Neo4J Ontology Extensions

Collection of plug-ins and extensions to simplify access to the ontology-related properties and the annotation set hierarchy

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Content:

• 1. Installation
• 2. Endpoints
• 3. Usage

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1. Installation

For the sake of concision I assume that Neo4J has been installed in /neo4j/. Make sure to adjust it to your set-up accordingly.

1. Stop Neo4J

   neo4j stop
   
   $ neo4j start
   

2. Download or compile the JAR and copy it to Neo4J's plug-in directory.

   cp ./dist/ontology.jar /neo4j/plugins/
   

3. Enable unmanaged JAX-RS extensions. Open /neo4j/conf/neo4j-server.properties and ensure that the line starting with:

   org.neo4j.server.thirdparty_jaxrs_classes=
   

   looks like this:

   org.neo4j.server.thirdparty_jaxrs_classes=org.neo4j.ontology.server.unmanaged=/ontology/unmanaged
   

4. Start Neo4J

   neo4j start
   

5. OPTIONAL: Open http://localhost:7474 to check if everything works. In case nothing shows up check /path/to/neo4j/data/log/console.log and file an issue. Cheers.

Compile yourself

Travis-CI is automatically compiling the JAR for every release and attaches it to the release but you can surely compile the JAR yourself.

Requirements:

• Java RE 7
• Gradle

Compile:

gradlew build

2. Endpoints

Get the annotation set hierarchy

HTTP: GET

URL: http://localhost:7474/ontology/unmanaged/annotations/<USER_NAME>

Parameters:

• objectification: If true the response nodes property will be an object with the keys being the ontology term's URI. Default return type is an Array, i.e. false.

Description: Returns an object with all terms (or classes) directly or indirectly related to annotations of user's accessible data sets.

HTTP: POST

URL: http://localhost:7474/ontology/unmanaged/annotations/[<USER_NAME>]

Description: Labels ontology terms that belong to all (or a specific user's) annotation set hierarchy.

HTTP: DELETE

URL: http://localhost:7474/ontology/unmanaged/annotations/

Description: Remove all annotation set-related labels.

Get number of annotations per data set across the repository

URL: http://localhost:7474/db/data/ext/Annotations/graphdb/getNumAnnoPerDataSet

Description: A GET request returns the possible parameters and a POST request returns the actual results. The results could be used to draw a histogram to quickly confirm whether the annotations follow a Gaussian distribution or are biased.

3. Usage

1. Send a POST request to http://localhost:7474/ontology/unmanaged/annotations/ to prepare annotation sets for all users. Note, this step needs to be done whenever a user uploads, deletes or shares a data set.

2. Send a GET request to http://localhost:7474/ontology/unmanaged/annotations/<USER_NAME> to get the user's annotation set hierarchy.