From bdf58f09d47c72dd0a7fa2b3c2ab030aa5965cd4 Mon Sep 17 00:00:00 2001 From: eecavanna Date: Fri, 17 Jan 2025 13:07:57 -0800 Subject: [PATCH] 11.3.0 --- nmdc_schema/nmdc-pydantic.py | 798 +++++++++++++++--- nmdc_schema/nmdc.py | 16 +- nmdc_schema/nmdc.schema.json | 1 + .../nmdc_materialized_patterns.schema.json | 1 + nmdc_schema/nmdc_materialized_patterns.yaml | 48 +- 5 files changed, 747 insertions(+), 117 deletions(-) diff --git a/nmdc_schema/nmdc-pydantic.py b/nmdc_schema/nmdc-pydantic.py index 54e0a9ae16..0b4e843f4f 100644 --- a/nmdc_schema/nmdc-pydantic.py +++ b/nmdc_schema/nmdc-pydantic.py @@ -65,14 +65,19 @@ def __contains__(self, key:str) -> bool: linkml_meta = LinkMLMeta({'default_prefix': 'nmdc', 'default_range': 'string', - 'description': 'Schema for National Microbiome Data Collaborative (NMDC).\n' - 'This schema is organized into multiple modules, such as:\n' - '\n' - ' * a set of core types for representing data values\n' - ' * a subset of the mixs schema\n' - ' * an annotation schema\n' - ' * the NMDC schema itself, into which the other modules are ' - 'imported', + 'description': 'The NMDC Schema is a foundational framework designed to ' + 'standardize metadata for the National Microbiome Data ' + 'Collaborative (NMDC) and collaborating data providors. By ' + 'establishing a structured approach to metadata, the NMDC ' + 'Schema enables researchers to organize, share, and interpret ' + 'complex datasets with consistency and clarity. The NMDC ' + 'Schema is critical substrate used to facilitate ' + 'interoperability and collaboration, as it provide a common ' + 'language for data exchange across systems and disciplines. ' + 'In the context of the NMDC, this schema supports the ' + 'integration of microbiome data from medicine, agriculture, ' + 'bioenergy, and environmental science into a cohesive ' + 'platform.', 'emit_prefixes': ['KEGG.ORTHOLOGY', 'MASSIVE', 'biosample', @@ -2177,8 +2182,10 @@ class FileTypeEnum(str, Enum): LC_DDA_MSSOLIDUSMS_Raw_Data = "LC-DDA-MS/MS Raw Data" # A configuration toml file used by various programs to store settings that are specific to their respective software. Configuration_toml = "Configuration toml" - # LC-MS-based lipid assignment results table. + # LC-MS-based lipidomics analysis results table LC_MS_Lipidomics_Results = "LC-MS Lipidomics Results" + # Processed data for the LC-MS-based lipidomics analysis in hdf5 format + LC_MS_Lipidomics_Processed_Data = "LC-MS Lipidomics Processed Data" # FASTA amino acid file for contaminant proteins commonly observed in proteomics data. Contaminants_Amino_Acid_FASTA = "Contaminants Amino Acid FASTA" # A configuration file used by a single computational software tool that stores settings that are specific to that tool. @@ -2374,7 +2381,10 @@ class EukEval(ConfiguredBaseModel): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) completeness: Optional[float] = Field(None, description="""Estimate of the completeness of the metagenome-assembled genome, estimated by a tool like CheckM.""", ge=0, json_schema_extra = { "linkml_meta": {'alias': 'completeness', 'domain_of': ['EukEval', 'MagBin']} }) contamination: Optional[float] = Field(None, description="""Estimate of the completeness of the metagenome-assembled genome, estimated by a tool like CheckM.""", ge=0, json_schema_extra = { "linkml_meta": {'alias': 'contamination', 'domain_of': ['EukEval', 'MagBin']} }) ncbi_lineage_tax_ids: Optional[str] = Field(None, description="""Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId)""", json_schema_extra = { "linkml_meta": {'alias': 'ncbi_lineage_tax_ids', @@ -2449,7 +2459,10 @@ class FunctionalAnnotationAggMember(ConfiguredBaseModel): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('was_generated_by') def pattern_was_generated_by(cls, v): @@ -2573,7 +2586,10 @@ class MobilePhaseSegment(ConfiguredBaseModel): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) volume: Optional[QuantityValue] = Field(None, description="""The volume of a substance.""", json_schema_extra = { "linkml_meta": {'alias': 'volume', 'contributors': ['ORCID:0009-0001-1555-1601', 'ORCID:0000-0002-8683-0050'], 'domain_of': ['Extraction', @@ -2628,7 +2644,10 @@ class PortionOfSubstance(ConfiguredBaseModel): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) volume: Optional[QuantityValue] = Field(None, description="""The volume of a substance.""", json_schema_extra = { "linkml_meta": {'alias': 'volume', 'contributors': ['ORCID:0009-0001-1555-1601', 'ORCID:0000-0002-8683-0050'], 'domain_of': ['Extraction', @@ -2713,7 +2732,10 @@ class MagBin(ConfiguredBaseModel): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) eukaryotic_evaluation: Optional[EukEval] = Field(None, description="""Contains results from evaluating if a Metagenome-Assembled Genome is of eukaryotic lineage.""", json_schema_extra = { "linkml_meta": {'alias': 'eukaryotic_evaluation', 'domain_of': ['MagBin']} }) @@ -2754,7 +2776,10 @@ class MetaboliteIdentification(ConfiguredBaseModel): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('alternative_identifiers') def pattern_alternative_identifiers(cls, v): @@ -2831,7 +2856,10 @@ class GenomeFeature(ConfiguredBaseModel): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) feature_category: Optional[ControlledIdentifiedTermValue] = Field(None, description="""A Sequence Ontology term that describes the category of a feature""", json_schema_extra = { "linkml_meta": {'alias': 