diff --git a/docs/index.Rmd b/docs/index.Rmd index dc02a361..aa32f308 100644 --- a/docs/index.Rmd +++ b/docs/index.Rmd @@ -160,7 +160,7 @@ if(!params$use_cache) { PlateBasedReporterAssayTemplate = "Plate_Based_Reporter_Assay_Template", ClinicalAssayTemplate = "Clinical_Assay_Template", # PatientTimepointsTemplate = "Patient_Timepoints_Template", - ProtocolTemplate = "Protocol_Template", + Protocol = "Protocol", SourceCodeTemplate = "Source_Code_Template", LightScatteringAssayTemplate = "Light_Scattering_Assay_Template") diff --git a/docs/index.html b/docs/index.html index 3f037602..53b25245 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1629,553 +1629,28 @@ function(a,b,c){if(!Vd(b))throw Error(n(200));return Wd(null,a,b,!1,c)};Q.unmountComponentAtNode=function(a){if(!Vd(a))throw Error(n(40));return a._reactRootContainer?(zb(function(){Wd(null,null,a,!1,function(){a._reactRootContainer=null;a[Ja]=null})}),!0):!1};Q.unstable_batchedUpdates=Tf;Q.unstable_renderSubtreeIntoContainer=function(a,b,c,d){if(!Vd(c))throw Error(n(200));if(null==a||void 0===a._reactInternals)throw Error(n(38));return Wd(a,b,c,!1,d)};Q.version="18.2.0-next-9e3b772b8-20220608"}); })(); - + +
+
Epigenetics Assay
-
- +
+
WES Assay
-
- +
+
WGS Assay
-
- +
+
Bulk RNA-Seq Assay
-
- +
+
Single-cell RNA-Seq Assay
-
- +
+
Processed Aligned Reads
-
- +
+
Processed Variant Calls
-
- +
+
Processed Expression
-
- +
+
@@ -3449,34 +2924,34 @@

Proteomics Assay Templates

Proteomics Assay (Generic)
-
- +
+

Imaging Assay Templates

Imaging Assay (Generic)
-
- +
+
MRI Assay
-
- +
+

Other Assay Templates

Pharmacokinetics Assay
-
- +
+
Plate Based Reporter Assay
-
- +
+
@@ -3484,29 +2959,29 @@

