Add initial version of micronutrient extraction template (and other n…

…ew templates) (#469)

src/ontogpt/templates/ecosim_methods.yaml

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+id: http://w3id.org/ontogpt/ecosim_methods
+name: ecosim_methods
+title: EcoSIM Methods Extraction Template
+description: >-
+  EcoSIM Methods Extraction Template
+license: https://creativecommons.org/publicdomain/zero/1.0/
+prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
+  linkml: https://w3id.org/linkml/
+  ecosim_simple: http://w3id.org/ontogpt/ecosim_simple
+  ecosim: http://purl.obolibrary.org/obo/ecosim
+
+default_prefix: ecosim_methods
+default_range: string
+
+imports:
+  - linkml:types
+  - core
+
+classes:
+  TermSet:
+    tree_root: true
+    is_a: NamedEntity
+    attributes:
+      locations:
+        range: Location
+        multivalued: true
+        description: >-
+          A semicolon-separated list of research locations.
+          Examples include: Vermont, New York City,
+          Ethiopia
+      methods:
+        range: Method
+        multivalued: true
+        description: >-
+          A semicolon-separated list of methods used in
+          environmental and earth science research. Examples
+          include: sampling, spectroscopy
+      variables:
+        range: Variable
+        description: >-
+          A semicolon-separated list of variables measured in
+          environmental and earth science research. Examples
+          include: root shape, biomass, water turbidity
+      equipments:
+        range: Equipment
+        description: >-
+          A semicolon-separated list of equipment used in
+          environmental and earth science research.
+      equipment_to_variable_relationships:
+        range: EquipmentMeasuresVariable
+        description: >-
+          A semicolon separated list of relationships
+          between specific equipment and variables
+          they are used to measure as described in the input.
+          Example: NMR spectrometer was used to measure
+          chemical content
+        multivalued: true
+        inlined: true
+
+  Location:
+    is_a: NamedEntity
+    annotations:
+      prompt: >-
+        The name of a location used in research.
+
+  Method:
+    is_a: NamedEntity
+    annotations:
+      annotators: bioportal:ECOSIM
+      prompt: >-
+        The name of a method used in environment and
+        earth science research.
+
+  Variable:
+    is_a: NamedEntity
+    annotations:
+      annotators: bioportal:ECOSIM
+      prompt: >-
+        The name of a variable measured in environment and
+        earth science research.
+
+  Equipment:
+    is_a: NamedEntity
+    annotations:
+      prompt: >-
+        The name of a piece of equipment used in
+        environment and earth science research.
+
+  EquipmentMeasuresVariable:
+    is_a: CompoundExpression
+    attributes:
+      equipment:
+        range: Equipment
+        description: Name of the equipment used to measure a variable.
+      variable:
+        range: Variable
+        description: Name of the variable being measured.
+