'feature_category', 'domain_of': ['GenomeFeature', 'FunctionalAnnotation']} }) @@ -2908,7 +2936,10 @@ class FunctionalAnnotation(ConfiguredBaseModel): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) feature_category: Optional[ControlledIdentifiedTermValue] = Field(None, description="""A Sequence Ontology term that describes the category of a feature""", json_schema_extra = { "linkml_meta": {'alias': 'feature_category', 'domain_of': ['GenomeFeature', 'FunctionalAnnotation']} }) @@ -2970,7 +3001,10 @@ class AttributeValue(ConfiguredBaseModel): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) class QuantityValue(AttributeValue): @@ -3028,7 +3062,10 @@ class QuantityValue(AttributeValue): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) class ImageValue(AttributeValue): @@ -3069,7 +3106,10 @@ class ImageValue(AttributeValue): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) class PersonValue(AttributeValue): @@ -3167,7 +3207,10 @@ class PersonValue(AttributeValue): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('websites') def pattern_websites(cls, v): @@ -3214,7 +3257,10 @@ class TextValue(AttributeValue): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) class TimestampValue(AttributeValue): @@ -3250,7 +3296,10 @@ class TimestampValue(AttributeValue): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) class ControlledTermValue(AttributeValue): @@ -3289,7 +3338,10 @@ class ControlledTermValue(AttributeValue): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) class ControlledIdentifiedTermValue(ControlledTermValue): @@ -3329,7 +3381,10 @@ class ControlledIdentifiedTermValue(ControlledTermValue): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) class GeolocationValue(AttributeValue): @@ -3382,7 +3437,10 @@ class GeolocationValue(AttributeValue): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) class NamedThing(ConfiguredBaseModel): @@ -3404,7 +3462,13 @@ class NamedThing(ConfiguredBaseModel): 'typecodes must correspond 1:1 to a class in the NMDC schema. this ' 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' - 'checked in the pattern']} }) + 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -3435,7 +3499,10 @@ class NamedThing(ConfiguredBaseModel): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -3484,7 +3551,13 @@ class GeneProduct(NamedThing): 'typecodes must correspond 1:1 to a class in the NMDC schema. this ' 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' - 'checked in the pattern']} }) + 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -3515,7 +3588,10 @@ class GeneProduct(NamedThing): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -3565,7 +3641,13 @@ class OntologyClass(NamedThing): 'examples': [{'description': 'https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248', 'value': 'nmdc:mgmag-00-x012.1_7_c1'}], 'notes': ["The identifiers for terms from external ontologies can't have " - 'their ids constrained to the nmdc namespace']} }) + 'their ids constrained to the nmdc namespace'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -3596,7 +3678,10 @@ class OntologyClass(NamedThing): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -3639,7 +3724,13 @@ class EnvironmentalMaterialTerm(OntologyClass): 'examples': [{'description': 'https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248', 'value': 'nmdc:mgmag-00-x012.1_7_c1'}], 'notes': ["The identifiers for terms from external ontologies can't have " - 'their ids constrained to the nmdc namespace']} }) + 'their ids constrained to the nmdc namespace'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -3670,7 +3761,10 @@ class EnvironmentalMaterialTerm(OntologyClass): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -3738,7 +3832,13 @@ class ChemicalEntity(OntologyClass): 'examples': [{'description': 'https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248', 'value': 'nmdc:mgmag-00-x012.1_7_c1'}], 'notes': ["The identifiers for terms from external ontologies can't have " - 'their ids constrained to the nmdc namespace']} }) + 'their ids constrained to the nmdc namespace'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -3769,7 +3869,10 @@ class ChemicalEntity(OntologyClass): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -3819,7 +3922,13 @@ class FunctionalAnnotationTerm(OntologyClass): 'examples': [{'description': 'https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248', 'value': 'nmdc:mgmag-00-x012.1_7_c1'}], 'notes': ["The identifiers for terms from external ontologies can't have " - 'their ids constrained to the nmdc namespace']} }) + 'their ids constrained to the nmdc namespace'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -3850,7 +3959,10 @@ class FunctionalAnnotationTerm(OntologyClass): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -3903,7 +4015,13 @@ class Pathway(FunctionalAnnotationTerm): 'examples': [{'description': 'https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248', 'value': 'nmdc:mgmag-00-x012.1_7_c1'}], 'notes': ["The identifiers for terms from external ontologies can't have " - 'their ids constrained to the nmdc namespace']} }) + 'their ids constrained to the nmdc namespace'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -3934,7 +4052,10 @@ class Pathway(FunctionalAnnotationTerm): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -3989,7 +4110,13 @@ class OrthologyGroup(FunctionalAnnotationTerm): 'examples': [{'description': 