Quick Start

General

The tool is invoked from the command line using the main script name, FAIRLinked, followed by a command and its specific arguments.

FAIRLinked [COMMAND] [OPTIONS]

To see the help message for any command, use the -h or --help flag.

FAIRLinked filter -h
FAIRLinked generate-template -help

InterfaceMDS Commands

These commands are used for interacting with the Materials Data Schema (MDS) ontology.

filter

Get terms associated with a certain Domain, Subdomain, or Study Stage.

Usage

FAIRLinked filter -t <SEARCH_TYPES> -q <QUERY_TERM> [OPTIONS]

Arguments

  • -q, --query_term: (Required) Enter the domain, subdomain, or study stage.

  • -t, --search_types: (Required) Specifies the search criteria. Choices: "Domain", "SubDomain", "Study Stage".

  • -op, --ontology_path: Path to the ontology file. Defaults to "default".

  • -te, --ttl_extr: Specifies whether user wants to save search results. Enter T or F. Defaults to "F".

  • -tp, --ttl_path: If user wants to save search results, provide path to save file. Append file name at the end of the path.

view-domains

Display unique Domains and SubDomains from the ontology.

Usage

FAIRLinked view-domains

dir-make

View and make directory tree of turtle files based on domains and subdomains.

Usage

FAIRLinked dir-make

add-terms

Add new terms to an existing ontology file via an interactive session.

Usage

FAIRLinked add-terms -op <PATH_TO_ONTOLOGY>

RDFTableConversion Commands

These commands facilitate the conversion of tabular data (CSV) to and from RDF (JSON-LD format).

generate-template

Generate a JSON-LD template based on a CSV file.

Usage

FAIRLinked generate-template -cp <CSV_PATH> -out <OUTPUT_PATH> -lp <LOG_PATH> [OPTIONS]

Arguments

  • -cp, --csv_path: (Required) Path to CSV file.

  • -out, --output_path: (Required) Path to output JSON-LD file.

  • -lp, --log_path: (Required) Path to store files that log labels that could/couldn’t be matched to a term in MDS-Onto.

  • -op, --ontology_path: Path to ontology. To get official MDS-Onto choose ‘default’.

serialize-data

Create a directory of JSON-LDs from a single CSV file.

Usage

FAIRLinked serialize-data -mdt <TEMPLATE_PATH> -cf <CSV_FILE> -rkc <ROW_KEY_COLS> ...

Arguments

  • -mdt, --metadata_template: (Required) Metadata template (path to JSON file if using CLI).

  • -cf, --csv_file: (Required) Path to the CSV file containing the data.

  • -rkc, --row_key_cols: (Required) Comma-separated list of column names used to uniquely identify rows (e.g. col1,col2,col3).

  • -orc, --orcid: (Required) ORCID identifier of the researcher.

  • -of, --output_folder: (Required) Directory where JSON-LD files will be saved.

  • -pc, --prop_col: Python dictionary literal to define relationships between columns.

  • -op, --ontology_path: Path to ontology. Must be provided if ‘prop_col’ is provided.

  • -base, --base_uri: Base URI used to construct subject and object URIs.

deserialize-data

Deserialize a directory of JSON-LDs back into a CSV.

Usage

FAIRLinked deserialize-data -jd <JSONLD_DIRECTORY> -on <OUTPUT_NAME> -od <OUTPUT_DIR>

Arguments

  • -jd, --jsonld_directory: (Required) Directory containing JSON-LD files.

  • -on, --output_name: (Required) Base name of output files.

  • -od, --output_dir: (Required) Path to directory to save the outputs.

QBWorkflow Commands

Commands related to the RDF Data Cube workflow.

data-cube-run

Start RDF Data Cube Workflow.

Description

This command launches an interactive workflow to create richly structured, multidimensional datasets that adhere to the RDF Data Cube vocabulary.

Usage

FAIRLinked data-cube-run