Clinical Assay Templates

Clinical Assay (Generic)
-
- +
+

Other Assays

Light Scattering
-
- +
+

Non-Assay Templates

Protocol
-
- +
+
Source Code
-
- +
+
@@ -3523,18 +2998,18 @@

Annotation Vocabulary

Assay

AssayEnum

-
+
- +


PlatformEnum

-
+
- +


Relations Graph
@@ -3553,34 +3028,34 @@
Relations Graph

Information Entity

Resource

-
+
- +


Data

-
+
- +


DataSubtypeEnum

-
+
- +


FileFormatEnum

-
+
- +


@@ -3598,82 +3073,82 @@

Sample

Tissue

-
+
- +


OrganismSubstance

-
+
- +


Tumor

-
+
- +


SexEnum

-
+
- +


DiagnosisEnum

-
+
- +


Genotype

-
+
- +


SpeciesEnum

-
+
- +


Cell

-
+
- +


CellLineModel

-
+
- +


MouseModel

-
+
- +


@@ -3684,10 +3159,10 @@

Experiment

TimeUnit

-
+
- +


diff --git a/docs/templates/Clinical_Assay_Template.csv b/docs/templates/Clinical_Assay_Template.csv index 3735df55..2ae2fe3f 100644 --- a/docs/templates/Clinical_Assay_Template.csv +++ b/docs/templates/Clinical_Assay_Template.csv @@ -1,27 +1,27 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" -"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.","true","#DataSubtypeEnum" +"assay","The technology used to generate the data in this file.","true","#" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"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","true","#FileFormatEnum" +","true","#" +"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","true","#" +"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","true","#" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#" -"resourceType","The type of resource being stored and annotated","true","#Resource" -"species","The name of a species (typically a taxonomic group) of organism.","true","#SpeciesEnum" -"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#Tumor" +"resourceType","The type of resource being stored and annotated","true","#" +"species","The name of a species (typically a taxonomic group) of organism.","true","#" +"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#" "Filename","The name of the file.","false","#" "age","A numeric value representing age of the individual. Use with `ageUnit`.","false","#" -"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit" +"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#" "comments","Brief free-text comments that may also be important to understanding the resource.","false","#" "compoundDose","A dose quantity for the treatment compound. To be used with compoundDoseUnit.","false","#" "compoundDoseUnit","A unit associated with the value(s) in compoundDose.","false","#" -"compoundName","Common name for a compound, e.g. “Selumetinib” (https://pubchem.ncbi.nlm.nih.gov/compound/10127622)","false","#" -"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","false","#DiagnosisEnum" +"compoundName","//pubchem.ncbi.nlm.nih.gov/compound/10127622)","false","#" "experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","false","#" -"experimentalFactor","An ontology concept for experimental factor measured with this data.","false","#Measurement" -"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): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#CellLineModel|#MouseModel" -"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#Genotype|#UnknownEnum" -"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#Genotype|#UnknownEnum" -"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.","false","#OrganEnum" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#SexEnum|#UnknownEnum|#NotApplicableEnum" -"timepointUnit","For timed experiments this represents the unit of time measured","false","#TimeUnit" +"experimentalFactor","An ontology concept for experimental factor measured with this data.","false","#" +"modelSystemName"," HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#" +"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#" +"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#" +"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.","false","#" +"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" +"timepointUnit","For timed experiments this represents the unit of time measured","false","#" diff --git a/docs/templates/Epigenetics_Assay_Template.csv b/docs/templates/Epigenetics_Assay_Template.csv index 13dfd598..0e607265 100644 --- a/docs/templates/Epigenetics_Assay_Template.csv +++ b/docs/templates/Epigenetics_Assay_Template.csv @@ -1,41 +1,41 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" -"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.","true","#DataSubtypeEnum" +"assay","The technology used to generate the data in this file.","true","#" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"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","true","#FileFormatEnum" +","true","#" +"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","true","#" +"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","true","#" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#" -"libraryPreparationMethod","Method by which library was prepared","true","#LibraryPreparationMethodEnum" -"libraryStrand","Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.","true","#StrandednessEnum|#NotApplicableEnum" -"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#PlatformEnum" -"resourceType","The type of resource being stored and annotated","true","#Resource" -"species","The name of a species (typically a taxonomic group) of organism.","true","#SpeciesEnum" +"libraryPreparationMethod","Method by which library was prepared","true","#" +"libraryStrand","Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.","true","#" +"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#" +"resourceType","The type of resource being stored and annotated","true","#" +"species","The name of a species (typically a taxonomic group) of organism.","true","#" "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. ","true","#" -"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","true","#SpecimenPreparationMethodEnum" -"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#Tumor" +"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","true","#" +"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#" "Filename","The name of the file.","false","#" "age","A numeric value representing age of the individual. Use with `ageUnit`.","false","#" -"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit" +"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#" "aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID.","false","#" "batchID","Batch identifier, can be used in any context where added batch information is helpful, such as different sequencing runs or collection times.","false","#" "bisulfiteConversionKitID","Name of kit used in bisulfite conversion.","false","#" "comments","Brief free-text comments that may also be important to understanding the resource.","false","#" -"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","false","#DiagnosisEnum" -"libraryPrep","The general strategy by which the library was prepared","false","#LibraryPrepEnum" -"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): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#CellLineModel|#MouseModel" -"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#Genotype|#UnknownEnum" -"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#Genotype|#UnknownEnum" -"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","false","#NucleicAcidSourceEnum" -"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.","false","#OrganEnum" +"libraryPrep","The general strategy by which the library was prepared","false","#" +"modelSystemName"," HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#" +"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#" +"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#" +"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","false","#" +"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.","false","#" "parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor that was subsectioned into several samples. The parentSpecimenID can be the same as specimenID when there is no subsectioning. ","false","#" "readDepth","If available, the coverage statistic as output from bedtools coverage or samtools stats.","false","#" "readLength","Number of base pairs (bp) sequenced for a read","false","#" "readPair","The read of origin, Read 1 or Read 2","false","#" -"runType","Sequencing run type.","false","#RunTypeEnum" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#SexEnum|#UnknownEnum|#NotApplicableEnum" +"runType","Sequencing run type.","false","#" +"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" "specimenType","The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances. -","false","#Tissue|#OrganismSubstance" +","false","#" "targetDepth","The targeted read depth prior to sequencing.","false","#" diff --git a/docs/templates/Genomics_Assay_Template.csv b/docs/templates/Genomics_Assay_Template.csv index ba985fbb..a48f93ea 100644 --- a/docs/templates/Genomics_Assay_Template.csv +++ b/docs/templates/Genomics_Assay_Template.csv @@ -1,40 +1,40 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" -"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.","true","#DataSubtypeEnum" +"assay","The technology used to generate the data in this