Example: Process → Experiment

This example maps instance data conforming to a Process/ProcessStep/Input/InputSettings design pattern to an Experiment/ExperimentSetup/Sample/Parameters design pattern.

The mapping

flowchart TD
    ex:Process[Process]
    ex:ProcessStep[ProcessStep]
    ex:Input[Input]
    ex:InputSettings[InputSettings]
    ex:ChemicalInvestigation([ChemicalInvestigation])
    ex:Setup([Setup])
    ex:realizedOccurent([realizedOccurent])
    ex:Specimen([Specimen])
    ex:Experiment(Experiment)
    ex:ExperimentSetup(ExperimentSetup)
    ex:Sample(Sample)
    ex:Parameters(Parameters)

    subgraph ShapeValidation
        subgraph CoreShapeInformation
        ex:Process ==>|hasPart| ex:ProcessStep
        ex:Input ==>|isInput| ex:ProcessStep
        ex:Input ==>|hasModifier| ex:InputSettings
        end

    ex:Process --->|isSome| ex:ChemicalInvestigation
    ex:Process --->|isSome| ex:realizedOccurent
    ex:ProcessStep --->|describes| ex:Setup
    ex:Input --->|is_a| ex:Specimen
    end

    subgraph TransformedGraph
    ex:Experiment -->|hasExperimentSetup| ex:ExperimentSetup
    ex:Experiment -->|hasSample| ex:Sample
    ex:ExperimentSetup -->|performedWith| ex:Parameters
    ex:Sample -->|hasConcentrations| ex:Parameters
    end

    ex:Process -.....->|SHACL_bridge| ex:Experiment
    ex:ProcessStep -.....->|SHACL_bridge| ex:ExperimentSetup
    ex:Input -.....->|SHACL_bridge| ex:Sample
    ex:InputSettings -.....->|SHACL_bridge| ex:Parameters

Node shapes: rectangle = core source class (bridged), stadium = peripheral source class (validation-only), rounded rectangle = target class.

Running the example

just example
# or directly:
python examples/process_to_experiment/run_example.py

Or step by step via the CLI:

# 1. Validate the mapping
shacl-bridges validate examples/process_to_experiment/mapping/bridge.yaml

# 2. Inspect the generated diagram
shacl-bridges diagram examples/process_to_experiment/mapping/bridge.yaml

# 3. Generate the SHACL shape
shacl-bridges generate examples/process_to_experiment/mapping/bridge.yaml \
  -o examples/process_to_experiment/bridge_shape.ttl

# 4. Run the bridge on the test data
shacl-bridges run \
  examples/process_to_experiment/mapping/bridge.yaml \
  tests/test_data/data.ttl \
  --expanded examples/process_to_experiment/expanded.ttl \
  --diff     examples/process_to_experiment/diff.ttl

Expected output:

Data conforms to source pattern.
Bridge added N new triple(s).
Written: examples/process_to_experiment/expanded.ttl
Written: examples/process_to_experiment/diff.ttl

The mapping file

The full mapping lives in examples/process_to_experiment/mapping/bridge.yaml:

--8<-- "examples/process_to_experiment/mapping/bridge.yaml"

What the generated SHACL looks like

The tool generates a shape targeting ex:Process (the declared root):

shapes:BridgeShape
    a sh:NodeShape ;
    sh:targetClass ex:Process ;
    sh:property [
        sh:path ex:hasPart ;
        sh:node [ a sh:NodeShape ; sh:class ex:ProcessStep ; ... ] ;
    ] ;
    sh:rule [
        a sh:SPARQLRule ;
        sh:construct """
            CONSTRUCT {
              ?this rdf:type ex:Experiment .
              ?this ex:hasExperimentSetup ?var_b .
              ...
            }
            WHERE {
              ?this rdf:type ex:Process .
              ?this ex:hasPart ?var_b .
              ?var_b rdf:type ex:ProcessStep .
              ...
            }
        """ ;
    ] ;
.

Reading the diff output

The diff graph (diff.ttl) contains only the triples introduced by the bridge — nothing that was already in the source graph or derivable from RDFS inference. This makes it easy to verify exactly what the bridge produced.