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IBD Literature Template

A template for extracting information from IBD literature


Name: ibd-literature-template

Schema Diagram

erDiagram IBDAnnotations { } DiseaseCellularProcessRelationship { } NamedEntity { string id string label } CellularProcess { string id string label } DiseaseToCellularProcessPredicate { string id string label } Disease { string id string label } GeneExposureRelationship { } Gene { string id string label } ChemicalExposureToGenePredicate { string id string label } ChemicalExposure { string id string label } IBDAnnotations ||--}o Gene : "genes" IBDAnnotations ||--}o ChemicalExposure : "exposures" IBDAnnotations ||--}o GeneExposureRelationship : "gene_exposures_relationships" IBDAnnotations ||--}o Disease : "diseases" IBDAnnotations ||--}o CellularProcess : "cellular_process" IBDAnnotations ||--}o DiseaseCellularProcessRelationship : "disease_cellular_process_relationships" DiseaseCellularProcessRelationship ||--|o Disease : "subject" DiseaseCellularProcessRelationship ||--|o DiseaseToCellularProcessPredicate : "predicate" DiseaseCellularProcessRelationship ||--|o CellularProcess : "object" DiseaseCellularProcessRelationship ||--|o NamedEntity : "subject_qualifier" DiseaseCellularProcessRelationship ||--|o NamedEntity : "object_qualifier" GeneExposureRelationship ||--|o ChemicalExposure : "subject" GeneExposureRelationship ||--|o ChemicalExposureToGenePredicate : "predicate" GeneExposureRelationship ||--|o Gene : "object" GeneExposureRelationship ||--|o NamedEntity : "subject_qualifier" GeneExposureRelationship ||--|o NamedEntity : "object_qualifier"


Class Description
AnnotatorResult None
Any None
CompoundExpression None
        DiseaseCellularProcessRelationship None
        GeneExposureRelationship None
        Triple Abstract parent for Relation Extraction tasks
ExtractionResult A result of extracting knowledge on text
IBDAnnotations None
NamedEntity None
        CellularProcess None
        ChemicalExposure None
        ChemicalExposureToGenePredicate None
        Disease None
        DiseaseToCellularProcessPredicate None
        Gene None
        RelationshipType None
Publication None
TextWithTriples None


Slot Description
abstract The abstract of the publication
cellular_process semicolon-separated list of cellular processes
disease_cellular_process_relationships semicolon-separated list of disease to cellular process relationships
diseases semicolon-separated list of diseases
exposures semicolon-separated list of exposures
extracted_object The complex objects extracted from the text
full_text The full text of the publication
gene_exposures_relationships semicolon-separated list of gene to molecular activity relationships
genes semicolon-separated list of genes
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 The name of the gene in the pair
object_qualifier An optional qualifier or modifier for the gene
predicate The name of the type of relationship between a chemical exposure and a gene
qualifier A qualifier for the statements, e
subject The name of the exposure, such as a exposure to a chemical toxin
subject_qualifier An optional qualifier or modifier for the chemical exposure
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