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Biological Process Template

A template for GO-CAMs

URI: https://w3id.org/ontogpt/biological_process

Name: biological-process-template

Schema Diagram

erDiagram BiologicalProcess { string label string description stringList synonyms string id } GeneMolecularActivityRelationship { } MolecularActivity { string id string label } Gene { string id string label } ChemicalEntity { string id string label } BiologicalProcess ||--|o BiologicalProcess : "subclass_of" BiologicalProcess ||--}o ChemicalEntity : "inputs" BiologicalProcess ||--}o ChemicalEntity : "outputs" BiologicalProcess ||--}o MolecularActivity : "steps" BiologicalProcess ||--}o Gene : "genes" BiologicalProcess ||--}o GeneMolecularActivityRelationship : "gene_activities" GeneMolecularActivityRelationship ||--|o Gene : "gene" GeneMolecularActivityRelationship ||--|o MolecularActivity : "molecular_activity"

Classes

Class Description
AnnotatorResult None
Any None
CompoundExpression None
        Triple Abstract parent for Relation Extraction tasks
ExtractionResult A result of extracting knowledge on text
GeneMolecularActivityRelationship None
NamedEntity None
        BiologicalProcess None
        ChemicalEntity None
        Gene None
        MolecularActivity None
        RelationshipType None
Publication None
TextWithTriples None

Slots

Slot Description
abstract The abstract of the publication
combined_text
description a textual description of the biological process
extracted_object The complex objects extracted from the text
full_text The full text of the publication
gene
gene_activities semicolon-separated list of gene to molecular activity relationships
genes
id A unique identifier for the named entity
input_id
input_text
input_title
inputs the inputs of the biological process
label the name of the biological process
molecular_activity
named_entities Named entities extracted from the text
object
object_id
object_qualifier An optional qualifier or modifier for the object of the statement, e
object_text
outputs the outputs of the biological process
predicate
prompt
publication
qualifier A qualifier for the statements, e
raw_completion_output
steps the steps involved in this biological process
subclass_of the category to which this biological process belongs
subject
subject_qualifier An optional qualifier or modifier for the subject of the statement, e
subject_text
synonyms alternative names of the biological process
title The title of the publication
triples

Enumerations

Enumeration Description
NullDataOptions

Types

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

Subsets

Subset Description