Linkml-model

Latest version: v1.8.0

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1.9.0rc1

What's Changed
* move array to slot_expression by sneakers-the-rat in https://github.com/linkml/linkml-model/pull/200
* add extra_slots metamodel slot by sneakers-the-rat in https://github.com/linkml/linkml-model/pull/205
* Add URI or CURIE range documentation by amc-corey-cox in https://github.com/linkml/linkml-model/pull/207
* Codespell inspired spelling fixes by kevinschaper in https://github.com/linkml/linkml-model/pull/212
* Add the alias slot to the class_definition class by kevinschaper in https://github.com/linkml/linkml-model/pull/211

New Contributors
* amc-corey-cox made their first contribution in https://github.com/linkml/linkml-model/pull/207
* kevinschaper made their first contribution in https://github.com/linkml/linkml-model/pull/212

**Full Changelog**: https://github.com/linkml/linkml-model/compare/v1.8.0...v1.9.0rc1

1.8.0

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:

yaml
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:

yaml
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:

yaml
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
* remove domain from is_a, mixin, mixins per ticket 1261 by sierra-moxon in https://github.com/linkml/linkml-model/pull/192
* Adding extended types. Fixes https://github.com/linkml/linkml/issues/1871 by cmungall in https://github.com/linkml/linkml-model/pull/185
* Allowing permissible_value to have implements and instantiates by cmungall in https://github.com/linkml/linkml-model/pull/194
* Adding is_a and mixins to slots for permissible_value. by cmungall in https://github.com/linkml/linkml-model/pull/195
* Adding enum bindings by cmungall in https://github.com/linkml/linkml-model/pull/193
* Adding type_mappings to metamodel by cmungall in https://github.com/linkml/linkml-model/pull/196
* Allowing multivalued to be used in slot expressions as well as top level slots. by cmungall in https://github.com/linkml/linkml-model/pull/197
* Update ifabsent metamodel by vincentkelleher in https://github.com/linkml/linkml-model/pull/198

New Contributors
* vincentkelleher made their first contribution in https://github.com/linkml/linkml-model/pull/198

**Full Changelog**: https://github.com/linkml/linkml-model/compare/v1.7.0...v1.8.0

1.8.0rc1

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:

yaml
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:

yaml
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:

yaml
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 https://github.com/linkml/linkml/issues/1261 by sierra-moxon in https://github.com/linkml/linkml-model/pull/192
* Adding is_a and mixins to slots for permissible_value. by cmungall in https://github.com/linkml/linkml-model/pull/195
* Allowing permissible_value to have implements and instantiates by cmungall in https://github.com/linkml/linkml-model/pull/194
* Adding extended types. Fixes https://github.com/linkml/linkml/issues/1871 by cmungall in https://github.com/linkml/linkml-model/pull/185
* Adding enum bindings by cmungall in https://github.com/linkml/linkml-model/pull/193
* Adding type_mappings to metamodel by cmungall in https://github.com/linkml/linkml-model/pull/196
* Allowing multivalued to be used in slot expressions as well as top level slots. by cmungall in https://github.com/linkml/linkml-model/pull/197
* Update ifabsent metamodel to allow for `EnumName(PermissibleValue)` by vincentkelleher in https://github.com/linkml/linkml-model/pull/198

New Contributors
* vincentkelleher made their first contribution in https://github.com/linkml/linkml-model/pull/198

**Full Changelog**: https://github.com/linkml/linkml-model/compare/v1.7.0...v1.8.0rc1

1.7.0

* Remove "has_extra_dimensions" by rly in https://github.com/linkml/linkml-model/pull/184
* 1.7.0rc3 by cmungall in https://github.com/linkml/linkml-model/pull/183

New Contributors
* nlharris made their first contribution in https://github.com/linkml/linkml-model/pull/170
* nicholsn made their first contribution in https://github.com/linkml/linkml-model/pull/171
* melonora made their first contribution in https://github.com/linkml/linkml-model/pull/172
* sneakers-the-rat made their first contribution in https://github.com/linkml/linkml-model/pull/177

**Full Changelog**: https://github.com/linkml/linkml-model/compare/v1.6.0...v1.7.0

1.7.0rc1

What's Changed
* Fix repository name in release workflow by pkalita-lbl in https://github.com/linkml/linkml-model/pull/169
* Include LABEL in Permissible Value Formula Options by nicholsn in https://github.com/linkml/linkml-model/pull/171
* XY alias removal of axes by melonora in https://github.com/linkml/linkml-model/pull/172
* Bump to latest linkml version for dev group by cmungall in https://github.com/linkml/linkml-model/pull/173
* Add missing oslc and bibo prefixes by sneakers-the-rat in https://github.com/linkml/linkml-model/pull/177
* Make maximum_value and minimum_value accept linkml:Any by sneakers-the-rat in https://github.com/linkml/linkml-model/pull/176
* Update array metamodel and examples by rly in https://github.com/linkml/linkml-model/pull/175
* Adding examples to test by cmungall in https://github.com/linkml/linkml-model/pull/174
* Adding mappings to SIO by cmungall in https://github.com/linkml/linkml-model/pull/178

New Contributors
* nlharris made their first contribution in https://github.com/linkml/linkml-model/pull/170
* nicholsn made their first contribution in https://github.com/linkml/linkml-model/pull/171
* melonora made their first contribution in https://github.com/linkml/linkml-model/pull/172
* sneakers-the-rat made their first contribution in https://github.com/linkml/linkml-model/pull/177

**Full Changelog**: https://github.com/linkml/linkml-model/compare/v1.6.0...v1.7.0rc1

1.6.0

Highlights

This release marks the start of versioned documentation deployment

https://linkml.io/linkml-model/1.6.x/docs/

What's Changed
* Adding instantiates metaslot by cmungall in https://github.com/linkml/linkml-model/pull/163
* Adding AnyValue to the metamodel by cmungall in https://github.com/linkml/linkml-model/pull/164
* changing the range of extensions from string to AnyValue by cmungall in https://github.com/linkml/linkml-model/pull/162
* proposal add jsonpointer path types by cmungall in https://github.com/linkml/linkml-model/pull/159
* basic repo maintenance by sierra-moxon in https://github.com/linkml/linkml-model/pull/167
* Add missing "not" to partial_match slot description by pkalita-lbl in https://github.com/linkml/linkml-model/pull/166
* Use versioned documentation deployment by pkalita-lbl in https://github.com/linkml/linkml-model/pull/168


**Full Changelog**: https://github.com/linkml/linkml-model/compare/v1.5.2...v1.6.0

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