+
Miscellaneous
-
System
+
System Properties
System 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.
-
@@ -459,7 +603,7 @@
Terms
// establish options
var options = {
- selectors: "h1,h2,h3,h4,h5",
+ selectors: "h1,h2,h3,h4",
theme: "bootstrap3",
context: '.toc-content',
hashGenerator: function (text) {
diff --git a/docs/templates/Epigenetics_Assay_Template.csv b/docs/templates/Epigenetics_Assay_Template.csv
new file mode 100644
index 00000000..6313004e
--- /dev/null
+++ b/docs/templates/Epigenetics_Assay_Template.csv
@@ -0,0 +1,33 @@
+"Field","Description","Required","ControlledVocab","Note"
+"Filename","The name of the file. ","required","","Automatically filled when using the curator app."
+"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",""
+"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",""
+"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",""
+"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",""
+"assay","The technology used to generate the data in this file","required","#Assay",""
+"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",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"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",""
+"genePerturbationType","Specific way in which a single gene was perturbed in a sample","optional","#Gene_Perturbation",""
+"genePerturbationTechnology","Technology used to perform gene perturbation","optional","#Gene_Perturbation_Technology",""
+"genePerturbed","The HUGO gene symbol for the gene that is perturbed. ","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."
+"specimenID","A unique identifier (non-PII) that represents the specimen (sample) from which the data came. e.g. an ID that indicates a specific tumor specimen.","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"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",""
+"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",""
+"isCellLine","Boolean flag indicating whether or not sample source is a cell line. (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE",""
+"isPrimaryCell","Boolean flag indicating whether or not cellType is primary (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE",""
+"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",""
+"assayTarget","The HUGO gene symbol that represents the target analyte assayed.","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","",""
+"timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"readDepth","Average number of reads obtained","optional","",""
+"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","optional","#Nucleic_Acid_Source",""
+"comments","Brief free-text comments that may also be important to understanding the data. ","optional","",""
diff --git a/docs/templates/Genomics_Assay_Template.csv b/docs/templates/Genomics_Assay_Template.csv
new file mode 100644
index 00000000..c683221a
--- /dev/null
+++ b/docs/templates/Genomics_Assay_Template.csv
@@ -0,0 +1,42 @@
+"Field","Description","Required","ControlledVocab","Note"
+"Filename","The name of the file. ","required","","Automatically filled when using the curator app."
+"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",""
+"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",""
+"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",""
+"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",""
+"assay","The technology used to generate the data in this file","required","#Assay",""
+"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",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"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",""
+"genePerturbationType","Specific way in which a single gene was perturbed in a sample","optional","#Gene_Perturbation",""
+"genePerturbationTechnology","Technology used to perform gene perturbation","optional","#Gene_Perturbation_Technology",""
+"genePerturbed","The HUGO gene symbol for the gene that is perturbed. ","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."
+"specimenID","A unique identifier (non-PII) that represents the specimen (sample) from which the data came. e.g. an ID that indicates a specific tumor specimen.","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"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",""
+"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",""
+"isCellLine","Boolean flag indicating whether or not sample source is a cell line. (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE",""
+"isPrimaryCell","Boolean flag indicating whether or not cellType is primary (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE",""
+"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",""
+"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","",""
+"timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"runType","Is the sequencing run single or paired end?","optional","#Run_Type",""
+"readPair","The read of origin","optional","#Read_Pair",""
+"isStranded","Whether or not the library is stranded. (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE",""
+"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",""
+"libraryPrep","The general strategy by which the library was prepared","optional","#Library_Prep",""
+"libraryPreparationMethod","Method by which library was prepared","optional","#Library_Preparation_Method",""
+"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","optional","#Nucleic_Acid_Source",""
+"dissociationMethod","Procedure by which a biological specimen is dissociated into individual cells or a cell suspension","optional","#Dissociation_Method",""
+"readLength","Number of base pairs (bp) sequenced for a read","optional","",""
+"readDepth","Average number of reads obtained","optional","",""
+"comments","Brief free-text comments that may also be important to understanding the data. ","optional","",""
diff --git a/docs/templates/Imaging_Assay_Template.csv b/docs/templates/Imaging_Assay_Template.csv
new file mode 100644
index 00000000..6051a72d
--- /dev/null
+++ b/docs/templates/Imaging_Assay_Template.csv
@@ -0,0 +1,31 @@
+"Field","Description","Required","ControlledVocab","Note"
+"Filename","The name of the file. ","required","","Automatically filled when using the curator app."
