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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 { } 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"


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
TextWithTriples None


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
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
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