Represent ontologies and ontology-encoded knowledge in a Neo4j graph.
SciGraph aims to represent ontologies and data described using ontologies as a Neo4j graph. SciGraph reads ontologies with owlapi and ingests ontology formats available to owlapi (OWL, RDF, OBO, TTL, etc). Have a look at how SciGraph translates some simple ontologies.
- OWL 2 Support
- Provide a simple, usable, Neo4j representation
- Efficient, parallel ontology ingestion
- Provide basic "vocabulary" support
- Stay domain agnostic
- Create ontologies based on the graph
- Reasoning support
SciGraph can be used in a number of ways. After the graph is generated it could be used in an application with no SciGraph dependency.
It could be used in an application with the
scigraph-core dependency which adds some convenience methods and includes "vocabulary" support. "Vocabulary" support resolves
labels to graph nodes, auto-complete functionality, OpenRefine resolution services, and CURIE to
IRI resolution. Additional support for identifying these vocabulary entities
in free text can be found in the
SciGraph can also be used as a stand-alone Dropwizard web service (via
scigraph-services). SciGraph services support adding custom Cypher
queries during application configuration to keep the code base domain agnostic.
Note that SciGraph is "OWL-centric". If you have, for example, and arbitrary SKOS ontology that doesn't assert skos:Concept as an owl:Class these skos:Concepts will not be visible to the owlapi and not loaded in the resulting Neo4j graph.
- the Monarch Initiative uses SciGraph for both ontologies and biological data modeling
- SciCrunch uses SciGraph for vocabulary and annotation services
- CINERGI uses SciGraph for vocabulary and annotation services
- the Human Brain project uses SciGraph for vocabulary and annotation services
curl https://raw.githubusercontent.com/SciGraph/SciGraph/master/src/test/resources/vagrant/Vagrantfile -o Vagrantfile vagrant up vagrant ssh
Note that because Neo4j is using memory mapped IO the database cannot be stored in a Vagrant shared directory
If you're not using the vagrant box make sure you have
java available. Java should be version 7 or better.
Clone and compile the project:
git clone https://github.com/SciGraph/SciGraph; cd SciGraph; mvn -DskipTests -DskipITs install
Build the graph:
cd SciGraph-core mvn exec:java -Dexec.mainClass="io.scigraph.owlapi.loader.BatchOwlLoader" -Dexec.args="-c src/test/resources/pizzaExample.yaml"
Run the services:
cd ../SciGraph-services mvn exec:java -Dexec.mainClass="io.scigraph.services.MainApplication" -Dexec.args="server src/test/resources/pizzaConfiguration.yaml"
Check out some of the REST endpoints (the Vagrant box has port 9000 mapped so you can use your host browser to check these out):
Also browse the generated REST documentation to see some of the other resources.
Thanks to YourKit for providing an Open Source license.
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