file.","true","#" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"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","true","#FileFormatEnum" +","true","#" +"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","true","#" +"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","true","#" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#" -"libraryPreparationMethod","Method by which library was prepared","true","#LibraryPreparationMethodEnum" -"libraryStrand","Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.","true","#StrandednessEnum|#NotApplicableEnum" -"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#PlatformEnum" -"resourceType","The type of resource being stored and annotated","true","#Resource" -"species","The name of a species (typically a taxonomic group) of organism.","true","#SpeciesEnum" +"libraryPreparationMethod","Method by which library was prepared","true","#" +"libraryStrand","Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.","true","#" +"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#" +"resourceType","The type of resource being stored and annotated","true","#" +"species","The name of a species (typically a taxonomic group) of organism.","true","#" "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. ","true","#" -"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","true","#SpecimenPreparationMethodEnum" -"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#Tumor" +"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","true","#" +"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#" "Filename","The name of the file.","false","#" "age","A numeric value representing age of the individual. Use with `ageUnit`.","false","#" -"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit" +"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#" "aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID.","false","#" "batchID","Batch identifier, can be used in any context where added batch information is helpful, such as different sequencing runs or collection times.","false","#" "comments","Brief free-text comments that may also be important to understanding the resource.","false","#" -"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","false","#DiagnosisEnum" -"libraryPrep","The general strategy by which the library was prepared","false","#LibraryPrepEnum" -"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): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#CellLineModel|#MouseModel" -"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#Genotype|#UnknownEnum" -"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#Genotype|#UnknownEnum" -"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","false","#NucleicAcidSourceEnum" -"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.","false","#OrganEnum" +"libraryPrep","The general strategy by which the library was prepared","false","#" +"modelSystemName"," HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#" +"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#" +"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#" +"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","false","#" +"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.","false","#" "parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor that was subsectioned into several samples. The parentSpecimenID can be the same as specimenID when there is no subsectioning. ","false","#" "readDepth","If available, the coverage statistic as output from bedtools coverage or samtools stats.","false","#" "readLength","Number of base pairs (bp) sequenced for a read","false","#" "readPair","The read of origin, Read 1 or Read 2","false","#" -"runType","Sequencing run type.","false","#RunTypeEnum" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#SexEnum|#UnknownEnum|#NotApplicableEnum" +"runType","Sequencing run type.","false","#" +"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" "specimenType","The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances. -","false","#Tissue|#OrganismSubstance" +","false","#" "targetDepth","The targeted read depth prior to sequencing.","false","#" diff --git a/docs/templates/Imaging_Assay_Template.csv b/docs/templates/Imaging_Assay_Template.csv index f4c206b4..66a5fbc9 100644 --- a/docs/templates/Imaging_Assay_Template.csv +++ b/docs/templates/Imaging_Assay_Template.csv @@ -1,25 +1,25 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" -"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.","true","#DataSubtypeEnum" +"assay","The technology used to generate the data in this file.","true","#" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"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","true","#FileFormatEnum" +","true","#" +"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","true","#" +"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","true","#" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#" -"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#PlatformEnum" -"resourceType","The type of resource being stored and annotated","true","#Resource" -"species","The name of a species (typically a taxonomic group) of organism.","true","#SpeciesEnum" -"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#Tumor" +"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#" +"resourceType","The type of resource being stored and annotated","true","#" +"species","The name of a species (typically a taxonomic group) of organism.","true","#" +"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#" "Filename","The name of the file.","false","#" "age","A numeric value representing age of the individual. Use with `ageUnit`.","false","#" -"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit" +"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#" "assayTarget","Target of the assay such as a HUGO gene symbol, cell type, or tissue region depending on the capabilities of the assay.","false","#" "auxiliaryAsset","URI to supplemental asset(s), e.g. QC reports or other auxiliary files to support the processing, analysis, or interpretation of the current entity. ","false","#" "comments","Brief free-text comments that may also be important to understanding the resource.","false","#" -"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","false","#DiagnosisEnum" -"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): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#CellLineModel|#MouseModel" -"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#Genotype|#UnknownEnum" -"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#Genotype|#UnknownEnum" -"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.","false","#OrganEnum" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#SexEnum|#UnknownEnum|#NotApplicableEnum" +"modelSystemName"," HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#" +"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#" +"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#" +"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.","false","#" +"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" diff --git a/docs/templates/Light_Scattering_Assay_Template.csv b/docs/templates/Light_Scattering_Assay_Template.csv index 825636f9..54d9bb73 100644 --- a/docs/templates/Light_Scattering_Assay_Template.csv +++ b/docs/templates/Light_Scattering_Assay_Template.csv @@ -1,16 +1,18 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" -"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.","true","#DataSubtypeEnum" +"assay","The technology used to generate the data in this file.","true","#" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#PlatformEnum" -"resourceType","The type of resource being stored and annotated","true","#Resource" +","true","#" +"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","true","#" +"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#" +"resourceType","The type of resource being stored and annotated","true","#" "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. ","true","#" +"Filename","The name of the file.","false","#" "concentrationMaterial","Numeric value for concentration of the material","false","#" -"concentrationMaterialUnit","Unit used for the material concentration, e.g. mg/mL","false","#ConcentrationUnit" +"concentrationMaterialUnit","Unit used for the material concentration, e.g. mg/mL","false","#" "concentrationNaCl","Numeric value for NaCl concentration","false","#" -"concentrationNaClUnit","Unit used for the NaCl concentration, e.g. mM","false","#ConcentrationUnit" +"concentrationNaClUnit","Unit used for the NaCl concentration, e.g. mM","false","#" "materialType","Type of material in the characterization","false","#" "pH","Numeric value for pH (range 0-14)","false","#" diff --git a/docs/templates/MRI_Assay_Template.csv b/docs/templates/MRI_Assay_Template.csv index c325e870..2e503cff 100644 --- a/docs/templates/MRI_Assay_Template.csv +++ b/docs/templates/MRI_Assay_Template.csv @@ -1,30 +1,30 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" -"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.","true","#DataSubtypeEnum" +"assay","The technology used to generate the data in this file.","true","#" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"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","true","#FileFormatEnum" +","true","#" +"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","true","#" +"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","true","#" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#" -"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#PlatformEnum" -"resourceType","The