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structured_format.pattern-style permissible value creation eg for MIxS #785

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merged 9 commits into from
Jul 31, 2024

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turbomam
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@turbomam turbomam commented Jul 23, 2024

I destructively edited src/oaklib/utilities/subsets/value_set_expander.py. I think the real solution will require adding a new permissible value for the pv_formula slot in the metamodel

my idea can be interactively illustrated with

vskit expand --schema mixs_inspired_schema.yaml --output mixs_inspired_schema_expanded.yaml 
linkml-validate --schema mixs_inspired_schema_expanded.yaml --target-class Sample mixs_inspired_data.yaml 

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@cmungall
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This should be done by passing a syntax string like “{label} [{id}]”

  • Longer term: add linkmlml metamodel element for pv_syntax (e.g. “{label} {id}”
  • Interim: Do this as a command line option on vskit E.g. –pv-syntax “{label} {id}”

@turbomam turbomam linked an issue Jul 26, 2024 that may be closed by this pull request
@turbomam turbomam changed the title crude MIXS style permissible value illustration structured_format.pattern-style permissible value creation eg for MIxS Jul 26, 2024
@turbomam turbomam requested review from hrshdhgd and cmungall July 26, 2024 21:48
@turbomam turbomam marked this pull request as ready for review July 26, 2024 21:49
@cmungall cmungall merged commit 8d3d2db into main Jul 31, 2024
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@turbomam turbomam deleted the mixs-style-expander branch July 31, 2024 20:57
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vskit expander should support PVs in the MIxS label [id] style
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