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GLOMICON / asvBiomXchange

A repository to develop an exchange format for molecular biodiversity data
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Define minimal metadata set to include in BIOM #2

Open pbuttigieg opened 5 years ago

jdeck88 commented 5 years ago

Use Case #1: BIOME with ASVs only and a link to identifiers pointing to metadata (e.g. GEOME created identifiers)

Use Case #2: BIOME with ASVs and all metadata included. For ALL metadata define the minimum requirements for each use case here: water, soil, populations of spiders, etc...

pbuttigieg commented 4 years ago

Use Case #1: BIOME with ASVs only and a link to identifiers pointing to metadata (e.g. GEOME created identifiers)

The linked data aspect appeals to me here. I like this use case as if we have agreed metadata storage formats across resources like GEOME, PANGAEA, etc, we can keep the BIOM files slim.

Use Case #2: BIOME with ASVs and all metadata included. For ALL metadata define the minimum requirements for each use case here: water, soil, populations of spiders, etc...

Yes, we should include this use case too. Until we have fixity of external repositories, I would encourage this route. Use Case 1 would be "how it should be" in the near future.

pbuttigieg commented 4 years ago

In a sync call today (Francisco, Chris, Neil, and I), we agreed to use the core MIxS fields in the metadata slot of the BIOM file, just to get the ball rolling. Participants can extend that later on.

@ramonawalls if we have IRIs on the MIxS fields/variables (Cross-link: https://github.com/GenomicsStandardsConsortium/mixs/issues/27) this would greatly reduce ambiguity. Are they available yet?