Add rdf to prefixes on templates to avoid extra warnings (#339)

OWL export produces warnings when rdf prefix isn't defined, so now it's
in the YAML templates.

src/ontogpt/templates/biological_process.yaml

@@ -5,6 +5,7 @@ description: >-
   A template for GO-CAMs
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
   CHEBI: http://purl.obolibrary.org/obo/CHEBI_
   CL: http://purl.obolibrary.org/obo/CL_
   GO: http://purl.obolibrary.org/obo/GO_

src/ontogpt/templates/biotic_interaction.yaml

@@ -5,6 +5,7 @@ description: >-
   A template for biotic interactions
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
   MESH: http://identifiers.org/mesh/
   NCBITaxon: http://purl.obolibrary.org/obo/NCBITAXON_
   RO: http://purl.obolibrary.org/obo/RO_

src/ontogpt/templates/cell_type.yaml

@@ -5,6 +5,7 @@ description: >-
   A template for representing cell types
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
   AUTO: http://w3id.org/ontogpt/auto/
   BFO: http://purl.obolibrary.org/obo/BFO_
   CHEBI: http://purl.obolibrary.org/obo/CHEBI_

src/ontogpt/templates/class_enrichment.yaml

@@ -6,6 +6,7 @@ description: >-
 license: https://creativecommons.org/publicdomain/zero/1.0/
 
 prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
   OBI: http://purl.obolibrary.org/obo/OBI_
   STATO: http://purl.obolibrary.org/obo/STATO_
   bpa: https://bioportal.bioontology.org/annotator/

src/ontogpt/templates/composite_disease.yaml

@@ -5,6 +5,7 @@ description: >-
   A template for representing composite disease concepts
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
   CHEBI: http://purl.obolibrary.org/obo/CHEBI_
   HGNC: http://identifiers.org/hgnc/
   HP: http://purl.obolibrary.org/obo/HP_

src/ontogpt/templates/core.yaml

@@ -3,6 +3,7 @@ name: core
 title: AI core Template
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
   NCIT: http://purl.obolibrary.org/obo/NCIT_
   RO: http://purl.obolibrary.org/obo/RO_
   biolink: https://w3id.org/biolink/vocab/

src/ontogpt/templates/ctd.yaml

@@ -13,6 +13,7 @@ see_also:
 source: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-v/track-3-cdr/
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
   MESH: http://identifiers.org/mesh/
   drug: http://w3id.org/ontogpt/drug/
   linkml: https://w3id.org/linkml/

src/ontogpt/templates/ctd_ner.yaml

@@ -15,6 +15,7 @@ source: >-
   https://biocreative.bioinformatics.udel.edu/tasks/biocreative-v/track-3-cdr/
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
   MESH: http://identifiers.org/mesh/
   ctdner: http://w3id.org/ontogpt/ctd_ner
   linkml: https://w3id.org/linkml/

src/ontogpt/templates/data_sheets_schema.yaml

@@ -9,6 +9,7 @@ see_also:
   - https://bridge2ai.github.io/data-sheets-schema
 
 prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
   biolink: https://w3id.org/biolink/
   csvw: http://www.w3.org/ns/csvw#
   data_sheets_schema: https://w3id.org/bridge2ai/data-sheets-schema/

src/ontogpt/templates/datasheet.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 from datetime import datetime, date
 from enum import Enum
+
 from typing import List, Dict, Optional, Any, Union
 from pydantic import BaseModel as BaseModel, ConfigDict,  Field, field_validator
 import re
@@ -21,6 +22,7 @@ class ConfiguredBaseModel(BaseModel):
         extra = 'forbid',
         arbitrary_types_allowed=True,
         use_enum_values = True)
+    pass
 
 
 class NullDataOptions(str, Enum):
@@ -46,14 +48,14 @@ class ExtractionResult(ConfiguredBaseModel):
     extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""")
     named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""")
 
-        
+
 
 class NamedEntity(ConfiguredBaseModel):
 
     id: str = Field(..., description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
 
-        
+
 
 class Dataset(NamedEntity):
     """
@@ -72,20 +74,20 @@ class Dataset(NamedEntity):
     id: str = Field(..., description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
 
-        
+
 
 class Organization(NamedEntity):
 
     id: str = Field(..., description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
 
-        
+
 
 class CompoundExpression(ConfiguredBaseModel):
 
     None
 
-        
+
 
 class Triple(CompoundExpression):
     """
@@ -98,7 +100,7 @@ class Triple(CompoundExpression):
     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\"""")
     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\"""")
 
-        
+
 
 class TextWithTriples(ConfiguredBaseModel):
     """
@@ -107,7 +109,7 @@ class TextWithTriples(ConfiguredBaseModel):
     publication: Optional[Publication] = Field(None)
     triples: Optional[List[Triple]] = Field(default_factory=list)
 
-        
+
 
 class TextWithEntity(ConfiguredBaseModel):
     """
@@ -116,14 +118,14 @@ class TextWithEntity(ConfiguredBaseModel):
     publication: Optional[Publication] = Field(None)
     entities: Optional[List[str]] = Field(default_factory=list)
 
-        
+
 
 class RelationshipType(NamedEntity):
 
     id: str = Field(..., description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
 
-        
+
 
 class Publication(ConfiguredBaseModel):
 
@@ -133,15 +135,15 @@ class Publication(ConfiguredBaseModel):
     combined_text: Optional[str] = Field(None)
     full_text: Optional[str] = Field(None, description="""The full text of the publication""")
 