+"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",""
+"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",""
+"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",""
+"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",""
+"assay","The technology used to generate the data in this file","required","#Assay",""
+"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",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"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",""
+"genePerturbationType","Specific way in which a single gene was perturbed in a sample","optional","#Gene_Perturbation",""
+"genePerturbationTechnology","Technology used to perform gene perturbation","optional","#Gene_Perturbation_Technology",""
+"genePerturbed","The HUGO gene symbol for the gene that is perturbed. ","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."
+"specimenID","A unique identifier (non-PII) that represents the specimen (sample) from which the data came. e.g. an ID that indicates a specific tumor specimen.","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"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",""
+"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",""
+"isCellLine","Boolean flag indicating whether or not sample source is a cell line. (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE",""
+"isPrimaryCell","Boolean flag indicating whether or not cellType is primary (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE",""
+"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",""
+"assayTarget","The HUGO gene symbol that represents the target analyte assayed.","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","",""
+"timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"comments","Brief free-text comments that may also be important to understanding the data. ","optional","",""
diff --git a/docs/templates/MRI_Assay_Template.csv b/docs/templates/MRI_Assay_Template.csv
new file mode 100644
index 00000000..f4a91466
--- /dev/null
+++ b/docs/templates/MRI_Assay_Template.csv
@@ -0,0 +1,24 @@
+"Field","Description","Required","ControlledVocab","Note"
+"Filename","The name of the file. ","required","","Automatically filled when using the curator app."
+"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",""
+"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",""
+"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",""
+"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",""
+"assay","The technology used to generate the data in this file","required","#Assay",""
+"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",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"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",""
+"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."
+"specimenID","A unique identifier (non-PII) that represents the specimen (sample) from which the data came. e.g. an ID that indicates a specific tumor specimen.","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"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",""
+"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",""
+"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","",""
+"timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"MRISequence","The scanning sequence/modality that is used for a conventional MRI scan. ","optional","T1-weighted,T2-weighted,PD-weighted,Short Tau Inversion Recovery",""
+"comments","Brief free-text comments that may also be important to understanding the data. ","optional","",""
diff --git a/docs/templates/Patient_Timepoints_Template.csv b/docs/templates/Patient_Timepoints_Template.csv
new file mode 100644
index 00000000..d58abff6
--- /dev/null
+++ b/docs/templates/Patient_Timepoints_Template.csv
@@ -0,0 +1,11 @@
+"Field","Description","Required","ControlledVocab","Note"
+"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",""
+"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",""
+"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","",""
+"timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
+"comments","Brief free-text comments that may also be important to understanding the data. ","optional","",""
diff --git a/docs/templates/Pharmacokinetics_Assay_Template.csv b/docs/templates/Pharmacokinetics_Assay_Template.csv
new file mode 100644
index 00000000..f543fa01
--- /dev/null
+++ b/docs/templates/Pharmacokinetics_Assay_Template.csv
@@ -0,0 +1,31 @@
+"Field","Description","Required","ControlledVocab","Note"
+"Filename","The name of the file. ","required","","Automatically filled when using the curator app."
+"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",""
+"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",""
+"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",""
+"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",""
+"assay","The technology used to generate the data in this file","required","#Assay",""
+"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",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"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",""
+"genePerturbationType","Specific way in which a single gene was perturbed in a sample","optional","#Gene_Perturbation",""
+"genePerturbationTechnology","Technology used to perform gene perturbation","optional","#Gene_Perturbation_Technology",""
+"genePerturbed","The HUGO gene symbol for the gene that is perturbed. ","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."
+"specimenID","A unique identifier (non-PII) that represents the specimen (sample) from which the data came. e.g. an ID that indicates a specific tumor specimen.","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"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",""
+"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",""
+"isCellLine","Boolean flag indicating whether or not sample source is a cell line. (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE",""
+"isPrimaryCell","Boolean flag indicating whether or not cellType is primary (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE",""
+"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",""
+"assayTarget","The HUGO gene symbol that represents the target analyte assayed.","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","",""
+"timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
+"experimentId","When applicable, an optional identifier that can be used to distinguish or group the experiments that generated the data; also can be used to denote internal batch reference if needed.","optional","",""
+"comments","Brief free-text comments that may also be important to understanding the data. ","optional","",""
diff --git a/docs/templates/Plate_Based_Reporter_Assay_Template.csv b/docs/templates/Plate_Based_Reporter_Assay_Template.csv
new file mode 100644
index 00000000..a469da89
--- /dev/null
+++ b/docs/templates/Plate_Based_Reporter_Assay_Template.csv
@@ -0,0 +1,32 @@
+"Field","Description","Required","ControlledVocab","Note"
+"Filename","The name of the file. ","required","","Automatically filled when using the curator app."
