diff --git a/pr-preview/pr-564/Dockerfile b/pr-preview/pr-564/Dockerfile deleted file mode 100644 index 6a5b7bf6..00000000 --- a/pr-preview/pr-564/Dockerfile +++ /dev/null @@ -1,9 +0,0 @@ -FROM ghcr.io/nf-osi/nfportalutils:develop - -WORKDIR /app - -RUN apt-get -yq install pandoc - -RUN R -e "install.packages(c('rmarkdown', 'reactable', 'visNetwork'), repos='http://cran.rstudio.com/')" - -ENTRYPOINT ["/bin/bash", "R", "-e", "rmarkdown::render('docs/index.Rmd')"] diff --git a/pr-preview/pr-564/custom.css b/pr-preview/pr-564/custom.css deleted file mode 100644 index b6fe531c..00000000 --- a/pr-preview/pr-564/custom.css +++ /dev/null @@ -1,119 +0,0 @@ -@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; -} - -.tag { - width: 30px; - height: 30px; - border: 1px solid rgba(0, 0, 0, 0.03); - border-radius: 20%; - color: #000; - font-size: 13px; - letter-spacing: -2px; -} - -.warning { - color: #000; - background-color: orange; -} - -.good { - color: #000; - background-color: #50C878; -} - -div.info { - padding: 1em; - margin: 1em 0; - padding-left: 80px; - background-size: 30px; - background-repeat: no-repeat; - background-image: url("info_icon.svg"); - background-position: 15px center; - background-color: rgba(18,94,129,.05); - -} - -.term-table { - margin-top: 16px; - border: 1px solid hsl(213, 33%, 93%); - border-radius: 4px; - box-shadow: 0 4px 8px 0 rgba(0, 0, 0, 0.1); -} - -.template-title { - font-size: 14px; -} - -.detail { - padding: 24px; - box-shadow: inset 0 1px 3px #dbdbdb; - background: hsl(213, 20%, 99%); -} - -.detail-label { - margin: 20px 0 4px; - font-size: 14px; - color: rgba(0, 0, 0, 0.6); -} - -.detail-header { - margin-bottom: 16px; - font-size: 20px; - font-weight: 600; -} - -.detail-title { - margin-left: 18px; - font-size: 14px; - font-weight: 400; - color: rgba(0, 0, 0, 0.6); -} - -/* Custom tab pills */ - -.nav-pills > li > a { - background-color: #fff; - border: 1px solid #e2e8f0; - border-radius: 0.5rem; - box-sizing: border-box; - color: #0d172a; - cursor: pointer; - display: inline-block; - font-family: "Basier circle",-apple-system,system-ui,"Segoe UI",Roboto,"Helvetica Neue",Arial,"Noto Sans",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji"; - font-size: 1.1rem; - font-weight: 600; - line-height: 1; - padding: 1rem 1.6rem; - text-align: center; - text-decoration: none #0d172a solid; - text-decoration-thickness: auto; - 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:rgb(64, 75, 99) !important; - color: #fff; -} - -/* TOC */ - -.list-group-item.active, .list-group-item.active:hover, .list-group-item.active:focus { - z-index: 2; - color: #ffffff; - background-color: rgb(64, 75, 99); - border-color: rgb(64, 75, 99); -} diff --git a/pr-preview/pr-564/docTemplate.R b/pr-preview/pr-564/docTemplate.R deleted file mode 100644 index b481b51d..00000000 --- a/pr-preview/pr-564/docTemplate.R +++ /dev/null @@ -1,114 +0,0 @@ -read_properties <- function(file = "../modules/props.yaml") { - props <- yaml::read_yaml(file)$slots - # props <- rbindlist(props, fill = TRUE, idcol = "Property") - props -} - -# The range of prop `assay` is anything of class `Assay` -- -# However, the json-ld does not make this so conceptually concise for props, instead listing all possible values -# In the docs, we don't want to enumerate all values and instead want to create a _link_ to a class that defines the range -# To do this, we can infer class by look up the class of the first listed enum for that prop -# The range could also be inferred to be a boolean or string/integer rather than a class -summarize_range <- function(prop_id, schema, return_labels = FALSE) { - - enums <- nfportalutils::get_by_prop_from_json_schema(id = prop_id, - prop = "schema:rangeIncludes", - schema = schema, - return_labels = FALSE) - - # handle how enums are presented - if(is.null(enums)) return("") - if(length(enums) < 5) return(paste(gsub("bts:", "", enums), collapse = ",")) - if("bts:Yes" %in% enums) return("Y/N") - - enum1 <- enums[1] - - # additional lookup class - class <- nfportalutils::get_by_prop_from_json_schema(enum1, - prop = "rdfs:subClassOf", - schema = schema, - return_labels = FALSE)[[1]] - if(length(class) > 1) warning(enum1, " has multiple parent classes") - class <- sub("bts:", "", class[1]) # use first but warn - class <- paste0("#", class) - class -} - -#' @param prop_id Namespaced id, e.g. "bts:tumorType" -summarize_range_linkml <- function(prop_id, props) { - prop_id <- sub("^bts:", "", prop_id) - - # union ranges - if(!is.null(props[[prop_id]]$any_of)) { - paste0("#", unlist(props[[prop_id]]$any_of, use.names = F), collapse = "|") - - } else { - class <- props[[prop_id]]$range - if(is.null(range)) class <- "" - paste0("#", class) - } -} - - -#' Generate template documentation -#' -#' Basically tries to present a template in a conventional format similar to: -#' 1. [GDC viewer](https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads) -#' 