sorting of linkml document

[wdduncan]

• Linkml can sort them alphabetically or by rank (which would be an annotation property that we aren’t using yet)
• We should request that alphabetical sorting list required fields first then others

cc @ramonawalls @turbomam @only1chunts @lschriml

[turbomam]

When we say "LinkML can sort them", are we saying that software could be written to generate derived files, with terms/slots arranged in either alphabetical or rank order? Like for ordering columns in a tabular output?

That's not really the same as sorting the LinkML document itself. Maybe that capability could be adde to gen-linkml (which deprecates gen-yaml for those who remember that.)

For the record, DataHarmonizer already does arrange slots into groups, and sorts both the groups and the columns, according to rank

You can see that by looking at

• The nmdc_submission_schema_generated schema
• A DataHarmonizer interface generated from the soil_emsl_jgi_mg template in that schema

Note that the Sample ID section comes first, and the "globally unique ID" comes first in that section. (2022-07-26)

Relevant snapshots of the schema from the same time include

soil_emsl_jgi_mg:
  is_a: dh_interface
  slot_usage:
    source_mat_id:
      title: globally unique ID
      rank: 1
      is_a: nucleic acid sequence source field
      slot_uri: MIXS:0000026
      multivalued: false
      identifier: true
      slot_group: Sample ID
      range: string
      required: true
      recommended: true

And

Sample ID:
  name: Sample ID
  rank: 1
  is_a: dh_section

[turbomam]

See https://github.com/linkml/linkml/issues/885

[ramonawalls]

Sorting happens in the spreadsheet one might be working with for linkml (such as schemasheets). Not a MIxS issue, except around editing workflow.

We could add rank if we want.

[ramonawalls]

@wdduncan can this issue be closed or do you still have questions?

[wdduncan]

@ramonawalls This issue can be closed if you are satisfied. IIRC, I opened it during a call in regards to this question coming up by others.