Knowledge Graph Building (Semantic Uplifting)

This section describes how EMO-BON data is transformed into linked data and integrated into a knowledge graph.

Semantic Uplifting Process¶

RO-Crate SemBench Setup¶

The rocrate-sembench-setup action makes preparations for semantic uplifting by:

• Initializing an RO-Crate from a default profile if necessary

• Assembling required files and variables into the ~sembench_data_cache folder (files coming from the observatory-profile)

• Creating the ~sembench_kwargs.json file with configuration parameters

These steps separate RO-Crate-specific logic from pysembench logic on a conceptual level. The utility files produced by this action are untracked via the .gitignore.

Semantify Action¶

The semantify action performs:

• Generate TTL (Turtle format RDF) using pysubyt task

• Validate TTL using pyshacl task

• Generate LDES feed for linked data event streams

• Create list of generated items for reuse by rocrate-validate

RO-Crate Validation¶

The rocrate-validate process:

• Validates the RO-Crate structure and content

• Repairs issues where possible

• Reports validation results

Publishing to Pages¶

The rocrate-to-pages process:

• Converts RO-Crate to HTML for GitHub Pages

• Generates human-readable views of the data

Triple Store Construction¶

The EMO-BON triple store is built through a dockerized stack that:

1. Harvests links to datasets from data.emobon.embrc.eu/

2. Applies extensive harvest tricks to assemble ALL linked triples (including data turtle inside RO-Crates)

3. Exposes the triple store / SPARQL-endpoint at public URL (e.g., sparql.- or api.emobon.embrc.eu)

Catalogue Integration¶

Metadata is integrated into catalogues (e.g., FAIR EASE IDDAS) through:

1. Dockerized process execution

2. Harvesting links to datasets from data.emobon.embrc.eu/

3. Applying semantic harvest tricks to assemble linked triples (minimally ro-crate-metadata.json)

4. Exporting harvest result into dump file for import in asset catalogue