Removed extra copies of output & changed parser files

docs/biological_process/AnnotatorResult.md

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+
+# Class: AnnotatorResult
+
+
+
+
+URI: [bp:AnnotatorResult](http://w3id.org/ontogpt/biological-process-templateAnnotatorResult)
+
+
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])
+
+## Attributes
+
+
+### Own
+
+ * [➞subject_text](annotatorResult__subject_text.md)  <sub>0..1</sub>
+     * Range: [String](types/String.md)
+ * [➞object_id](annotatorResult__object_id.md)  <sub>0..1</sub>
+     * Range: [String](types/String.md)
+ * [➞object_text](annotatorResult__object_text.md)  <sub>0..1</sub>
+     * Range: [String](types/String.md)

docs/biological_process/Any.md

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+
+# Class: Any
+
+
+
+
+URI: [bp:Any](http://w3id.org/ontogpt/biological-process-templateAny)
+
+
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])
+
+## Referenced by Class
+
+ *  **None** *[➞extracted_object](extractionResult__extracted_object.md)*  <sub>0..1</sub>  **[Any](Any.md)**
+ *  **None** *[➞named_entities](extractionResult__named_entities.md)*  <sub>0..\*</sub>  **[Any](Any.md)**
+
+## Attributes
+
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Mappings:** | | linkml:Any |
+

docs/biological_process/BiologicalProcess.md

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+
+# Class: BiologicalProcess
+
+
+
+
+URI: [bp:BiologicalProcess](http://w3id.org/ontogpt/biological-process-templateBiologicalProcess)
+
+
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MolecularActivity],[GeneMolecularActivityRelationship],[Gene],[ChemicalEntity],[GeneMolecularActivityRelationship]<gene_activities%200..*-++[BiologicalProcess&#124;label:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string],[Gene]<genes%200..*-%20[BiologicalProcess],[MolecularActivity]<steps%200..*-%20[BiologicalProcess],[ChemicalEntity]<outputs%200..*-%20[BiologicalProcess],[ChemicalEntity]<inputs%200..*-%20[BiologicalProcess],[BiologicalProcess]<subclass_of%200..1-%20[BiologicalProcess],[NamedEntity]^-[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MolecularActivity],[GeneMolecularActivityRelationship],[Gene],[ChemicalEntity],[GeneMolecularActivityRelationship]<gene_activities%200..*-++[BiologicalProcess&#124;label:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string],[Gene]<genes%200..*-%20[BiologicalProcess],[MolecularActivity]<steps%200..*-%20[BiologicalProcess],[ChemicalEntity]<outputs%200..*-%20[BiologicalProcess],[ChemicalEntity]<inputs%200..*-%20[BiologicalProcess],[BiologicalProcess]<subclass_of%200..1-%20[BiologicalProcess],[NamedEntity]^-[BiologicalProcess])
+
+## Parents
+
+ *  is_a: [NamedEntity](NamedEntity.md)
+
+## Referenced by Class
+
+ *  **None** *[➞subclass_of](biologicalProcess__subclass_of.md)*  <sub>0..1</sub>  **[BiologicalProcess](BiologicalProcess.md)**
+
+## Attributes
+
+
+### Own
+
+ * [➞label](biologicalProcess__label.md)  <sub>0..1</sub>
+     * Description: the name of the biological process
+     * Range: [String](types/String.md)
+ * [➞description](biologicalProcess__description.md)  <sub>0..1</sub>
+     * Description: a textual description of the biological process
+     * Range: [String](types/String.md)
+ * [➞synonyms](biologicalProcess__synonyms.md)  <sub>0..\*</sub>
+     * Description: alternative names of the biological process
+     * Range: [String](types/String.md)
+ * [➞subclass_of](biologicalProcess__subclass_of.md)  <sub>0..1</sub>
+     * Description: the category to which this biological process belongs
+     * Range: [BiologicalProcess](BiologicalProcess.md)
+ * [➞inputs](biologicalProcess__inputs.md)  <sub>0..\*</sub>
+     * Description: the inputs of the biological process
+     * Range: [ChemicalEntity](ChemicalEntity.md)
+ * [➞outputs](biologicalProcess__outputs.md)  <sub>0..\*</sub>
+     * Description: the outputs of the biological process
+     * Range: [ChemicalEntity](ChemicalEntity.md)
+ * [➞steps](biologicalProcess__steps.md)  <sub>0..\*</sub>
+     * Description: the steps involved in this biological process
+     * Range: [MolecularActivity](MolecularActivity.md)
+ * [➞genes](biologicalProcess__genes.md)  <sub>0..\*</sub>
+     * Range: [Gene](Gene.md)
+ * [➞gene_activities](biologicalProcess__gene_activities.md)  <sub>0..\*</sub>
+     * Description: semicolon-separated list of gene to molecular activity relationships
+     * Range: [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md)
+
+### Inherited from NamedEntity:
+
+ * [➞id](namedEntity__id.md)  <sub>1..1</sub>
+     * Description: A unique identifier for the named entity
+     * Range: [String](types/String.md)

