Skip to content

Latest commit

 

History

History
76 lines (46 loc) · 2.72 KB

README.md

File metadata and controls

76 lines (46 loc) · 2.72 KB
Raw

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. If you would like to deploy the entire OntoTools stack (OLS, OxO, and ZOOMA), check out the OntoTools Docker Config repository. If you would like to deploy OxO only, read on.

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.

Customisation

It is possible to customise several branding options in oxo-web/src/main/resources/application.properties:

  • oxo.customisation.debrand — If set to true, removes the EBI header and footer, documentation, and about page
  • oxo.customisation.title — A custom title for your instance, e.g. "My OxO Instance"
  • oxo.customisation.short-title — A shorter version of the custom title, e.g. "MYOxO"
  • oxo.customisation.description — A description of the instance
  • oxo.customisation.org — The organisation hosting your instance