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

Question

[edward.messick]

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

Answer 1

[Tm]

Hi Edward,

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

[edward.messick]

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?

Answer 2

[erictleung]

The closest databases I can think of are

• Repositive (https://discover.repositive.io/), which is more general purpose sequencing data
• Qiita (https://qiita.ucsd.edu/), which is microbial sequencing specific
• American Gut Project (http://americangut.org/), where some data can be found at https://github.com/biocore/American-Gut

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