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The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.

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Thursday, June 29 • 15:40 - 17:00
P13: Prioritizing SNPs using the Neo4j Galaxy Interactive Environment

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Lose Thoba 1, Ziphozakhe Mashologu 1, Peter Van Heusden 1*, Alan Christoffels 1*
1 : South African National Bioinformatics Institute  (SANBI)
* : Corresponding author

Graph database implementation such as Neo4J are increasingly used within the biomedical research space, eg. disease network underpinned by a protein and metabolic framework. We previously developed a Galaxy datatype and an interactive environment for storing and exploring Neo4j graph databases within Galaxy. Building on this work we generate a M. tuberculosis genomic database from multiple sources of annotation. This database follows a Chado-like schema with graph nodes named according to sequence ontology terms. Thus, making it natural to the researcher to make queries using the Cypher query language. NGS data is processed to yield novel variants that are stored in the database using a schema derived from the GA4GH variant model. Using the resultant Neo4j database and Cypher queries in the context Mycobacterium tuberculosis drug resistance, we able to prioritize SNPs for further experimental investigation of their association with multi-drug resistance in Mtb.


Peter Van Heusden

South African National Bioinformatics Institute (SANBI)
avatar for Ziphozakhe Mashologu

Ziphozakhe Mashologu

Developer, UWC - South African National Bioinformatics Institute
South African National Bioinformatics Institute (SANBI)

Lose Thoba

South African National Bioinformatics Institute (SANBI)

Thursday June 29, 2017 15:40 - 17:00
Le Corum Le Corum

Attendees (3)