'https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248', 'value': 'nmdc:mgmag-00-x012.1_7_c1'}], 'notes': ["The identifiers for terms from external ontologies can't have " - 'their ids constrained to the nmdc namespace']} }) + 'their ids constrained to the nmdc namespace'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -4020,7 +4147,10 @@ class OrthologyGroup(FunctionalAnnotationTerm): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -4098,7 +4228,10 @@ class OntologyRelation(ConfiguredBaseModel): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) subject: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'subject', 'domain_of': ['FunctionalAnnotation', 'OntologyRelation']} }) predicate: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'predicate', 'domain_of': ['OntologyRelation']} }) object: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'object', 'domain_of': ['OntologyRelation']} }) @@ -4140,7 +4273,10 @@ class FailureCategorization(ConfiguredBaseModel): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) class MaterialEntity(NamedThing): @@ -4161,7 +4297,13 @@ class MaterialEntity(NamedThing): 'typecodes must correspond 1:1 to a class in the NMDC schema. this ' 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' - 'checked in the pattern']} }) + 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -4192,7 +4334,10 @@ class MaterialEntity(NamedThing): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -4238,7 +4383,13 @@ class Sample(MaterialEntity): 'typecodes must correspond 1:1 to a class in the NMDC schema. this ' 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' - 'checked in the pattern']} }) + 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -4269,7 +4420,10 @@ class Sample(MaterialEntity): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -10769,6 +10923,12 @@ class Biosample(Sample): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -10801,7 +10961,10 @@ class Biosample(Sample): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('associated_studies') def pattern_associated_studies(cls, v): @@ -11032,6 +11195,12 @@ class ProcessedSample(Sample): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -11064,7 +11233,10 @@ class ProcessedSample(Sample): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('external_database_identifiers') def pattern_external_database_identifiers(cls, v): @@ -11121,7 +11293,13 @@ class Site(MaterialEntity): 'typecodes must correspond 1:1 to a class in the NMDC schema. this ' 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' - 'checked in the pattern']} }) + 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -11152,7 +11330,10 @@ class Site(MaterialEntity): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -11284,6 +11465,12 @@ class FieldResearchSite(Site): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -11316,7 +11503,10 @@ class FieldResearchSite(Site): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('part_of') def pattern_part_of(cls, v): @@ -11382,6 +11572,12 @@ class Instrument(MaterialEntity): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -11414,7 +11610,10 @@ class Instrument(MaterialEntity): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -11477,7 +11676,13 @@ class PlannedProcess(NamedThing): 'typecodes must correspond 1:1 to a class in the NMDC schema. this ' 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' - 'checked in the pattern']} }) + 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -11508,7 +11713,10 @@ class PlannedProcess(NamedThing): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -11599,6 +11807,12 @@ class CollectingBiosamplesFromSite(PlannedProcess): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -11631,7 +11845,10 @@ class CollectingBiosamplesFromSite(PlannedProcess): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('has_input') def pattern_has_input(cls, v): @@ -11756,6 +11973,12 @@ class ProtocolExecution(PlannedProcess): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -11788,7 +12011,10 @@ class ProtocolExecution(PlannedProcess): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('has_process_parts') def pattern_has_process_parts(cls, v): @@ -11935,6 +12161,12 @@ class StorageProcess(PlannedProcess): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:storpr-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -11967,7 +12199,10 @@ class StorageProcess(PlannedProcess): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('has_input') def pattern_has_input(cls, v): @@ -12078,7 +12313,13 @@ class MaterialProcessing(PlannedProcess): 'typecodes must correspond 1:1 to a class in the NMDC schema. this ' 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' - 'checked in the pattern']} }) + 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -12109,7 +12350,10 @@ class MaterialProcessing(PlannedProcess): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('has_input') def pattern_has_input(cls, v): @@ -12227,6 +12471,12 @@ class Pooling(MaterialProcessing): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -12259,7 +12509,10 @@ class Pooling(MaterialProcessing): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('has_input') def pattern_has_input(cls, v): @@ -12401,6 +12654,12 @@ class Extraction(MaterialProcessing): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -12433,7 +12692,10 @@ class Extraction(MaterialProcessing): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('has_input') def pattern_has_input(cls, v): @@ -12601,6 +12863,12 @@ class LibraryPreparation(MaterialProcessing): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -12633,7 +12901,10 @@ class LibraryPreparation(MaterialProcessing): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('has_input') def pattern_has_input(cls, v): @@ -12795,6 +13066,12 @@ class SubSamplingProcess(MaterialProcessing): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -12827,7 +13104,10 @@ class SubSamplingProcess(MaterialProcessing): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('has_input') def pattern_has_input(cls, v): @@ -12958,6 +13238,12 @@ class MixingProcess(MaterialProcessing): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'syntax': '{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', @@ -12989,7 +13275,10 @@ class MixingProcess(MaterialProcessing): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('has_input') def pattern_has_input(cls, v): @@ -13139,6 +13428,12 @@ class FiltrationProcess(MaterialProcessing): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:filtpr-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -13171,7 +13466,10 @@ class FiltrationProcess(MaterialProcessing): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('has_input') def pattern_has_input(cls, v): @@ -13304,6 +13602,12 @@ class ChromatographicSeparationProcess(MaterialProcessing): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'syntax': '{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', @@ -13335,7 +13639,10 @@ class ChromatographicSeparationProcess(MaterialProcessing): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('has_input') def pattern_has_input(cls, v): @@ -13464,6 +13771,12 @@ class DissolvingProcess(MaterialProcessing): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -13496,7 +13809,10 @@ class DissolvingProcess(MaterialProcessing): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('has_input') def pattern_has_input(cls, v): @@ -13630,6 +13946,12 @@ class ChemicalConversionProcess(MaterialProcessing): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -13662,7 +13984,10 @@ class ChemicalConversionProcess(MaterialProcessing): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('has_input') def pattern_has_input(cls, v): @@ -13744,7 +14069,10 @@ class Protocol(ConfiguredBaseModel): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) class CreditAssociation(ConfiguredBaseModel): @@ -13789,7 +14117,10 @@ class CreditAssociation(ConfiguredBaseModel): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) class Doi(ConfiguredBaseModel): @@ -13852,7 +14183,10 @@ class Doi(ConfiguredBaseModel): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('doi_value') def pattern_doi_value(cls, v): @@ -14254,6 +14588,12 @@ class Study(NamedThing): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', @@ -14294,7 +14634,10 @@ class Study(NamedThing): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('emsl_project_identifiers') def pattern_emsl_project_identifiers(cls, v): @@ -14475,7 +14818,13 @@ class InformationObject(NamedThing): 'typecodes must correspond 1:1 to a class in the NMDC schema. this ' 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' - 'checked in the pattern']} }) + 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -14506,7 +14855,10 @@ class InformationObject(NamedThing): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -14554,7 +14906,13 @@ class Configuration(InformationObject): 'typecodes must correspond 1:1 to a class in the NMDC schema. this ' 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' - 'checked in the pattern']} }) + 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -14585,7 +14943,10 @@ class Configuration(InformationObject): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -14654,6 +15015,12 @@ class MassSpectrometryConfiguration(Configuration): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'}} }) name: str = Field(..., description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -14686,7 +15053,10 @@ class MassSpectrometryConfiguration(Configuration): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -14759,6 +15129,12 @@ class ChromatographyConfiguration(Configuration): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'}} }) name: str = Field(..., description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -14791,7 +15167,10 @@ class ChromatographyConfiguration(Configuration): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -14845,6 +15224,12 @@ class Manifest(InformationObject): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'syntax': '{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', @@ -14876,7 +15261,10 @@ class Manifest(InformationObject): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('id') def pattern_id(cls, v): @@ -14951,6 +15339,12 @@ class CalibrationInformation(InformationObject): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -14983,7 +15377,10 @@ class CalibrationInformation(InformationObject): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('calibration_object') def pattern_calibration_object(cls, v): @@ -15048,7 +15445,10 @@ class DataObject(InformationObject): data_object_type: Optional[FileTypeEnum] = Field(None, description="""The type of file represented by the data object.""", json_schema_extra = { "linkml_meta": {'alias': 'data_object_type', 'domain_of': ['DataObject'], 'examples': [{'value': 'FT ICR-MS Analysis Results'}, - {'value': 'GC-MS