics, image, geneExpression, isoformExpression, proteomics, kinomics, drugScreen, drugCombinationScreen, cellularPhysiology, chromatinActivity, surveyData, network, clinical, immunoassay, electrophysiology, raw counts, mask image,AlignedReads,SomaticVariants,AnnotatedSomaticVariants,StructuralVariants,GermlineVariants",dataSubtype,TRUE,,experimentalData,,,,dataType,Property,Data,annotationProperty,,Data,one,
+expressionUnit,"Measure used for transcript expression quantification","TPM,RPKM,FPKM,Counts,Other",,TRUE,,experimentalData,,,,expressionUnit,DataProperty,Data,annotationProperty,,,,
failedQC,Whether the sample or data failed QC checks (Yes; No),"Yes, No",,TRUE,,experimentalData,,,,failedQC,DataProperty,Data,annotationProperty,,,,
Filename,The name of the file.,,"entityId,fileFormat",TRUE,Sage Bionetworks,NF,,,,fileName,Class,Data,annotationProperty,fileName,,one,Automatically filled when using the curator app.
programmingLanguage,A computer programming language,"Python, R, MATLAB, Java, C, C++, C#, Javascript, bash",,FALSE,Sage Bionetworks,,,,,programmingLanguage,Property,Data,annotationProperty,ngsParameter,,,
diff --git a/modules/Processing/annotationProperty.csv b/modules/Processing/annotationProperty.csv
new file mode 100644
index 00000000..99402226
--- /dev/null
+++ b/modules/Processing/annotationProperty.csv
@@ -0,0 +1,13 @@
+Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules,.ID,.Type,.Module,.Root,.SubOf,.Range,.Cardinality,.EditorNote
+workflow,"Name and version of the workflow used to generate/analyze the data",,workflowLink,FALSE,,,,,,workflow,Property,Processing,annotationProperty,,,,
+workflowLink,"Workflow URL reference",,,FALSE,,,,,,workflowLink,Property,Processing,annotationProperty,,,,
+genomicReference,"Version of genome reference used for alignment in processing workflow",,,FALSE,,,,,,genomicReference,Property,Processing,annotationProperty,,,,
+averageInsertSize,"Average insert size as reported by samtools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=average_insert_size,,,,,averageInsertSize,Property,Processing,annotationProperty,,,,
+averageReadLength,"Average read length collected from samtools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=average_read_length,,,,,averageReadLength,Property,Processing,annotationProperty,,,,
+averageBaseQuality,"Average base quality collected from samtools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=average_base_quality,,,,,averageBaseQuality,Property,Processing,annotationProperty,,,,
+pairsOnDifferentChr,"Pairs on different chromosomes collected from samtools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=pairs_on_diff_chr,,,,,pairsOnDifferentChr,Property,Processing,annotationProperty,,,,
+readsDuplicatedPercent,"Percent of duplicated reads collected from samtools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=proportion_reads_duplicated,,,,,readsDuplicatedPercent,Property,Processing,annotationProperty,,,,
+readsMappedPercent,"Percent of mapped reads collected from samtools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=proportion_reads_mapped,,,,,readsMappedPercent,Property,Processing,annotationProperty,,,,
+meanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard Tools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=mean_coverage,,,,,meanCoverage,Property,Processing,annotationProperty,,,,
+proportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=proportion_coverage_10x,,,,,proportionCoverage10x,Property,Processing,annotationProperty,,,,
+proportionCoverage30x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools",,,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads&anchor=proportion_coverage_30x,,,,,proportionCoverage30x,Property,Processing,annotationProperty,,,,
diff --git a/modules/Template/Template.csv b/modules/Template/Template.csv
index f46c2a2b..b93160f8 100644
--- a/modules/Template/Template.csv
+++ b/modules/Template/Template.csv
@@ -1,28 +1,35 @@
-Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules,.ID,.Type,.Module,.Root,.SubOf,.Range,.Cardinality,.EditorNote
-genomicsAssayTemplate_Normalized,"Generic template for describing data from a genomic type assay (RNA-seq, Exome-seq, etc) WITHOUT full individual and biospecimen data. To link individual and biospecimen metadata, an additional “biospecimenTemplate_Default” must be additionally completed with either specimenID or aliquotID available for joining. This is a two-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,specimenID,aliquotID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Normalized,Class,Template,Template,Assay_Template,,,
-genomicsAssayTemplate,"Generic denormalized template for describing data from a genomic type assay (RNA-seq, Exome-seq, etc) along with individual, biospecimen and experimental metadata. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template,Class,Template,Template,Assay_Template,,,
