AOP-CAM Knowledge Provider database pipeline

This repository contains a makefile and resources for constructing the RDF triplestore used in the AOP-CAM Knowledge Provider prototype for NCATS Data Translator. Source code for the web service API used to query this data can be found at TranslatorIIPrototypes/cam-api. The web service API can be tested from within its Swagger API documentation. The current version of this database can queried with SPARQL using the endpoint https://stars-app.renci.org/cam/sparql.

Development of the prototype is led by Jim Balhoff (RENCI, UNC-Chapel Hill) and Stephen Edwards (RTI International), funded by the National Center for Advancing Translational Sciences.

Data sources

Ontologies

This resources integrates a broad set of ontologies developed as part of the OBO Library. The complete list can be see in the OWL imports declarations within https://github.com/TranslatorIIPrototypes/cam-pipeline/blob/master/ontologies.ofn.

Data

The data sets integrated into the database consist of independent OWL instance models making use of the terms and relations defined within the combined ontology (as described in 'Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems'). Currently three main types of data are included:

Causal Activity Models annotated by Gene Ontology biocurators (see http://geneontology.org/go-cam)
Causal Activity Models automatically translated from Reactome pathways (see geneontology/pathways2GO)
Causal Activity Models automatically translated from Comparative Toxicogenomics Database chemical–gene interactions (see balhoff/ctd-to-owl)

Building the database

Prerequisites

A Unix-like environment with the GNU Make workflow tool
Java 8 or higher
These tools on your PATH:
Clone the Gene Ontology Noctua models repo in ../noctua-models
Clone the Gene Ontology Noctua models repo in ../noctua-models-dev and git checkout dev in that directory (this is to obtain the converted Reactome pathways, which are not yet officially released)

Running

First ensure enough memory is available for all the commands:

   export JVM_ARGS=-Xmx256G
   export ROBOT_JAVA_ARGS=-Xmx256G
   export JAVA_OPTS=-Xmx256G

Run make cam-db-reasoned.jnl
Wait a few days...