src/ontogpt/templates/ecosim_simple.py

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+from __future__ import annotations 
+from datetime import (
+    datetime,
+    date,
+    time
+)
+from decimal import Decimal 
+from enum import Enum 
+import re
+import sys
+from typing import (
+    Any,
+    ClassVar,
+    List,
+    Literal,
+    Dict,
+    Optional,
+    Union
+)
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator
+)
+metamodel_version = "None"
+version = "None"
+
+
+class ConfiguredBaseModel(BaseModel):
+    model_config = ConfigDict(
+        validate_assignment = True,
+        validate_default = True,
+        extra = "forbid",
+        arbitrary_types_allowed = True,
+        use_enum_values = True,
+        strict = False,
+    )
+    pass
+
+
+
+
+class LinkMLMeta(RootModel):
+    root: Dict[str, Any] = {}
+    model_config = ConfigDict(frozen=True)
+
+    def __getattr__(self, key:str):
+        return getattr(self.root, key)
+
+    def __getitem__(self, key:str):
+        return self.root[key]
+
+    def __setitem__(self, key:str, value):
+        self.root[key] = value
+
+    def __contains__(self, key:str) -> bool:
+        return key in self.root
+
+
+linkml_meta = LinkMLMeta({'default_prefix': 'ecosim_simple',
+     'default_range': 'string',
+     'description': 'Simple EcoSIM Extraction Template',
+     'id': 'http://w3id.org/ontogpt/ecosim_simple',
+     'imports': ['linkml:types', 'core'],
+     'license': 'https://creativecommons.org/publicdomain/zero/1.0/',
+     'name': 'ecosim_simple',
+     'prefixes': {'ecosim': {'prefix_prefix': 'ecosim',
+                             'prefix_reference': 'http://purl.obolibrary.org/obo/ecosim'},
+                  'ecosim_simple': {'prefix_prefix': 'ecosim_simple',
+                                    'prefix_reference': 'http://w3id.org/ontogpt/ecosim_simple'},
+                  'linkml': {'prefix_prefix': 'linkml',
+                             'prefix_reference': 'https://w3id.org/linkml/'},
+                  'rdf': {'prefix_prefix': 'rdf',
+                          'prefix_reference': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'}},
+     'source_file': '/home/harry/ontogpt/src/ontogpt/templates/ecosim_simple.yaml',
+     'title': 'Simple EcoSIM Extraction Template'} )
+
+class NullDataOptions(str, Enum):
+    UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION"
+    NOT_APPLICABLE = "NOT_APPLICABLE"
+    NOT_MENTIONED = "NOT_MENTIONED"
+
+
+
+class ExtractionResult(ConfiguredBaseModel):
+    """
+    A result of extracting knowledge on text
+    """
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'})
+
+    input_id: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'input_id', 'domain_of': ['ExtractionResult']} })
+    input_title: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'input_title', 'domain_of': ['ExtractionResult']} })
+    input_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'input_text', 'domain_of': ['ExtractionResult']} })
+    raw_completion_output: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'raw_completion_output', 'domain_of': ['ExtractionResult']} })
+    prompt: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'prompt', 'domain_of': ['ExtractionResult']} })
+    extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""", json_schema_extra = { "linkml_meta": {'alias': 'extracted_object', 'domain_of': ['ExtractionResult']} })
+    named_entities: Optional[List[Any]] = Field(None, description="""Named entities extracted from the text""", json_schema_extra = { "linkml_meta": {'alias': 'named_entities', 'domain_of': ['ExtractionResult']} })
+
+
+class NamedEntity(ConfiguredBaseModel):
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'http://w3id.org/ontogpt/core'})
+
+    id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id',
+         'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}},
+         'comments': ['this is populated during the grounding and normalization step'],
+         'domain_of': ['NamedEntity', 'Publication']} })
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label',
+         'aliases': ['name'],
+         'annotations': {'owl': {'tag': 'owl',
+                                 'value': 'AnnotationProperty, AnnotationAssertion'}},
+         'domain_of': ['NamedEntity'],
+         'slot_uri': 'rdfs:label'} })
+
+
+class CompoundExpression(ConfiguredBaseModel):
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'http://w3id.org/ontogpt/core'})
+
+    pass
+
+
+class Triple(CompoundExpression):
+    """
+    Abstract parent for Relation Extraction tasks
+    """
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'http://w3id.org/ontogpt/core'})
+
+    subject: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'subject', 'domain_of': ['Triple']} })
+    predicate: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'predicate', 'domain_of': ['Triple']} })
+    object: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'object', 'domain_of': ['Triple']} })
+    qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""", json_schema_extra = { "linkml_meta": {'alias': 'qualifier', 'domain_of': ['Triple']} })
+    subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""", json_schema_extra = { "linkml_meta": {'alias': 'subject_qualifier', 'domain_of': ['Triple']} })
+    object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""", json_schema_extra = { "linkml_meta": {'alias': 'object_qualifier', 'domain_of': ['Triple']} })
+
+
+class TextWithTriples(ConfiguredBaseModel):
+    """
+    A text containing one or more relations of the Triple type.
+    """
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'})
+
+    publication: Optional[Publication] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'publication',
+         'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}},
+         'domain_of': ['TextWithTriples', 'TextWithEntity']} })
+    triples: Optional[List[Triple]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'triples', 'domain_of': ['TextWithTriples']} })
+
+
+class TextWithEntity(ConfiguredBaseModel):
+    """
+    A text containing one or more instances of a single type of entity.
+    """
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'})
+