Metabolomics Results'}]} }) + {'value': 'GC-MS Metabolomics Results'}], + 'structured_aliases': {'data_object_type': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_type', + 'predicate': 'EXACT_SYNONYM'}}} }) file_size_bytes: Optional[int] = Field(None, description="""Size of the file in bytes""", json_schema_extra = { "linkml_meta": {'alias': 'file_size_bytes', 'domain_of': ['DataObject']} }) insdc_experiment_identifiers: Optional[List[str]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'insdc_experiment_identifiers', 'domain_of': ['NucleotideSequencing', 'DataObject'], @@ -15086,6 +15486,12 @@ class DataObject(InformationObject): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'}} }) name: str = Field(..., description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -15118,7 +15524,10 @@ class DataObject(InformationObject): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('insdc_experiment_identifiers') def pattern_insdc_experiment_identifiers(cls, v): @@ -15269,7 +15678,13 @@ class DataGeneration(PlannedProcess): 'typecodes must correspond 1:1 to a class in the NMDC schema. this ' 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' - 'checked in the pattern']} }) + 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -15300,7 +15715,10 @@ class DataGeneration(PlannedProcess): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('associated_studies') def pattern_associated_studies(cls, v): @@ -15471,6 +15889,12 @@ class NucleotideSequencing(DataGeneration): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:(dgns|omprc)-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -15503,7 +15927,10 @@ class NucleotideSequencing(DataGeneration): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('gold_sequencing_project_identifiers') def pattern_gold_sequencing_project_identifiers(cls, v): @@ -15712,6 +16139,12 @@ class MassSpectrometry(DataGeneration): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:(dgms|omprc)-{id_shoulder}-{id_blade}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -15744,7 +16177,10 @@ class MassSpectrometry(DataGeneration): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('generates_calibration') def pattern_generates_calibration(cls, v): @@ -15912,7 +16348,10 @@ class WorkflowExecution(PlannedProcess): version: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'version', 'domain_of': ['WorkflowExecution']} }) was_informed_by: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'was_informed_by', 'domain_of': ['WorkflowExecution'], - 'mappings': ['prov:wasInformedBy']} }) + 'mappings': ['prov:wasInformedBy'], + 'structured_aliases': {'was_informed_by': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'was_informed_by', + 'predicate': 'EXACT_SYNONYM'}}} }) has_input: List[str] = Field(..., description="""An input to a process.""", json_schema_extra = { "linkml_meta": {'alias': 'has_input', 'aliases': ['input'], 'domain_of': ['PlannedProcess'], @@ -15951,7 +16390,13 @@ class WorkflowExecution(PlannedProcess): 'typecodes must correspond 1:1 to a class in the NMDC schema. this ' 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' - 'checked in the pattern']} }) + 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) description: Optional[str] = Field(None, description="""a human-readable description of a thing""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['ImageValue', 'NamedThing'], @@ -15982,7 +16427,10 @@ class WorkflowExecution(PlannedProcess): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('ended_at_time') def pattern_ended_at_time(cls, v): @@ -16119,6 +16567,9 @@ class MetagenomeAnnotation(WorkflowExecution): was_informed_by: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'was_informed_by', 'domain_of': ['WorkflowExecution'], 'mappings': ['prov:wasInformedBy'], + 'structured_aliases': {'was_informed_by': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'was_informed_by', + 'predicate': 'EXACT_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'}} }) has_input: List[str] = Field(..., description="""An input to a process.""", json_schema_extra = { "linkml_meta": {'alias': 'has_input', @@ -16160,6 +16611,12 @@ class MetagenomeAnnotation(WorkflowExecution): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -16192,7 +16649,10 @@ class MetagenomeAnnotation(WorkflowExecution): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('img_identifiers') def pattern_img_identifiers(cls, v): @@ -16429,6 +16889,9 @@ class MetagenomeAssembly(WorkflowExecution): was_informed_by: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'was_informed_by', 'domain_of': ['WorkflowExecution'], 'mappings': ['prov:wasInformedBy'], + 'structured_aliases': {'was_informed_by': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'was_informed_by', + 'predicate': 'EXACT_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'}} }) has_input: List[str] = Field(..., description="""An input to a process.""", json_schema_extra = { "linkml_meta": {'alias': 'has_input', @@ -16470,6 +16933,12 @@ class MetagenomeAssembly(WorkflowExecution): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -16502,7 +16971,10 @@ class MetagenomeAssembly(WorkflowExecution): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('insdc_assembly_identifiers') def pattern_insdc_assembly_identifiers(cls, v): @@ -16722,6 +17194,9 @@ class MetatranscriptomeAssembly(WorkflowExecution): was_informed_by: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'was_informed_by', 