entity_extraction schema

linkml-schema/entity_extraction.yaml

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+name: EntityExtraction
+title: Entity Extraction Schema
+id: https:/w3id.org/brain-bican/entity-extraction
+imports:
+- linkml:types
+prefixes:
+  bican: https://identifiers.org/brain-bican/vocab/
+  prov: https://www.w3.org/TR/prov-o/#
+  linkml: https://w3id.org/linkml/
+default_prefix: bican
+default_range: string
+classes:
+  ExtractedEntity:
+    from_schema: https:/w3id.org/brain-bican/entity-extraction
+    attributes:
+      id:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        identifier: true
+        range: string
+      term:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        range: string
+      label:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        range: string
+      ontology_id:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        range: uriorcurie
+      ontology_label:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        range: string
+      sentence:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        range: string
+      start_index:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        range: integer
+      end_index:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        range: integer
+      judge_score:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        range: float
+      remarks:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        range: string
+      paper_location:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        range: string
+      paper:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        range: Paper
+  JudgeExtraction:
+    from_schema: https:/w3id.org/brain-bican/entity-extraction
+    is_a: Activity
+    attributes:
+      id:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        identifier: true
+        range: string
+      generated:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        slot_uri: prov:generated
+        range: ExtractedEntity
+        multivalued: true
+      startedAtTime:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        slot_uri: prov:startedAtTime
+        range: datetime
+  Paper:
+    from_schema: https:/w3id.org/brain-bican/entity-extraction
+    attributes:
+      id:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        identifier: true
+        range: string
+      title:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        range: string
+      doi:
+        from_schema: https:/w3id.org/brain-bican/entity-extraction
+        range: string

linkml-schema/source_entity_extraction/gsheet.yaml

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+gsheet_id: "1gziX3bgw_I0BDchi1FH2JSTUEOHjfVCUrQFsRwiXogs"
+sheets:
+  - name: "Classes"
+    gid: "0"
+  - name: "Attributes"
+    gid: "205457862"
+  # - name: "Slots"
+  #   gid: "1496475127"
+  - name: "Prefixes"
+    gid: "2018832318"
+  - name: "Schema"
+    gid: "1640492340"
+
+

linkml-schema/source_entity_extraction/gsheet_output/Attributes.tsv

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+SubGroup/LinkML Class Name	LinkML Slot or Attribute Name	BICAN UUID	Definition	Identifier	Data Type	Data Examples	Nullable	Multivalued	Permissible Values	Subsets	Notes
+> class	attribute	slot_uri	description	identifier	range	ignore	ignore	multivalued	ignore	in_subset	ignore
+>										internal_separator: "|"	
+ExtractedEntity	id 			TRUE	string						
+ExtractedEntity	term				string						
+ExtractedEntity	label				string						
+ExtractedEntity	ontology_id				uriorcurie						
+ExtractedEntity	ontology_label				string						
+ExtractedEntity	sentence				string						
+ExtractedEntity	start_index				integer						
+ExtractedEntity	end_index				integer						
+ExtractedEntity	judge_score				float						
+ExtractedEntity	remarks				string						
+ExtractedEntity	paper_location				string						
+ExtractedEntity	paper				Paper						
+JudgeExtraction	id 			TRUE	string						
+JudgeExtraction	generated	prov:generated			ExtractedEntity			TRUE			
+JudgeExtraction	startedAtTime	prov:startedAtTime			datetime						
+Paper	id 			TRUE	string						
+Paper	title				string						
+Paper	doi				string						

linkml-schema/source_entity_extraction/gsheet_output/Classes.tsv

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+class	Inheritance: is_a	Inheritance: mixin	Subsets	Definition		
+> class	is_a	mixins	in_subset	description	class_uri	mixin
+>		internal_separator: "|"	internal_separator: "|"			
+ExtractedEntity						
+JudgeExtraction	Activity					
+Paper						

linkml-schema/source_entity_extraction/gsheet_output/Prefixes.tsv

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+prefix	URI
+> prefix	prefix_reference
+bican	https://identifiers.org/brain-bican/vocab/
+prov	https://www.w3.org/TR/prov-o/#

linkml-schema/source_entity_extraction/gsheet_output/Schema.tsv

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+schema	uri	description	schema prefix	imports	title
+> schema	id	description	default_prefix	imports	title
+>				internal_separator: "|"	
+EntityExtraction	https:/w3id.org/brain-bican/entity-extraction		bican		Entity Extraction Schema