+    publication: Optional[Publication] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'publication',
+         'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}},
+         'domain_of': ['TextWithTriples', 'TextWithEntity']} })
+    entities: Optional[List[str]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'entities', 'domain_of': ['TextWithEntity']} })
+
+
+class RelationshipType(NamedEntity):
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core',
+         'id_prefixes': ['RO', 'biolink']})
+
+    id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id',
+         'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}},
+         'comments': ['this is populated during the grounding and normalization step'],
+         'domain_of': ['NamedEntity', 'Publication']} })
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label',
+         'aliases': ['name'],
+         'annotations': {'owl': {'tag': 'owl',
+                                 'value': 'AnnotationProperty, AnnotationAssertion'}},
+         'domain_of': ['NamedEntity'],
+         'slot_uri': 'rdfs:label'} })
+
+
+class Publication(ConfiguredBaseModel):
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'})
+
+    id: Optional[str] = Field(None, description="""The publication identifier""", json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['NamedEntity', 'Publication']} })
+    title: Optional[str] = Field(None, description="""The title of the publication""", json_schema_extra = { "linkml_meta": {'alias': 'title', 'domain_of': ['Publication']} })
+    abstract: Optional[str] = Field(None, description="""The abstract of the publication""", json_schema_extra = { "linkml_meta": {'alias': 'abstract', 'domain_of': ['Publication']} })
+    combined_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'combined_text', 'domain_of': ['Publication']} })
+    full_text: Optional[str] = Field(None, description="""The full text of the publication""", json_schema_extra = { "linkml_meta": {'alias': 'full_text', 'domain_of': ['Publication']} })
+
+
+class AnnotatorResult(ConfiguredBaseModel):
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'})
+
+    subject_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'subject_text', 'domain_of': ['AnnotatorResult']} })
+    object_id: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'object_id', 'domain_of': ['AnnotatorResult']} })
+    object_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'object_text', 'domain_of': ['AnnotatorResult']} })
+
+
+class TermSet(NamedEntity):
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/ecosim_simple', 'tree_root': True})
+
+    terms: Optional[List[str]] = Field(None, description="""A semicolon-separated list of variables for earth system simulation. Do not include abbreviations in parentheses, e.g., \"Carbon (C)\" should be represented as \"carbon\". Examples include:          carboxylation, sodium, underground irrigation.""", json_schema_extra = { "linkml_meta": {'alias': 'terms', 'domain_of': ['TermSet']} })
+    id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id',
+         'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}},
+         'comments': ['this is populated during the grounding and normalization step'],
+         'domain_of': ['NamedEntity', 'Publication']} })
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label',
+         'aliases': ['name'],
+         'annotations': {'owl': {'tag': 'owl',
+                                 'value': 'AnnotationProperty, AnnotationAssertion'}},
+         'domain_of': ['NamedEntity'],
+         'slot_uri': 'rdfs:label'} })
+
+
+class Term(NamedEntity):
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'annotations': {'annotators': {'tag': 'annotators',
+                                        'value': 'bioportal:ECOSIM'},
+                         'prompt': {'tag': 'prompt',
+                                    'value': 'The name of a variable for earth system '
+                                             'simulation.'}},
+         'from_schema': 'http://w3id.org/ontogpt/ecosim_simple'})
+
+    id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id',
+         'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}},
+         'comments': ['this is populated during the grounding and normalization step'],
+         'domain_of': ['NamedEntity', 'Publication']} })
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label',
+         'aliases': ['name'],
+         'annotations': {'owl': {'tag': 'owl',
+                                 'value': 'AnnotationProperty, AnnotationAssertion'}},
+         'domain_of': ['NamedEntity'],
+         'slot_uri': 'rdfs:label'} })
+
+
+# Model rebuild
+# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
+ExtractionResult.model_rebuild()
+NamedEntity.model_rebuild()
+CompoundExpression.model_rebuild()
+Triple.model_rebuild()
+TextWithTriples.model_rebuild()
+TextWithEntity.model_rebuild()
+RelationshipType.model_rebuild()
+Publication.model_rebuild()
+AnnotatorResult.model_rebuild()
+TermSet.model_rebuild()
+Term.model_rebuild()

src/ontogpt/templates/ecosim_simple.yaml

@@ -0,0 +1,39 @@
+id: http://w3id.org/ontogpt/ecosim_simple
+name: ecosim_simple
+title: Simple EcoSIM Extraction Template
+description: >-
+  Simple EcoSIM Extraction Template
+license: https://creativecommons.org/publicdomain/zero/1.0/
+prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
+  linkml: https://w3id.org/linkml/
+  ecosim_simple: http://w3id.org/ontogpt/ecosim_simple
+  ecosim: http://purl.obolibrary.org/obo/ecosim
+
+default_prefix: ecosim_simple
+default_range: string
+
+imports:
+  - linkml:types
+  - core
+
+classes:
+  TermSet:
+    tree_root: true
+    is_a: NamedEntity
+    attributes:
+      terms:
+        range: Term
+        multivalued: true
+        description: >-
+          A semicolon-separated list of variables
+          for earth system simulation. Do not include
+          abbreviations in parentheses, e.g., "Carbon (C)"
+          should be represented as "carbon". Examples include:          carboxylation, sodium, underground irrigation.
+
+  Term:
+    is_a: NamedEntity
+    annotations:
+      annotators: bioportal:ECOSIM
+      prompt: >-
+        The name of a variable for earth system simulation.