'domain_of': ['WorkflowExecution'], 'mappings': ['prov:wasInformedBy'], + 'structured_aliases': {'was_informed_by': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'was_informed_by', + 'predicate': 'EXACT_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'}} }) has_input: List[str] = Field(..., description="""An input to a process.""", json_schema_extra = { "linkml_meta": {'alias': 'has_input', @@ -16763,6 +17238,12 @@ class MetatranscriptomeAssembly(WorkflowExecution): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -16795,7 +17276,10 @@ class MetatranscriptomeAssembly(WorkflowExecution): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('insdc_assembly_identifiers') def pattern_insdc_assembly_identifiers(cls, v): @@ -16961,6 +17445,9 @@ class MetatranscriptomeAnnotation(WorkflowExecution): was_informed_by: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'was_informed_by', 'domain_of': ['WorkflowExecution'], 'mappings': ['prov:wasInformedBy'], + 'structured_aliases': {'was_informed_by': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'was_informed_by', + 'predicate': 'EXACT_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'}} }) has_input: List[str] = Field(..., description="""An input to a process.""", json_schema_extra = { "linkml_meta": {'alias': 'has_input', @@ -17002,6 +17489,12 @@ class MetatranscriptomeAnnotation(WorkflowExecution): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -17034,7 +17527,10 @@ class MetatranscriptomeAnnotation(WorkflowExecution): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('img_identifiers') def pattern_img_identifiers(cls, v): @@ -17197,6 +17693,9 @@ class MetatranscriptomeExpressionAnalysis(WorkflowExecution): was_informed_by: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'was_informed_by', 'domain_of': ['WorkflowExecution'], 'mappings': ['prov:wasInformedBy'], + 'structured_aliases': {'was_informed_by': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'was_informed_by', + 'predicate': 'EXACT_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'}} }) has_input: List[str] = Field(..., description="""An input to a process.""", json_schema_extra = { "linkml_meta": {'alias': 'has_input', @@ -17238,6 +17737,12 @@ class MetatranscriptomeExpressionAnalysis(WorkflowExecution): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:wfmtex-{id_shoulder}-{id_blade}{id_version}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -17270,7 +17775,10 @@ class MetatranscriptomeExpressionAnalysis(WorkflowExecution): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('img_identifiers') def pattern_img_identifiers(cls, v): @@ -17428,6 +17936,9 @@ class MagsAnalysis(WorkflowExecution): was_informed_by: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'was_informed_by', 'domain_of': ['WorkflowExecution'], 'mappings': ['prov:wasInformedBy'], + 'structured_aliases': {'was_informed_by': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'was_informed_by', + 'predicate': 'EXACT_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'}} }) has_input: List[str] = Field(..., description="""An input to a process.""", json_schema_extra = { "linkml_meta": {'alias': 'has_input', @@ -17469,6 +17980,12 @@ class MagsAnalysis(WorkflowExecution): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -17501,7 +18018,10 @@ class MagsAnalysis(WorkflowExecution): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('img_identifiers') def pattern_img_identifiers(cls, v): @@ -17644,6 +18164,9 @@ class MetagenomeSequencing(WorkflowExecution): was_informed_by: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'was_informed_by', 'domain_of': ['WorkflowExecution'], 'mappings': ['prov:wasInformedBy'], + 'structured_aliases': {'was_informed_by': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'was_informed_by', + 'predicate': 'EXACT_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'}} }) has_input: List[str] = Field(..., description="""An input to a process.""", json_schema_extra = { "linkml_meta": {'alias': 'has_input', @@ -17685,6 +18208,12 @@ class MetagenomeSequencing(WorkflowExecution): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -17717,7 +18246,10 @@ class MetagenomeSequencing(WorkflowExecution): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('ended_at_time') def pattern_ended_at_time(cls, v): @@ -17858,6 +18390,9 @@ class ReadQcAnalysis(WorkflowExecution): was_informed_by: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'was_informed_by', 'domain_of': ['WorkflowExecution'], 'mappings': ['prov:wasInformedBy'], + 'structured_aliases': {'was_informed_by': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'was_informed_by', + 'predicate': 'EXACT_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'}} }) has_input: List[str] = Field(..., description="""An input to a process.""", json_schema_extra = { "linkml_meta": {'alias': 'has_input', @@ -17899,6 +18434,12 @@ class ReadQcAnalysis(WorkflowExecution): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -17931,7 +18472,10 @@ class ReadQcAnalysis(WorkflowExecution): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('ended_at_time') def pattern_ended_at_time(cls, v): @@ -18058,6 +18602,9 @@ class ReadBasedTaxonomyAnalysis(WorkflowExecution): was_informed_by: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'was_informed_by', 'domain_of': ['WorkflowExecution'], 'mappings': ['prov:wasInformedBy'], + 