type of resource being stored and annotated","true","#Resource" -"species","The name of a species (typically a taxonomic group) of organism.","true","#SpeciesEnum" -"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#Tumor" +"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#" +"resourceType","The type of resource being stored and annotated","true","#" +"species","The name of a species (typically a taxonomic group) of organism.","true","#" +"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#" "Filename","The name of the file.","false","#" "MRISequence","A mode used in MRI imaging","false","#MRISequenceEnum" "age","A numeric value representing age of the individual. Use with `ageUnit`.","false","#" -"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit" +"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#" "assayTarget","Target of the assay such as a HUGO gene symbol, cell type, or tissue region depending on the capabilities of the assay.","false","#" "auxiliaryAsset","URI to supplemental asset(s), e.g. QC reports or other auxiliary files to support the processing, analysis, or interpretation of the current entity. ","false","#" -"bodySite","Sample location referring to a named area of the body, inclusive of gross anatomical structures and organ parts.","false","#BodyPartEnum" +"bodySite","Sample location referring to a named area of the body, inclusive of gross anatomical structures and organ parts.","false","#" "comments","Brief free-text comments that may also be important to understanding the resource.","false","#" -"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","false","#DiagnosisEnum" "experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","false","#" "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","false","#" -"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): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#CellLineModel|#MouseModel" -"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#Genotype|#UnknownEnum" -"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#Genotype|#UnknownEnum" -"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.","false","#OrganEnum" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#SexEnum|#UnknownEnum|#NotApplicableEnum" -"timepointUnit","For timed experiments this represents the unit of time measured","false","#TimeUnit" +"modelSystemName"," HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#" +"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#" +"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#" +"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.","false","#" +"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" +"timepointUnit","For timed experiments this represents the unit of time measured","false","#" diff --git a/docs/templates/Pharmacokinetics_Assay_Template.csv b/docs/templates/Pharmacokinetics_Assay_Template.csv index 6381dfef..aff7aaab 100644 --- a/docs/templates/Pharmacokinetics_Assay_Template.csv +++ b/docs/templates/Pharmacokinetics_Assay_Template.csv @@ -1,33 +1,33 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" -"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.","true","#DataSubtypeEnum" +"assay","The technology used to generate the data in this file.","true","#" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"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","true","#FileFormatEnum" +","true","#" +"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","true","#" +"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","true","#" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#" -"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#PlatformEnum" -"resourceType","The type of resource being stored and annotated","true","#Resource" -"species","The name of a species (typically a taxonomic group) of organism.","true","#SpeciesEnum" +"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#" +"resourceType","The type of resource being stored and annotated","true","#" +"species","The name of a species (typically a taxonomic group) of organism.","true","#" "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. ","true","#" -"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#Tumor" +"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#" "Filename","The name of the file.","false","#" "age","A numeric value representing age of the individual. Use with `ageUnit`.","false","#" -"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit" +"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#" "aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID.","false","#" "comments","Brief free-text comments that may also be important to understanding the resource.","false","#" "compoundDose","A dose quantity for the treatment compound. To be used with compoundDoseUnit.","false","#" "compoundDoseUnit","A unit associated with the value(s) in compoundDose.","false","#" -"compoundName","Common name for a compound, e.g. “Selumetinib” (https://pubchem.ncbi.nlm.nih.gov/compound/10127622)","false","#" -"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","false","#DiagnosisEnum" +"compoundName","//pubchem.ncbi.nlm.nih.gov/compound/10127622)","false","#" "experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","false","#" "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","false","#" -"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): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#CellLineModel|#MouseModel" -"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#Genotype|#UnknownEnum" -"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#Genotype|#UnknownEnum" -"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.","false","#OrganEnum" +"modelSystemName"," HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#" +"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#" +"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#" +"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.","false","#" "parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor that was subsectioned into several samples. The parentSpecimenID can be the same as specimenID when there is no subsectioning. ","false","#" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#SexEnum|#UnknownEnum|#NotApplicableEnum" -"timepointUnit","For timed experiments this represents the unit of time measured","false","#TimeUnit" +"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" +"timepointUnit","For timed experiments this represents the unit of time measured","false","#" diff --git a/docs/templates/Plate_Based_Reporter_Assay_Template.csv b/docs/templates/Plate_Based_Reporter_Assay_Template.csv index c566b2b7..22772c35 100644 --- a/docs/templates/Plate_Based_Reporter_Assay_Template.csv +++ b/docs/templates/Plate_Based_Reporter_Assay_Template.csv @@ -1,36 +1,36 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" -"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.","true","#DataSubtypeEnum" +"assay","The technology used to generate the data in this file.","true","#" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"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","true","#FileFormatEnum" +","true","#" +"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","true","#" +"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","true","#" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#" -"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#PlatformEnum" -"resourceType","The type of resource being stored and annotated","true","#Resource" -"species","The name of a species (typically a taxonomic group) of organism.","true","#SpeciesEnum" +"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#" +"resourceType","The type of resource being stored and annotated","true","#" +"species","The name of a species (typically a taxonomic group) of organism.","true","#" "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. ","true","#" -"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#Tumor" +"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#" "Filename","The name of the file.","false","#" "age","A numeric value representing age of the individual. Use with `ageUnit`.","false","#" -"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit" +"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#" "aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID.","false","#" "assayTarget","Target of the assay such as a HUGO gene symbol, cell type, or tissue region depending on the capabilities of the assay.","false","#" "comments","Brief free-text comments that may also be important to understanding the resource.","false","#" "compoundDose","A dose quantity for the treatment compound. To be used with compoundDoseUnit.","false","#" "compoundDoseUnit","A unit associated with the value(s) in compoundDose.","false","#" -"compoundName","Common name for a compound, e.g. “Selumetinib” (https://pubchem.ncbi.nlm.nih.gov/compound/10127622)","false","#" -"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","false","#DiagnosisEnum" +"compoundName","//pubchem.ncbi.nlm.nih.gov/compound/10127622)","false","#" "experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","false","#" "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","false","#" -"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): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#CellLineModel|#MouseModel" -"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#Genotype|#UnknownEnum" -"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#Genotype|#UnknownEnum" -"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.","false","#OrganEnum" +"modelSystemName"," HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#" +"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#" +"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#" +"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.","false","#" "parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor