Does anyone know good open data sources for metagenomic data linked to a given condition?
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6.6 years ago

I'm looking for either a database (like SRA) or even a study that provides its data that has labels associated with the data. Ideally, this would be metagenomic data (either sequences or abundance tables) in a study that has a strong link between a feature like a species and the condition being studied.

Just reaching out because I haven't been able to find any studies that have enough data for my application (implementing machine learning algorithms) - so ideally we are talking about at least 100 samples for the condition being studied (controls, maybe the same).

Any help is appreciated. Thanks guys

metagenomics databases open data • 1.6k views
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6.6 years ago
Tm ★ 1.1k

Hi Edward,

You can check below mentioned post. It may solve your purpose http://github.com/gjospin/PhyloSift/issues/59.

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thanks! I'll look through that post... of course I'm probably being a little too nitpicky with my search... we'll never really find ideal data in the real world, will we?

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6.6 years ago
erictleung ▴ 110

The closest databases I can think of are

The American Gut project has the quantity of data, so that might be the most interest to you for machine learning purposes. Good luck.

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