SchemaLoader should not inject additional slots for slot_usage and attributes

[cmungall]

Currently SchemaLoader will manipulate the SchemaDefinition object, doing many useful things. However, this can make it hard to access the intended meaning of the slot.

In particular, when slot_usage is used for s on c, this has the effect of making SL inject additional slots, c_s.

Currently this "leaks out" all over the place for example, e.g.

https://biolink.github.io/biolink-model/docs/SequenceVariant.html

id is shown twice, as if they are different. In fact they should not be treated as distinct. in fact SequenceVariant is simply defining some context-specific examples for the generic id property

  sequence variant:
    aliases: ['allele']
...
    slot_usage:
      has gene:
        multivalued: true
        description: Each allele can be associated with any number of genes
      has biological sequence:
        description: >-
          The state of the sequence w.r.t a reference sequence
      id:
        examples:
          - value: ZFIN:ZDB-ALT-980203-1091
            description: ti282a allele from ZFIN
          - value: ClinVarVariant:17681
            description: NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)

I think the datamodel should work like the owlapi

The SD object should not be manipulated. Instead there should be utility or wrapper classes that can be used to do things like look up something in the whole imports closure, or return inferred values of slots based on class context

[cmungall]

See also

• slot_usage -- injects a global slot into the namespace #59 from @jiaola
• slot_usage induces new sub-slots, these should be hidden in many exports #48
• induced slots should inherit metaslots from parent slot #270
• Replace simple_name with name in the Slot header in the Markdown generator #240

[cmungall]

This PR addresses this issue:

linkml/linkml-runtime#25