Building a repository of biomedical ontologies with Neo4j

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Petra Selmer

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Nov 9, 2015, 5:14:02 PM11/9/15
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Hi all

I thought I would pass on a link to the slides of a very interesting talk given recently by Simon Jupp, from the European Bioinformatics Institute. The presentation was about building a repository of biomedical ontologies using Neo4j (please see the abstract towards the bottom of this email).


We are hoping to have a webinar on this project in the near future - I will keep you posted on details for this.

Best wishes
Petra

Here is the abstract:

Data integration is intrinsic to how modern research is undertaken in areas such as genomics, drug development and personalised medicine. To better enable this integration a large number of biomedical ontologies have been developed by the community to provide common metadata vocabularies.   

There are now over one hundred biomedical ontologies in widespread use that describe concepts such as genes, molecules, drugs and diseases. This amounts to millions of terms that are interconnected via relationships that naturally form a graph of biological knowledge.   

The European Bioinformatics Institute (EMBL-EBI)  has been hosting a repository of these ontologies for the past 10 years and has recently undertaken a project to re-engineer this service from the ground up using the Spring Data Framework and Neo4j. 

Simon will  discuss the design of the system and their rationale for choosing Neo4j. He will also discuss how this work relates to other activities in the area of linked data, RDF and semantics at the EBI. 

EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in academia and industry.
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