2. [Bioschema profile](https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE) -#' 3. [FAIRplus example](https://fairplus.github.io/the-fair-cookbook/content/recipes/interoperability/transcriptomics-metadata.html#assay-metadata) -#' 4. [Immport template doc](https://www.immport.org/shared/templateDocumentation?tab=1&template=bioSamples.txt) -#' 5. [LINCS template doc](https://lincsproject.org/LINCS/files//2020_exp_meta_stand/General_Proteomics.pdf) -#' -#' In general it looks like a table with one row per property and informational columns for: -#' - [x] controlled values (valid values for schematic) / range of property -#' - [ ] marginality (required vs. recommended vs. optional) -#' - [ ] cardinality (one or many values allowed) -#' - [x] notes / comments -#' -#' Currently, schematic templates allow modeling more on the simplistic side and -#' don't formally express all these, so only a few are checked. -#' Currently, the jsonld version loses some information when translated from the csv source -#' (mainly the summary Range definition corresponding to https://www.w3.org/TR/rdf-schema/#ch_range and EditorNote). -#' -#' @param templates Named vector of templates to process, -#' where names corresponds to id without prefix (currently whatever follows "bts:"), -#' and value is the real internal ID (in .ID). -#' @param schema Schema list object parsed from a schematic jsonld. -#' @param prefix Namespace prefix. -#' @param savedir Directory where template representations will be outputted. -#' @param verbose Whether to be verbose about what's going on. -docTemplate <- function(templates, - schema, - prefix = "bts:", - savedir = "templates/", - verbose = TRUE) { - - - for(x in names(templates)) { # e.g. x <- "GenomicsAssayTemplate" - # For template, parse DependsOn to get all props present in manifest - prop_ids <- nfportalutils::get_dependency_from_json_schema(paste0(prefix, x), - schema = schema, - return_labels = FALSE) - - - prop_ref <- read_properties() - - sms <- Filter(function(x) x$`@id` %in% prop_ids, schema) - sms <- lapply(sms, function(x) { - list(Field = x$`sms:displayName`, - Description = if(!is.null(x$`rdfs:comment`)) x$`rdfs:comment` else " ", - Required = if(!is.null(x$`sms:required`)) sub("sms:", "", x$`sms:required`) else "?", - ValidRange = summarize_range_linkml(prop_id = x$`@id`, props = prop_ref)) - }) - tt <- rbindlist(sms) - - # Sort to show by required, then alphabetically - tt <- tt[order(-Required, Field), ] - - template_id <- templates[x] - filepath <- paste0(savedir, template_id, ".csv") - write.csv(tt, file = filepath, row.names = F) - } -} - - diff --git a/pr-preview/pr-564/graph.R b/pr-preview/pr-564/graph.R deleted file mode 100644 index 6a4d6785..00000000 --- a/pr-preview/pr-564/graph.R +++ /dev/null @@ -1,102 +0,0 @@ -library(visNetwork) - -#-------------------------------------------------------------------------------# - -# Reads a main extended schematic .csv file and its extended definitions -# (which are separate files named `ext_classes.csv` and `ext_relations.csv`, -# respectively) -# usage example: -# schema <- readExtSchema("NF.csv") -readExtSchema <- function(schema_csv, ext_classes_csv = "ext_classes.csv") { - schema <- read.csv(schema_csv) %>% - dplyr::select(label = Attribute, id = .ID, Root = .Root, SubOf = .SubOf) - - # Extended class definitions - ext_classes <- read.csv(ext_classes_csv) %>% - select(label = Attribute, id = .ID, Root = .Root, SubOf = .SubOf) - - ext_schema <- rbind(schema, ext_classes) - ext_schema -} - -#' Make required node and edge data for specified cluster -#' Usage: -#' assay <- getNodesEdges(schema, "Assay", "A", -#' nodes = list(color = list(A = "plum", C = "indigo"))) -#' template <- getNodesEdges(schema, "Template", "T", use_id = T, -#' nodes = list(color = list(A = "pink", C = "firebrick"))) -getNodesEdges <- function(schema, cluster_root, - prefix, use_id = F, - nodes = list(color = list(A = "black", C = "black"), - font.color = list(A = "white", C = "white")) - ) { - cluster <- schema %>% - dplyr::filter(Root == cluster_root) - - # Namespaces for cluster ancestor vs Children - A <- paste(prefix, "A", sep = "_") - C <- paste(prefix, "C", sep = "_") - nodes <- cluster %>% - select(id, label, SubOf) %>% - mutate(group = ifelse(SubOf %in% c(cluster_root, ""), A, C), - color = ifelse(group == A, nodes$color$A, nodes$color$C), - font.color = ifelse(group == A, nodes$font.color$A, nodes$font.color$C)) - - if(use_id) { - nodes <- nodes %>% - mutate(label = id) - } - - edges <- cluster %>% - filter(SubOf != "") %>% # Remove root from edges - select(from = id, to = SubOf) - - return(list(nodes = nodes, edges = edges)) -} - -# Convenience wrapper to extract and combine two clusters into a graph df -# given schema and extensions -# usage example: -# c2Cluster(assay, template) -c2Cluster <- function(cluster_1, cluster_2, connect_by, - ext_relations_csv = "ext_relations.csv", - viz = list(color = "firebrick", width = 4)) { - - # Configure between-cluster relations - relations <- read.csv(ext_relations_csv, header = T) - edges <- relations %>% - dplyr::filter(property == connect_by) - relations$color <- viz$color - relations$width <- viz$width - - # Concatenate clusters - g_nodes <- rbind(cluster_1$nodes, cluster_2$nodes) - g_edges <- rbind(cluster_1$edges, cluster_2$edges) - g_edges$color <- "gray" # non-configurable default for now - g_edges$width <- 1 # non-configurable default for now - g_edges <- rbind(g_edges, relations[, c("from", "to", "color", "width")]) - return(list(nodes = g_nodes, edges = g_edges)) -} - -# Generate default graph -defaultGraph <- function(graph, height = 800) { - visNetwork(graph$nodes, graph$edges, height = height) %>% - visEdges(arrows = "To") %>% - visIgraphLayout() %>% - visNodes(shape = "box", - font = list(size = 30), - shadow = list(enabled = TRUE), - physics = F) %>% - visOptions(nodesIdSelection = TRUE, - highlightNearest = list(enabled = T, hover = T) - ) -} - -# Simple graph function meant for checking an extracted portion of graph -basicGraph <- function(g) { - visNetwork(g$nodes, g$edges) %>% - visEdges(arrows = "To") %>% - visIgraphLayout() -} - -# ------------------------------------------------------------------------------# diff --git a/pr-preview/pr-564/index.Rmd b/pr-preview/pr-564/index.Rmd deleted file mode 100644 index aa32f308..00000000 --- a/pr-preview/pr-564/index.Rmd +++ /dev/null @@ -1,540 +0,0 @@ ---- -title: "NF Vocabulary / Schema" -author: "NF-OSI DCC" -date: "Last updated on `r Sys.Date()`" -output: - html_document: - theme: lumen - css: custom.css - toc: true - toc_float: - collapsed: false - toc_depth: 4 -params: - schema_json: "../NF.jsonld" - ext_classes_csv: "../ext_classes.csv" - ext_relations_csv: "../ext_relations.csv" - graph_view: false - use_cache: false ---- - -```{r setup, include=FALSE} -knitr::opts_chunk$set(echo = TRUE) -library(data.table) -library(reactable) -library(htmltools) -# library(visNetwork) - -source("graph.R") -source("docTemplate.R") - - -basicTable <- function(dt, columns = c("Attribute", "Description")) { - reactable(dt[, columns], - filterable = if(nrow(dt) > 20) TRUE else FALSE, - pagination = FALSE, - columns = list( - Attribute = colDef(name = "Label", maxWidth = 250) - ), - wrap = FALSE, - class = "term-table" - ) -} - -expandedTable <- function(dt) { - row_details <- function(index) { - expanded <- dt[index, ] - detail <- div( - class = "detail", - div(class = "detail-header", expanded$Attribute, - span(class = "detail-title", expanded$Description)) - ) - detail - } - - - - reactable(dt[, c("Attribute", "Description")], - filterable = TRUE, - pagination = FALSE, - onClick = "expand", - columns = list( - Attribute = colDef(name = "Label", maxWidth = 250) - # DependsOn = colDef(name = "Fields") - ), - details = row_details, - wrap = FALSE, - class = "term-table" - ) -} - -templateTable <- function(dt) { - # Reference range by linking to relevant class sections within document - # or returning range values in plain text - refRange <- function(value, index) { - values <- strsplit(value, split = "|", fixed = TRUE)[[1]] - if(any(grepl("#", values))) { - htmltools::div( - lapply(values, function(value) htmltools::p( - htmltools::tags$a(href = value, sub("#", "", value)), " ")) - ) - } else { - value - } - } - - reactable(dt, - columns = list( - Field = colDef(minWidth = 180, - cell = function(value, index) { div(style = list(fontWeight = 600), value)}), - Description = colDef(minWidth = 300), - Required = colDef(maxWidth = 100), - ValidRange = colDef(name = "Valid Range", cell = refRange) - ), - rowStyle = function(index) { - if (dt[index, "Required"]) { - list(background = "lemonchiffon") - } - }, - pagination = FALSE, - wrap = TRUE, - class = "term-table") -} - - -module_section <- function(module, - submodule, - submodule_id = submodule) { - - file <- glue::glue("../modules/{module}/{submodule}.yaml") - data <- yaml::read_yaml(file) - - for(key in submodule_id) { - data <- data$enums[[key]]$permissible_values - - cat(paste0("\n", "#### ", key, " {#", key, " .tabset .tabset-fade .tabset-pills}", "\n")) - - table <- rbindlist(data, fill = TRUE, idcol = "Attribute") - setnames(table, "description", "Description", skip_absent = TRUE) - if(!"Description" %in% names(table)) table[, Description := ""] - - table <- table[, .