that was subsectioned into several samples. The parentSpecimenID can be the same as specimenID when there is no subsectioning. ","false","#" "reporterGene","A gene which produces an easily assayed phenotype. Often used for expression studies of heterologous promoters.","false","#" "reporterSubstance","A biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.","false","#" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#SexEnum|#UnknownEnum|#NotApplicableEnum" -"timepointUnit","For timed experiments this represents the unit of time measured","false","#TimeUnit" +"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" +"timepointUnit","For timed experiments this represents the unit of time measured","false","#" diff --git a/docs/templates/Processed_Aligned_Reads_Template.csv b/docs/templates/Processed_Aligned_Reads_Template.csv index 396898d6..0c1700ac 100644 --- a/docs/templates/Processed_Aligned_Reads_Template.csv +++ b/docs/templates/Processed_Aligned_Reads_Template.csv @@ -1,38 +1,40 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" -"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.","true","#DataSubtypeEnum" +"assay","The technology used to generate the data in this file.","true","#" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"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","true","#FileFormatEnum" +","true","#" +"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","true","#" +"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","true","#" "genomicReference","Version of genome reference used for alignment in processing workflow","true","#" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#" -"resourceType","The type of resource being stored and annotated","true","#Resource" -"species","The name of a species (typically a taxonomic group) of organism.","true","#SpeciesEnum" -"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#Tumor" +"resourceType","The type of resource being stored and annotated","true","#" +"species","The name of a species (typically a taxonomic group) of organism.","true","#" +"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. +","true","#" +"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#" "Filename","The name of the file.","false","#" "age","A numeric value representing age of the individual. Use with `ageUnit`.","false","#" -"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit" +"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#" "auxiliaryAsset","URI to supplemental asset(s), e.g. QC reports or other auxiliary files to support the processing, analysis, or interpretation of the current entity. ","false","#" "averageBaseQuality","Average base quality collected from samtools","false","#" "averageInsertSize","Average insert size as reported by samtools","false","#" "averageReadLength","Average read length collected from samtools","false","#" "comments","Brief free-text comments that may also be important to understanding the resource.","false","#" -"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","false","#DiagnosisEnum" "genomicReferenceLink","Link to genome reference data file used for alignment in processing workflow","false","#" "meanCoverage","Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard Tools","false","#" -"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): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#CellLineModel|#MouseModel" -"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#Genotype|#UnknownEnum" -"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#Genotype|#UnknownEnum" -"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.","false","#OrganEnum" +"modelSystemName"," HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#" +"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#" +"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#" +"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.","false","#" "pairsOnDifferentChr","Pairs on different chromosomes collected from samtools","false","#" "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","#" "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","#" "readDepth","If available, the coverage statistic as output from bedtools coverage or samtools stats.","false","#" "readsDuplicatedPercent","Percent of duplicated reads collected from samtools","false","#" "readsMappedPercent","Percent of mapped reads collected from samtools","false","#" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#SexEnum|#UnknownEnum|#NotApplicableEnum" +"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" "totalReads","If available, the total number of reads collected from samtools.","false","#" -"workflow","Name and version of the workflow used to generate/analyze the data","false","#WorkflowEnum" +"workflow","Name and version of the workflow used to generate/analyze the data","false","#" "workflowLink","Workflow URL reference","false","#" diff --git a/docs/templates/Processed_Expression_Template.csv b/docs/templates/Processed_Expression_Template.csv index 80aec501..b992b3e0 100644 --- a/docs/templates/Processed_Expression_Template.csv +++ b/docs/templates/Processed_Expression_Template.csv @@ -1,26 +1,28 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" -"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.","true","#DataSubtypeEnum" +"assay","The technology used to generate the data in this file.","true","#" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"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","true","#FileFormatEnum" +","true","#" +"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","true","#" +"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","true","#" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#" -"resourceType","The type of resource being stored and annotated","true","#Resource" -"species","The name of a species (typically a taxonomic group) of organism.","true","#SpeciesEnum" -"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#Tumor" +"resourceType","The type of resource being stored and annotated","true","#" +"species","The name of a species (typically a taxonomic group) of organism.","true","#" +"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. +","true","#" +"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#" "Filename","The name of the file.","false","#" "age","A numeric value representing age of the individual. Use with `ageUnit`.","false","#" -"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit" +"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#" "auxiliaryAsset","URI to supplemental asset(s), e.g. QC reports or other auxiliary files to support the processing, analysis, or interpretation of the current entity. ","false","#" "comments","Brief free-text comments that may also be important to understanding the resource.","false","#" -"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","false","#DiagnosisEnum" -"expressionUnit","Measure used for transcript expression quantification","false","#ExpressionUnitEnum" -"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): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#CellLineModel|#MouseModel" -"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#Genotype|#UnknownEnum" -"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#Genotype|#UnknownEnum" -"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.","false","#OrganEnum" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#SexEnum|#UnknownEnum|#NotApplicableEnum" -"workflow","Name and version of the workflow used to generate/analyze the data","false","#WorkflowEnum" +"expressionUnit","Measure used for transcript expression quantification","false","#" +"modelSystemName"," HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#" +"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#" +"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#" +"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.","false","#" +"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" +"workflow","Name and version of the workflow used to generate/analyze the data","false","#" "workflowLink","Workflow URL reference","false","#" diff --git a/docs/templates/Processed_Variant_Calls_Template.csv b/docs/templates/Processed_Variant_Calls_Template.csv index f6c011b5..3092fb6f 100644 --- a/docs/templates/Processed_Variant_Calls_Template.csv +++ b/docs/templates/Processed_Variant_Calls_Template.csv @@ -1,26 +1,28 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" -"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.","true","#DataSubtypeEnum" +"assay","The technology used to generate the data in this file.","true","#" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"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","true","#FileFormatEnum" +","true","#" +"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","true","#" +"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","true","#" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#" -"resourceType","The