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Diagnostic Procedure Template

A template for clinical diagnostic procedures and the phenotypes they may contribute to.


Name: diagnostic_procedure

Schema Diagram

erDiagram DiagnosticProceduretoPhenotypeAssociation { string qualifier } DiagnosticProceduretoAttributeAssociation { string qualifier } DiagnosticProcedure { string id string label } Phenotype { string id string label } ClinicalAttribute { string id string label } Quality { string id string label } ProcedureToPhenotypePredicate { string id string label } ProcedureToAttributePredicate { string id string label } Unit { 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 } DiagnosticProceduretoPhenotypeAssociation ||--|o DiagnosticProcedure : "subject" DiagnosticProceduretoPhenotypeAssociation ||--|o ProcedureToPhenotypePredicate : "predicate" DiagnosticProceduretoPhenotypeAssociation ||--}o Phenotype : "object" DiagnosticProceduretoPhenotypeAssociation ||--|o NamedEntity : "subject_qualifier" DiagnosticProceduretoPhenotypeAssociation ||--|o NamedEntity : "object_qualifier" DiagnosticProceduretoAttributeAssociation ||--|o DiagnosticProcedure : "subject" DiagnosticProceduretoAttributeAssociation ||--|o ProcedureToAttributePredicate : "predicate" DiagnosticProceduretoAttributeAssociation ||--}o ClinicalAttribute : "object" DiagnosticProceduretoAttributeAssociation ||--|o NamedEntity : "subject_qualifier" DiagnosticProceduretoAttributeAssociation ||--|o Quality : "object_qualifier" ClinicalAttribute ||--|o Unit : "unit" 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
                DiagnosticProceduretoAttributeAssociation A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., "blood pressure measurement" is associated with "blood pressure" (or in OBA, something like OBA:VT0000183, "blood pressure trait").
                DiagnosticProceduretoPhenotypeAssociation A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., "blood pressure measurement" is associated with "high blood pressure".
ExtractionResult A result of extracting knowledge on text
NamedEntity None
        ClinicalAttribute None
        DiagnosticProcedure None
        Phenotype None
        Quality None
        RelationshipType None
                ProcedureToAttributePredicate A predicate for procedure to attribute relationships, defining "this procedure is a measurement of this attribute".
                ProcedureToPhenotypePredicate A predicate for procedure to phenotype relationships, defining "this procedure is intended to provide support for/against this phenotype".
        Unit 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
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
unit the unit used to measure the attribute


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