(Attribute, Description)] - - print( - tagList( - expandedTable(table), tags$br())) - } -} - - -``` - -```{r process_schema_table, echo=FALSE} - -schema <- jsonlite::read_json(params$schema_json) -schema <- schema$`@graph` - -if(!params$use_cache) { - templates <- c(# genomics/transcriptomics - GenomicsAssayTemplate = "Genomics_Assay_Template", - WGSTemplate = "WGS_Template", - WESTemplate = "WES_Template", - EpigeneticsAssayTemplate = "Epigenetics_Assay_Template", - RNASeqTemplate = "RNASeq_Template", - ScRNASeqTemplate = "ScRNASeq_Template", - - # genomics/transcriptomics -- processed - ProcessedAlignedReadsTemplate = "Processed_Aligned_Reads_Template", - ProcessedVariantCallsTemplate = "Processed_Variant_Calls_Template", - ProcessedExpressionTemplate = "Processed_Expression_Template", - - # proteomics - ProteomicsAssayTemplate = "Proteomics_Assay_Template", - - # imaging - ImagingAssayTemplate = "Imaging_Assay_Template", - MRIAssayTemplate = "MRI_Assay_Template", - - # other - PharmacokineticsAssayTemplate = "Pharmacokinetics_Assay_Template", # drug assays type - PlateBasedReporterAssayTemplate = "Plate_Based_Reporter_Assay_Template", - ClinicalAssayTemplate = "Clinical_Assay_Template", - # PatientTimepointsTemplate = "Patient_Timepoints_Template", - Protocol = "Protocol", - SourceCodeTemplate = "Source_Code_Template", - LightScatteringAssayTemplate = "Light_Scattering_Assay_Template") - - docTemplate(templates, schema = schema) -} - -# Splits terms into Property or Class using `Type` -# schema_class <- schema %>% -# filter(Type == "Class") - -# Not displayed yet -# schema_prop <- schema %>% -# filter(Type == "Property") - -``` - -## Annotation Templates - -:::info - -Annotation templates are spreadsheet templates that allow contributors to annotate resources uploaded to the repository. -See interactive use of these templates at our [NF Data Curator App](https://shiny.synapse.org/users/rallaway/NF_data_curator/). -Templates implement "minimum metadata" standards specific to the type of data/resource (hence variants exist for assay types and "raw" vs "processed" data). -Templates also contain common components, e.g. many will collect core sample info associated with the data. - -Unless the template field is free-text, it is meant to be filled by the contributor using the ontology terms/controlled vocabulary defined here. -For example, the "assay" property allows the contributor to use [terms under Assay](#assay). - -::: - -#### Genomics Assay Data Templates {#Genomics_Assay_Templates .tabset .tabset-fade .tabset-pills} - -:::info - -Raw or processed data files from a genomics assay should be annotated using one of these templates. - -::: - -##### Genomics Assay (Generic) - -```{r echo=FALSE } - -templateTable(read.csv("templates/Genomics_Assay_Template.csv")) - -``` - -##### Epigenetics Assay -```{r echo=FALSE } - -templateTable(read.csv("templates/Epigenetics_Assay_Template.csv")) - -``` - - -##### WES Assay - -```{r echo=FALSE } - -templateTable(read.csv("templates/WES_Template.csv")) - -``` - -##### WGS Assay - -```{r echo=FALSE } - -templateTable(read.csv("templates/WGS_Template.csv")) - -``` - -##### Bulk RNA-Seq Assay - -```{r echo=FALSE } - -templateTable(read.csv("templates/RNASeq_Template.csv")) - -``` - -##### Single-cell RNA-Seq Assay - -```{r echo=FALSE } - -templateTable(read.csv("templates/ScRNASeq_Template.csv")) - -``` - - -##### Processed Aligned Reads - -```{r echo=FALSE } - -templateTable(read.csv("templates/Processed_Aligned_Reads_Template.csv")) - -``` - -##### Processed Variant Calls - -```{r echo=FALSE } - -templateTable(read.csv("templates/Processed_Variant_Calls_Template.csv")) - -``` - -##### Processed Expression - -```{r echo=FALSE } - -templateTable(read.csv("templates/Processed_Expression_Template.csv")) - -``` - -#### Proteomics Assay Templates {#Proteomics_Assay_Templates .tabset .tabset-fade .tabset-pills} - -##### Proteomics Assay (Generic) -```{r echo=FALSE } - -templateTable(read.csv("templates/Proteomics_Assay_Template.csv")) - -``` - - -#### Imaging Assay Templates {#Imaging_Assay_Templates .tabset .tabset-fade .tabset-pills} - -##### Imaging Assay (Generic) -```{r echo=FALSE } - -templateTable(read.csv("templates/Imaging_Assay_Template.csv")) - -``` - -##### MRI Assay -```{r echo=FALSE } - -templateTable(read.csv("templates/MRI_Assay_Template.csv")) - -``` - -#### Other Assay Templates {#Other_Assay_Templates .tabset .tabset-fade .tabset-pills} - -##### Pharmacokinetics Assay - -```{r echo=FALSE } - -templateTable(read.csv("templates/Pharmacokinetics_Assay_Template.csv")) - -``` - -##### Plate Based Reporter Assay -```{r echo=FALSE } - -templateTable(read.csv("templates/Plate_Based_Reporter_Assay_Template.csv")) - -``` - -#### Clinical Assay Templates {#Clinical_Assay_Templates .tabset .tabset-fade .tabset-pills} - -##### Clinical Assay (Generic) -```{r echo=FALSE } - -templateTable(read.csv("templates/Clinical_Assay_Template.csv")) - -``` - -#### Other Assays {.tabset .tabset-fade .tabset-pills} - - -##### Light Scattering -```{r echo=FALSE } - -templateTable(read.csv("templates/Light_Scattering_Assay_Template.csv")) - -``` - -#### Non-Assay Templates {#Non_Assay_Template .tabset .tabset-fade .tabset-pills} - -##### Protocol -```{r echo=FALSE } - -templateTable(read.csv("templates/Protocol_Template.csv")) - -``` - -##### Source Code -```{r echo=FALSE } - -templateTable(read.csv("templates/Source_Code_Template.csv")) - -``` - - -## Annotation Vocabulary - -:::info - -These are standard terms available to NF resource contributors for annotation of their resource. -Terms are grouped into modules. -When using these terms, contributors are helping to label and classify resources using standard semantics for improved interoperability and findability. - -::: - -### Assay - -```{r assay, echo=FALSE,results='asis'} - -module_section("Assay", "Assay", "AssayEnum") - -``` - -```{r platform, echo=FALSE,results='asis'} - -module_section("Assay", "Platform", "PlatformEnum") - -``` - -##### Relations Graph - -:::info - -This partial graph view logically relates **assays** to metadata **templates** available at the [NF Data Curator App](https://shiny.synapse.org/users/rallaway/NF_data_curator/). -For example, assays under the classification of `Imaging_Assay` currently uses a generic `Imaging_Assay_Template` for annotation. -More specialized templates may be made available as needed for specific assays. - -::: - -```{r schema_ext_assay_template, out.width="100%", echo=FALSE, eval=params$graph_view} - -schema_ext <- readExtSchema(params$schema_csv, params$ext_classes_csv) -assay <- getNodesEdges(schema_ext, "Assay", "A", - nodes = list(color = list(A = "plum", C = "indigo"), - font.color = list(A = "black", C = "white"))) -template <- getNodesEdges(schema_ext, "Template", "T", use_id = T, - nodes = list(color = list(A = "pink", C = "firebrick"), - font.color = list(A = "black", C = "white"))) -g_assay_template <- c2Cluster(assay, template, "suggests", params$ext_relations_csv) -defaultGraph(g_assay_template) - -``` - - -### Information Entity - -```{r resource, echo=FALSE, results='asis'} - -module_section("Data", "Resource", "Resource") -``` - -```{r data, echo=FALSE, results='asis'} - -module_section("Data", "Data", "Data") -``` - -```{r datasubtype, echo=FALSE, results='asis'} - -module_section("Data", "Data", "DataSubtypeEnum") -``` - - -```{r fileformat, echo=FALSE, results='asis'} - -module_section("Data", "FileFormat", "FileFormatEnum") -``` - - -### Sample - -:::info - -Sample typically refers to a **biosample**, but on some rare occasions can refer to an inorganic sample from which data are generated. -For biosamples, there is a distinction between individual-level and specimen-level data. -Data can be linked to individual-level sample information such as sex, species, diagnosis, and genotype. -Data can be linked to specimen-level information such as sample site (the organ or body part), specimen type or cell type, tumor class (if specimen is a tumor), and specimen state. - -::: - - -```{r sample_specimenType_tissue, echo=FALSE, results='asis'} - -module_section("Sample", "SpecimenType", "Tissue") - -``` - -```{r sample_specimenType_other, echo=FALSE, results='asis'} - -module_section("Sample", "SpecimenType", "OrganismSubstance") - -``` - - -```{r sample_tumor, echo=FALSE, results='asis'} - -module_section("Sample", "Tumor", "Tumor") - -``` - -```{r sample_sex, echo=FALSE, results='asis'} - -module_section("Sample", "Sex", "SexEnum") - -``` - -```{r sample_diagonosis, echo=FALSE, results='asis'} - -module_section("Sample", "Diagnosis", "DiagnosisEnum") - -``` - - -```{r sample_genotype, echo=FALSE, results='asis'} - -module_section("Sample", "Genotype", "Genotype") - -``` - - -```{r sample_species, echo=FALSE, results='asis'} - -module_section("Sample", "Species", "SpeciesEnum") - -``` - -```{r sample_cell, echo=FALSE, results='asis'} - -module_section("Sample", "Cell", "Cell") - -``` - -```{r sample_cellmodel, echo=FALSE, results='asis'} - -module_section("Sample", "CellLineModel", "CellLineModel") - -``` - - -```{r sample_mousemodel, echo=FALSE, results='asis'} - -module_section("Sample", "MouseModel", "MouseModel") - -``` - - -### Experiment - -:::info - -Terminology to help characterize experiment. - -::: - -```{r biosample_module, echo=FALSE, results='asis'} - -module_section("Experiment", "Unit", "TimeUnit") - -``` - - -## Other - -#### Reserved Properties {#reserved .tabset .tabset-fade .tabset-pills} - -:::info - -Reserved annotation properties also describe the resource in some way, but they are not expected to be edited directly by contributors. -They are computed/automated annotations set by the data platform and DCC activities. - -::: - -##### Terms -```{r reserved_properties_table, echo=FALSE,eval=F} - -reserved_properties_table <- schema %>% - filter(SubOf %in% c("dccProperty", "synapseProperty")) %>% - select(Attribute, Description, DependsOn) - -basicTable(reserved_properties_table) -``` - - diff --git a/pr-preview/pr-564/index.html b/pr-preview/pr-564/index.html deleted file mode 100644 index 37befd61..00000000 --- a/pr-preview/pr-564/index.html +++ /dev/null @@ -1,3790 +0,0 @@ - - - - - - - - - - - - - - -NF Vocabulary / Schema - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Annotation Templates

