process_ontology_files {FAIRmaterials}

Process Ontology CSV Files

Description

This function reads, processes, and combines ontology CSV files from a specified folder. These CSV files must be formatted with template from:

https://docs.google.com/spreadsheets/d/1k7gFRc1Yslc-m65aWfFCxqk5UtrKZl9c3GyEFQvLSFU/edit?usp=drive_link

It can handle subdirectories by producing separate unmerged outputs for each subdirectory. The function generates an ontology tree plot, saves it as SVG, and serializes the RDF object to Turtle and JSON-LD formats in the specified folder. Additionally, it allows for the merging of multiple ontologies, with options to customize the merged RDF dataset's metadata.

Usage

process_ontology_files(
  folder_path,
  add_external_onto_info = FALSE,
  include_graph_valuetype = TRUE,
  merge_base_uri = NULL,
  merge_title = NULL,
  merge_author = NULL,
  merge_version = NULL,
  merge_description = NULL
)

Arguments

folder_path

Path to the folder containing ontology CSV files.

add_external_onto_info

Logical indicating whether to update information in RDF.

include_graph_valuetype

Logical indicating whether to include value types in the graph.

merge_base_uri

String containing base URI for the merged ontology. Defaults to NULL but is required for merging ontologies. Leave as default when only processing one ontology.

merge_title

String containing title for the merged ontology.. Defaults to NULL will concatenate titles of all merged ontologies. Leave as default when only processing one ontology.

merge_author

One String containing authors for the merged ontology. Defaults to NULL will concatenate all unique Author names of merged ontologies. Leave as default when only processing one ontology.

merge_version

String containing version for the merged ontology.. Defaults to NULL will leave version blank. Leave as default when only processing one ontology.

merge_description

String containing description for the merged ontology. Defaults to NULL will concatenate descriptions of all merged ontologies with relative titles as prefixes. Leave as default when only processing one ontology.

Details

This function processes ontology CSV files in a specified folder and its subdirectories. For each subdirectory, it creates separate unmerged outputs named with the folder name prefix. The merged output is generated in the main folder path.

If you have a single ontology, place all CSV files in the specified folder and run the function with default parameters. The function will generate outputs for this single ontology, including an ontology tree plot and serialized RDF formats.

For multiple ontologies across different subdirectories, the function will process each subdirectory separately. Each subdirectories ontology will have its own set of outputs. Additionally the function will merge the ontologies from all subdirectories. This merged output can have customized metadata such as title, authors, version, URL, and description. If no metadata is specified the merging process concatenates titles, authors, and descriptions from all included ontologies. Note that specifying a base uri is required for merging ontologies.

Examples

# Create temporary directory
temp_dir <- tempdir()
XRay_test_folder <- file.path(temp_dir, "XRay")
dir.create(XRay_test_folder, recursive = TRUE)

# Copy CSV files from the package's extdata to the temporary directory
extdata_path <- system.file("extdata", "XRay", package = "FAIRmaterials")
file.copy(from = list.files(extdata_path, full.names = TRUE),
  to = XRay_test_folder, recursive = TRUE)

# Process the CSV files in temp the XRay folder
process_ontology_files(XRay_test_folder, add_external_onto_info = FALSE)

# Clean up
unlink(temp_dir, recursive = TRUE)