Define BIOM archive requirements

GLOMICON / asvBiomXchange

A repository to develop an exchange format for molecular biodiversity data

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Define BIOM archive requirements #12

Open pbuttigieg opened 4 years ago

pbuttigieg commented 4 years ago

The service / system that hosts BIOM files should consider the following:

Version control on each slot of the file (OTU table, metadata, taxonomy)
some form of provenance tracking on each slot (e.g. what docker container was used to create the BIOM #11, what curation was done post-submission)
Links to the source sequence files in an INSDC database to (with the docker container) allow reproducibility

(please add more in this thread)

cuttlefishh commented 4 years ago

As I mentioned in #8, my approach has been to keep metadata separate from the BIOM file, as this is the format supported by QIIME 2. The same is true for taxonomy data, which is kept as a separate file (a QIIME 2 artifact).

pbuttigieg commented 4 years ago

Thanks @cuttlefishh

We have to avoid locking in the exchange format to any specific workflow, but your point here and in #8 about handling the metadata and taxonomy files separately is well taken.