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Neo4J Ontology Extensions Build Status

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


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/ and ensure that the line starting with:


    looks like this:

  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.



gradlew build

2. Endpoints

Get the annotation set hierarchy


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


  • 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.


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.


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.

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