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reaction Template

A template for reactions


Name: reaction-template

Schema Diagram

erDiagram Reaction { string label string description stringList synonyms string id } GeneToReaction { } ReactionDocument { } GeneReactionPairing { } ReactionGrouping { string id string label } ChemicalEntity { string id string label } Evidence { string id string label } Gene { string id string label } Organism { 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 } Reaction ||--|o ReactionGrouping : "subclass_of" Reaction ||--}o ChemicalEntity : "left_side" Reaction ||--}o ChemicalEntity : "right_side" GeneToReaction ||--|o Gene : "gene" GeneToReaction ||--}o Reaction : "reactions" GeneToReaction ||--|o Organism : "organism" ReactionDocument ||--}o Gene : "genes" ReactionDocument ||--}o Reaction : "reactions" ReactionDocument ||--}o GeneReactionPairing : "gene_reaction_pairings" ReactionDocument ||--|o Organism : "organism" ReactionDocument ||--}o Evidence : "has_evidence" GeneReactionPairing ||--|o Gene : "gene" GeneReactionPairing ||--|o Reaction : "reaction" 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
        GeneReactionPairing None
        Triple Abstract parent for Relation Extraction tasks
ExtractionResult A result of extracting knowledge on text
GeneToReaction None
NamedEntity None
        ChemicalEntity None
        Evidence None
        Gene None
        Organism None
        Reaction None
        ReactionGrouping None
        RelationshipType None
Publication None
ReactionDocument None
TextWithEntity A text containing one or more instances of a single type of entity.
TextWithTriples A text containing one or more relations of the Triple type.


Slot Description
abstract The abstract of the publication
description a textual description of the reaction
extracted_object The complex objects extracted from the text
full_text The full text of the publication
gene name of the gene that catalyzes the reaction
gene_reaction_pairings semicolon separated list of gene to reaction pairings
genes semicolon separated list of genes that catalyzes the mentioned reactions
has_evidence evidence for the reaction
id A unique identifier for the named entity
label the name of the reaction
left_side semicolon separated list of chemical entities on the left side
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
reaction equation describing the reaction (e
reactions semicolon separated list of reaction equations (e
right_side semicolon separated list of chemical entities on the right side
subclass_of the category to which this biological process belongs
subject_qualifier An optional qualifier or modifier for the subject of the statement, e
synonyms alternative names of the reaction
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