Reasoning

DAG IDs: reason (Sunlet), reason_openllet_new (Openllet) Schedule: Manual trigger only Files: dags/reason-spreadsheets.py, dags/reason_openlletnew.py

What It Does

Performs OWL 2 DL reasoning over the MSE-KG to materialise implicit knowledge that is only derivable from the ontological axioms defined in MWO, NFDIcore, and BFO. The reasoner computes the deductive closure of the ABox with respect to the TBox, generating inferred class assertions, subclass relationships, property assertions, and inverse property entailments that are not explicitly stated in the input graph but are logically entailed by the ontology.

The pipeline uses Openllet, an open-source OWL 2 DL reasoner forked from Pellet, which supports the full $\mathcal{SROIQ}(\mathcal{D})$ description logic. Openllet is invoked as an external process that reads the pre-filtered ontology and produces an OWL file containing only the inferred axioms.

Two reasoner variants

Two variants exist: reason uses the Sunlet reasoner, while reason_openllet_new uses Openllet. The latter is the current default used by all harvesters and the core pipeline.

Task Chain

graph LR
    A["init_data_dir"] --> B["pre_filter<br/>━━━━━━━━━━━<br/>ROBOT remove"]
    B --> C["openllet_reasoning<br/>━━━━━━━━━━━<br/>Openllet extract"]
    C --> D["robot_convert<br/>━━━━━━━━━━━<br/>OWL → Turtle"]
    D --> E["mark_success"]

    style A fill:#e8eaf6,stroke:#283593
    style B fill:#fff3e0,stroke:#e65100
    style C fill:#e3f2fd,stroke:#1565c0
    style D fill:#f3e5f5,stroke:#6a1b9a
    style E fill:#e8f5e9,stroke:#2e7d32

Step 1: Axiom Pre-Filtering

Before reasoning, the pipeline uses ROBOT to remove axioms that cause reasoning difficulties or are deprecated:

robot remove --input input.ttl \
  --term http://purl.obolibrary.org/obo/RO_0000057 \
  --axioms SubPropertyChainOf \
  remove \
  --term http://purl.obolibrary.org/obo/BFO_0000118 \
  --term http://purl.obolibrary.org/obo/BFO_0000181 \
  --term http://purl.obolibrary.org/obo/BFO_0000138 \
  --term http://purl.obolibrary.org/obo/BFO_0000136 \
  --output filtered.ttl

Removed Term	Reason
RO_0000057 (SubPropertyChainOf only)	Property chain axioms on has_participant cause reasoning complexity explosion
BFO_0000118	Deprecated BFO class
BFO_0000181	Deprecated BFO class
BFO_0000138	Deprecated BFO class
BFO_0000136	Deprecated BFO class

Why filter before reasoning?

SubPropertyChainOf axioms on has_participant (RO_0000057) interact with the large ABox to produce combinatorial explosion in reasoning time. Removing these chain axioms preserves the core semantics while making reasoning tractable. Deprecated BFO terms are removed to prevent spurious inferences from obsolete class definitions.

Step 2: Openllet Reasoning

The reasoner is invoked with an explicit selection of which axiom types to extract:

openllet extract \
  -s "PropertyAssertion SubPropertyOf InverseProperties SubClassOf ClassAssertion" \
  input-filtered.ttl > output_inferences.owl

Generated Axiom Types

Axiom Type	Description	Example
ClassAssertion	Inferred rdf:type statements	A person bearing an AgentRole is inferred to be an Agent
SubClassOf	Inferred class subsumption	ArtificialIntelligence ⊑ ComputerScience
SubPropertyOf	Inferred property hierarchies	Specialised participation relations
PropertyAssertion	Inferred object/data property values	Inverse of participates_in yields has_participant
InverseProperties	Materialised inverse property pairs	RO_0000056 ↔ RO_0000057

Why these axiom types?

This selection covers the axioms needed for SPARQL query answering: class assertions enable ?x a ?Class patterns, property assertions enable ?x ?prop ?y traversals, and subsumption enables hierarchical queries. Axiom types like DisjointClasses or EquivalentClasses are not extracted because they are schema-level (TBox) and already present in the input ontology.

Step 3: Conversion to Turtle

The OWL/XML output from Openllet is converted to Turtle using ROBOT:

robot convert --input inferences.owl --output inferences.ttl

The pipeline validates that the output is well-formed Turtle (not accidentally RDF/XML) by checking the file header.

Input

Source	Description
matwerk_sharedfs	Shared filesystem path
matwerk_last_successful_merge_run	Source directory (if source_run_dir not in conf)
openlletnewcmd	Openllet command path

Conf parameters (from triggering DAG or UI):

Parameter	Default	Description
artifact	spreadsheets	Name of the artifact being reasoned
in_ttl	spreadsheets_asserted.ttl	Input TTL filename
source_run_dir	(from Variable)	Custom source directory
target_run_dir	(auto-created)	Custom target directory

Output

Output	Description
{artifact}-filtered.ttl	Pre-processed TTL (problematic axioms removed)
{artifact}_inferences.owl	Openllet reasoning output (OWL/XML)
{artifact}_inferences.ttl	Converted Turtle inferences

Variables set on success:

• matwerk_last_successful_reason_run (if artifact is spreadsheets)
• matwerk_last_successful_reason_run__{artifact} (always)

Downstream

None. Trigger validation_checks after this DAG succeeds.