microbiomedata / sheets_and_friends

Enhance a LinkML model with imported and optionally modified slots
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geographical terms/"is it modified?" parent issue #68

Closed turbomam closed 2 years ago

turbomam commented 2 years ago

@pvangay collecting some of your issues here

@mslarae13 you might be interested in this too but I don't have any specific requests

see

turbomam commented 2 years ago

Regarding the requirement for geo_loc_name "geographic location (country and/or sea,region)" and lat_lon "geographic location (latitude and longitude)" and the resulting DH section assignment:

For the SNTC/DataHarmonizer workflow, I was taking MIxS' soil class as the source of truth. Now, in nmdc-dh-sheets/sheets_and_friends, I'm using the MIxS checklist/environmental combination soil MIMS as the source of truth, so the usage of environmental terms is clearer. That explains why I waffled on whether these fields were required in our soil_emsl_jgi_mg interface for GSP.

Having said that, we are modifying the validation pattern for lat_lon from the string serialization of {float} {float} to the regular expression ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ so we won't get locations like "1000.1 555.5". So it is modified in that sense.

You can see all of MIxS' metadata on these two terms in three different contexts below. Again, I am using soil MIMS (aka soil microbiome) as the reference now.

class_name slot_name title recommended required from_schema is_a multivalued owner range slot_uri string_serialization
soil MIMS geo_loc_name geographic location (country and/or sea,region)   True http://w3id.org/mixs/terms environment field False soil MIMS string MIXS:0000010 {term}: {term}, {text}
soil MIMS lat_lon geographic location (latitude and longitude)   True http://w3id.org/mixs/terms environment field False soil MIMS string MIXS:0000009 {float} {float}
soil geo_loc_name geographic location (country and/or sea,region)     http://w3id.org/mixs/terms environment field False soil string MIXS:0000010 {term}: {term}, {text}
soil lat_lon geographic location (latitude and longitude)     http://w3id.org/mixs/terms environment field False soil string MIXS:0000009 {float} {float}
MIMS geo_loc_name geographic location (country and/or sea,region)   True http://w3id.org/mixs/terms environment field False MIMS string MIXS:0000010 {term}: {term}, {text}
MIMS lat_lon geographic location (latitude and longitude)   True http://w3id.org/mixs/terms environment field False MIMS string MIXS:0000009 {float} {float}