The MO-LD project, Enhancing the FAIRness of Yeast and other model organism data

Presenting Author Information 


Michel Dumontier


Stanford University

BD2K Grant Number



Michel Dumontier

ORCID (optional)



Phone Number

(650) 497-3260

Additional Author Information 

Maxime Deraspe2, Gail Binkley3, Kalpana Karra3, Gos Micklem4, Julie Sullivan4, Michael J. Cherry4, and Michel Dumontier1

1Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, United States;

2Department of Molecular Medicine, Université Laval, Quebec, Canada;

3Department of Genetics, Stanford University, Stanford, United States; 4Department of Genetics, University of Cambridge, Cambridge, United Kingdom

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Abstract Title

The MO-LD project, Enhancing the FAIRness of Yeast and other model organism data

Abstract Description

Model organisms such as budding yeast provide a common platform to interrogate and understand cellular and physiological processes. Knowledge about model organisms, whether generated during the course of scientific investigations, or extracted from published articles, are integrated and made available by model organism databases (MODs) such as the Saccharomyces Genome Database (SGD). SGD and many MODs use InterMine, a system for integrating, analysing, and republishing biological data from multiple sources that also enables data-driven bioinformatic analyses through a web user interface and programmatic web services.

Here, we developed a cloud-ready dockerized platform that uses Semantic Web technologies to transform and make available model organism data in a manner that makes it easier to discover, explore, and query. First, we developed a pipeline to extract, transform, and load a Linked Data representation of the InterMine store. Second, we use Docker to package both software and data for local or remote deployment. Third, we built a lightweight dashboard that packages together existing and SPARQL-aware applications to search, browse, explore, and query the InterMine-based data. Our work extends the InterMine platform, and supports new query functionality across InterMine installations and the network of open Linked Data.

Release Date: 
November 29, 2016
Author List: 
Maxime Deraspe, Gail Binkley, Kalpana Karra, Gos Micklem, Julie Sullivan, Michael J. Cherry, Michel Dumontier
Artifact Type: 
Last Updated: 
May 12 2017 - 1:56pm