type of resource being stored and annotated","true","#Resource" -"species","The name of a species (typically a taxonomic group) of organism.","true","#SpeciesEnum" -"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#Tumor" +"resourceType","The type of resource being stored and annotated","true","#" +"species","The name of a species (typically a taxonomic group) of organism.","true","#" +"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. +","true","#" +"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#" "Filename","The name of the file.","false","#" "age","A numeric value representing age of the individual. Use with `ageUnit`.","false","#" -"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit" +"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#" "auxiliaryAsset","URI to supplemental asset(s), e.g. QC reports or other auxiliary files to support the processing, analysis, or interpretation of the current entity. ","false","#" "comments","Brief free-text comments that may also be important to understanding the resource.","false","#" -"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","false","#DiagnosisEnum" "isFilteredReads","Whether the reads in the processed result has been filtered by adding a 'PASS' filter or other filters as determined by the data generator","false","#" -"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): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#CellLineModel|#MouseModel" -"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#Genotype|#UnknownEnum" -"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#Genotype|#UnknownEnum" -"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.","false","#OrganEnum" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#SexEnum|#UnknownEnum|#NotApplicableEnum" -"workflow","Name and version of the workflow used to generate/analyze the data","false","#WorkflowEnum" +"modelSystemName"," HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#" +"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#" +"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#" +"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.","false","#" +"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" +"workflow","Name and version of the workflow used to generate/analyze the data","false","#" "workflowLink","Workflow URL reference","false","#" diff --git a/docs/templates/Proteomics_Assay_Template.csv b/docs/templates/Proteomics_Assay_Template.csv index 04b33622..8a2a7ed5 100644 --- a/docs/templates/Proteomics_Assay_Template.csv +++ b/docs/templates/Proteomics_Assay_Template.csv @@ -1,29 +1,29 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" +"assay","The technology used to generate the data in this file.","true","#" "dataCollectionMode","Mode of data collection in tandem MS assays. Either DDA (data-dependent acquisition) or DIA (data-independent) acquisition.","true","#" -"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.","true","#DataSubtypeEnum" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"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","true","#FileFormatEnum" +","true","#" +"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","true","#" +"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","true","#" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#" -"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#PlatformEnum" -"resourceType","The type of resource being stored and annotated","true","#Resource" -"species","The name of a species (typically a taxonomic group) of organism.","true","#SpeciesEnum" +"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#" +"resourceType","The type of resource being stored and annotated","true","#" +"species","The name of a species (typically a taxonomic group) of organism.","true","#" "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. ","true","#" -"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#Tumor" +"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#" "Filename","The name of the file.","false","#" "age","A numeric value representing age of the individual. Use with `ageUnit`.","false","#" -"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit" +"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#" "aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID.","false","#" "comments","Brief free-text comments that may also be important to understanding the resource.","false","#" -"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","false","#DiagnosisEnum" -"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): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#CellLineModel|#MouseModel" -"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#Genotype|#UnknownEnum" -"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#Genotype|#UnknownEnum" -"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.","false","#OrganEnum" +"modelSystemName"," HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#" +"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#" +"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#" +"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.","false","#" "parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor that was subsectioned into several samples. The parentSpecimenID can be the same as specimenID when there is no subsectioning. ","false","#" -"proteinExtractSource","Source of the extracted protein used in the experiment","false","#ProteinExtractSourceEnum" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#SexEnum|#UnknownEnum|#NotApplicableEnum" +"proteinExtractSource","Source of the extracted protein used in the experiment","false","#" +"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" diff --git a/docs/templates/Protocol.csv b/docs/templates/Protocol.csv new file mode 100644 index 00000000..3c3dddff --- /dev/null +++ b/docs/templates/Protocol.csv @@ -0,0 +1,10 @@ +"Field","Description","Required","ValidRange" +"title","Title of a resource.","true","#" +"author","The author of the resource; preferably use an ORCID ID, GitHub profile link, etc., if available and a text name if not.","false","#" +"citation","Citation (e.g. doi) that usage of data or resource should be cited with.","false","#" +"comments","Brief free-text comments that may also be important to understanding the resource.","false","#" +"license","Link to a license or name of license applicable for the resource.","false","#" +"protocolAssay","Main assay type that this protocol is related to, e.g. this is a prep protocol for single-cell RNA-seq assay. This is especially helpful for newly-developed or in-house assays. +","false","#" +"protocolPurpose","Brief description of the protocol purpose.","false","#" +"sampleType","Type of sample used","false","#" diff --git a/docs/templates/RNASeq_Template.csv b/docs/templates/RNASeq_Template.csv index ba985fbb..1e8f26e4 100644 --- a/docs/templates/RNASeq_Template.csv +++ b/docs/templates/RNASeq_Template.csv @@ -1,40 +1,44 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" -"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.","true","#DataSubtypeEnum" +"assay","The technology used to generate the data in this file.","true","#" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"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","true","#FileFormatEnum" +","true","#" +"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","true","#" +"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","true","#" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#" -"libraryPreparationMethod","Method by which library was prepared","true","#LibraryPreparationMethodEnum" -"libraryStrand","Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.","true","#StrandednessEnum|#NotApplicableEnum" -"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#PlatformEnum" -"resourceType","The type of resource being stored and annotated","true","#Resource" -"species","The name of a species (typically a taxonomic group) of organism.","true","#SpeciesEnum" +"libraryPreparationMethod","Method by which library was prepared","true","#" +"libraryStrand","Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.","true","#" +"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#" +"resourceType","The type of resource being stored and annotated","true","#" +"species","The name of a species (typically a taxonomic group) of organism.","true","#" "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. ","true","#" -"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","true","#SpecimenPreparationMethodEnum" -"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#Tumor" +"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","true","#" +"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#" "Filename","The name of the file.","false","#" "age","A numeric value representing age of the individual. Use with `ageUnit`.","false","#" -"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit" +"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#" "aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID.","false","#" "batchID","Batch identifier, can be used in any context where added batch information is helpful, such as different sequencing runs or collection times.","false","#" "comments","Brief free-text comments that may also be important to understanding the resource.","false","#" -"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","false","#DiagnosisEnum" -"libraryPrep","The