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Chemical and Disease Entity Recognition Template

A template for Chemical and Disease named entity recognition. This template is intended to represent entities (chemicals and diseases), and for evaluating SPIRES against the BioCreative V Disease Named Entity Recognition (DNER) results. As the test set also contains chemical names, it is also appropriate to use this template for evaluating chemical NER.


Name: ctd_ner

Schema Diagram

erDiagram ChemicalToDiseaseDocument { } Chemical { string id string label } Disease { string id string label } Any { } ExtractionResult { string input_id string input_title string input_text string raw_completion_output string prompt } NamedEntity { string id string label } CompoundExpression { } Triple { string qualifier } TextWithTriples { } TextWithEntity { } RelationshipType { string id string label } Publication { string id string title string abstract string combined_text string full_text } AnnotatorResult { string subject_text string object_id string object_text } ChemicalToDiseaseDocument ||--}o Chemical : "chemicals" ChemicalToDiseaseDocument ||--}o Disease : "diseases" ChemicalToDiseaseDocument ||--|o Publication : "publication" ChemicalToDiseaseDocument ||--}o NamedEntity : "entities" ExtractionResult ||--|o Any : "extracted_object" ExtractionResult ||--}o Any : "named_entities" Triple ||--|o NamedEntity : "subject" Triple ||--|o RelationshipType : "predicate" Triple ||--|o NamedEntity : "object" Triple ||--|o NamedEntity : "subject_qualifier" Triple ||--|o NamedEntity : "object_qualifier" TextWithTriples ||--|o Publication : "publication" TextWithTriples ||--}o Triple : "triples" TextWithEntity ||--|o Publication : "publication" TextWithEntity ||--}o NamedEntity : "entities"


Class Description
AnnotatorResult None
Any None
CompoundExpression None
        Triple Abstract parent for Relation Extraction tasks
ExtractionResult A result of extracting knowledge on text
NamedEntity None
        Chemical None
        Disease None
        RelationshipType None
Publication None
TextWithEntity A text containing one or more instances of a single type of entity.
        ChemicalToDiseaseDocument A document that contains chemical and disease entities.
TextWithTriples A text containing one or more relations of the Triple type.


Slot Description
abstract The abstract of the publication
chemicals One or more chemical substances, drugs, or small molecules
diseases One or more diseases or conditions
extracted_object The complex objects extracted from the text
full_text The full text of the publication
id A unique identifier for the named entity
label The label (name) of the named thing
named_entities Named entities extracted from the text
object_qualifier An optional qualifier or modifier for the object of the statement, e
qualifier A qualifier for the statements, e
subject_qualifier An optional qualifier or modifier for the subject of the statement, e
title The title of the publication


Enumeration Description


Type Description
Boolean A binary (true or false) value
Curie a compact URI
Date a date (year, month and day) in an idealized calendar
DateOrDatetime Either a date or a datetime
Datetime The combination of a date and time
Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double A real number that conforms to the xsd:double specification
Float A real number that conforms to the xsd:float specification
Integer An integer
Jsonpath A string encoding a JSON Path
Jsonpointer A string encoding a JSON Pointer
Ncname Prefix part of CURIE
Nodeidentifier A URI, CURIE or BNODE that represents a node in a model
Objectidentifier A URI or CURIE that represents an object in the model
Sparqlpath A string encoding a SPARQL Property Path
String A character string
Time A time object represents a (local) time of day, independent of any particular...
Uri a complete URI
Uriorcurie a URI or a CURIE


Subset Description