Chapter 5 Appendix

5.1 Appendix A – Description of ASPAR_KR packages.

A package is a variation of the classes in Figure 2.1. A list of the packages, and the fields available in them is present in the the terms overview. If a package you need is not available, please refer to Annex 5.2.

5.1.1 Observation unit packages

Default: Standard observational unit. Here you fill in treatments that were applied on the experimental unit itself.

5.1.2 Sample packages

Compost: A sample of compost. It is important to indicate whether it is has azoles in it.
CFUCountCulture: Results of a plate count assay. One can use this package if you put material which originates from a single Sample on plate culture.
AirStrip: A airstrip sample taken according to Kortenbosch et al. (2022).

5.1.3 Assay packages

Like a PCR test result, can be added upon request.

5.2 Appendix B – Extend ASPAR_KR with your own packages.

5.2.1 Planning the addition.

Since it is not possible for the developer of ASPAR_KR to know about all the research data that should be standardised with ASPAR_KR, a package can be requested on gitlab ² If you want to add the package yourself, it is possible, by understanding the class structure of ASPAR_KR Figure 5.1.

Figure 5.1: Classes availible within the ASPAR KR database. Each class `owns’ lower level classess. For example, a sample has associated assays.

5.2.2 Adding the packages.³

First we obtain the latest version of the metadata files as such:

suppressMessages(require(tidyverse))
#' Constructs the download link to the FAIRDS metadata files.
#' @param type The type of metadata to obtain.
.meta_data_link_builder <- function(type = "terms") {
  .accepted <- c("terms", "Sample", "Investigation", "ObservationUnit", "Assay")
  if (!(type %in% .accepted)) {
    stop(paste("Given type", type, " is not within", .accepted))
  }
  paste0("https://gitlab.com/m-unlock/fairds-metadata/-/raw/main/", 
         type, ".tsv?ref_type=heads", collapse = "")
}

# Download the terms sheet.
terms <- readr::read_delim(.meta_data_link_builder("terms"))

## Rows: 682 Columns: 7
## ── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (7): Item label, Requirement, Value syntax, Example, Preferred unit, URL...
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

sample_meta_data <- readr::read_delim(.meta_data_link_builder("Sample"))

## Rows: 2421 Columns: 4
## ── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (4): # Level, Package name, Item label, Requirement
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Then we can add a sample:

# add a sample.

.add_package <- function(packages,
                        level = NA,
                        name = NA,
                        label = NA,
                        requirement = NA) {
  .accepted_requirement <- c("optional", "manditory", "ignore");
  for (re in requirement) {
    if (!(requirement %in% .accepted_requirement)) {
      stop(paste("Given requirement", re, 
                 " is not within", .accepted_requirement))
    }  
  }
  
  df <- dplyr::tibble("# Level" = level,
                      "Package name" = name,
                      "Item label" = label,
                      "Requirement" = requirement)
  rbind(df, packages)
}

new_packages <- .add_package(sample_meta_data,
                             level = "Sample",
                             name = "test",
                             label = "label",
                             requirement = "optional")
new_packages

## # A tibble: 2,422 × 4
##    `# Level` `Package name` `Item label`                Requirement
##    <chr>     <chr>          <chr>                       <chr>      
##  1 Sample    test           label                       optional   
##  2 Sample    default        sample identifier           mandatory  
##  3 Sample    default        sample description          mandatory  
##  4 Sample    default        sample name                 mandatory  
##  5 Sample    default        ncbi taxonomy id            mandatory  
##  6 Sample    default        scientific name             mandatory  
##  7 Sample    default        biosafety level             mandatory  
##  8 Sample    default        sampling strategy           optional   
##  9 Sample    default        sample treatment            optional   
## 10 Sample    default        observation unit identifier mandatory  
## # ℹ 2,412 more rows

References

Kortenbosch, Hylke H., Fabienne Van Leuven, Bas J. Zwaan, and Eveline Snelders. 2022. “Catching More Air: An Effective and Simple-to-Use Air Sampling Approach to Assess Aerial Resistance Fractions in Aspergillus Fumigatus.” Preprint. Microbiology. https://doi.org/10.1101/2022.11.03.515058.

See ‘filing issues’ for more information on how to do this.↩︎
Note: It is possible to add packages completely by your self after obtaining push permissions from Jasper Koehorst, but this is out of the scope of this guide.↩︎