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Annotation templates are spreadsheet templates that allow -contributors to annotate resources uploaded to the repository. See -interactive use of these templates at our NF Data -Curator App. Templates implement “minimum metadata” standards -specific to the type of data/resource (hence variants exist for assay -types and “raw” vs “processed” data). Templates also contain common -components, e.g. many will collect core sample info associated with the -data.

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Unless the template field is free-text, it is meant to be filled by -the contributor using the ontology terms/controlled vocabulary defined -here. For example, the “assay” property allows the contributor to use terms under Assay.

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Genomics Assay Data -Templates

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Raw or processed data files from a genomics assay should be annotated -using one of these templates.

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Genomics Assay (Generic)
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Epigenetics Assay
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WES Assay
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WGS Assay
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Bulk RNA-Seq Assay
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Single-cell RNA-Seq Assay
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Processed Aligned Reads
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Processed Variant Calls
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Processed Expression
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Proteomics Assay -Templates

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Proteomics Assay (Generic)
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Imaging Assay Templates

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Imaging Assay (Generic)
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MRI Assay
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Other Assay Templates

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Pharmacokinetics Assay
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Plate Based Reporter Assay
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Clinical Assay -Templates

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Clinical Assay (Generic)
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Other Assays

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Light Scattering
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Non-Assay Templates

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Protocol
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Source Code
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Annotation Vocabulary

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These are standard terms available to NF resource contributors for -annotation of their resource. Terms are grouped into modules. When using -these terms, contributors are helping to label and classify resources -using standard semantics for improved interoperability and -findability.

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Assay

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AssayEnum

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PlatformEnum

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Relations Graph
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This partial graph view logically relates assays to -metadata templates available at the NF Data -Curator App. For example, assays under the classification of -Imaging_Assay currently uses a generic -Imaging_Assay_Template for annotation. More specialized -templates may be made available as needed for specific assays.

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Information Entity

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Resource

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Data

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DataSubtypeEnum

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FileFormatEnum

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Sample

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Sample typically refers to a biosample, but on some -rare occasions can refer to an inorganic sample from which data are -generated. For biosamples, there is a distinction between -individual-level and specimen-level data. Data can be linked to -individual-level sample information such as sex, species, diagnosis, and -genotype. Data can be linked to specimen-level information such as -sample site (the organ or body part), specimen type or cell type, tumor -class (if specimen is a tumor), and specimen state.

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Tissue

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OrganismSubstance

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Tumor

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- -
- -


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SexEnum

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- -


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DiagnosisEnum

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- -
- -


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Genotype

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- -


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SpeciesEnum

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- -
- -


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Cell

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- -
- -


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CellLineModel

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- -
- -


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MouseModel

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- -


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Experiment

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Terminology to help characterize experiment.

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TimeUnit

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- -


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Other

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Reserved Properties

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Reserved annotation properties also describe the resource in some -way, but they are not expected to be edited directly by contributors. -They are computed/automated annotations set by the data platform and DCC -activities.

