FAQ

• How can SciGraph be added to my build?

<dependency>
  <groupId>io.scigraph</groupId>
  <artifactId>scigraph-core</artifactId>
  <version>2.0</version>
  <type>jar</type>
  <scope>compile</scope>
</dependency>

• How can an ontology be loaded into a Neo4j graph from the command line?

mvn exec:java -Dexec.mainClass=io.scigraph.owlapi.OwlLoader -Dexec.arguments="-c src/test/resources/loadExample.yaml" Customize loadExample.yaml as necessary. You may also want to set your MAVEN_OPTS environment variable to allow better performance: -server -d64 -XX:+UseParNewGC -XX:+UseConcMarkSweepGC -XX:+CMSParallelRemarkEnabled -XX:+AggressiveOpts -XX:+UseFastAccessorMethods -XX:+UseBiasedLocking -XX:NewRatio=2 -Xms8G -Xmx16G -XX:-ReduceInitialCardMarks (depending on the memory available to you).

• How can an ontology be loaded into a Neo4j graph from Java?

OntologyConfiguration ontologyConfiguration = new OntologyConfiguration();
ontologyConfiguration.setGraphLocation(graphLocation);
OwlLoadConfiguration config = new OwlLoadConfiguration();
config.setOntologyConfiguration(ontologyConfiguration);
config.getOntologyUrls().add(url);
OwlLoader.load(config);

• What can be specified in the yaml load configuration?

ontologyConfiguration:
   # Indicated the path containing the neo4j graph. 
   # Note that if a graph exists in this location the loader will append to the existing graph
   graphLocation: /tmp/generatedGraph

ontologyUrls:
  # URLs to load into the graph
  # They can be local paths:
  - /tmp/someLocalOntology.owl
  # Remote URLs
  - http://example.org/wine.owl
  # This can be any format that owl-api can read
  - http://example.org/wineBottles.ttl

categories:
  # Categories are applied after the graph has been loaded. They propagate from the
  # from the parent URI and add a property attribute to all subclasses. A concept
  # may have multiple categories.
  http://example.org/wine/WINE_Red : red-wine
  http://example.org/wine/WINE_White : white-wine

mappedProperties:
  # Controls how ontology properties are mapped to Neo4j properties.
  - name: label # The name of the neo4j property
    properties: # A list of properties to map to the neo4j property
    - http://www.w3.org/2000/01/rdf-schema#label
  - name: synonym
    properties: # Properties are appended so there may be multiple values
    - http://example.org/wine#hasExactSynonym
    - http://example.org/wine#AKA

• What can be specified in the runtime configuration?

curies:
  # CURIEs are mapped during runtime time.
  http://example.org/wine/WINE_ : WINE
  http://example.org/other/OTHER_ : OTHER

serviceMetadata:
  # Application specific OpenRefine settings 
  name: 'SciGraph Reconciliation Service'
  identifierSpace: 'http://example.org'
  schemaSpace: 'http://example.org'
  view: {
    url: 'http://localhost:9000/scigraph/refine/view/{{id}}'
  }
  preview: {
    url: 'http://localhost:9000/scigraph/refine/preview/{{id}}',
    width: 400,
    height: 400
 }