OWL Reasoning

Hermes provides optional OWL reasoning for post-coordinated expressions using the OWL API and the ELK reasoner.

OWL reasoning provides:

• Classification — determine equivalent concepts, direct super-concepts and proximal primitive supertypes for post-coordinated expressions
• Subsumption — more accurate than structural subsumption for complex expressions, correctly handling GCI axioms
• Necessary Normal Form (NNF) — a canonical representation with proximal primitive supertypes as focus concepts and all necessary relationships

Availability

OWL reasoning is opt-in. The OWL libraries are not included in the release jar or Homebrew install — they add ~30MB and most users don't need them.

Install method	OWL support
Homebrew (hermes)	No
Release jar (hermes.jar)	No
From source with :owl alias	Yes

Without OWL, hermes still provides structural subsumption and expression validation — which handles the majority of use cases.

Setup

1. Import with OWL axioms

OWL axiom reference set files must be imported. Use the --owl flag during import:

clj -M:run:owl --db snomed.db import ~/Downloads/snomed-2024/ --owl
clj -M:run:owl --db snomed.db index compact

Or with automated download:

clj -M:run:owl --progress --db snomed.db \
  install --dist uk.nhs/sct-clinical --api-key trud-api-key.txt --cache-dir /tmp/trud --owl \
  index compact

2. Run with OWL enabled

# HTTP server
clj -M:run:owl --db snomed.db --owl serve

# MCP server
clj -M:run:owl --db snomed.db --owl mcp

The reasoner initialises at startup. Check its status:

curl -s 'http://localhost:8080/v1/snomed/status' | jq .reasoningStatus
# => "active", "inactive", or "unavailable"

HTTP endpoints

Classify expression

curl -s 'http://localhost:8080/v1/snomed/classify?expression=73211009:363698007=84301002' | jq .

Returns:

• equivalent-concepts — pre-coordinated concepts equivalent to the expression
• direct-super-concepts — immediate supertypes
• proximal-primitive-supertypes — nearest primitive ancestors

Necessary Normal Form

curl -s 'http://localhost:8080/v1/snomed/necessary-normal-form?expression=73211009:363698007=84301002' | jq .

The NNF uses proximal primitive supertypes as focus concepts with all necessary relationships — a canonical form useful for comparison and storage.

Expression subsumption (OWL mode)

curl -s 'http://localhost:8080/v1/snomed/subsumes?a=73211009&b=73211009:363698007=84301002&mode=owl' | jq .

The mode=owl parameter uses the ELK reasoner instead of structural comparison.

Structural vs OWL subsumption

	Structural (default)	OWL
Available in	All installs	Source with :owl alias only
Handles GCI axioms	No	Yes
Handles role composition	No	Yes
Speed	Microseconds	Milliseconds
Sufficient for most use cases	Yes	—

Structural subsumption normalises both expressions and compares them structurally. This works correctly for the vast majority of cases. OWL reasoning is needed only when GCI axioms or advanced DL features affect the subsumption relationship.

Library usage

Add the OWL dependencies to your project:

;; deps.edn
net.sourceforge.owlapi/owlapi-apibinding {:mvn/version "5.5.1"
                                           :exclusions  [net.sourceforge.owlapi/owlapi-rio
                                                         net.sourceforge.owlapi/owlapi-oboformat
                                                         net.sourceforge.owlapi/owlapi-tools]}
io.github.liveontologies/elk-owlapi      {:mvn/version "0.6.0"}

Then:

(require '[com.eldrix.hermes.core :as hermes])

(def svc (hermes/open "snomed.db"))
(hermes/activate-reasoner svc)
(hermes/reasoning-status svc)  ;; => :active

;; Classify
(hermes/classify-expression svc "73211009:363698007=84301002")

;; OWL subsumption
(hermes/subsumes svc "73211009" "73211009:363698007=84301002" :mode :owl)

;; Necessary Normal Form
(hermes/necessary-normal-form svc "73211009:363698007=84301002")