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Terms
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-
-
- - - -
-
- -
- - - - - - - - - - - - - - - - diff --git a/pr-preview/pr-564/info_icon.svg b/pr-preview/pr-564/info_icon.svg deleted file mode 100644 index a2bebb9a..00000000 --- a/pr-preview/pr-564/info_icon.svg +++ /dev/null @@ -1,17 +0,0 @@ - - - - - - - image/svg+xml - - - - - - - - - - \ No newline at end of file diff --git a/pr-preview/pr-564/templates/Clinical_Assay_Template.csv b/pr-preview/pr-564/templates/Clinical_Assay_Template.csv deleted file mode 100644 index 2ae2fe3f..00000000 --- a/pr-preview/pr-564/templates/Clinical_Assay_Template.csv +++ /dev/null @@ -1,27 +0,0 @@ -"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","#" -"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","#" -"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","#" -"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","#" -"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","//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","#" -"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/pr-preview/pr-564/templates/Dynamic_Light_Scattering_Template.csv b/pr-preview/pr-564/templates/Dynamic_Light_Scattering_Template.csv deleted file mode 100644 index b12e1e77..00000000 --- a/pr-preview/pr-564/templates/Dynamic_Light_Scattering_Template.csv +++ /dev/null @@ -1,15 +0,0 @@ -"Field","Description","Required","ControlledVocab","Note" -"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" -"Filename","The name of the file.","required","","Automatically filled when using the curator app." -"assay","The technology used to generate the data in this file","required","#Assay","" -"dataSubtype","Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","required","#Data_Level","" -"dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data","" -"fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format","" -"resourceType","The type of resource being stored and annotated","required","#Resource","" -"concentrationMaterial","Numeric value for concentration of the material","optional","","" -"concentrationMaterialUnit","Unit used for the material concentration, e.g. mg/mL","optional","mg/mL,mM","" -"concentrationNaCl","Numeric value for NaCl concentration","optional","","" -"concentrationNaClUnit","Unit used for the NaCl concentration, e.g. mM","optional","mg/mL,mM","" -"materialType","Type of material in the characterization","optional","nanoparticles,polymeric nanoparticles,small molecule,DNA","" -"pH","Numeric value for pH sample parameter","optional","","" -"entityId",NA,NA,NA,NA diff --git a/pr-preview/pr-564/templates/Epigenetics_Assay_Template.csv b/pr-preview/pr-564/templates/Epigenetics_Assay_Template.csv deleted file mode 100644 index 0e607265..00000000 --- a/pr-preview/pr-564/templates/Epigenetics_Assay_Template.csv +++ /dev/null @@ -1,41 +0,0 @@ -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"targetDepth","The targeted read depth prior to sequencing.","false","#" diff --git a/pr-preview/pr-564/templates/Genomics_Assay_Template.csv b/pr-preview/pr-564/templates/Genomics_Assay_Template.csv deleted file mode 100644 index a48f93ea..00000000 --- a/pr-preview/pr-564/templates/Genomics_Assay_Template.csv +++ /dev/null @@ -1,40 +0,0 @@ -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"targetDepth","The targeted read depth prior to sequencing.","false","#" diff --git a/pr-preview/pr-564/templates/Imaging_Assay_Template.csv b/pr-preview/pr-564/templates/Imaging_Assay_Template.csv deleted file mode 100644 index 66a5fbc9..00000000 --- a/pr-preview/pr-564/templates/Imaging_Assay_Template.csv +++ /dev/null @@ -1,25 +0,0 @@ -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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/pr-preview/pr-564/templates/Light_Scattering_Assay_Template.csv b/pr-preview/pr-564/templates/Light_Scattering_Assay_Template.csv deleted file mode 100644 index 54d9bb73..00000000 --- a/pr-preview/pr-564/templates/Light_Scattering_Assay_Template.csv +++ /dev/null @@ -1,18 +0,0 @@ -"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","#" -"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","#" -"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","#" -"concentrationNaCl","Numeric value for NaCl concentration","false","#" -"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/pr-preview/pr-564/templates/MRI_Assay_Template.csv b/pr-preview/pr-564/templates/MRI_Assay_Template.csv deleted file mode 100644 index 2e503cff..00000000 --- a/pr-preview/pr-564/templates/MRI_Assay_Template.csv +++ /dev/null @@ -1,30 +0,0 @@ -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"comments","Brief free-text comments that may also be important to understanding the resource.","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"," 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/pr-preview/pr-564/templates/Pharmacokinetics_Assay_Template.csv b/pr-preview/pr-564/templates/Pharmacokinetics_Assay_Template.csv deleted file mode 100644 index aff7aaab..00000000 --- a/pr-preview/pr-564/templates/Pharmacokinetics_Assay_Template.csv +++ /dev/null @@ -1,33 +0,0 @@ -"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","#" -"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","#" -"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","#" -"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","#" -"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","//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"," 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","#" -"timepointUnit","For timed experiments this represents the unit of time