v1.11.0-rc1

What's Changed

• Update metamodel files by @matentzn in #241
• Submit releases to the LinkML Zenodo community by @dalito in #240
• 1.11.0rc1 by @matentzn in #245
• Fix incorrect use of value slots in extra_slots examples. by @gouttegd in #243
• Fix invalid slot_usage on axis slot in array.yaml by @matentzn in #246

New Contributors

• @gouttegd made their first contribution in #243

Full Changelog: v1.10.0...v1.11.0-rc1

v1.10.0 release

What's Changed

• move array to slot_expression by @sneakers-the-rat in #200
• add extra_slots metamodel slot by @sneakers-the-rat in #205
• Add URI or CURIE range documentation by @amc-corey-cox in #207
• Codespell inspired spelling fixes by @kevinschaper in #212
• Add the alias slot to the class_definition class by @kevinschaper in #211
• Remove ifabsent: false on extra_slots by @cmungall in #215
• README: Fix a grammatical error by @hoijui in #222
• Update GitHub Actions workflows (sync with other repos in org) by @sujaypatil96 in #225
• add LICENSE, CITATION.cff, .zenodo.json by @sierra-moxon in #228
• Quote Python version in release workflow by @matentzn in #230
• Minimal changes to support windows by @dalito in #224
• Update the linkml-model files with linkml 1.10.0-rc4 by @matentzn in #236
• Update to RC5 by @matentzn in #238
• Modernize: Drop py39, add py313 compatibility, switch to uv by @dalito in #237
• Bump the github-actions group with 3 updates by @dependabot[bot] in #239
• Use anonymous_slot_expression instead of range_expression for extra_slots by @sneakers-the-rat in #227
• Refresh linkml-model documentation pages with latest and greatest features by @sujaypatil96 in #226

New Contributors

• @amc-corey-cox made their first contribution in #207
• @kevinschaper made their first contribution in #212
• @hoijui made their first contribution in #222
• @matentzn made their first contribution in #230
• @dependabot[bot] made their first contribution in #239

Full Changelog: v1.8.0...v1.10.0

v1.10.0-rc2

What's Changed

• Quote Python version in release workflow by @matentzn in #230

New Contributors

• @matentzn made their first contribution in #230

Full Changelog: v1.10.0-rc1...v1.10.0-rc2

v1.10.0-rc1

What's Changed

• Remove ifabsent: false on extra_slots by @cmungall in #215
• README: Fix a grammatical error by @hoijui in #222
• Update GitHub Actions workflows (sync with other repos in org) by @sujaypatil96 in #225
• add LICENSE, CITATION.cff, .zenodo.json by @sierra-moxon in #228

New Contributors

• @hoijui made their first contribution in #222

Full Changelog: v1.9.0rc1...v1.10.0-rc1

v1.9.0-rc2

What's Changed

• Remove ifabsent: false on extra_slots by @cmungall in #215
• README: Fix a grammatical error by @hoijui in #222
• Update GitHub Actions workflows (sync with other repos in org) by @sujaypatil96 in #225
• add LICENSE, CITATION.cff, .zenodo.json by @sierra-moxon in #228

New Contributors

• @hoijui made their first contribution in #222

Full Changelog: v1.9.0rc1...v1.9.0-rc2

v1.9.0rc1

What's Changed

• move array to slot_expression by @sneakers-the-rat in #200
• add extra_slots metamodel slot by @sneakers-the-rat in #205
• Add URI or CURIE range documentation by @amc-corey-cox in #207
• Codespell inspired spelling fixes by @kevinschaper in #212
• Add the alias slot to the class_definition class by @kevinschaper in #211

New Contributors

• @amc-corey-cox made their first contribution in #207
• @kevinschaper made their first contribution in #212

Full Changelog: v1.8.0...v1.9.0rc1

v1.8.0

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:

  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

• remove domain from is_a, mixin, mixins per ticket 1261 by @sierra-moxon in #192
• Adding extended types. Fixes linkml/linkml#1871 by @cmungall in #185
• Allowing permissible_value to have implements and instantiates by @cmungall in #194
• Adding is_a and mixins to slots for permissible_value. by @cmungall in #195
• 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 by @vincentkelleher in #198

New Contributors

• @vincentkelleher made their first contribution in #198

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

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

v1.7.0

Array Support

The 1.7.x series of LinkML sees the introduction of first-class array support through the introduction of the linkml:array metamodel slot.

Basic example of usage, to define a 3D array:

TemperatureDataset:
    attributes:
      temperature_matrix:
        range: float
        unit:
         ucum_code: K
        array:
          exact_number_dimensions: 3

Individual axes can be named and constrained. See #181 for a log of discussions. Additional documentation will be added to the main LinkML site.

Thanks to the work of the @linkml/ndarray-wg

• @bendichter
• @ialarmedalien
• @jmchandonia
• @melonora
• @nicholsn
• @oruebel
• @rly
• @sneakers-the-rat

This work was conducted as part of the LinkML Neurodata Hackashop sponsored by NeurodataWithoutBorders and DANDI and organized by @satra and @oruebel at Berkeley in Feb 2024.

Additional Highights

• Include LABEL in Permissible Value Formula Options by @nicholsn in #171
• Make maximum_value and minimum_value accept linkml:Any by @sneakers-the-rat in #176

What's Changed

• Fix repository name in release workflow by @pkalita-lbl in #169
• Remove Mark from author list by @nlharris in #170
• Include LABEL in Permissible Value Formula Options by @nicholsn in #171
• XY alias removal of axes by @melonora in #172
• Bump to latest linkml version for dev group by @cmungall in #173
• Add missing oslc and bibo prefixes by @sneakers-the-rat in #177
• Make maximum_value and minimum_value accept linkml:Any by @sneakers-the-rat in #176
• Update array metamodel and examples by @rly in #175
• Adding examples to test by @cmungall in #174
• Adding mappings to SIO by @cmungall in #178
• Mention BasicSubset just once by @yarikoptic in #182
• First pass at native NDArray support. by @cmungall in #181
• 1.7.0 release candidate by @cmungall in #179
• Remove "has_extra_dimensions" by @rly in #184
• 1.7.0rc3 by @cmungall in #183

New Contributors

• @nlharris made their first contribution in #170
• @nicholsn made their first contribution in #171
• @melonora made their first contribution in #172
• @sneakers-the-rat made their first contribution in #177

Full Changelog: v1.6.0...v1.7.0

v1.7.0rc1

What's Changed

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

New Contributors

• @nlharris made their first contribution in #170
• @nicholsn made their first contribution in #171
• @melonora made their first contribution in #172
• @sneakers-the-rat made their first contribution in #177

Full Changelog: v1.6.0...v1.7.0rc1