Patch docs (#404)

* Update docs after changes in #401

* Regenerate

* Update CSS

docs/custom.css

@@ -1,3 +1,12 @@
+@font-face {
+  font-family: DM Sans,sans-serif;
+  src: url(https://fonts.googleapis.com/css2?family=DM+Sans:ital,opsz,wght@0,9..40,100..1000;1,9..40,100..100);
+}
+
+body {
+  font-family: DM Sans,sans-serif;
+}
+
 div.main-container {
   max-width: 1200px !important;
 }
@@ -30,7 +39,7 @@ div.info {
   background-repeat: no-repeat;
   background-image: url("info_icon.svg");
   background-position: 15px center;
-  background-color: aliceblue;
+  background-color: rgba(18,94,129,.05);
 
 }
 
@@ -74,8 +83,8 @@ div.info {
 
 .nav-pills > li > a {
   background-color: #fff;
-  border: 0 solid #e2e8f0;
-  border-radius: 1rem;
+  border: 1px solid #e2e8f0;
+  border-radius: 0.5rem;
   box-sizing: border-box;
   color: #0d172a;
   cursor: pointer;
@@ -88,16 +97,15 @@ div.info {
   text-align: center;
   text-decoration: none #0d172a solid;
   text-decoration-thickness: auto;
-  transition: all .1s cubic-bezier(.4, 0, .2, 1);
-  box-shadow: 0px 1px 2px rgba(166, 175, 195, 0.25);
+  transition: all .1s cubic-bezier(.1, 0, .2, 1);
   user-select: none;
   -webkit-user-select: none;
   touch-action: manipulation;
 }
 
 
 .nav-pills > li.active > a:hover, .nav-pills > li.active > a {
-  background-color: #1e293b !important;
+  background-color:rgb(64, 75, 99) !important;
   color: #fff;
 }
 
@@ -106,6 +114,6 @@ div.info {
 .list-group-item.active, .list-group-item.active:hover, .list-group-item.active:focus {
     z-index: 2;
     color: #ffffff;
-    background-color: #1e293b;
-    border-color: #1e293b;
+    background-color: rgb(64, 75, 99);
+    border-color: rgb(64, 75, 99);
 }

docs/index.Rmd

@@ -414,7 +414,7 @@ module_section("Data", "Data", "Data")
 
 ```{r datasubtype, echo=FALSE, results='asis'}
 
-module_section("Data", "Data", "DataSubtype")
+module_section("Data", "Data", "DataSubtypeEnum")
 ```
 
 

docs/templates/Clinical_Assay_Template.csv

@@ -1,25 +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","#DataSubtype"
-"dataType","A type of data -- experimental, clinical, or other. Most typically refers to a high-level data type that can be related to an assay type.  For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.
+"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"
+"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"
 "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"
 "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"
 "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","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","false","#DiagnosisEnum"
+"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","#"
 "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"

docs/templates/Epigenetics_Assay_Template.csv

@@ -1,8 +1,8 @@
 "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","#DataSubtype"
-"dataType","A type of data -- experimental, clinical, or other. Most typically refers to a high-level data type that can be related to an assay type.  For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.
+"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"
+"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"
 "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#"
@@ -21,18 +21,21 @@
 "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","#"
-"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","false","#DiagnosisEnum"
+"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"
 "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"
+"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"
 "targetDepth","The targeted read depth prior to sequencing.","false","#"
-"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","false","#TissueEnum"

docs/templates/Genomics_Assay_Template.csv

@@ -1,8 +1,8 @@
 "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","#DataSubtype"
-"dataType","A type of data -- experimental, clinical, or other. Most typically refers to a high-level data type that can be related to an assay type.  For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.
+"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"
+"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"
 "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","true","#"
@@ -20,18 +20,21 @@
 "ageUnit","A time unit that can be used with a given age value, e.g. years.","false","#TimeUnit"
 "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","#"
-"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","false","#DiagnosisEnum"
+"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"
 "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"
+"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"
 "targetDepth","The targeted read depth prior to sequencing.","false","#"
-"tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","false","#TissueEnum"

docs/templates/Imaging_Assay_Template.csv

@@ -1,21 +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","#DataSubtype"
-"dataType","A type of data -- experimental, clinical, or other. Most typically refers to a high-level data type that can be related to an assay type.  For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.
+"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"
+"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"
 "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"
 "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"
+"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","#"
-"diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","false","#DiagnosisEnum"
+"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"

docs/templates/Light_Scattering_Assay_Template.csv

@@ -1,8 +1,8 @@
 "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","#DataSubtype"
-"dataType","A type of data -- experimental, clinical, or other. Most typically refers to a high-level data type that can be related to an assay type.  For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.
+"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"
+"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"