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I took a stab at it. |
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The definition states this object property is to be used to relate "...one individual to another...". I would interpret that to mean that--using your example--x 'has substitutable entity' y. Perhaps the definition is not phrased as intended? I also think that the last part, "...in its other relations to other individuals", can be omitted. |
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I will try to reword to clarify. All of the lowercase letters are meant to be individuals, and |
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@nataled I updated the example of usage to the following:
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wdduncan
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cmungall
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This commit introduces high-level convenience methods for creating protein complexes and entity sets (paralogy groups) in GO-CAM models, along with corresponding CLI commands. ## Core Library Changes ### New Pydantic Models (src/noctua/models.py) - Add ProteinComplexComponent model for specifying complex components - Fields: entity_id (required), label, evidence_type, reference - Includes comprehensive doctests demonstrating usage - Add EntitySetMember model for specifying functionally interchangeable entities - Same field structure as ProteinComplexComponent - Used for paralogy groups and other substitutable entity sets ### New BaristaClient Methods (src/noctua/barista.py) - Add add_protein_complex() method (lines 1386-1491) - Creates protein-containing complex (GO:0032991 by default) - Links components using BFO:0000051 (has part) relation - Supports optional labels and evidence for each component - Uses atomic batch execution with automatic rollback - Returns BaristaResponse with created complex and relationships - Add add_entity_set() method (lines 1493-1599) - Creates entity set (CHEBI:33695 information biomacromolecule by default) - Links members using RO:0019003 (has substitutable entity) relation - Supports optional labels and evidence for each member - Uses atomic batch execution with automatic rollback - Returns BaristaResponse with created set and relationships - Replace print statements with proper logging (lines 6, 46, 661, 826-827) - Use logging.getLogger(__name__) pattern - Appropriate log levels (warning, error, info) ### CLI Commands (src/noctua/cli.py) - Add _parse_component_spec() helper function (lines 1106-1145) - Parses pipe-delimited format: entity_id|label=X|evidence=Y|ref=Z - Returns dict with entity_id, label, evidence_type, reference - Includes doctests for format validation - Add barista add-protein-complex command (lines 1148-1230) - Syntax: --component "UniProtKB:P12345|label=X|evidence=Y|ref=Z" - Repeatable --component flag for multiple components - Default class: GO:0032991 (protein-containing complex) - Optional --var for variable assignment - Optional --session for variable persistence - Supports --dry-run mode for safe preview - Add barista add-entity-set command (lines 1233-1315) - Syntax: --member "UniProtKB:P27361|label=X|evidence=Y|ref=Z" - Repeatable --member flag for multiple members - Default class: CHEBI:33695 (information biomacromolecule) - Optional --var for variable assignment - Optional --session for variable persistence - Supports --dry-run mode for safe preview ## Testing ### New Test Files - tests/test_protein_complex.py (5 tests) - test_add_protein_complex_simple: Basic two-component complex - test_add_protein_complex_with_evidence: Complex with evidence annotations - test_add_protein_complex_no_components_error: Error handling validation - test_add_protein_complex_missing_entity_id: Pydantic validation - test_add_protein_complex_custom_class: Custom complex class usage - tests/test_entity_set.py (6 tests) - test_add_entity_set_simple: Basic two-member set - test_add_entity_set_with_evidence: Set with evidence annotations - test_add_entity_set_no_members_error: Error handling validation - test_add_entity_set_missing_entity_id: Pydantic validation - test_add_entity_set_custom_class: Custom set class usage - test_add_entity_set_paralogy_group: Real-world ERK1/ERK2 example - tests/test_cli_complex_and_set.py (6 tests) - test_add_protein_complex_dry_run: CLI dry-run with full options - test_add_entity_set_dry_run: CLI dry-run with full options - test_add_protein_complex_custom_class: Custom class via CLI - test_add_entity_set_simple: Minimal CLI arguments - test_protein_complex_help: Help text verification - test_entity_set_help: Help text verification ## Design Decisions ### Pipe-Delimited CLI Syntax Chose pipe-delimited format (entity_id|label=X|evidence=Y|ref=Z) for CLI as a practical compromise between expressiveness and command-line usability. Alternatives considered: - JSON: Too verbose and error-prone for shell usage - Multiple flags: Would require --entity, --label, etc. per component - YAML: Requires multiline input or files ### Ontology Terms Based on GO-CAM project requirements: - Protein complexes use BFO:0000051 (has part) - standard mereological relation - Entity sets use RO:0019003 (has substitutable entity) - new relation for functionally interchangeable entities (see oborel/obo-relations#865) - Set class is CHEBI:33695 (information biomacromolecule) - appropriate for representing gene products as information-bearing entities ### Session Integration Both CLI commands support --session flag to save the created variable to a persistent session, enabling workflows like: noctua-py barista add-entity-set --session mysession --var erk_set ... noctua-py barista add-fact --session mysession --subject erk_set ... ## Test Results - 145 total tests passed (+17 new tests) - 51 doctests passed (+3 new doctests) - mypy: No type errors - ruff: No linting issues ## Related Issues - Implements protein complex functionality per internal requirements - Implements entity sets per geneontology/project-management#114 - Uses has_substitutable_entity relation per oborel/obo-relations#865 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