-genomicsAssayTemplate_Extended,"Template for describing data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,runType,libraryPrep,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Extended,Class,Template,Template,Assay_Template,,,
-imagingAssayTemplate,"Generic template for describing data from an imaging type assay (IHC, etc). This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,comments",TRUE,Sage Bionetworks,template,,,,Imaging_Assay_Template,Class,Template,Template,Assay_Template,,,
-imagingAssayTemplate_Extended,"Template for describing data from an imaging type assay (IHC, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points.. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Imaging_Assay_Template_Extended,Class,Template,Template,Assay_Template,,,
-MRIAssayTemplate,Generic template for describing data from an MRI assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,MRISequence,comments",TRUE,Sage Bionetworks,template,,,,MRI_Assay_Template,Class,Template,Template,Assay_Template,,,
-epigeneticsAssayTemplate,Generic template for describing data from an epigenetics assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Epigenetics_Assay_Template,Class,Template,Template,Assay_Template,,,
-pharmacokineticsAssayTemplate,Generic template for describing data from a pharmacokinetics assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Pharmacokinetics_Assay_Template,Class,Template,Template,Assay_Template,,,
-proteomicsAssayTemplate,Generic template for describing data from a proteomics assay. Note that specialized proteomics assays may have their own template to capture more detailed information. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,proteinExtractSource,comments ",TRUE,Sage Bionetworks,template,,,,Proteomics_Assay_Template,Class,Template,Template,Assay_Template,,,
-plateBasedReporterAssayTemplate,Generic template for describing data from a plate-based reporter assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,reporterGene,reporterSubstance,comments",TRUE,Sage Bionetworks,template,,,,Plate_Based_Reporter_Assay_Template,Class,Template,Template,Assay_Template,,,
-patientTimepointsTemplate,Template for capturing individual-level metadata with time points. Do not use for data file annotation.,,"Component,individualID,experimentalTimepoint",TRUE,Sage Bionetworks,template,,,,Patient_Timepoints_Template,Class,Template,Template,Non_Assay_Template,,,
-clinicalAssayTemplate,"Annotation template for simple endpoint data from clinical assays often used in diagnostic practice or clinical trials; may include repeated measures and a treatment/intervention context. Examples include bloodwork results (creatine assay, serum antibody assay), tumor size measurements, or medication adherence. Note that clinical data are from human individuals, therefore species should be “human”. ",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,comments",TRUE,Sage Bionetworks,template,,,,Clinical_Assay_Template,Class,Template,Template,Assay_Template,,,
-clinicalAssayTemplate_Extended,Annotation template for simple endpoint data from clinical assays often used in diagnostic practice or clinical trials; may include repeated measures and a treatment/intervention context. Extended to capture additional drug/treatment parameters.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,compoundName,compoundDose,comments",TRUE,Sage Bionetworks,template,,,,Clinical_Assay_Template_Extended,Class,Template,Template,Assay_Template,,,
-behavioralAssayTemplate,"Generic template for describing data from behavioral assays such as “adaptive n-back task” (for humans) or “shock-probe defensive burying test” (for mice). If another modality is used as part of the behavioral assay, e.g. fMRI, that data can be linked.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,experimentalCondition,experimentalTimepoint,comments",TRUE,Sage Bionetworks,template,,,,Behavioral_Assay_Template,Class,Template,Template,Assay_Template,,,
-sourceCodeTemplate,Template for describing scripts or source code files for a software application.,,"Component,Filename,resourceType,programmingLanguage,documentation,runtimePlatform,comments",TRUE,Sage Bionetworks,template,,,,Source_Code_Template,Class,Template,Template,Non_Assay_Template,,,
-protocolTemplate,Template for describing a protocol document. (BETA) Adapted from https://bioschema.org/profiles/LabProtocol/0.6-DRAFT-2020_12_08,,"Component,Filename,resourceType,author,citation,license,comments",TRUE,Sage Bionetworks,template,,,,Protocol_Template,Class,Template,Template,Non_Assay_Template,,,
-pdxGenomicsAssay,Template for describing PDX assay data that extends genomicsAssay.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,transplantationType,genePerturbed,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,PDX_Genomics_Assay_Template,Class,Template,Template,Assay_Template,,,