-        
+
 
 class AnnotatorResult(ConfiguredBaseModel):
 
     subject_text: Optional[str] = Field(None)
     object_id: Optional[str] = Field(None)
     object_text: Optional[str] = Field(None)
 
-        
+
 
 
 # Model rebuild

src/ontogpt/templates/datasheet.yaml

@@ -10,6 +10,7 @@ description: >-
 
 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/
   d4d: http://w3id.org/ontogpt/datasheet
 

src/ontogpt/templates/desiccation.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 from datetime import datetime, date
 from enum import Enum
+
 from typing import List, Dict, Optional, Any, Union
 from pydantic import BaseModel as BaseModel, ConfigDict,  Field, field_validator
 import re
@@ -21,6 +22,7 @@ class ConfiguredBaseModel(BaseModel):
         extra = 'forbid',
         arbitrary_types_allowed=True,
         use_enum_values = True)
+    pass
 
 
 class NullDataOptions(str, Enum):
@@ -46,14 +48,14 @@ class ExtractionResult(ConfiguredBaseModel):
     extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""")
     named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""")
 
-        
+
 
 class NamedEntity(ConfiguredBaseModel):
 
     id: str = Field(..., description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
 
-        
+
 
 class EntityContainingDocument(NamedEntity):
 
@@ -63,34 +65,34 @@ class EntityContainingDocument(NamedEntity):
     id: str = Field(..., description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
 
-        
+
 
 class EnvironmentalCondition(NamedEntity):
 
     id: str = Field(..., description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
 
-        
+
 
 class Taxon(NamedEntity):
 
     id: str = Field(..., description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
 
-        
+
 
 class Trait(NamedEntity):
 
     id: str = Field(..., description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
 
-        
+
 
 class CompoundExpression(ConfiguredBaseModel):
 
     None
 
-        
+
 
 class Triple(CompoundExpression):
     """
@@ -103,7 +105,7 @@ class Triple(CompoundExpression):
     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\"""")
     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\"""")
 
-        
+
 
 class TextWithTriples(ConfiguredBaseModel):
     """
@@ -112,7 +114,7 @@ class TextWithTriples(ConfiguredBaseModel):
     publication: Optional[Publication] = Field(None)
     triples: Optional[List[Triple]] = Field(default_factory=list)
 
-        
+
 
 class TextWithEntity(ConfiguredBaseModel):
     """
@@ -121,14 +123,14 @@ class TextWithEntity(ConfiguredBaseModel):
     publication: Optional[Publication] = Field(None)
     entities: Optional[List[str]] = Field(default_factory=list)
 
-        
+
 
 class RelationshipType(NamedEntity):
 
     id: str = Field(..., description="""A unique identifier for the named entity""")
     label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
 
-        
+
 
 class Publication(ConfiguredBaseModel):
 
@@ -138,15 +140,15 @@ class Publication(ConfiguredBaseModel):
     combined_text: Optional[str] = Field(None)
     full_text: Optional[str] = Field(None, description="""The full text of the publication""")
 
-        
+
 
 class AnnotatorResult(ConfiguredBaseModel):
 
     subject_text: Optional[str] = Field(None)
     object_id: Optional[str] = Field(None)
     object_text: Optional[str] = Field(None)
 
-        
+
 
 
 # Model rebuild

src/ontogpt/templates/desiccation.yaml

@@ -5,6 +5,7 @@ description: >-
   A template for extracting ChEBI, GO, NCBITAXON, PO, TO, PECO
 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/
   desiccation: http://w3id.org/ontogpt/desiccation
 

src/ontogpt/templates/diagnostic_procedure.yaml

@@ -6,6 +6,7 @@ description: >-
   phenotypes they may contribute to.
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
   HP: http://purl.obolibrary.org/obo/HP_
   LOINC: http://loinc.org/rdf/
   OBA: http://purl.obolibrary.org/obo/OBA_

src/ontogpt/templates/dietitian_notes.yaml

@@ -7,6 +7,7 @@ description: >-
   and Alyson Lawrence, RD, CNSC
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
   EFO: http://www.ebi.ac.uk/efo/EFO_
   FOODON: http://purl.obolibrary.org/obo/FOODON_
   HP: http://purl.obolibrary.org/obo/HP_

src/ontogpt/templates/drug.yaml

@@ -5,6 +5,7 @@ description: >-
   A template for Drugs and drug mechanism
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
   HGNC: http://identifiers.org/hgnc/
   MESH: http://identifiers.org/mesh/
   drug: http://w3id.org/ontogpt/drug/

src/ontogpt/templates/emapa_simple.yaml

@@ -5,6 +5,7 @@ description: >-
   Simple Mouse Developmental Anatomy Ontology Extraction Template
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
   EMAPA: http://purl.obolibrary.org/obo/EMAPA_
   GO: http://purl.obolibrary.org/obo/GO_
   emapa_simple: http://w3id.org/ontogpt/emapa_simple

src/ontogpt/templates/environmental_metadata.yaml

@@ -6,6 +6,7 @@ description: >-
   data entries. See https://github.com/EDIorg/EDIorg-repository-index
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
   ENVO: http://purl.obolibrary.org/obo/ENVO_
   envmd: http://w3id.org/ontogpt/environmental-metadata
   linkml: https://w3id.org/linkml/

src/ontogpt/templates/environmental_sample.yaml

@@ -5,6 +5,7 @@ description: >-
   A template for Environmental Samples
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
   ENVO: http://purl.obolibrary.org/obo/ENVO_
   PATO: http://purl.obolibrary.org/obo/PATO_
   UO: http://purl.obolibrary.org/obo/UO_