docs/biological_process/ChemicalEntity.md

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+
+# Class: ChemicalEntity
+
+
+
+
+URI: [bp:ChemicalEntity](http://w3id.org/ontogpt/biological-process-templateChemicalEntity)
+
+
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20inputs%200..*>[ChemicalEntity|id(i):string;label(i):string%20%3F],[BiologicalProcess]-%20outputs%200..*>[ChemicalEntity],[NamedEntity]^-[ChemicalEntity],[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20inputs%200..*>[ChemicalEntity|id(i):string;label(i):string%20%3F],[BiologicalProcess]-%20outputs%200..*>[ChemicalEntity],[NamedEntity]^-[ChemicalEntity],[BiologicalProcess])
+
+## Identifier prefixes
+
+ * CHEBI
+
+## Parents
+
+ *  is_a: [NamedEntity](NamedEntity.md)
+
+## Referenced by Class
+
+ *  **None** *[➞inputs](biologicalProcess__inputs.md)*  <sub>0..\*</sub>  **[ChemicalEntity](ChemicalEntity.md)**
+ *  **None** *[➞outputs](biologicalProcess__outputs.md)*  <sub>0..\*</sub>  **[ChemicalEntity](ChemicalEntity.md)**
+
+## Attributes
+
+
+### Inherited from NamedEntity:
+
+ * [➞id](namedEntity__id.md)  <sub>1..1</sub>
+     * Description: A unique identifier for the named entity
+     * Range: [String](types/String.md)
+ * [➞label](namedEntity__label.md)  <sub>0..1</sub>
+     * Description: The label (name) of the named thing
+     * Range: [String](types/String.md)

docs/biological_process/CompoundExpression.md

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+
+# Class: CompoundExpression
+
+
+
+
+URI: [bp:CompoundExpression](http://w3id.org/ontogpt/biological-process-templateCompoundExpression)
+
+
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])
+
+## Children
+
+ * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks
+
+## Referenced by Class
+
+
+## Attributes
+

docs/biological_process/ExtractionResult.md

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+
+# Class: ExtractionResult
+
+
+A result of extracting knowledge on text
+
+URI: [bp:ExtractionResult](http://w3id.org/ontogpt/biological-process-templateExtractionResult)
+
+
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult&#124;input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult&#124;input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])
+
+## Attributes
+
+
+### Own
+
+ * [➞input_id](extractionResult__input_id.md)  <sub>0..1</sub>
+     * Range: [String](types/String.md)
+ * [➞input_title](extractionResult__input_title.md)  <sub>0..1</sub>
+     * Range: [String](types/String.md)
+ * [➞input_text](extractionResult__input_text.md)  <sub>0..1</sub>
+     * Range: [String](types/String.md)
+ * [➞raw_completion_output](extractionResult__raw_completion_output.md)  <sub>0..1</sub>
+     * Range: [String](types/String.md)
+ * [➞prompt](extractionResult__prompt.md)  <sub>0..1</sub>
+     * Range: [String](types/String.md)
+ * [➞extracted_object](extractionResult__extracted_object.md)  <sub>0..1</sub>
+     * Description: The complex objects extracted from the text
+     * Range: [Any](Any.md)
+ * [➞named_entities](extractionResult__named_entities.md)  <sub>0..\*</sub>
+     * Description: Named entities extracted from the text
+     * Range: [Any](Any.md)