'structured_aliases': {'was_informed_by': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'was_informed_by', + 'predicate': 'EXACT_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'}} }) has_input: List[str] = Field(..., description="""An input to a process.""", json_schema_extra = { "linkml_meta": {'alias': 'has_input', @@ -18099,6 +18646,12 @@ class ReadBasedTaxonomyAnalysis(WorkflowExecution): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -18131,7 +18684,10 @@ class ReadBasedTaxonomyAnalysis(WorkflowExecution): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('ended_at_time') def pattern_ended_at_time(cls, v): @@ -18263,6 +18819,9 @@ class MetabolomicsAnalysis(WorkflowExecution): was_informed_by: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'was_informed_by', 'domain_of': ['WorkflowExecution'], 'mappings': ['prov:wasInformedBy'], + 'structured_aliases': {'was_informed_by': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'was_informed_by', + 'predicate': 'EXACT_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'}} }) has_input: List[str] = Field(..., description="""An input to a process.""", json_schema_extra = { "linkml_meta": {'alias': 'has_input', @@ -18304,6 +18863,12 @@ class MetabolomicsAnalysis(WorkflowExecution): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -18336,7 +18901,10 @@ class MetabolomicsAnalysis(WorkflowExecution): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('uses_calibration') def pattern_uses_calibration(cls, v): @@ -18473,6 +19041,9 @@ class MetaproteomicsAnalysis(WorkflowExecution): was_informed_by: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'was_informed_by', 'domain_of': ['WorkflowExecution'], 'mappings': ['prov:wasInformedBy'], + 'structured_aliases': {'was_informed_by': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'was_informed_by', + 'predicate': 'EXACT_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'}} }) has_input: List[str] = Field(..., description="""An input to a process.""", json_schema_extra = { "linkml_meta": {'alias': 'has_input', @@ -18514,6 +19085,12 @@ class MetaproteomicsAnalysis(WorkflowExecution): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -18546,7 +19123,10 @@ class MetaproteomicsAnalysis(WorkflowExecution): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('ended_at_time') def pattern_ended_at_time(cls, v): @@ -18676,6 +19256,9 @@ class NomAnalysis(WorkflowExecution): was_informed_by: str = Field(..., json_schema_extra = { "linkml_meta": {'alias': 'was_informed_by', 'domain_of': ['WorkflowExecution'], 'mappings': ['prov:wasInformedBy'], + 'structured_aliases': {'was_informed_by': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'was_informed_by', + 'predicate': 'EXACT_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'}} }) has_input: List[str] = Field(..., description="""An input to a process.""", json_schema_extra = { "linkml_meta": {'alias': 'has_input', @@ -18717,6 +19300,12 @@ class NomAnalysis(WorkflowExecution): 'will be checked via per-class id slot usage assertions', 'minting authority shoulders should probably be enumerated and ' 'checked in the pattern'], + 'structured_aliases': {'data_object_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'data_object_id', + 'predicate': 'NARROW_SYNONYM'}, + 'workflow_execution_id': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_id', + 'predicate': 'NARROW_SYNONYM'}}, 'structured_pattern': {'interpolated': True, 'syntax': '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$'}} }) name: Optional[str] = Field(None, description="""A human readable label for an entity""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['PersonValue', 'NamedThing', 'Protocol']} }) @@ -18749,7 +19338,10 @@ class NomAnalysis(WorkflowExecution): 'see_also': ['https://github.com/microbiomedata/nmdc-schema/issues/1048', 'https://github.com/microbiomedata/nmdc-schema/issues/1233', 'https://github.com/microbiomedata/nmdc-schema/issues/248'], - 'slot_uri': 'rdf:type'} }) + 'slot_uri': 'rdf:type', + 'structured_aliases': {'workflow_execution_class': {'contexts': ['https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml'], + 'literal_form': 'workflow_execution_class', + 'predicate': 'NARROW_SYNONYM'}}} }) @field_validator('uses_calibration') def pattern_uses_calibration(cls, v): diff --git a/nmdc_schema/nmdc.py b/nmdc_schema/nmdc.py index ba1b1827d2..10706ae73e 100644 --- a/nmdc_schema/nmdc.py +++ b/nmdc_schema/nmdc.py @@ -1,15 +1,9 @@ # Auto generated from nmdc.yaml by pythongen.py version: 0.0.1 -# Generation date: 2025-01-08T12:52:37 +# Generation date: 2025-01-17T21:04:40 # Schema: NMDC # # id: https://w3id.org/nmdc/nmdc -# description: Schema for National Microbiome Data Collaborative (NMDC). -# This schema is organized into multiple modules, such as: -# -# * a set of core types for representing data values -# * a subset of the mixs schema -# * an annotation schema -# * the NMDC schema itself, into which the other modules are imported +# description: The NMDC Schema is a foundational framework designed to standardize metadata for the National Microbiome Data Collaborative (NMDC) and collaborating data providors. By establishing a structured approach to metadata, the NMDC Schema enables researchers to organize, share, and interpret complex datasets with consistency and clarity. The NMDC Schema is critical substrate used to facilitate interoperability and collaboration, as it provide a common