cmungall
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Oct 24, 2025
This commit introduces high-level convenience methods for creating protein complexes and entity sets (paralogy groups) in GO-CAM models, along with corresponding CLI commands. - Add ProteinComplexComponent model for specifying complex components - Fields: entity_id (required), label, evidence_type, reference - Includes comprehensive doctests demonstrating usage - Add EntitySetMember model for specifying functionally interchangeable entities - Same field structure as ProteinComplexComponent - Used for paralogy groups and other substitutable entity sets - Add add_protein_complex() method (lines 1386-1491) - Creates protein-containing complex (GO:0032991 by default) - Links components using BFO:0000051 (has part) relation - Supports optional labels and evidence for each component - Uses atomic batch execution with automatic rollback - Returns BaristaResponse with created complex and relationships - Add add_entity_set() method (lines 1493-1599) - Creates entity set (CHEBI:33695 information biomacromolecule by default) - Links members using RO:0019003 (has substitutable entity) relation - Supports optional labels and evidence for each member - Uses atomic batch execution with automatic rollback - Returns BaristaResponse with created set and relationships - Replace print statements with proper logging (lines 6, 46, 661, 826-827) - Use logging.getLogger(__name__) pattern - Appropriate log levels (warning, error, info) - Add _parse_component_spec() helper function (lines 1106-1145) - Parses pipe-delimited format: entity_id|label=X|evidence=Y|ref=Z - Returns dict with entity_id, label, evidence_type, reference - Includes doctests for format validation - Add barista add-protein-complex command (lines 1148-1230) - Syntax: --component "UniProtKB:P12345|label=X|evidence=Y|ref=Z" - Repeatable --component flag for multiple components - Default class: GO:0032991 (protein-containing complex) - Optional --var for variable assignment - Optional --session for variable persistence - Supports --dry-run mode for safe preview - Add barista add-entity-set command (lines 1233-1315) - Syntax: --member "UniProtKB:P27361|label=X|evidence=Y|ref=Z" - Repeatable --member flag for multiple members - Default class: CHEBI:33695 (information biomacromolecule) - Optional --var for variable assignment - Optional --session for variable persistence - Supports --dry-run mode for safe preview - tests/test_protein_complex.py (5 tests) - test_add_protein_complex_simple: Basic two-component complex - test_add_protein_complex_with_evidence: Complex with evidence annotations - test_add_protein_complex_no_components_error: Error handling validation - test_add_protein_complex_missing_entity_id: Pydantic validation - test_add_protein_complex_custom_class: Custom complex class usage - tests/test_entity_set.py (6 tests) - test_add_entity_set_simple: Basic two-member set - test_add_entity_set_with_evidence: Set with evidence annotations - test_add_entity_set_no_members_error: Error handling validation - test_add_entity_set_missing_entity_id: Pydantic validation - test_add_entity_set_custom_class: Custom set class usage - test_add_entity_set_paralogy_group: Real-world ERK1/ERK2 example - tests/test_cli_complex_and_set.py (6 tests) - test_add_protein_complex_dry_run: CLI dry-run with full options - test_add_entity_set_dry_run: CLI dry-run with full options - test_add_protein_complex_custom_class: Custom class via CLI - test_add_entity_set_simple: Minimal CLI arguments - test_protein_complex_help: Help text verification - test_entity_set_help: Help text verification Chose pipe-delimited format (entity_id|label=X|evidence=Y|ref=Z) for CLI as a practical compromise between expressiveness and command-line usability. Alternatives considered: - JSON: Too verbose and error-prone for shell usage - Multiple flags: Would require --entity, --label, etc. per component - YAML: Requires multiline input or files Based on GO-CAM project requirements: - Protein complexes use BFO:0000051 (has part) - standard mereological relation - Entity sets use RO:0019003 (has substitutable entity) - new relation for functionally interchangeable entities (see oborel/obo-relations#865) - Set class is CHEBI:33695 (information biomacromolecule) - appropriate for representing gene products as information-bearing entities Both CLI commands support --session flag to save the created variable to a persistent session, enabling workflows like: noctua-py barista add-entity-set --session mysession --var erk_set ... noctua-py barista add-fact --session mysession --subject erk_set ... - 145 total tests passed (+17 new tests) - 51 doctests passed (+3 new doctests) - mypy: No type errors - ruff: No linting issues - Implements protein complex functionality per internal requirements - Implements entity sets per geneontology/project-management#114 - Uses has_substitutable_entity relation per oborel/obo-relations#865 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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Fixes #863.
Label: has substitutable entity
Definition: Relates one individual to another which is capable of standing in for the first individual in its other relations to other individuals.
Example of usage: Given individuals f, i, x, and y, where f is a 'molecular function', i is an 'information biomacromolecule', and x and y are instances of different types of gene products, if f 'enabled by' i within an OWL model of a biological pathway, and i 'has substitutable entity' both x and y, then either x or y are valid enablers of function f within the modeled biological context.