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https://github.com/flekschas/owl2neo4j
Convert OWL to labeled property graph and import into Neo4J
https://github.com/flekschas/owl2neo4j
gradle import java neo4j ontology owl
Last synced: 2 months ago
JSON representation
Convert OWL to labeled property graph and import into Neo4J
- Host: GitHub
- URL: https://github.com/flekschas/owl2neo4j
- Owner: flekschas
- License: mit
- Created: 2015-07-13T17:31:07.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2021-09-07T22:48:35.000Z (over 3 years ago)
- Last Synced: 2024-03-19T00:44:38.293Z (10 months ago)
- Topics: gradle, import, java, neo4j, ontology, owl
- Language: Java
- Size: 30.3 MB
- Stars: 46
- Watchers: 6
- Forks: 9
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Citation: CITATION.bib
Awesome Lists containing this project
README
# OWL 2 Neo4J [](https://travis-ci.org/flekschas/owl2neo4j)
Convert [OWL](owl) schema ontologies to labeled property graph and import into [Neo4J](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](jre7) or [Java 8](jre8) or [Java 11](jdk11)
* [Gradle](gradle)
```
git clone https://github.com/flekschas/owl2neo4j && cd owl2neo4j
gradle build
```
## Import ontology
**Requirements**:
* [Neo4J](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 -b [--eqp ] [-h]
[-i] [-l] -n -o [-p ] [-s ] [-u
] [-v] [--version]
Import OWL into Neo4J as a labeled property graph.
-a,--abbreviation Ontology abbreviation (E.g. go)
-b,--batch Path to JSON file
--eqp 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 Ontology name (E.g. Gene Ontology)
-o,--owl Path to OWL file
-p,--password Neo4J user password
-s,--server Neo4J server root URL [Default:
http://localhost:7474]
-u,--user Neo4J user name
-v,--verbosity Verbose output
--version Show version
```
For detailed instructions and help regarding the different options please refer to the [wiki](./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=` 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 ...
```
[gradle]:https://gradle.org/
[jre7]:http://www.oracle.com/technetwork/java/javase/downloads/jre7-downloads-1880261.html
[jre8]:http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html
[jre11]:http://jdk.java.net/11/
[neo4j]:http://neo4j.com/
[owl]:www.w3.org/2004/OWL/