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Create a catalogue of samples (XML + TTL + validation)

Source: R/functions.R
specimen_catalogue.Rd

[Stable] This function reads a specimen spreadsheet template (e.g. 'specimen_template.xlsx') and generates, for each row in the SpecimenInfo sheet:

  • an XML representation of the sample, following the IGSN / ODM2 model;

  • a Turtle (TTL) representation using SOSA/SSN, PROV-O, DCAT and related vocabularies;

  • a SHACL-like validation report on each TTL file (via specimen_validate_ttl()).

The XML files are created by specimen_XML(), while the TTL files and the validation are handled by specimen_ttl().

Usage

specimen_catalogue(
  excel_path = NULL,
  creator_name = NULL,
  creator_surname = NULL,
  creator_orcid = NULL
)

Arguments

excel_path

A character string with the path to the spreadsheet template (typically 'specimen_template.xlsx').

creator_name

Character. First name of the sample(s) creator to be used in the TTL provenance metadata (DCMI / PROV).

creator_surname

Character. Last name of the sample(s) creator.

creator_orcid

Character. ORCID of the sample(s) creator (e.g. "0000-0002-1825-0097"). It will be normalised to a full ORCID URL (https://orcid.org/...) if needed.

Value

A list with:

  • output_dir – the root directory created for this run

  • specimen_uuids – vector of UUIDs assigned to specimens

  • validation – list of tibbles, one per TTL file, as returned by specimen_ttl() / specimen_validate_ttl().

The function also writes XML and TTL files to disk under output_dir.

Author

Alessandro Oggioni, PhD (2023–2025) oggioni.a@cnr.it

Examples

if (FALSE) { # \dontrun{
specimen_catalogue(
  excel_path = "./specimen_template.xlsx",
  creator_name = "Alessandro",
  creator_surname = "Oggioni",
  creator_orcid = "0000-0002-7997-219X"
)
} # }