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GenomicsStandardsConsortium / mixs

Minimum Information about any (X) Sequence” (MIxS) specification
https://w3id.org/mixs
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restore some 'Expected value' content that was lost in MIxS v6.2.0 #740

Open turbomam opened 6 months ago

turbomam commented 6 months ago

MIxS v6.2.0 is based on the following input: https://github.com/GenomicsStandardsConsortium/mixs/raw/issue-610-temp-mixs-xlsx-home/mixs/excel/mixs_v6.xlsx

See the mixs6.2_release_candidate repo's project.Makefile for elaboration

The following spreadsheet was used to convert MIxS Value syntaxes and Expected values into LinkML ranges and patterns: https://github.com/GenomicsStandardsConsortium/mixs6.2_release_candidate/blob/main/config/mixs-valsyns-expvals-to-linkml-ranges-patterns.tsv

Some content may have been lost, like

The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]

for env_medium/MIXS:0000014

turbomam commented 6 months ago

To what extent do the Expected values need to be reiterated verbatim in one of the SlotDefinition metaslots?

hysterectomy has this Expected value: 'hysterectomy status'

After the range/pattern conversion, that Expected value is not present anymore.

  hysterectomy:
    description: Specification of whether hysterectomy was performed
    title: hysterectomy
    examples:
      - value: 'no'
    slot_uri: MIXS:0000287
    range: boolean

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