Find replacements for GENEPIO and OMIT mappings if possible and/or define prefixes

[turbomam]

Thanks for providing these mappings, @aculm.

GENEPIO and OMIT aren't defined as prefixes yet. That's an error condition but it isn't super visible in the standard build process. We haven't used them before (although GENEPIO appears in an un-checked example in the mixs.yaml file). We should be conservative about adding new namespaces to the schema, especially if they aren't clearly authorities on the concepts being addressed.

Examples:

  members_id:
    range: string
    multivalued: true
    description: Names of the contigs that make up a metagenome-assembled genome.
    close_mappings:
      - GENEPIO:0100596

and

  num_5s:
    description: Number of 5s seqeuences detected, a subunit of ribosomes.
    range: integer
    minimum_value: 0
    broad_mappings:
      - OMIT:0013248

[eecavanna]

When I ran make squeaky-clean all test today in order to generate release artifacts for 11.1.0, I saw this at the end of the console output:

# ...
mkdir -p examples/output
poetry run linkml-run-examples \
        --schema nmdc_schema/nmdc_materialized_patterns.yaml \
        --input-directory src/data/valid \
        --counter-example-input-directory src/data/invalid \
        --output-directory examples/output > examples/output/README.md
Unrecognized prefix: GENEPIO
Unrecognized prefix: OMIT

The final two lines caught my eye. I think they are what @turbomam was referring to when he said this error currently "isn't super visible in the standard build process."