docs/biological_process/Gene.md

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+
+# Class: Gene
+
+
+
+
+URI: [bp:Gene](http://w3id.org/ontogpt/biological-process-templateGene)
+
+
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20genes%200..*>[Gene|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20gene%200..1>[Gene],[NamedEntity]^-[Gene],[GeneMolecularActivityRelationship],[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20genes%200..*>[Gene|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20gene%200..1>[Gene],[NamedEntity]^-[Gene],[GeneMolecularActivityRelationship],[BiologicalProcess])
+
+## Identifier prefixes
+
+ * HGNC
+
+## Parents
+
+ *  is_a: [NamedEntity](NamedEntity.md)
+
+## Referenced by Class
+
+ *  **None** *[➞genes](biologicalProcess__genes.md)*  <sub>0..\*</sub>  **[Gene](Gene.md)**
+ *  **None** *[➞gene](geneMolecularActivityRelationship__gene.md)*  <sub>0..1</sub>  **[Gene](Gene.md)**
+
+## Attributes
+
+
+### Inherited from NamedEntity:
+
+ * [➞id](namedEntity__id.md)  <sub>1..1</sub>
+     * Description: A unique identifier for the named entity
+     * Range: [String](types/String.md)
+ * [➞label](namedEntity__label.md)  <sub>0..1</sub>
+     * Description: The label (name) of the named thing
+     * Range: [String](types/String.md)

docs/biological_process/GeneMolecularActivityRelationship.md

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+
+# Class: GeneMolecularActivityRelationship
+
+
+
+
+URI: [bp:GeneMolecularActivityRelationship](http://w3id.org/ontogpt/biological-process-templateGeneMolecularActivityRelationship)
+
+
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[MolecularActivity],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship],[BiologicalProcess]++-%20gene_activities%200..*>[GeneMolecularActivityRelationship],[Gene],[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[MolecularActivity],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship],[BiologicalProcess]++-%20gene_activities%200..*>[GeneMolecularActivityRelationship],[Gene],[BiologicalProcess])
+
+## Referenced by Class
+
+ *  **None** *[➞gene_activities](biologicalProcess__gene_activities.md)*  <sub>0..\*</sub>  **[GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md)**
+
+## Attributes
+
+
+### Own
+
+ * [➞gene](geneMolecularActivityRelationship__gene.md)  <sub>0..1</sub>
+     * Range: [Gene](Gene.md)
+ * [➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md)  <sub>0..1</sub>
+     * Range: [MolecularActivity](MolecularActivity.md)

docs/biological_process/MolecularActivity.md

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+
+# Class: MolecularActivity
+
+
+
+
+URI: [bp:MolecularActivity](http://w3id.org/ontogpt/biological-process-templateMolecularActivity)
+
+
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20steps%200..*>[MolecularActivity|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20molecular_activity%200..1>[MolecularActivity],[NamedEntity]^-[MolecularActivity],[GeneMolecularActivityRelationship],[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20steps%200..*>[MolecularActivity|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20molecular_activity%200..1>[MolecularActivity],[NamedEntity]^-[MolecularActivity],[GeneMolecularActivityRelationship],[BiologicalProcess])
+
+## Identifier prefixes
+
+ * GO
+
+## Parents
+
+ *  is_a: [NamedEntity](NamedEntity.md)
+
+## Referenced by Class
+
+ *  **None** *[➞steps](biologicalProcess__steps.md)*  <sub>0..\*</sub>  **[MolecularActivity](MolecularActivity.md)**
+ *  **None** *[➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md)*  <sub>0..1</sub>  **[MolecularActivity](MolecularActivity.md)**
+
+## Attributes
+
+
+### Inherited from NamedEntity:
+
+ * [➞id](namedEntity__id.md)  <sub>1..1</sub>
+     * Description: A unique identifier for the named entity
+     * Range: [String](types/String.md)
+ * [➞label](namedEntity__label.md)  <sub>0..1</sub>
+     * Description: The label (name) of the named thing
+     * Range: [String](types/String.md)

