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GLOMICON / asvBiomXchange

A repository to develop an exchange format for molecular biodiversity data
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Identify sequence sets to BIOMise #1

Open pbuttigieg opened 5 years ago

pbuttigieg commented 5 years ago

We will need a few sets of sequence data to work on in order to generate our data products.

We should aim to have a few taxonomic marker genes represented. I can arrange some 16S/18S rRNA gene sequences.

chrispmeyer commented 5 years ago

I can bring in COI, but it will be from ARMS, not water. I'd like the ARMS data to come in metadata-naked (linked only to existing BioSample and EventID already existing in GEOME) - and think about GEOME asking for an augmented metadata layer currently consistent and based on what Francisco is providing and then see what else we might need

pbuttigieg commented 5 years ago

Thanks @chrispmeyer

I can bring in COI, but it will be from ARMS, not water.

Shouldn't be an issue.

I'd like the ARMS data to come in metadata-naked (linked only to existing BioSample and EventID already existing in GEOME)

Yes, @jdeck88 sketched that out as a Use Case in https://github.com/GLOMICON/asvBiomXchange/issues/2#issuecomment-505137038. It would be a good example of using linked open data approaches here.

@jdeck88 It's important that the link and the resource it resolves to also returns metadata in a standardised format. We'll define that in #8

However, we should have a few BIOM files with metadata bundled in, in a standardised way.

... and think about GEOME asking for an augmented metadata layer currently consistent and based on what Francisco is providing and then see what else we might need

Not sure I follow this, could you elaborate?