-updateMilestoneReport,Defines a metadata template for updating milestone report values in NF studies -- currently a supported feature for NTAP and GFF.,,"Component,Filename,resourceType,progressReportNumber",FALSE,Sage Bionetworks,template,,,,Update_Milestone_Report,Class,Template,Template,Non_Assay_Template,,,
-template,Parent attribute for the manifest template attributes.,,,FALSE,Sage Bionetworks,template,,,,Template,Class,Template,Template,,,,
-individualTemplate,Base template for minimal information describing individual-level data within the NF scope. Not called “patientTemplate_Default” because individuals can be a non-human organism.,"individualID,sex,age,ageUnit,species,diagnosis,nf1Genotype,nf2Genotype","Component,individualID,sex,age,ageUnit,species,diagnosis,nf1Genotype,nf2Genotype",FALSE,Sage Bionetworks,template,,,,Individual_Template,Class,Template,Template,Non_Assay_Template,,,
-biospecimenTemplate_Normalized,Base template for describing biospecimen-level data.,"parentSpecimenID,specimenID,aliquotID,organ,tissue,isCellLine,isPrimaryCell,cellType,tumorType,specimenPreparationMethod,modelSystemName","Component,parentSpecimenID,specimenID,aliquotID,organ,tissue,isCellLine,isPrimaryCell,cellType,tumorType,specimenPreparationMethod,modelSystemName",FALSE,Sage Bionetworks,template,,,,Biospecimen_Template_Normalized,Class,Template,Template,Non_Assay_Template,,,
-biospecimenTemplate,Denormalized template for describing biospecimen data that includes all individual-level data as well.,,"Component,individualID,parentSpecimenID",FALSE,Sage Bionetworks,template,,,,Biospecimen_Template,Class,Template,Template,Non_Assay_Template,,,
-dataFileComponent,Template component for describing a data file resource that extends fileTemplate_Default with required properties dataType and dataSubtype.,"Filename,entityId,fileFormat,resourceType,dataType,dataSubtype","Filename,entityId,fileFormat,resourceType,dataType,dataSubtype",FALSE,Sage Bionetworks,template,,,,Data_File_Component,Class,Template,TemplateComponent,,,,
-experimentComponent,Template component for describing core experimental parameters.,"experimentalCondition,experimentalTimepoint","experimentalCondition,experimentalTimepoint",FALSE,Sage Bionetworks,template,,,,Experiment_Component,Class,Template,TemplateComponent,,,,
-genePerturbComponent,Template component for adding genetic perturbation metadata. This applies only to some assays and does not make sense with e.g. behavioral assays.,"genePerturbed,genePerturbationType,genePerturbationTechnology","genePerturbed,genePerturbationType,genePerturbationTechnology",FALSE,Sage Bionetworks,template,,,,Gene_Perturb_Component,Class,Template,TemplateComponent,,,,
-fileComponent,Template component for describing some file on the NF-OSI Synapse platform.,"Filename,entityId,fileFormat,resourceType","Filename,entityId,fileFormat,resourceType",FALSE,Sage Bionetworks,template,,,,File_Component,Class,Template,TemplateComponent,,,,
+Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules,.ID,.Type,.Module,.Root,.SubOf,.Range,.Cardinality,.EditorNote
+genomicsAssayTemplate_Normalized,"Generic template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) WITHOUT full individual and biospecimen data. To link individual and biospecimen metadata, an additional “biospecimenTemplate_Default” must be additionally completed with either specimenID or aliquotID available for joining. This is a two-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,specimenID,aliquotID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Normalized,Class,Template,Template,Assay_Template,,,
+genomicsAssayTemplate,"Generic denormalized template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) along with individual, biospecimen and experimental metadata. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template,Class,Template,Template,Assay_Template,,,
+genomicsAssayTemplate_Extended,"Template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,runType,libraryPrep,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Extended,Class,Template,Template,Assay_Template,,,
+WGSTemplate,"Template for describing raw data from Whole Genome Sequencing (WGS)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,WGS_Template,Class,Template,Template,Assay_Template,,,
+WESTemplate,"Template for describing raw data from Whole Exome Sequencing (WES)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,targetCaptureKitID,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,WES_Template,Class,Template,Template,Assay_Template,,,
+RNASeqTemplate,"Template for describing raw data from (bulk) RNA-sequencing",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,targetDepth,comments",TRUE,Sage Bionetworks,template,,,,RNA_Seq_Template,Class,Template,Template,Assay_Template,,,