+"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",""
+"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",""
+"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",""
+"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",""
+"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."
+"specimenID","A unique identifier (non-PII) that represents the specimen (sample) from which the data came. e.g. an ID that indicates a specific tumor specimen.","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"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",""
+"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",""
+"genePerturbationType","Specific way in which a single gene was perturbed in a sample","optional","#Gene_Perturbation",""
+"genePerturbationTechnology","Technology used to perform gene perturbation","optional","#Gene_Perturbation_Technology",""
+"genePerturbed","The HUGO gene symbol for the gene that is perturbed. ","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."
+"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",""
+"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",""
+"isCellLine","Boolean flag indicating whether or not sample source is a cell line. (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE",""
+"isPrimaryCell","Boolean flag indicating whether or not cellType is primary (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE",""
+"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",""
+"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",""
+"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","",""
+"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","",""
+"timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
+"comments","Brief free-text comments that may also be important to understanding the data. ","optional","",""
diff --git a/docs/templates/Proteomics_Assay_Template.csv b/docs/templates/Proteomics_Assay_Template.csv
new file mode 100644
index 00000000..b5d2ef6c
--- /dev/null
+++ b/docs/templates/Proteomics_Assay_Template.csv
@@ -0,0 +1,31 @@
+"Field","Description","Required","ControlledVocab","Note"
+"Filename","The name of the file. ","required","","Automatically filled when using the curator app."
+"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",""
+"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",""
+"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",""
+"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",""
+"assay","The technology used to generate the data in this file","required","#Assay",""
+"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",""
+"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
+"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",""
+"genePerturbationType","Specific way in which a single gene was perturbed in a sample","optional","#Gene_Perturbation",""
+"genePerturbationTechnology","Technology used to perform gene perturbation","optional","#Gene_Perturbation_Technology",""
+"genePerturbed","The HUGO gene symbol for the gene that is perturbed. ","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."
+"specimenID","A unique identifier (non-PII) that represents the specimen (sample) from which the data came. e.g. an ID that indicates a specific tumor specimen.","optional","","Typically annotated with a single ID, but many allowed for summary data."
+"proteinExtractSource","Source of the extracted protein used in the experiment","required","cell lysate, nuclei, mitochondria, cytoplasm",""
+"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",""
+"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",""
+"isCellLine","Boolean flag indicating whether or not sample source is a cell line. (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE",""
+"isPrimaryCell","Boolean flag indicating whether or not cellType is primary (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE",""
+"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",""
+"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","",""
+"timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"comments","Brief free-text comments that may also be important to understanding the data. ","optional","",""
diff --git a/ext_classes.csv b/ext_classes.csv
index 6abbbba7..edf69cdc 100644
--- a/ext_classes.csv
+++ b/ext_classes.csv
@@ -17,3 +17,15 @@ Assay_Template,Assay_Template,Class,Template,Manifest_Template
Non_Assay_Template,Non_Assay_Template,Class,Template,Template
Manifest_Template,Manifest_Template,Class,Template,Template
Update_Milestone_Report_Template,Update_Milestone_Report_Template,Class,Template,Non_Assay_Template
+Resource,Resource,Class,Resource,
+Species,Species,Class,Species,
+Model_System,Model_System,Class,Model_System,
+Model_Organism,Model_Organism,Class,Model_System,Model_System
+Cell_Line_Model,Cell_Line_Model,Class,Model_System,Model_System
+Genotype,Genotype,Class,Class,
+Methods,Methods,Class,Class,
+NGS_Parameter,NGS_Parameter,Class,Class,Methods
+Unit,Unit,Class,Class,
+Time_Unit ,Time_Unit ,Class,Class,Unit
+Tissue,Tissue,Class,Class,
+Data,Data,Class,Class,