general strategy by which the library was prepared","false","#LibraryPrepEnum" -"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): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#CellLineModel|#MouseModel" -"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#Genotype|#UnknownEnum" -"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#Genotype|#UnknownEnum" -"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","false","#NucleicAcidSourceEnum" -"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.","false","#OrganEnum" +"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","false","#" +"genePerturbationTechnology","Technology used to perturb gene","false","#" +"genePerturbationType","Specific way in which a single gene was perturbed in a sample","false","#" +"genePerturbed","The HUGO gene symbol for the gene that is perturbed.","false","#" +"libraryPrep","The general strategy by which the library was prepared","false","#" +"modelSystemName"," HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#" +"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#" +"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#" +"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","false","#" +"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.","false","#" "parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor that was subsectioned into several samples. The parentSpecimenID can be the same as specimenID when there is no subsectioning. ","false","#" "readDepth","If available, the coverage statistic as output from bedtools coverage or samtools stats.","false","#" "readLength","Number of base pairs (bp) sequenced for a read","false","#" "readPair","The read of origin, Read 1 or Read 2","false","#" -"runType","Sequencing run type.","false","#RunTypeEnum" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#SexEnum|#UnknownEnum|#NotApplicableEnum" +"runType","Sequencing run type.","false","#" +"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" "specimenType","The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances. -","false","#Tissue|#OrganismSubstance" +","false","#" "targetDepth","The targeted read depth prior to sequencing.","false","#" diff --git a/docs/templates/ScRNASeq_Template.csv b/docs/templates/ScRNASeq_Template.csv index a112e0e9..4639e75e 100644 --- a/docs/templates/ScRNASeq_Template.csv +++ b/docs/templates/ScRNASeq_Template.csv @@ -1,44 +1,49 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" -"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.","true","#DataSubtypeEnum" +"assay","The technology used to generate the data in this file.","true","#" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"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","true","#FileFormatEnum" +","true","#" +"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","true","#" +"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","true","#" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#" -"libraryPreparationMethod","Method by which library was prepared","true","#LibraryPreparationMethodEnum" -"libraryStrand","Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.","true","#StrandednessEnum|#NotApplicableEnum" -"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#PlatformEnum" -"resourceType","The type of resource being stored and annotated","true","#Resource" -"species","The name of a species (typically a taxonomic group) of organism.","true","#SpeciesEnum" +"libraryKitID","Library kit ID.","true","#" +"libraryPreparationMethod","Method by which library was prepared","true","#" +"libraryStrand","Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.","true","#" +"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#" +"resourceType","The type of resource being stored and annotated","true","#" +"species","The name of a species (typically a taxonomic group) of organism.","true","#" "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. ","true","#" -"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","true","#SpecimenPreparationMethodEnum" -"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#Tumor" +"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","true","#" +"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#" "Filename","The name of the file.","false","#" "age","A numeric value representing age of the individual. Use with `ageUnit`.","false","#" -"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit" +"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#" "aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID.","false","#" "auxiliaryAsset","URI to supplemental asset(s), e.g. QC reports or other auxiliary files to support the processing, analysis, or interpretation of the current entity. ","false","#" "batchID","Batch identifier, can be used in any context where added batch information is helpful, such as different sequencing runs or collection times.","false","#" "cellID","Also known as cell barcode, this value can be added for single-cell experiments to identify data at the cell level.","false","#" -"cellType","A cell type is a distinct morphological or functional form of cell.","false","#Cell" +"cellType","A cell type is a distinct morphological or functional form of cell.","false","#" "comments","Brief free-text comments that may also be important to understanding the resource.","false","#" -"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","false","#DiagnosisEnum" -"dissociationMethod","Procedure by which a biological specimen is dissociated into individual cells or a cell suspension","false","#DissociationMethodEnum" -"isCellLine","Whether or not sample source is a cell line (Yes; No)","false","#BooleanEnum" -"libraryPrep","The general strategy by which the library was prepared","false","#LibraryPrepEnum" -"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): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#CellLineModel|#MouseModel" -"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#Genotype|#UnknownEnum" -"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#Genotype|#UnknownEnum" -"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","false","#NucleicAcidSourceEnum" -"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.","false","#OrganEnum" +"dissociationMethod","Procedure by which a biological specimen is dissociated into individual cells or a cell suspension","false","#" +"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","false","#" +"genePerturbationTechnology","Technology used to perturb gene","false","#" +"genePerturbationType","Specific way in which a single gene was perturbed in a sample","false","#" +"genePerturbed","The HUGO gene symbol for the gene that is perturbed.","false","#" +"isCellLine","Whether or not sample source is a cell line (Yes; No)","false","#" +"libraryPrep","The general strategy by which the library was prepared","false","#" +"modelSystemName"," HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#" +"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#" +"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#" +"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","false","#" +"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.","false","#" "parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor that was subsectioned into several samples. The parentSpecimenID can be the same as specimenID when there is no subsectioning. ","false","#" "readDepth","If available, the coverage statistic as output from bedtools coverage or samtools stats.","false","#" "readLength","Number of base pairs (bp) sequenced for a read","false","#" "readPair","The read of origin, Read 1 or Read 2","false","#" -"runType","Sequencing run type.","false","#RunTypeEnum" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#SexEnum|#UnknownEnum|#NotApplicableEnum" +"runType","Sequencing run type.","false","#" +"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" "targetDepth","The targeted read depth prior to sequencing.","false","#" diff --git a/docs/templates/Source_Code_Template.csv b/docs/templates/Source_Code_Template.csv index f190b55a..5b507101 100644 --- a/docs/templates/Source_Code_Template.csv +++ b/docs/templates/Source_Code_Template.csv @@ -1,8 +1,8 @@ "Field","Description","Required","ValidRange" -"title","Title of a resource.","true","#string" +"title","Title of a resource.","true","#" "author","The author of the resource; preferably use an ORCID ID, GitHub profile link, etc., if available and a text name if not.","false","#" "citation","Citation (e.g. doi) that usage of data or resource should be cited with.","false","#" "documentation","URL to any documentation describing the resource and its use.","false","#" -"license","Link to a license or name of license applicable for the resource.","false","#string" +"license","Link to a license or name of license applicable for the resource.","false","#" "programmingLanguage","A computer programming language","false","#" "runtimePlatform","Runtime platform or script interpreter dependencies (e.g. Java v1, Python 2.3).","false","#" diff --git a/docs/templates/WES_Template.csv b/docs/templates/WES_Template.csv index 66541b45..e6153d70 100644 --- a/docs/templates/WES_Template.csv +++ b/docs/templates/WES_Template.csv @@ -1,42 +1,42 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" -"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.","true","#DataSubtypeEnum" +"assay","The