v1.8.0rc1

Highlights

New primitive types for use in scientific computing

Provides new primitives such as uint32 for precise specification of numeric base types

https://github.com/linkml/linkml-model/pull/185/files

This work was done by the @linkml/ndarray-wg as part of the Berkeley neuro-hackathon

Enum model enhancements

permissible_values now allows for many of the same slots as other elements, allowing for placement in an is-a hierarchy. See #192, #194, #195

This metamodel also introduces the concept of enum bindings. See the examples here: https://github.com/linkml/linkml-model/blob/main/tests/input/examples/schema_definition-enum_bindings-1.yaml

For example, given a class for modeling concepts or vocabulary terms in your model:

  Concept:
    description: A generic class for representing an element from a vocabulary or ontology.
    attributes:
      id:
        identifier: true
        description: CURIE/identifier for the concept. E.g. ENVO:1234567
      name:
        description: human-readable label of the concept. E.g. "blood"
      vocabulary:
        description: E.g. UBERON, PO, ENVO, NCIT

and a class that uses it:

  EnvironmentalMaterialSample:
    attributes:
      name:
        description: E.g. my blood sample
      sample_material_type:
        range: Concept

This allows for a great deal of flexibility. But what if we want to restrict the values of the id field of the referenced concept based on a (static of dynamic) enum?

We can modify the attribute or slot:

  sample_material_type:
        range: Concept
        bindings:
          - binds_value_of: id
            range: ENVOMaterialEnum
            obligation_level: RECOMMENDED
            description: Material type from the ENVO ontology

Currently this only serves as documentation as logic to validate bindings is not yet implemented

What's Changed

• Relax domain on is_a, mixin, mixins such that inheritance is valid for permissible values; fixes linkml/linkml#1261 by @sierra-moxon in #192
• Adding is_a and mixins to slots for permissible_value. by @cmungall in #195
• Allowing permissible_value to have implements and instantiates by @cmungall in #194
• Adding extended types. Fixes linkml/linkml#1871 by @cmungall in #185
• Adding enum bindings by @cmungall in #193
• Adding type_mappings to metamodel by @cmungall in #196
• Allowing multivalued to be used in slot expressions as well as top level slots. by @cmungall in #197
• Update ifabsent metamodel to allow for EnumName(PermissibleValue) by @vincentkelleher in #198

New Contributors

• @vincentkelleher made their first contribution in #198

Full Changelog: v1.7.0...v1.8.0rc1