OxO is a service for finding mappings (or cross-references) between terms from ontologies, vocabularies and coding standards. OxO imports mappings from a variety of sources including the Ontology Lookup Service and a subset of mappings provided by the UMLS.

OxO with Docker

OxO is comprised of three components:

• The loader scripts (oxo-loader/), which pull data about terms and mappings from the OLS, OBO xrefs, and UMLS and upload them to neo4j
• The indexer (oxo-indexer/), which indexes terms and mappings found in neo4j in solr
• The Web application (oxo-web/), which provides the user interface

The preferred method of deployment for OxO is using Docker. First, create the necessary volumes:

docker volume create --name=oxo-neo4j-data
docker volume create --name=oxo-neo4j-import
docker volume create --name=oxo-mongo-data
docker volume create --name=oxo-solr-data
docker volume create --name=oxo-hsqldb

Then, start OxO:

docker-compose up

The OxO instance will be empty until the loader and indexer have been executed.

Running the loader

The loader scripts are documented in the README of the oxo-loader/ directory.

Running the indexer

After using the loader to load data into neo4j, the indexer can be executed using Docker:

docker run --net=host ebispot/oxo-indexer:dev

OxO without Docker

Sometimes it is impractical to use Docker (e.g. for local development). To get OxO up and running without Docker, first install:

• neo4j community edition 3.1.1
• solr 5.3.0
• Java 1.8
• Maven

The instructions for the loader are not Docker-specific, and can be found in the oxo-loader/ directory. For the indexer and Web application, first compile the project using Maven:

mvn clean package

Then run the indexer:

java -Xmx10g -jar oxo-indexer.jar

The Web application is a standard WAR and can be deployed using e.g. Tomcat.