docs/biological_process/NamedEntity.md

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+
+# Class: NamedEntity
+
+
+
+
+URI: [bp:NamedEntity](http://w3id.org/ontogpt/biological-process-templateNamedEntity)
+
+
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[MolecularActivity],[NamedEntity]^-[Gene],[NamedEntity]^-[ChemicalEntity],[NamedEntity]^-[BiologicalProcess],[Triple],[MolecularActivity],[Gene],[ChemicalEntity],[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[MolecularActivity],[NamedEntity]^-[Gene],[NamedEntity]^-[ChemicalEntity],[NamedEntity]^-[BiologicalProcess],[Triple],[MolecularActivity],[Gene],[ChemicalEntity],[BiologicalProcess])
+
+## Children
+
+ * [BiologicalProcess](BiologicalProcess.md)
+ * [ChemicalEntity](ChemicalEntity.md)
+ * [Gene](Gene.md)
+ * [MolecularActivity](MolecularActivity.md)
+ * [RelationshipType](RelationshipType.md)
+
+## Referenced by Class
+
+ *  **None** *[➞object](triple__object.md)*  <sub>0..1</sub>  **[NamedEntity](NamedEntity.md)**
+ *  **None** *[➞object_qualifier](triple__object_qualifier.md)*  <sub>0..1</sub>  **[NamedEntity](NamedEntity.md)**
+ *  **None** *[➞subject](triple__subject.md)*  <sub>0..1</sub>  **[NamedEntity](NamedEntity.md)**
+ *  **None** *[➞subject_qualifier](triple__subject_qualifier.md)*  <sub>0..1</sub>  **[NamedEntity](NamedEntity.md)**
+
+## Attributes
+
+
+### Own
+
+ * [➞id](namedEntity__id.md)  <sub>1..1</sub>
+     * Description: A unique identifier for the named entity
+     * Range: [String](types/String.md)
+ * [➞label](namedEntity__label.md)  <sub>0..1</sub>
+     * Description: The label (name) of the named thing
+     * Range: [String](types/String.md)

docs/biological_process/NullDataOptions.md

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+
+# Enum: NullDataOptions
+
+
+
+
+URI: [bp:NullDataOptions](http://w3id.org/ontogpt/biological-process-templateNullDataOptions)
+
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+
+## Permissible Values
+
+| Text | Description | Meaning | Other Information |
+| :--- | :---: | :---: | ---: |
+| UNSPECIFIED_METHOD_OF_ADMINISTRATION |  | NCIT:C149701 |  |
+| NOT_APPLICABLE |  | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} |
+| NOT_MENTIONED |  |  |  |
+

docs/biological_process/Publication.md

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+
+# Class: Publication
+
+
+
+
+URI: [bp:Publication](http://w3id.org/ontogpt/biological-process-templatePublication)
+
+
+[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])
+
+## Referenced by Class
+
+ *  **None** *[➞publication](textWithTriples__publication.md)*  <sub>0..1</sub>  **[Publication](Publication.md)**
+
+## Attributes
+
+
+### Own
+
+ * [➞id](publication__id.md)  <sub>0..1</sub>
+     * Description: The publication identifier
+     * Range: [String](types/String.md)
+ * [➞title](publication__title.md)  <sub>0..1</sub>
+     * Description: The title of the publication
+     * Range: [String](types/String.md)
+ * [➞abstract](publication__abstract.md)  <sub>0..1</sub>
+     * Description: The abstract of the publication
+     * Range: [String](types/String.md)
+ * [➞combined_text](publication__combined_text.md)  <sub>0..1</sub>
+     * Range: [String](types/String.md)
+ * [➞full_text](publication__full_text.md)  <sub>0..1</sub>
+     * Description: The full text of the publication
+     * Range: [String](types/String.md)