language for data exchange across systems and disciplines. In the context of the NMDC, this schema supports the integration of microbiome data from medicine, agriculture, bioenergy, and environmental science into a cohesive platform. # license: https://creativecommons.org/publicdomain/zero/1.0/ import dataclasses @@ -7626,7 +7620,11 @@ def _addvals(cls): setattr(cls, "LC-MS Lipidomics Results", PermissibleValue( text="LC-MS Lipidomics Results", - description="LC-MS-based lipid assignment results table.")) + description="LC-MS-based lipidomics analysis results table")) + setattr(cls, "LC-MS Lipidomics Processed Data", + PermissibleValue( + text="LC-MS Lipidomics Processed Data", + description="Processed data for the LC-MS-based lipidomics analysis in hdf5 format")) setattr(cls, "Contaminants Amino Acid FASTA", PermissibleValue( text="Contaminants Amino Acid FASTA", diff --git a/nmdc_schema/nmdc.schema.json b/nmdc_schema/nmdc.schema.json index 4463c8625c..0548a0563b 100644 --- a/nmdc_schema/nmdc.schema.json +++ b/nmdc_schema/nmdc.schema.json @@ -8026,6 +8026,7 @@ "LC-DDA-MS/MS Raw Data", "Configuration toml", "LC-MS Lipidomics Results", + "LC-MS Lipidomics Processed Data", "Contaminants Amino Acid FASTA", "Analysis Tool Parameter File", "Workflow Operation Summary", diff --git a/nmdc_schema/nmdc_materialized_patterns.schema.json b/nmdc_schema/nmdc_materialized_patterns.schema.json index dec5e8a2f6..0d8c155b5d 100644 --- a/nmdc_schema/nmdc_materialized_patterns.schema.json +++ b/nmdc_schema/nmdc_materialized_patterns.schema.json @@ -8042,6 +8042,7 @@ "LC-DDA-MS/MS Raw Data", "Configuration toml", "LC-MS Lipidomics Results", + "LC-MS Lipidomics Processed Data", "Contaminants Amino Acid FASTA", "Analysis Tool Parameter File", "Workflow Operation Summary", diff --git a/nmdc_schema/nmdc_materialized_patterns.yaml b/nmdc_schema/nmdc_materialized_patterns.yaml index 4b91ca8eab..26b4c52149 100644 --- a/nmdc_schema/nmdc_materialized_patterns.yaml +++ b/nmdc_schema/nmdc_materialized_patterns.yaml @@ -1,8 +1,13 @@ name: NMDC -description: "Schema for National Microbiome Data Collaborative (NMDC).\nThis schema\ - \ is organized into multiple modules, such as:\n\n * a set of core types for representing\ - \ data values\n * a subset of the mixs schema\n * an annotation schema\n * the NMDC\ - \ schema itself, into which the other modules are imported" +description: The NMDC Schema is a foundational framework designed to standardize metadata + for the National Microbiome Data Collaborative (NMDC) and collaborating data providors. + By establishing a structured approach to metadata, the NMDC Schema enables researchers + to organize, share, and interpret complex datasets with consistency and clarity. + The NMDC Schema is critical substrate used to facilitate interoperability and collaboration, + as it provide a common language for data exchange across systems and disciplines. In + the context of the NMDC, this schema supports the integration of microbiome data + from medicine, agriculture, bioenergy, and environmental science into a cohesive + platform. title: NMDC Schema notes: - not importing any MIxS terms where the relationship between the name (SCN) and the @@ -4114,7 +4119,11 @@ enums: - edam.format:4005 LC-MS Lipidomics Results: text: LC-MS Lipidomics Results - description: LC-MS-based lipid assignment results table. + description: LC-MS-based lipidomics analysis results table + LC-MS Lipidomics Processed Data: + text: LC-MS Lipidomics Processed Data + description: Processed data for the LC-MS-based lipidomics analysis in hdf5 + format Contaminants Amino Acid FASTA: text: Contaminants Amino Acid FASTA description: FASTA amino acid file for contaminant proteins commonly observed @@ -17120,6 +17129,12 @@ slots: was_informed_by: name: was_informed_by from_schema: https://w3id.org/nmdc/nmdc + structured_aliases: + was_informed_by: + literal_form: was_informed_by + predicate: EXACT_SYNONYM + contexts: + - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml mappings: - prov:wasInformedBy range: DataGeneration @@ -17301,6 +17316,12 @@ slots: - value: FT ICR-MS Analysis Results - value: GC-MS Metabolomics Results from_schema: https://w3id.org/nmdc/nmdc + structured_aliases: + data_object_type: + literal_form: data_object_type + predicate: EXACT_SYNONYM + contexts: + - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml range: FileTypeEnum data_category: name: data_category @@ -17744,6 +17765,12 @@ slots: - https://github.com/microbiomedata/nmdc-schema/issues/1048 - https://github.com/microbiomedata/nmdc-schema/issues/1233 - https://github.com/microbiomedata/nmdc-schema/issues/248 + structured_aliases: + workflow_execution_class: + literal_form: workflow_execution_class + predicate: NARROW_SYNONYM + contexts: + - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml slot_uri: rdf:type designates_type: true range: uriorcurie @@ -17809,6 +17836,17 @@ slots: - value: nmdc:mgmag-00-x012.1_7_c1 description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248 from_schema: https://w3id.org/nmdc/nmdc + structured_aliases: + workflow_execution_id: + literal_form: workflow_execution_id + predicate: NARROW_SYNONYM + contexts: + - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml + data_object_id: + literal_form: data_object_id + predicate: NARROW_SYNONYM + contexts: + - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml identifier: true range: uriorcurie required: true