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Update terms and template docs (#90)
* Remove another deprecated modelSystemStrainNomenclature * Update schema csv and jsonld Add to modelSystemName, make dataType required, rewording some descriptions, add backend class notation, range and editor note (mainly for docs) * Update ext_classes * Add documentation functions and sections, regenerate * Revise new extended classes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| #' Function to generate template documentation | ||
| #' | ||
| #' Creates one row per property and selected informational columns for: | ||
| #' - marginality (required vs. recommended vs. optional; in our case, recommended/optional collapsed to optional) | ||
| #' - controlled values / constraints on fields | ||
| #' - cardinality (one or many values allowed) *currently omitted, see additional notes | ||
| #' Example related resources for what this can look like: | ||
| #' 1. https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE | ||
| #' 2. https://fairplus.github.io/the-fair-cookbook/content/recipes/interoperability/transcriptomics-metadata.html#assay-metadata | ||
| #' 3. https://www.immport.org/shared/templateDocumentation?tab=1&template=bioSamples.txt | ||
| #' 4. https://lincsproject.org/LINCS/files//2020_exp_meta_stand/General_Proteomics.pdf | ||
| #' Marginality is mentioned in all examples. | ||
| #' CV is mentioned for #1,2,3. | ||
| #' Cardinality is mentioned in #1 only, so it's not prioritized. | ||
| docTemplate <- function(schema, savedir = "templates/") { | ||
| templates <- schema %>% | ||
| filter(Root == "Template" & SubclassOf != "") %>% | ||
| select(ID, DependsOn) | ||
| for(template in templates$ID) { | ||
| fields <- schema %>% | ||
| filter(template == ID) %>% | ||
| pull(DependsOn) %>% | ||
| strsplit(split = ", ?") %>% | ||
| unlist() | ||
| index <- match(fields, schema$Attribute) | ||
| # ControlledVocab col is handled specially and is derived from the Range col | ||
| # Range is either filled with a class or blank, where blank means free text or Boolean values | ||
| # Bools are "controlled vocabulary" vs. true ontology terms | ||
| range <- dplyr::if_else(schema[index, "Range"] != "", paste0("#", schema[index, "Range"]), schema[index, "Valid.Values"]) | ||
| template_tab <- data.frame(Field = fields, | ||
| Description = schema[index, "Description"], | ||
| Required = ifelse(schema[index, "Required"], "required", "optional"), | ||
| ControlledVocab = range, | ||
| # Cardinality = schema[index, "Cardinality"], | ||
| Note = schema[index, "EditorNote"]) | ||
| write.csv(template_tab, file = paste0(savedir, template, ".csv"), row.names = F) | ||
| } | ||
| } | ||
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