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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
        CellType None
        ChemicalEntity None
        Gene None
        MolecularActivity 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.

Slots

Slot Description
abstract The abstract of the publication
combined_text
description a textual description of the biological process
entities
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
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

Subsets

Subset Description