Owlery API

The Owlery API is VFB’s OWL (Web Ontology Language) reasoning service, providing advanced query capabilities over the ontologies used in VFB. It enables Description Logic (DL) queries, SPARQL queries with OWL reasoning, and access to multiple knowledgebases.

API Endpoint

Base URL: https://owl.virtualflybrain.org/kbs/vfb/

Note: VFB provides a single knowledgebase (vfb) containing all VFB ontologies and reasoning data.

DL Queries (Description Logic)

Owlery provides standard OWL DL query operations for reasoning over class hierarchies and relationships.

Subclasses

GET /kbs/vfb/subclasses/{class}

Get all subclasses of a named class or class expression.

Parameters:

• class: Class IRI or expression

Query Parameters:

• direct: true for direct subclasses only (default: false)

Superclasses

GET /kbs/vfb/superclasses/{class}

Get all superclasses of a named class or class expression.

Equivalent Classes

GET /kbs/vfb/equivalent/{class}

Get classes equivalent to the specified class.

Instances

GET /kbs/vfb/instances/{class}

Get all instances (individuals) of a class.

Types

GET /kbs/vfb/types/{individual}

Get all types (classes) of a named individual.

Satisfiability

GET /kbs/vfb/satisfiable/{class}

Check if a class expression is satisfiable (consistent).

SPARQL Services

Owlery provides SPARQL query capabilities with OWL reasoning support.

SPARQL Endpoint

GET /kbs/vfb/sparql?query={sparql_query}
POST /kbs/vfb/sparql

Execute SPARQL queries with OWL reasoning. Supports Owlet-style embedded class expressions.

Query Parameters (GET):

• query: URL-encoded SPARQL query

Request Body (POST):

• Content-Type: application/sparql-query
• Body: SPARQL query text

SPARQL Query Expander

GET /kbs/vfb/expand?query={sparql_query}
POST /kbs/vfb/expand

Expand a SPARQL query by transforming Owlet-style embedded class expressions into FILTER clauses.

VFB Query Integration

Owlery is extensively used in VFB’s high-level query chains. The following table shows how VFB’s named query operations map to Owlery API endpoints:

Common VFB Query Patterns

Find all anatomical subclasses of the adult brain

GET /kbs/vfb/subclasses/FBbt_00003624

Used in: PartsOf, SubclassesOf queries

Find all neurons that are part of a specific type

GET /kbs/vfb/instances/FBbt_00005106

Used in: NeuronsPartHere, neuron classification queries

Find all synaptic neuropils in the brain

GET /kbs/vfb/subclasses/FBbt_00005106?direct=true

Used in: NeuronsSynaptic, connectivity queries

Check if a class expression is valid

GET /kbs/vfb/satisfiable/FBbt_00003624

Used in: Query validation and reasoning checks

Complex Query Examples

Many VFB queries combine Owlery with other services. For example, the “Neurons with presynaptic terminals in antennal lobe” query typically involves:

1. Owlery reasoning: Find anatomical subclasses of the antennal lobe
2. Neo4j lookup: Find neurons with presynaptic terminals in those regions
3. SOLR search: Retrieve associated images and metadata

While these complex queries are handled by VFB’s query orchestration system, the individual Owlery components can be called directly for custom analyses.

Usage Examples

Note: VFB supports both full IRIs (e.g., http://purl.obolibrary.org/obo/FBbt_00003624) and short forms (e.g., FBbt_00003624) for class identifiers.

Basic Ontology Queries

Find all parts of the adult brain

GET /kbs/vfb/subclasses/FBbt_00003624
# or using full IRI:
GET /kbs/vfb/subclasses/http://purl.obolibrary.org/obo/FBbt_00003624

Find all neurons in the antennal lobe

GET /kbs/vfb/instances/FBbt_00007484

Find all synaptic neuropil subclasses

GET /kbs/vfb/subclasses/FBbt_00005106

SPARQL Reasoning Examples

Find GABAergic neurons using OWL reasoning

PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?neuron ?label
WHERE {
  ?neuron rdfs:subClassOf <http://purl.obolibrary.org/obo/FBbt_00005106> .
  ?neuron rdfs:label ?label .
  FILTER(CONTAINS(?label, "GABA"))
}

Find anatomical parts with expression data

PREFIX owl: <http://www.w3.org/2002/07/owl#>
SELECT ?part ?expression
WHERE {
  ?part rdfs:subClassOf <http://purl.obolibrary.org/obo/FBbt_00003624> .
  ?expression <http://purl.obolibrary.org/obo/RO_0002292> ?part .
}

Response Formats

Owlery returns results in JSON format by default. Available formats include:

• application/json (default)
• text/plain
• application/rdf+xml
• text/turtle

Specify format using the Accept header or format query parameter.

Error Handling

Owlery returns standard HTTP status codes:

• 200: Success
• 400: Bad request (invalid query/parameters)
• 404: Knowledgebase or resource not found
• 500: Server error

Error responses include JSON with error details:

{
  "error": "Error message",
  "details": "Additional information"
}

Integration with VFB

Owlery is a core component of VFB’s query system, providing the reasoning capabilities that power complex anatomical and connectivity queries. It’s used in combination with the PDB (Neo4j) and SOLR search services to deliver comprehensive results to users.