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weecology / retriever

Quickly download, clean up, and install public datasets into a database management system
http://data-retriever.org
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Support for BIOM format (biological observation matrix) #195

Closed davidelliott closed 3 years ago

davidelliott commented 10 years ago

The BIOM format is described at http://biom-format.org as "a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project."

The format is used by many microbial ecology tools like QIIME, Phyloseq, and MG-RAST which is also a repository. Support for this format might therefore help bring microbial data into the retriever.

Just a suggestion. Regards

David

ethanwhite commented 10 years ago

Thanks for the recommendation @davidelliott. We have a few of these alternative input format request in the pile at this point (also XML and HDF5) and I think it would be great to spend some time on this. Since BIOM is HDF5 at its core that should make these efforts line up well.

We're participating in an effort that involves professional developers teaming up with scientists to work on scientific software, and adding new input/output formats is one of the things on our list. I'll definitely add BIOM to the list of formats before that effort goes live. And of course we're very open to pull requests and providing support along the way if you have the time/energy/background to explore this possibility.

davidelliott commented 10 years ago

Partnering professional developers with scientists sounds like a good idea. My experience with BIOM is only as a user so I probably can't contribute a lot but I'm keen to make microbial data more accessible. I'll keep an eye on your project.

ethanwhite commented 10 years ago

My experience with BIOM is only as a user so I probably can't contribute a lot but I'm keen to make microbial data more accessible.

I totally understand. Just wanted to make sure that you felt welcome if you had the ability. I'm definitively excited about the possibility of supporting microbial data, especially since my group has been starting to use it, so stay tuned and we'll see what we can do.

ethanwhite commented 3 years ago

Closing since this is really stale and is the kind of special format that we'd need an expert to help support.