Update workflow context to point to bioschemas and add dct namespace636 compact computational workflow

[stuzart]

• Recreates Update workflow context to point to bioschemas and add dct namespace #2482 combined with bioschemas additions  #2553

• Partly resolves Workflow validation against bioschemas profile - description of errors #781 and Compact ComputationalWorkflow JSON-LD against schema.org context #636

Extend the context to add bioschemas terms used in Workflows.
Extend the context to add dct namespace

Already approved but waiting for RO-Crate synchronization ( see #2482 (review) )

[Copilot]

Pull request overview

This PR updates SEEK’s Bioschemas/Schema.org JSON-LD generation to use an inline @context with @vocab and a dct prefix, and extends Workflow/SOP/Event/Sample contexts with Bioschemas terms so generated JSON-LD can be compacted/validated more cleanly (notably for ComputationalWorkflow/FormalParameter and dct:conformsTo).

Changes:

• Switch Schema.org context handling to an object-based @context (@vocab + dct) and merge in additional context gathered from associated resources.
• Add explicit Bioschemas mappings for Workflow (ComputationalWorkflow, FormalParameter, input/output), SOP (LabProtocol, computationalTool), Event (contact/hostInstitution/eventType), and Sample type; align Sample PropertyValue field to propertyID.
• Update tests and bump ro-crate gem version and expected RO-Crate context version.

Reviewed changes

Copilot reviewed 12 out of 13 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
lib/seek/bio_schema/serializer.rb	Introduces @vocab + dct context constants and merges in additional context after attribute generation.
lib/seek/bio_schema/resource_decorators/base_decorator.rb	Makes decorator context an object (with @vocab/dct) and accumulates additional context from associated resources.
lib/seek/bio_schema/resource_decorators/workflow.rb	Adds Bioschemas term mappings for Workflow types and input/output/formal parameters.
lib/seek/bio_schema/resource_decorators/sop.rb	Adds Bioschemas LabProtocol/computationalTool mappings to SOP context.
lib/seek/bio_schema/resource_decorators/sample.rb	Adds Sample type mapping and updates propertyId → propertyID for Schema.org compliance.
lib/seek/bio_schema/resource_decorators/event.rb	Adds Bioschemas term mappings for Event-specific properties into context.
lib/seek/bio_schema/resource_decorators/person.rb	Removes Person conformance emission from this decorator.
lib/seek/bio_schema/resource_decorators/organism.rb	Fixes grammar in decorator comment (“an Organism”).
test/unit/bio_schema/schema_ld_generation_test.rb	Updates expected @context structure and adds schema.org term validation checks.
test/unit/bio_schema/decorator_test.rb	Updates decorator context expectation to match new object-based context.
test/unit/bio_schema/data_dump_test.rb	Adjusts dump size expectation to reflect updated output.
test/unit/ro_crate/workflow_crate_test.rb	Updates expected RO-Crate version in conformsTo.
Gemfile.lock	Bumps ro-crate gem from 0.6.0 to 0.7.0.

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