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« ABiC 2014: We Salute You! | Main | 18 sleeps to go before an explosion of systems biology connection »
Friday
Sep052014

Need help to get your genomes globally available?

Pretty. And pretty deadly. Neutrophil and Methicillin-resistant Staphylococccus aureus (MRSA) Bacteria . (Credit: NIAID)Science is all about turning data into information, information into knowledge, and knowledge into understanding.

So, it would seem like sharing data is a very good thing for science and the benefits it delivers. But…

"If people can't reuse your data, what's the point in sharing it?" says Dr Lien Le.

Lien and her team at the Bioinformatics Resource Australia EMBL (BRAEMBL) deal with large-scale genomic data on a daily basis.

Surely these days, once you've done all the hard work of genome sequencing and assembly, don't you just push a button to upload the whole shebang to the EBI?

This ain't just a file upload

"Uploading genomic data into the major global collections is one thing," says Lien, "but without the right metadata to accompany it, the chances are slim that other researchers will get much value from it. And getting the metadata right is fiddly and time consuming... especially if you are only doing that from time to time."

Clearly, metadata is not just a headache for politicians, but thanks to BRAEMBL, there is a remedy for Australian genome researchers and bioinformaticians.

Chaperoning your data to the world

BRAEMBL's newly created Data Integration (DI) Team has already been busy helping Australian scientists submiting their data into global collections.

"Scott Beatson's Group at UQ has been one of the first to take advantage of the DI Team's assistance," says Lien. "Together, we've helped deliver 10 studies to the EBI. That's a total of 314 strains of bacteria, including assembled data that is now globally available and reusable."

Now will you go and wash your hands please? Scanning electron micrograph of Group A Streptococcus bacteria on primary human neutrophil. (Credit: NIH NIAID)Spreading germs... well, germ genomes

Given that microbes rule the planet, it is vital that we humans learn to live in harmony with them. Especially the ones that can kill us.

The Beatson group is passionate about deadly bugs. They are particularly interesting in understanding how they evolve and change to become even deadlier and drug resistant.

"The Beatson Group's interests are like a Who's Who of human pathogens," says Lien, "including
Escherichia coli, Pseudomonas aeruginosa, Staphylococcus, Streptococcus, Legionella pneumophila and Acinetobacter baumannii."

"It's vital that we get data and knowledge about these pathogens out to the world. This is a great example of science that needs international collaboration to deliver benefits to humanity."

Piping hot

The DI Team at BRAEMBL have developed templates and a batch submission pipeline for the Beatson Group to make sharing data—sharing reusable data—a lot easier.

"Different research communities, say, microbiologists or medical scientists or plant researchers, expect different kinds of metadata," says Lein. "Sure you can use the 'generic default metadata' settings, but without explaining the experiments and protocols that generated the data, you've basically uploaded a pretty useless file."

"We want to help Australian researchers deliver high-quality, high-value, and highly-reusable genome data to the world," says Lien.

Follow these links for more information about BRAMBL's Data Integration Team, the Data Submission Service, and how you can get help in getting your genomes globally available.


BRAEMBL is funded by the Australian government and the Data Submission Service, like all other services of BRAEMBL, is provided free of charge to Australian researchers... Thank you Australian Government!