measured","false","#" diff --git a/pr-preview/pr-564/templates/Plate_Based_Reporter_Assay_Template.csv b/pr-preview/pr-564/templates/Plate_Based_Reporter_Assay_Template.csv deleted file mode 100644 index 22772c35..00000000 --- a/pr-preview/pr-564/templates/Plate_Based_Reporter_Assay_Template.csv +++ /dev/null @@ -1,36 +0,0 @@ -"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","#" -"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","#" -"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","#" -"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","#" -"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","//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"," 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","#" -"timepointUnit","For timed experiments this represents the unit of time measured","false","#" diff --git a/pr-preview/pr-564/templates/Processed_Aligned_Reads_Template.csv b/pr-preview/pr-564/templates/Processed_Aligned_Reads_Template.csv deleted file mode 100644 index 0c1700ac..00000000 --- a/pr-preview/pr-564/templates/Processed_Aligned_Reads_Template.csv +++ /dev/null @@ -1,40 +0,0 @@ -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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"," 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","#" -"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","#" -"workflowLink","Workflow URL reference","false","#" diff --git a/pr-preview/pr-564/templates/Processed_Expression_Template.csv b/pr-preview/pr-564/templates/Processed_Expression_Template.csv deleted file mode 100644 index b992b3e0..00000000 --- a/pr-preview/pr-564/templates/Processed_Expression_Template.csv +++ /dev/null @@ -1,28 +0,0 @@ -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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/pr-preview/pr-564/templates/Processed_Variant_Calls_Template.csv b/pr-preview/pr-564/templates/Processed_Variant_Calls_Template.csv deleted file mode 100644 index 3092fb6f..00000000 --- a/pr-preview/pr-564/templates/Processed_Variant_Calls_Template.csv +++ /dev/null @@ -1,28 +0,0 @@ -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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"," 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/pr-preview/pr-564/templates/Proteomics_Assay_Template.csv b/pr-preview/pr-564/templates/Proteomics_Assay_Template.csv deleted file mode 100644 index 8a2a7ed5..00000000 --- a/pr-preview/pr-564/templates/Proteomics_Assay_Template.csv +++ /dev/null @@ -1,29 +0,0 @@ -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","false","#" diff --git a/pr-preview/pr-564/templates/Protocol.csv b/pr-preview/pr-564/templates/Protocol.csv deleted file mode 100644 index 3c3dddff..00000000 --- a/pr-preview/pr-564/templates/Protocol.csv +++ /dev/null @@ -1,10 +0,0 @@ -"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/pr-preview/pr-564/templates/Protocol_Template.csv b/pr-preview/pr-564/templates/Protocol_Template.csv deleted file mode 100644 index ab848ad7..00000000 --- a/pr-preview/pr-564/templates/Protocol_Template.csv +++ /dev/null @@ -1,10 +0,0 @@ -"Field","Description","Required","ValidRange" -"title","Title of a resource.","true","#string" -"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","#string" -"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","#AssayEnum" -"protocolPurpose","Brief description of the protocol purpose.","false","#" -"sampleType","Type of sample used","false","#" diff --git a/pr-preview/pr-564/templates/RNASeq_Template.csv b/pr-preview/pr-564/templates/RNASeq_Template.csv deleted file mode 100644 index 1e8f26e4..00000000 --- a/pr-preview/pr-564/templates/RNASeq_Template.csv +++ /dev/null @@ -1,44 +0,0 @@ -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"targetDepth","The targeted read depth prior to sequencing.","false","#" diff --git a/pr-preview/pr-564/templates/ScRNASeq_Template.csv b/pr-preview/pr-564/templates/ScRNASeq_Template.csv deleted file mode 100644 index 4639e75e..00000000 --- a/pr-preview/pr-564/templates/ScRNASeq_Template.csv +++ /dev/null @@ -1,49 +0,0 @@ -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"comments","Brief free-text comments that may also be important to understanding the resource.","false","#" -"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","#" -"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/pr-preview/pr-564/templates/Source_Code_Template.csv b/pr-preview/pr-564/templates/Source_Code_Template.csv deleted file mode 100644 index 5b507101..00000000 --- a/pr-preview/pr-564/templates/Source_Code_Template.csv +++ /dev/null @@ -1,8 +0,0 @@ -"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","#" -"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","#" -"programmingLanguage","A computer programming language","false","#" -"runtimePlatform","Runtime platform or script interpreter dependencies (e.g. Java v1, Python 2.3).","false","#" diff --git a/pr-preview/pr-564/templates/WES_Template.csv b/pr-preview/pr-564/templates/WES_Template.csv deleted file mode 100644 index e6153d70..00000000 --- a/pr-preview/pr-564/templates/WES_Template.csv +++ /dev/null @@ -1,42 +0,0 @@ -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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/pr-preview/pr-564/templates/WGS_Template.csv b/pr-preview/pr-564/templates/WGS_Template.csv deleted file mode 100644 index a48f93ea..00000000 --- a/pr-preview/pr-564/templates/WGS_Template.csv +++ /dev/null @@ -1,40 +0,0 @@ -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"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","#" -"targetDepth","The targeted read depth prior to sequencing.","false","#"