Datasheet update

src/ontogpt/templates/biolog_simple.py

@@ -0,0 +1,124 @@
+from __future__ import annotations 
+
+import re
+import sys
+from datetime import (
+    date,
+    datetime,
+    time
+)
+from decimal import Decimal 
+from enum import Enum 
+from typing import (
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Literal,
+    Optional,
+    Union
+)
+
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    RootModel,
+    field_validator
+)
+
+
+metamodel_version = "None"
+version = "0.1.0"
+
+
+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': 'https://example.org/PaperExtractionSchema/',
+     'description': 'A simplified schema describing the fields to extract from a '
+                    'paper that includes study metadata and a minimal notion of '
+                    'experiments.\n',
+     'id': 'https://example.org/PaperExtractionSchema',
+     'imports': ['linkml:types'],
+     'name': 'PaperExtractionSchema',
+     'prefixes': {'linkml': {'prefix_prefix': 'linkml',
+                             'prefix_reference': 'https://w3id.org/linkml/'},
+                  'xsd': {'prefix_prefix': 'xsd',
+                          'prefix_reference': 'http://www.w3.org/2001/XMLSchema#'}},
+     'source_file': 'src/ontogpt/templates/biolog_simple.yaml',
+     'title': 'Paper Extraction Schema',
+     'types': {'boolean': {'base': 'bool',
+                           'from_schema': 'https://example.org/PaperExtractionSchema',
+                           'name': 'boolean'},
+               'string': {'base': 'str',
+                          'from_schema': 'https://example.org/PaperExtractionSchema',
+                          'name': 'string'}}} )
+
+
+class Paper(ConfiguredBaseModel):
+    """
+    Top-level class representing a single paper/study.
+    """
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://example.org/PaperExtractionSchema', 'tree_root': True})
+
+    study_title: str = Field(default=..., description="""Title of the study.""", json_schema_extra = { "linkml_meta": {'alias': 'study_title', 'domain_of': ['Paper']} })
+    authors: List[Author] = Field(default=..., description="""List of authors of the paper.""", json_schema_extra = { "linkml_meta": {'alias': 'authors', 'domain_of': ['Paper']} })
+    doi: Optional[str] = Field(default=None, description="""DOI of the publication.""", json_schema_extra = { "linkml_meta": {'alias': 'doi', 'domain_of': ['Paper']} })
+    date: Optional[str] = Field(default=None, description="""Date of the publication or the study.""", json_schema_extra = { "linkml_meta": {'alias': 'date', 'domain_of': ['Paper']} })
+    experiments: Optional[List[Experiment]] = Field(default=None, description="""List of experiments mentioned in the paper.""", json_schema_extra = { "linkml_meta": {'alias': 'experiments', 'domain_of': ['Paper']} })
+
+
+class Author(ConfiguredBaseModel):
+    """
+    Represents an author of the paper.
+    """
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://example.org/PaperExtractionSchema'})
+
+    name: str = Field(default=..., description="""Name of the author.""", json_schema_extra = { "linkml_meta": {'alias': 'name', 'domain_of': ['Author']} })
+
+
+class Experiment(ConfiguredBaseModel):
+    """
+    A minimal experiment class (could be Biolog or otherwise).
+    """
+    linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://example.org/PaperExtractionSchema'})
+
+    experiment_title: Optional[str] = Field(default=None, description="""Title or short description of the experiment.""", json_schema_extra = { "linkml_meta": {'alias': 'experiment_title', 'domain_of': ['Experiment']} })
+    is_biolog_experiment: Optional[bool] = Field(default=None, description="""Flag indicating if this experiment is a Biolog experiment.""", json_schema_extra = { "linkml_meta": {'alias': 'is_biolog_experiment', 'domain_of': ['Experiment']} })
+
+
+# Model rebuild
+# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
+Paper.model_rebuild()
+Author.model_rebuild()
+Experiment.model_rebuild()
+

src/ontogpt/templates/biolog_simple.yaml

@@ -0,0 +1,98 @@
+id: https://example.org/PaperExtractionSchema
+name: PaperExtractionSchema
+title: Paper Extraction Schema
+description: >
+  A simplified schema describing the fields to extract from a paper that includes
+  study metadata and a minimal notion of experiments.
+version: 0.1.0
+
+prefixes:
+  linkml: "https://w3id.org/linkml/"
+  xsd: "http://www.w3.org/2001/XMLSchema#"
+
+imports:
+  - linkml:types
+
+types:
+  string:
+    base: str
+  boolean:
+    base: bool
+
+########################
+# CLASSES
+########################
+
+classes:
+  # The top-level class (root) for the paper
+  Paper:
+    description: "Top-level class representing a single paper/study."
+    tree_root: true
+    slots:
+      - study_title
+      - authors
+      - doi
+      - date
+      - experiments
+
+  Author:
+    description: "Represents an author of the paper."
+    slots:
+      - name
+
+  Experiment:
+    description: "A minimal experiment class (could be Biolog or otherwise)."
+    slots:
+      - experiment_title
+      - is_biolog_experiment
+
+########################
+# SLOTS
+########################
+
+slots:
+  # Paper-level slots
+  study_title:
+    description: "Title of the study."
+    range: string
+    required: true
+
+  authors:
+    description: "List of authors of the paper."
+    range: Author
+    multivalued: true
+    required: true
+
+  doi:
+    description: "DOI of the publication."
+    range: string
+    required: false
+
+  date:
+    description: "Date of the publication or the study."
+    range: string
+    required: false
+
+  experiments:
+    description: "List of experiments mentioned in the paper."
+    range: Experiment
+    multivalued: true
+    required: false
+
+  # Author-level slot
+  name:
+    description: "Name of the author."
+    range: string
+    required: true
+
+  # Experiment-level slots
+  experiment_title:
+    description: "Title or short description of the experiment."
+    range: string
+    required: false
+
+  is_biolog_experiment:
+    description: "Flag indicating if this experiment is a Biolog experiment."
+    range: boolean
+    required: false
+