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Class: GenomicSequenceLocalization

A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig.

URI: biolink:GenomicSequenceLocalization

classDiagram class GenomicSequenceLocalization SequenceAssociation <|-- GenomicSequenceLocalization GenomicSequenceLocalization : aggregator_knowledge_source GenomicSequenceLocalization : category GenomicSequenceLocalization : description GenomicSequenceLocalization : end_interbase_coordinate GenomicSequenceLocalization : genome_build GenomicSequenceLocalization --|> StrandEnum : genome_build GenomicSequenceLocalization : has_attribute GenomicSequenceLocalization --|> attribute : has_attribute GenomicSequenceLocalization : has_evidence GenomicSequenceLocalization --|> evidence type : has_evidence GenomicSequenceLocalization : id GenomicSequenceLocalization : iri GenomicSequenceLocalization : knowledge_source GenomicSequenceLocalization : name GenomicSequenceLocalization : negated GenomicSequenceLocalization : object GenomicSequenceLocalization --|> nucleic acid entity : object GenomicSequenceLocalization : object_category GenomicSequenceLocalization --|> ontology class : object_category GenomicSequenceLocalization : object_category_closure GenomicSequenceLocalization --|> ontology class : object_category_closure GenomicSequenceLocalization : object_closure GenomicSequenceLocalization : object_label_closure GenomicSequenceLocalization : object_namespace GenomicSequenceLocalization : original_object GenomicSequenceLocalization : original_predicate GenomicSequenceLocalization : original_subject GenomicSequenceLocalization : phase GenomicSequenceLocalization --|> PhaseEnum : phase GenomicSequenceLocalization : predicate GenomicSequenceLocalization : primary_knowledge_source GenomicSequenceLocalization : publications GenomicSequenceLocalization --|> publication : publications GenomicSequenceLocalization : qualifiers GenomicSequenceLocalization --|> ontology class : qualifiers GenomicSequenceLocalization : retrieval_source_ids GenomicSequenceLocalization --|> retrieval source : retrieval_source_ids GenomicSequenceLocalization : start_interbase_coordinate GenomicSequenceLocalization : strand GenomicSequenceLocalization --|> StrandEnum : strand GenomicSequenceLocalization : subject GenomicSequenceLocalization --|> nucleic acid entity : subject GenomicSequenceLocalization : subject_category GenomicSequenceLocalization --|> ontology class : subject_category GenomicSequenceLocalization : subject_category_closure GenomicSequenceLocalization --|> ontology class : subject_category_closure GenomicSequenceLocalization : subject_closure GenomicSequenceLocalization : subject_label_closure GenomicSequenceLocalization : subject_namespace GenomicSequenceLocalization : timepoint GenomicSequenceLocalization : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
start_interbase_coordinate 0..1
Integer		 The position at which the subject nucleic acid entity starts on the chromosom... direct
end_interbase_coordinate 0..1
Integer		 The position at which the subject nucleic acid entity ends on the chromosome ... direct
genome_build 0..1
StrandEnum		 The version of the genome on which a feature is located direct
strand 0..1
StrandEnum		 The strand on which a feature is located direct
phase 0..1
PhaseEnum		 The phase for a coding sequence entity direct
subject 1..1
NucleicAcidEntity		 connects an association to the subject of the association Association
predicate 1..1
PredicateType		 A high-level grouping for the relationship type Association
object 1..1
NucleicAcidEntity		 connects an association to the object of the association Association
negated 0..1
Boolean		 if set to true, then the association is negated i Association
qualifiers 0..*
OntologyClass		 connects an association to qualifiers that modify or qualify the meaning of t... Association
publications 0..*
Publication		 One or more publications that report the statement expressed in an Associati... Association
has_evidence 0..*
EvidenceType		 connects an association to an instance of supporting evidence Association
knowledge_source 0..1
String		 An Information Resource from which the knowledge expressed in an Association ... Association
primary_knowledge_source 0..1
String		 The most upstream source of the knowledge expressed in an Association that an... Association
aggregator_knowledge_source 0..*
String		 An intermediate aggregator resource from which knowledge expressed in an Asso... Association
timepoint 0..1
TimeType		 a point in time Association
original_subject 0..1
String		 used to hold the original subject of a relation (or predicate) that an extern... Association
original_predicate 0..1
Uriorcurie		 used to hold the original relation/predicate that an external knowledge sourc... Association
original_object 0..1
String		 used to hold the original object of a relation (or predicate) that an externa... Association
subject_category 0..1
OntologyClass		 Used to hold the biolink class/category of an association Association
object_category 0..1
OntologyClass		 Used to hold the biolink class/category of an association Association
subject_closure 0..*
String		 Used to hold the subject closure of an association Association
object_closure 0..*
String		 Used to hold the object closure of an association Association
subject_category_closure 0..*
OntologyClass		 Used to hold the subject category closure of an association Association
object_category_closure 0..*
OntologyClass		 Used to hold the object category closure of an association Association
subject_namespace 0..1
String		 Used to hold the subject namespace of an association Association
object_namespace 0..1
String		 Used to hold the object namespace of an association Association
subject_label_closure 0..*
String		 Used to hold the subject label closure of an association Association
object_label_closure 0..*
String		 Used to hold the object label closure of an association Association
retrieval_source_ids 0..*
RetrievalSource		 A list of retrieval sources that served as a source of knowledge expressed in... Association
id 1..1
String		 A unique identifier for an entity Entity
iri 0..1
IriType		 An IRI for an entity Entity
category 0..*
CategoryType		 Name of the high level ontology class in which this entity is categorized Entity
type 0..*
String		 rdf:type of biolink:Association should be fixed at rdf:Statement Entity
name 0..1
LabelType		 A human-readable name for an attribute or entity Entity
description 0..1
NarrativeText		 a human-readable description of an entity Entity
has_attribute 0..*
Attribute		 connects any entity to an attribute Entity

Usages

used by used in type used
GenomicSequenceLocalization start_interbase_coordinate domain GenomicSequenceLocalization
GenomicSequenceLocalization end_interbase_coordinate domain GenomicSequenceLocalization
GenomicSequenceLocalization genome_build domain GenomicSequenceLocalization
GenomicSequenceLocalization strand domain GenomicSequenceLocalization

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/biolink/biolink-model

Mappings

Mapping Type Mapped Value
self biolink:GenomicSequenceLocalization
native biolink:GenomicSequenceLocalization
exact dcid:GenomeAnnotation
broad dcid:Chromosome

LinkML Source

Direct

name: genomic sequence localization
description: A relationship between a sequence feature and a nucleic acid entity it
  is localized to. The reference entity may be a chromosome, chromosome region or
  information entity such as a contig.
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- dcid:GenomeAnnotation
broad_mappings:
- dcid:Chromosome
is_a: sequence association
slots:
- start interbase coordinate
- end interbase coordinate
- genome build
- strand
- phase
slot_usage:
  subject:
    name: subject
    aliases:
    - sequence feature
    domain_of:
    - association
    range: nucleic acid entity
  object:
    name: object
    aliases:
    - reference
    domain_of:
    - association
    range: nucleic acid entity
  predicate:
    name: predicate
    domain_of:
    - predicate mapping
    - association
    subproperty_of: has sequence location