+ScRNASeqTemplate,"Template for describing raw data from single-cell RNA-sequencing (scRNA-seq)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,ScRNA_Seq_Template,Class,Template,Template,Assay_Template,,,
+ProcessedAlignedReadsTemplate,"Template for describing aligned reads output data (i.e. BAM)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,averageInsertSize,averageReadLength,averageBaseQuality,pairsOnDifferentChr,readsDuplicatedPercent,readsMappedPercent,meanCoverage,proportionCoverage10x,proportionCoverage30x,readDepth,totalReads,workflow,genomicReference,comments",TRUE,Sage Bionetworks,template,,,,Processed_Aligned_Reads_Template,Class,Template,Template,Assay_Template,,,
+ProcessedVariantCallsTemplate,"Template for describing either germline or variant calls output data (i.e. VCF/MAF)",,"Component,Filename,resourceType,progressReportNumber,specimenID,dataType,assay,individualID,workflow,comments",TRUE,Sage Bionetworks,template,,,,Processed_Variant_Calls_Template,Class,Template,Template,Assay_Template,,,
+ProcessedExpressionTemplate,"Template for describing expression output data",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,individualID,specimenID,workflow,expressionUnit,comments",TRUE,Sage Bionetworks,template,,,,Processed_Expression_Template,Class,Template,Template,Assay_Template,,,
+imagingAssayTemplate,"Generic template for describing data from an imaging type assay (IHC, etc). This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,comments",TRUE,Sage Bionetworks,template,,,,Imaging_Assay_Template,Class,Template,Template,Assay_Template,,,
+imagingAssayTemplate_Extended,"Template for describing data from an imaging type assay (IHC, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Imaging_Assay_Template_Extended,Class,Template,Template,Assay_Template,,,
+MRIAssayTemplate,Generic template for describing data from an MRI assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,MRISequence,comments",TRUE,Sage Bionetworks,template,,,,MRI_Assay_Template,Class,Template,Template,Assay_Template,,,
+epigeneticsAssayTemplate,Generic template for describing data from an epigenetics assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Epigenetics_Assay_Template,Class,Template,Template,Assay_Template,,,
+pharmacokineticsAssayTemplate,Generic template for describing data from a pharmacokinetics assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Pharmacokinetics_Assay_Template,Class,Template,Template,Assay_Template,,,
+proteomicsAssayTemplate,Generic template for describing data from a proteomics assay. Note that specialized proteomics assays may have their own template to capture more detailed information. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,proteinExtractSource,comments ",TRUE,Sage Bionetworks,template,,,,Proteomics_Assay_Template,Class,Template,Template,Assay_Template,,,
+plateBasedReporterAssayTemplate,Generic template for describing data from a plate-based reporter assay. This is a one-step template.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,assay,platformTarget,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,reporterGene,reporterSubstance,comments",TRUE,Sage Bionetworks,template,,,,Plate_Based_Reporter_Assay_Template,Class,Template,Template,Assay_Template,,,
+patientTimepointsTemplate,Template for capturing individual-level metadata with time points. Do not use for data file annotation.,,"Component,individualID,experimentalTimepoint",TRUE,Sage Bionetworks,template,,,,Patient_Timepoints_Template,Class,Template,Template,Non_Assay_Template,,,
+clinicalAssayTemplate,"Annotation template for simple endpoint data from clinical assays often used in diagnostic practice or clinical trials; may include repeated measures and a treatment/intervention context. Examples include bloodwork results (creatine assay, serum antibody assay), tumor size measurements, or medication adherence. Note that clinical data are from human individuals, therefore species should be “human”. ",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,comments",TRUE,Sage Bionetworks,template,,,,Clinical_Assay_Template,Class,Template,Template,Assay_Template,,,
+clinicalAssayTemplate_Extended,Annotation template for simple endpoint data from clinical assays often used in diagnostic practice or clinical trials; may include repeated measures and a treatment/intervention context. Extended to capture additional drug/treatment parameters.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,compoundName,compoundDose,comments",TRUE,Sage Bionetworks,template,,,,Clinical_Assay_Template_Extended,Class,Template,Template,Assay_Template,,,
