How do you access genomic data? Bart’s Health Innovation Fiona Nielsen [email protected] o.uk Sept 30, 2014
How do you access genomics data? Barts Health Innovation Sept 2014
Nov 18, 2014
Nucleobase, the social enterprise spin-out of DNAdigest, is building a data discovery platform to ease the pain of finding and locating relevant genomic datasets for research. See also http://nucleobase.co.uk
The research described in this slide deck was published in Journal of Applied and Translational Genomics as an Open Access paper: http://www.sciencedirect.com/science/article/pii/S2212066114000386
DNAdigest works to promote and enable easier and more efficient sharing of genomics data for research. We educate and engage the community about the hurdles and dilemmas for data sharing as faced from the perspective of stakeholders in academia, industry and patient communities. As part of our work we are working with our community and supporters to prototype new mechanisms and concepts for data sharing and data access.
Please visit our website to learn more about our activities and events: http://DNAdigest.org
This deck was used also to present at the Cambridge Sequencing Informatics Meeting VI on September 29, 2014
The research described in this slide deck was published in Journal of Applied and Translational Genomics as an Open Access paper: http://www.sciencedirect.com/science/article/pii/S2212066114000386
DNAdigest works to promote and enable easier and more efficient sharing of genomics data for research. We educate and engage the community about the hurdles and dilemmas for data sharing as faced from the perspective of stakeholders in academia, industry and patient communities. As part of our work we are working with our community and supporters to prototype new mechanisms and concepts for data sharing and data access.
Please visit our website to learn more about our activities and events: http://DNAdigest.org
This deck was used also to present at the Cambridge Sequencing Informatics Meeting VI on September 29, 2014
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Transcript
The frustrated researcher!
How did this happen?
The long road to resultsRaw reads
Read QC
Variant calling
Analysis-readyreads
Analysis-readyvariants
Variant Annotation Genotype
Refinement Raw Indels
Raw SVs
Raw SNPs
Mapping
External Data
What do you do?
Sequence Read Archive
What do you do?
What do you do?
Yikes
What do you do?
PubMed?
What do you do?
What do you do?
Ask your PI
Write application
Apply for access
Wait…Wait…Wait…Wait…
Access requests can take months
You are not the only one
T. A. van Schaik et alThe need to redefine genomic data sharing: a focus on data
accessibility, Applied & Translational Genomics, 2014
10.1016/j.atg.2014.09.013
Researchers spend months to find and access genomic data, and often choose to not access
data at all
2006 2007 2008 2009 2010 2011 2012 2013 2014 2015
Genomes Sequenced
~400k genomes produced
And how do you keep up?
What IF?
You could search all available data?
You could rank data by relevance?
You could search directly through your scripts?
Search would be easy
figshare.com
Overview would be simple
Collaboration would be easy
My research
Through your daily work routine you gain visibility
for potential collaborators
You would discover new resources you did not
know existed
Making your contribution would be easy
We are building a tool for you
Interested? Sign up for our beta at nucleobase.co.uk
We are building a tool for you
Interested? Sign up for our beta at nucleobase.co.uk
Adrian Alexa CTO & Data Scientist
Fiona NielsenFounder & CEO
And we are looking for more great people to make this happen. Interested? Get in touch
Thanks for listening!
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