baokunguo / owl2neo4j

Convert OWL to labeled property graph and import into Neo4J

OWL 2 Neo4J

Convert OWL schema ontologies to labeled property graph and import into Neo4J.

Note: currently the tool only converts the class hierarchy; instances are ignored for now.

Build

Each release comes with a precompiled JAR, created automatically by Travis-CI. To build the JAR file manually follow the three steps below. The JAR file will be created in dist.

Requirements:

• Java 7 or Java 8 or Java 11
• Gradle

git clone https://github.com/flekschas/owl2neo4j && cd owl2neo4j
gradle build

Import ontology

Requirements:

• Neo4J

A single file import is executed as follows:

java -jar ./dist/owl2neo4j.jar -o ./pizza.owl -n "Pizza Ontology" -a pizza

(To get pizza.owl run curl -O https://protege.stanford.edu/ontologies/pizza/pizza.owl.)

In order to import multiple ontologies at once create a JSON file:

{
	"server": "http://my-server:7474",
    "ontologies": [
        {
            "o": "./chebi.owl",
            "n": "Chemical Entities of Biological Interest",
            "a": "CHEBI"
        },
        {
            "o": "./cl.owl",
            "n": "Cell Ontology",
            "a": "CL",
            "i": true
        },
        {
            "o": "./efo.owl",
            "n": "Experimental Factor Ontology",
            "a": "EFO"
        }
    ]
}

a, i, n and o correspond to the CLI options. The only difference is that n, i.e. the path to the OWL file to be imported, should be relative to the JSON file. server is optional; when it's not defined, the default server url, i.e. http://127.0.0.1:7474, is used. Next you can import the everything with the following call:

$ java -jar ./dist/owl2neo4j.jar -b ./import.json

(Assuming that the file above is ./import.json.)

Command line options:

usage: java -jar owl2neo4j.jar -a <String> -b <Path> [--eqp <String>] [-h]
       [-i] [-l] -n <String> -o <Path> [-p <String>] [-s <URL>] [-u
       <String>] [-v] [--version]
Import OWL into Neo4J as a labeled property graph.

 -a,--abbreviation <String>   Ontology abbreviation (E.g. go)
 -b,--batch <Path>            Path to JSON file
    --eqp <String>            Existential quantification property (E.g.
                              http://www.co-ode.org/ontologies/pizza/pizza
                              .owl#hasTopping)
 -h,--help                    Shows this help
 -i,--incl-imports            Include import closure
 -l,--no-local                Don't scan for locally available OWL files
                              to ensure loading remote files.
 -n,--name <String>           Ontology name (E.g. Gene Ontology)
 -o,--owl <Path>              Path to OWL file
 -p,--password <String>       Neo4J user password
 -s,--server <URL>            Neo4J server root URL [Default:
                              http://localhost:7474]
 -u,--user <String>           Neo4J user name
 -v,--verbosity               Verbose output
    --version                 Show version

For detailed instructions and help regarding the different options please refer to the wiki.

Importing large ontologies:

By default the OWLAPI XML loader has a 64,000 triple limit. To increase the limit and being able to import larger ontologies start owl2neo4j.jar with DentityExpansionLimit=<LARGE_NUMBER> flag like so:

java -jar -DentityExpansionLimit=1000000 ./dist/owl2neo4j.jar -o ./extra-large-pizza.owl -n "Extra Large Pizza Ontology" -a elpo

Be sure that you have enough RAM to theoretical load 1000000 (or any other number), otherwise your system will complain.

Handshake error:

In case you see a handshake error of this form Remote host closed connection during handshake add the following parameter when calling java:

java -jar -Dhttps.protocols=TLSv1.1,TLSv1.2 ...