technology used to generate the data in this file.","true","#" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"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","true","#FileFormatEnum" +","true","#" +"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","true","#" +"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","true","#" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#" -"libraryPreparationMethod","Method by which library was prepared","true","#LibraryPreparationMethodEnum" -"libraryStrand","Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.","true","#StrandednessEnum|#NotApplicableEnum" -"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#PlatformEnum" -"resourceType","The type of resource being stored and annotated","true","#Resource" -"species","The name of a species (typically a taxonomic group) of organism.","true","#SpeciesEnum" +"libraryPreparationMethod","Method by which library was prepared","true","#" +"libraryStrand","Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.","true","#" +"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#" +"resourceType","The type of resource being stored and annotated","true","#" +"species","The name of a species (typically a taxonomic group) of organism.","true","#" "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. ","true","#" -"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","true","#SpecimenPreparationMethodEnum" -"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#Tumor" +"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","true","#" +"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#" "Filename","The name of the file.","false","#" "age","A numeric value representing age of the individual. Use with `ageUnit`.","false","#" -"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit" +"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#" "aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID.","false","#" "batchID","Batch identifier, can be used in any context where added batch information is helpful, such as different sequencing runs or collection times.","false","#" "comments","Brief free-text comments that may also be important to understanding the resource.","false","#" -"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","false","#DiagnosisEnum" -"libraryPrep","The general strategy by which the library was prepared","false","#LibraryPrepEnum" -"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): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#CellLineModel|#MouseModel" -"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#Genotype|#UnknownEnum" -"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#Genotype|#UnknownEnum" -"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","false","#NucleicAcidSourceEnum" -"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.","false","#OrganEnum" +"libraryPrep","The general strategy by which the library was prepared","false","#" +"modelSystemName"," HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#" +"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#" +"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#" +"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","false","#" +"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.","false","#" "parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor that was subsectioned into several samples. The parentSpecimenID can be the same as specimenID when there is no subsectioning. ","false","#" "readDepth","If available, the coverage statistic as output from bedtools coverage or samtools stats.","false","#" "readLength","Number of base pairs (bp) sequenced for a read","false","#" "readPair","The read of origin, Read 1 or Read 2","false","#" -"runType","Sequencing run type.","false","#RunTypeEnum" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#SexEnum|#UnknownEnum|#NotApplicableEnum" +"runType","Sequencing run type.","false","#" +"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" "specimenType","The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances. -","false","#Tissue|#OrganismSubstance" +","false","#" "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. ","false","#" "targetDepth","The targeted read depth prior to sequencing.","false","#" diff --git a/docs/templates/WGS_Template.csv b/docs/templates/WGS_Template.csv index ba985fbb..a48f93ea 100644 --- a/docs/templates/WGS_Template.csv +++ b/docs/templates/WGS_Template.csv @@ -1,40 +1,40 @@ "Field","Description","Required","ValidRange" "Component","Type of metadata template; provide the same one for all items/rows.","true","#" -"assay","The technology used to generate the data in this file.","true","#AssayEnum" -"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.","true","#DataSubtypeEnum" +"assay","The technology used to generate the data in this file.","true","#" +"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.","true","#" "dataType","Links an entity to data types that the entity represents/contains. This is closely tied to the assay property. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`. -","true","#Data|#Metadata" -"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","true","#FileFormatEnum" +","true","#" +"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","true","#" +"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","true","#" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#" -"libraryPreparationMethod","Method by which library was prepared","true","#LibraryPreparationMethodEnum" -"libraryStrand","Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.","true","#StrandednessEnum|#NotApplicableEnum" -"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#PlatformEnum" -"resourceType","The type of resource being stored and annotated","true","#Resource" -"species","The name of a species (typically a taxonomic group) of organism.","true","#SpeciesEnum" +"libraryPreparationMethod","Method by which library was prepared","true","#" +"libraryStrand","Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.","true","#" +"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","true","#" +"resourceType","The type of resource being stored and annotated","true","#" +"species","The name of a species (typically a taxonomic group) of organism.","true","#" "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. ","true","#" -"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","true","#SpecimenPreparationMethodEnum" -"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#Tumor" +"specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","true","#" +"tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","true","#" "Filename","The name of the file.","false","#" "age","A numeric value representing age of the individual. Use with `ageUnit`.","false","#" -"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit" +"ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#" "aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID.","false","#" "batchID","Batch identifier, can be used in any context where added batch information is helpful, such as different sequencing runs or collection times.","false","#" "comments","Brief free-text comments that may also be important to understanding the resource.","false","#" -"diagnosis","Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.","false","#DiagnosisEnum" -"libraryPrep","The general strategy by which the library was prepared","false","#LibraryPrepEnum" -"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): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#CellLineModel|#MouseModel" -"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#Genotype|#UnknownEnum" -"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#Genotype|#UnknownEnum" -"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","false","#NucleicAcidSourceEnum" -"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.","false","#OrganEnum" +"libraryPrep","The general strategy by which the library was prepared","false","#" +"modelSystemName"," HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","false","#" +"nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known.","false","#" +"nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","false","#" +"nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","false","#" +"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.","false","#" "parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor that was subsectioned into several samples. The parentSpecimenID can be the same as specimenID when there is no subsectioning. ","false","#" "readDepth","If available, the coverage statistic as output from bedtools coverage or samtools stats.","false","#" "readLength","Number of base pairs (bp) sequenced for a read","false","#" "readPair","The read of origin, Read 1 or Read 2","false","#" -"runType","Sequencing run type.","false","#RunTypeEnum" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#SexEnum|#UnknownEnum|#NotApplicableEnum" +"runType","Sequencing run type.","false","#" +"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" "specimenType","The type of a material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes. This includes particular types of cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory substances. -","false","#Tissue|#OrganismSubstance" +","false","#" "targetDepth","The targeted read depth prior to sequencing.","false","#"