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https://github.com/SciGraph/SciGraph

A Neo4j backed ontology store
https://github.com/SciGraph/SciGraph

java neo4j-graph ontologies scigraph

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A Neo4j backed ontology store

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README 

        
SciGraph

========

[![Build Status](https://travis-ci.org/SciGraph/SciGraph.svg?branch=master)](https://travis-ci.org/SciGraph/SciGraph)

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Represent ontologies and ontology-encoded knowledge in a Neo4j graph.



Motivation

----------

SciGraph aims to represent ontologies and data described using ontologies as a Neo4j graph. SciGraph

reads ontologies with [owlapi](http://owlapi.sourceforge.net/) and ingests

ontology formats available to owlapi (OWL, RDF, OBO, TTL, etc).

Have a look at [how SciGraph translates some simple ontologies](https://github.com/SciGraph/SciGraph/wiki/Neo4jMapping).



Goals:

* OWL 2 Support

* Provide a simple, usable, Neo4j representation

* Efficient, parallel ontology ingestion

* Provide basic "vocabulary" support

* Stay domain agnostic



Non-goals:

* Create ontologies based on the graph

* Reasoning support



What's Included?

----------------

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-entity` module.



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.



Alternatives

------------

* [tinkerpop sail implementation](https://github.com/tinkerpop/blueprints/wiki/Sail-Implementation)

* [owlapi](https://owlcs.github.io/owlapi/)

* [jena tdb](https://jena.apache.org/documentation/tdb/)



Applications

------------

 * the [Monarch Initiative](http://monarchinitiative.org/) uses SciGraph for both ontologies and biological data modeling

 * [SciCrunch](http://scicrunch.org/) uses SciGraph for vocabulary and annotation services

 * [CINERGI](http://earthcube.org/group/cinergi) uses SciGraph for vocabulary and annotation services

 * the [Human Brain project](https://nip.humanbrainproject.eu/) uses SciGraph for vocabulary and annotation services



Additional Documentation

------------------------



 * [Overview of SciGraph in NIF and Monarch](https://github.com/SciGraph/SciGraph/raw/master/docs/presentation/20150801%20SciGraph.pptx)



Getting Started

---------------

[A Docker container is included with instructions](https://github.com/SciGraph/SciGraph/tree/master/docker/)



Alternatively, a [Vagrant](https://www.vagrantup.com/) box is included if you don't want to modify your `localhost` (you'll also need [VirtualBox](https://www.virtualbox.org/)).

You can launch a provisioned box like this and then follow the steps below:



    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 or docker container make sure you have `git`, `maven`, and `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):



 - [Get autocomplete candidates for a prefix](http://localhost:9000/scigraph/vocabulary/autocomplete/Sp)



 - [Find a class based on an "exactish" term match](http://localhost:9000/scigraph/vocabulary/search/Shrimps)



 - [Get the graph neighborhood of a class](http://localhost:9000/scigraph/graph/neighbors/pizza:PrawnsTopping)



 - [Visualize the graph neighborhood of a class](http://localhost:9000/scigraph/graph/neighbors/pizza:AmericanHot.png)



 - [Visualize a custom, domain specific Cypher query](http://localhost:9000/scigraph/dynamic/toppings.png?pizza_id=pizza:FourSeasons)



Also browse the [generated REST documentation](http://localhost:9000/scigraph/docs/)

to see some of the other resources.



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Thanks to YourKit for providing an Open Source license.



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