OntoString

OntoString is a tool for curating mappings from free text to ontology terms. For a detailed description of the OntoString use case, see the OntoString Tutorial.

Build and run locally

Prerequisites

• Java 11
• MongoDB

Instructions

1. You need a local MongoDB instance running on port 27017
2. Add at least one super user in the DB in the users collection. From the Mongo shell:

db.users.insert({
  "name": "Super user",
  "email": "ontostring@ebi.ac.uk",
  "superUser": true,
  "roles": []
})

3. Set ontostring.auth.enabled to false in the dev profile in application.yml
4. Run mvn clean package -Dspring.profiles.active=dev
5. Then you can start the server: java -jar -Dspring.profiles.active=dev target/ontostring-*.war

OntoString should now be live at http://localhost:8080/spot/ontostring

Docker

To build a Docker image run the build.sh script under scripts