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/

Note: VFB provides a single knowledgebase (vfb) containing all VFB ontologies and reasoning data. All examples in this documentation use the vfb knowledgebase.

Knowledgebase Operations

Note: VFB provides access to a single knowledgebase (vfb) containing all VFB ontologies and reasoning data. The general /kbs endpoint is not accessible - all operations must use /kbs/vfb/.

Get Knowledgebase Information

GET /kbs/vfb

Display information and status for the VFB knowledgebase.

Response: JSON object with KB information

DL Queries (Description Logic)

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

Subclasses

GET /kbs/vfb/subclasses

Get subclasses of a named class or class expression.

Parameters:

• object (query): Manchester-syntax OWL class expression
• prefixes (query): JSON format prefix map for expanding prefixes
• direct (query): true for direct subclasses only (default: true)
• includeEquivalent (query): Include equivalent classes (default: false)
• includeNothing (query): Include owl:Nothing (default: false)
• includeDeprecated (query): Include deprecated terms (default: true)

Superclasses

GET /kbs/vfb/superclasses

Get superclasses of a named class or class expression.

Parameters:

• object (query): Manchester-syntax OWL class expression
• prefixes (query): JSON format prefix map
• direct (query): true for direct superclasses only (default: true)
• includeEquivalent (query): Include equivalent classes (default: false)
• includeThing (query): Include owl:Thing (default: false)
• includeDeprecated (query): Include deprecated terms (default: true)

Equivalent Classes

GET /kbs/vfb/equivalent

Get equivalent classes of a named class or class expression.

Parameters:

• object (query): Manchester-syntax OWL class expression
• prefixes (query): JSON format prefix map
• direct (query): true for direct equivalents only (default: true)
• includeDeprecated (query): Include deprecated terms (default: true)

Satisfiability

GET /kbs/vfb/satisfiable

Check if a class expression is satisfiable.

Parameters:

• object (query): Manchester-syntax OWL class expression
• prefixes (query): JSON format prefix map

Response: Boolean indicating satisfiability

Instances

GET /kbs/vfb/instances

Get instances of a named class or class expression.

Parameters:

• object (query): Manchester-syntax OWL class expression
• prefixes (query): JSON format prefix map
• direct (query): true for direct instances only (default: true)
• includeDeprecated (query): Include deprecated terms (default: true)

Types

GET /kbs/vfb/types

Get types (classes) of a named individual.

Parameters:

• object (query): Individual IRI
• prefixes (query): JSON format prefix map
• direct (query): true for direct types only (default: true)
• includeThing (query): Include owl:Thing (default: false)
• includeDeprecated (query): Include deprecated terms (default: true)

SPARQL Services

Owlery provides SPARQL query capabilities with OWL reasoning support using Owlet-style embedded class expressions.

SPARQL Query (GET)

GET /kbs/vfb/sparql

Perform SPARQL query encoded in URL parameter.

Parameters:

• query (query): SPARQL query string

Response: SPARQL results in XML format (application/sparql-results+xml)

SPARQL Query (POST)

POST /kbs/vfb/sparql

Perform SPARQL query contained in request body.

Request Body:

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

Response: SPARQL results

SPARQL Query Expansion (GET)

GET /kbs/vfb/expand

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

Parameters:

• query (query): SPARQL query string

Response: Expanded SPARQL query (application/sparql-query)

SPARQL Query Expansion (POST)

POST /kbs/vfb/expand

Expand a SPARQL query contained in request body.

Request Body:

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

Response: Expanded SPARQL query

VFB Query Integration

VFB extensively uses Owlery for its high-level query operations. The following table shows how VFB’s named query operations map to Owlery API endpoints, focusing on the vfb knowledgebase:

Common VFB Query Patterns

Find all anatomical subclasses of the adult brain

GET /kbs/vfb/subclasses?object=FBbt_00003624&direct=false&includeDeprecated=false&includeEquivalent=true

Used in: PartsOf, SubclassesOf queries

Find all neurons with some part in the antennal lobe

GET /kbs/vfb/subclasses?object=<http://purl.obolibrary.org/obo/FBbt_00005106> and <http://purl.obolibrary.org/obo/RO_0002131> some FBbt_00007484&direct=false&includeDeprecated=false&includeEquivalent=true

Used in: NeuronsPartHere, neuron classification queries

Find all synaptic neuropils in the brain

GET /kbs/vfb/subclasses?object=FBbt_00005106&direct=false&includeDeprecated=false&includeEquivalent=true

Used in: NeuronsSynaptic, connectivity queries

Check if a class expression is valid

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

Find all neurons in the antennal lobe

GET /kbs/vfb/instances?object=FBbt_00007484

Find all synaptic neuropil subclasses

GET /kbs/vfb/subclasses?object=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.