MIxS Change in geo_loc_name

[mslarae13]

See https://github.com/GenomicsStandardsConsortium/mixs/issues/79

GSC has changed the syntax for geo_loc_name to {text}:{text}, {text}

This is more aligned with INSDC.

Term name = geo_loc_name Term ID = MIXS:0000010 Structured comment name = geographic location (country and/or sea,region) Definition = The geographical origin of the sample as defined by the country or sea name followed by a specific region and/or a location name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ) Expected value = SeaOrCountry:Region, Specific location Value syntax = {text}:{text}, {text} Example = Belgium:Ghent, Bourgoyen nature reserve Preferred unit = none Package(s) = MIxS Core

I assume NMDC will make the same change, since @turbomam pulls the details for each term straight from MIxS. Does this affect any other downstream uses of this term?

[mslarae13]

@turbomam , @cmungall , @dehays , @wdduncan

Just bringing this to your attention because it was new to me. If it doesn't matter at all, we can just close this ticket.

[turbomam]

Thanks, @mslarae13

I am pulling geo_loc_name's string serialization from @cmungall and my MIxS LinkML because it appears with disposition 'use as-is' on the mixs_packages_x_slots tab

Note that the slot is still called pattern in the main branch of MIxS LinkML above, but that will soon be re-implemented as a string_serialization

Our MIxS LinkML currently has the string_serialization {term}: {term}, {text} and will only change when there's a change in the upstream Google Sheet

[turbomam]

Thanks, @mslarae13

I am pulling geo_loc_name's string serialization from @cmungall and my MIxS LinkML because it appears with disposition 'use as-is' on the mixs_packages_x_slots tab

Note that the slot is still called pattern in the main branch of MIxS LinkML above, but that will soon be re-implemented as a string_serialization

Our MIxS LinkML currently has the string_serialization {term}: {term}, {text} and will only change when there's a change in the upstream Google Sheet