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BeBOP-OBON / miop

Minimum Information about an Omics Protocol (MIOP) specifications
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Multi-value fields #2

Closed raissameyer closed 1 year ago

raissameyer commented 2 years ago

Examine all multi-value fields and see if multiple values are necessary.

Also offer multi-value examples.

raissameyer commented 2 years ago

Review for meth_cat

We previously noted multivalued as "false", this will be revised to allow multiple values. In the description we will add that we of course recommend the protocol to only fall into one meth_cat, but that it may also cover multiple.

Note: Can this field still be enum if we allow multiple values?

Note: In NCBI they note that you can use "|" to separate multiple values.

In MIxS, it is unclear (e.g. see heavy_metals term) - check with CIG.

raissameyer commented 2 years ago

Guidance from the GSC team (as shared by @pbuttigieg):

Multiple values in an enumerated field are allowed by LinkML. The values should be in a JSON list format, but tooling to expand pipe-separated values is available.

I think we should then default to | separators for meth_cat and others.

They'll document it and let us know if there are any surprise

raissameyer commented 1 year ago

Linking to a MIxS issue https://github.com/GenomicsStandardsConsortium/mixs/issues/484#issue-1346580520, in which the separator for multi-value fields is also noted as a pipe (|).

Based on this, I will go ahead and review our current MIOP examples to include single- and multi-value examples (the latter being separated by pipes), as appropriate.