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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
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
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
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