+behavioralAssayTemplate,"Generic template for describing data from behavioral assays such as “adaptive n-back task” (for humans) or “shock-probe defensive burying test” (for mice). If another modality is used as part of the behavioral assay, e.g. fMRI, that data can be linked.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,experimentalCondition,experimentalTimepoint,comments",TRUE,Sage Bionetworks,template,,,,Behavioral_Assay_Template,Class,Template,Template,Assay_Template,,,
+sourceCodeTemplate,Template for describing scripts or source code files for a software application.,,"Component,Filename,resourceType,programmingLanguage,documentation,runtimePlatform,comments",TRUE,Sage Bionetworks,template,,,,Source_Code_Template,Class,Template,Template,Non_Assay_Template,,,
+protocolTemplate,Template for describing a protocol document. (BETA) Adapted from https://bioschema.org/profiles/LabProtocol/0.6-DRAFT-2020_12_08,,"Component,Filename,resourceType,author,citation,license,comments",TRUE,Sage Bionetworks,template,,,,Protocol_Template,Class,Template,Template,Non_Assay_Template,,,
+pdxGenomicsAssay,Template for describing PDX assay data that extends genomicsAssay.,,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,experimentalCondition,experimentalTimepoint,transplantationType,genePerturbed,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,PDX_Genomics_Assay_Template,Class,Template,Template,Assay_Template,,,
+updateMilestoneReport,Defines a metadata template for updating milestone report values in NF studies -- currently a supported feature for NTAP and GFF.,,"Component,Filename,resourceType,progressReportNumber",FALSE,Sage Bionetworks,template,,,,Update_Milestone_Report,Class,Template,Template,Non_Assay_Template,,,
+template,Parent attribute for the manifest template attributes.,,,FALSE,Sage Bionetworks,template,,,,Template,Class,Template,Template,,,,
+individualTemplate,Base template for minimal information describing individual-level data within the NF scope. Not called “patientTemplate_Default” because individuals can be a non-human organism.,"individualID,sex,age,ageUnit,species,diagnosis,nf1Genotype,nf2Genotype","Component,individualID,sex,age,ageUnit,species,diagnosis,nf1Genotype,nf2Genotype",FALSE,Sage Bionetworks,template,,,,Individual_Template,Class,Template,Template,Non_Assay_Template,,,
+biospecimenTemplate_Normalized,Base template for describing biospecimen-level data.,"parentSpecimenID,specimenID,aliquotID,organ,tissue,isCellLine,isPrimaryCell,cellType,tumorType,specimenPreparationMethod,modelSystemName","Component,parentSpecimenID,specimenID,aliquotID,organ,tissue,isCellLine,isPrimaryCell,cellType,tumorType,specimenPreparationMethod,modelSystemName",FALSE,Sage Bionetworks,template,,,,Biospecimen_Template_Normalized,Class,Template,Template,Non_Assay_Template,,,
+biospecimenTemplate,Denormalized template for describing biospecimen data that includes all individual-level data as well.,,"Component,individualID,parentSpecimenID",FALSE,Sage Bionetworks,template,,,,Biospecimen_Template,Class,Template,Template,Non_Assay_Template,,,
+dataFileComponent,Template component for describing a data file resource that extends fileTemplate_Default with required properties dataType and dataSubtype.,"Filename,entityId,fileFormat,resourceType,dataType,dataSubtype","Filename,entityId,fileFormat,resourceType,dataType,dataSubtype",FALSE,Sage Bionetworks,template,,,,Data_File_Component,Class,Template,TemplateComponent,,,,
+experimentComponent,Template component for describing core experimental parameters.,"experimentalCondition,experimentalTimepoint","experimentalCondition,experimentalTimepoint",FALSE,Sage Bionetworks,template,,,,Experiment_Component,Class,Template,TemplateComponent,,,,
+genePerturbComponent,Template component for adding genetic perturbation metadata. This applies only to some assays and does not make sense with e.g. behavioral assays.,"genePerturbed,genePerturbationType,genePerturbationTechnology","genePerturbed,genePerturbationType,genePerturbationTechnology",FALSE,Sage Bionetworks,template,,,,Gene_Perturb_Component,Class,Template,TemplateComponent,,,,
+fileComponent,Template component for describing some file on the NF-OSI Synapse platform.,"Filename,entityId,fileFormat,resourceType","Filename,entityId,fileFormat,resourceType",FALSE,Sage Bionetworks,template,,,,File_Component,Class,Template,TemplateComponent,,,,
ngsComponent,Template component capturing Next Gen Sequencing/genomics attributes.,"runType,readPair,isStranded,readPairOrientation,readStrandOrigin,libraryPrep,libraryPreparationMethod,dissociationMethod,readLength,nucleicAcidSource","runType,readPair,isStranded,readPairOrientation,readStrandOrigin,libraryPrep,libraryPreparationMethod,dissociationMethod,readLength,nucleicAcidSource",FALSE,Sage Bionetworks,template,,,,NGS_Component,Class,Template,TemplateComponent,,,,
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