Show units for all quantitative values

microbiomedata / nmdc-server

Data portal client and server for NMDC.

https://data.microbiomedata.org

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Show units for all quantitative values #556

Closed ssarrafan closed 11 months ago

ssarrafan commented 2 years ago

All quantitative values should show units, this is stored in the JSON as both the verbatim value (e.g. 0.15m) and as a normalized tuple (value=0.15, unit=m)

Related to #448

ssarrafan commented 2 years ago

Brandon, please add T-Shirt size and any questions. Team is trying to get an idea of the time/effort to do this.

subdavis commented 2 years ago

Similar to #552, where should metadata about what fields are in what units be stored?

Can depth have values represented in different units? Can one sample be 15 CM and another sample be 15M?

ssarrafan commented 2 years ago

@cmungall @wdduncan @dehays can anyone respond to Brandon's question about where to store the information for units?

ssarrafan commented 1 year ago

@mslarae13 who is working on this? It's not currently assigned to anyone

ssarrafan commented 1 year ago

It looks like this is the backlog so I'll remove from the sprint. @mslarae13 if you plan to work on it next sprint let me know.

mslarae13 commented 1 year ago

@ssarrafan Need a sanity check/ to confirm that the problem we think this is addressing is correct.. but

This is related to how the depth or other quantitative values are displayed on the portal. Using depth as an example https://data.microbiomedata.org/details/sample/gold:Gb0126424

Depth unit is meters, but it's only captured in the column header.

What needs to happen?

confirm issue
If units are implied, how does the string or float in the submission schema go into the data portal? How do we get the units? -- could apply annotations to the schema? or to the Dataportal? (Probably not, prefer ucum) -- Nothing in the submission schema can have quantity value. The strings and floats need converted. -- LinkML unit infrastructure. Have a slot like elev (title: elevation, meters) has a unit slot that points to a ucum code "meters"

mslarae13 commented 1 year ago

Relates to https://github.com/microbiomedata/sample-annotator/issues/111

That issue is identifying which slots are assumed units vs not...

This issue then captures how to share those units on the dataportal

pkalita-lbl commented 1 year ago

how does the string or float in the submission schema go into the data portal? How do we get the units?

This is something that should be sorted out as part of https://github.com/microbiomedata/issues/issues/236

mslarae13 commented 11 months ago

closing in favor of https://github.com/microbiomedata/issues/issues/236 & https://github.com/microbiomedata/nmdc-schema/issues/1257