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Class: GenomeAnnotation

Location and nomenclature of genes and all of the coding regions in a genome assembly and the classification of genes and transcripts into types.

URI: bican:GenomeAnnotation

classDiagram class GenomeAnnotation click GenomeAnnotation href "../GenomeAnnotation" Genome <|-- GenomeAnnotation click Genome href "../Genome" GenomeAnnotation : authority GenomeAnnotation --> "0..1" AuthorityType : authority click AuthorityType href "../AuthorityType" GenomeAnnotation : category GenomeAnnotation : content_url GenomeAnnotation : deprecated GenomeAnnotation : description GenomeAnnotation : digest GenomeAnnotation : full_name GenomeAnnotation : has_attribute GenomeAnnotation --> "*" Attribute : has_attribute click Attribute href "../Attribute" GenomeAnnotation : has_biological_sequence GenomeAnnotation : id GenomeAnnotation : in_taxon GenomeAnnotation --> "*" OrganismTaxon : in_taxon click OrganismTaxon href "../OrganismTaxon" GenomeAnnotation : in_taxon_label GenomeAnnotation : iri GenomeAnnotation : name GenomeAnnotation : provided_by GenomeAnnotation : reference_assembly GenomeAnnotation : synonym GenomeAnnotation : type GenomeAnnotation : version GenomeAnnotation : xref

Inheritance

Slots

Name Cardinality and Range Description Inheritance
version 0..1
String		 direct
digest *
String or 
Checksum or 
String		 Stores checksum information direct
content_url *
String		 direct
authority 0..1
AuthorityType		 The organization responsible for publishing the data direct
reference_assembly 1
String or 
GenomeAssembly or 
String		 The reference genome assembly that this genome annotation was created from direct
id 1
String		 A unique identifier for an entity NamedThing, Entity, Genome, BiologicalEntity, OntologyClass
iri 0..1
IriType		 An IRI for an entity Genome, BiologicalEntity, NamedThing, Entity
category *
Curie		 Name of the high level ontology class in which this entity is categorized Genome, BiologicalEntity, NamedThing, Entity
type *
String		 Genome, BiologicalEntity, NamedThing, Entity
name 0..1
LabelType		 A human-readable name for an attribute or entity Genome, BiologicalEntity, NamedThing, Entity
description 0..1
NarrativeText		 a human-readable description of an entity Genome, BiologicalEntity, NamedThing, Entity
has_attribute *
Attribute		 connects any entity to an attribute Genome, BiologicalEntity, NamedThing, Entity
deprecated 0..1
Boolean		 A boolean flag indicating that an entity is no longer considered current or v... Genome, BiologicalEntity, NamedThing, Entity
provided_by *
String		 The value in this node property represents the knowledge provider that create... Genome, BiologicalEntity, NamedThing
xref *
Uriorcurie		 A database cross reference or alternative identifier for a NamedThing or edge... Genome, BiologicalEntity, NamedThing
full_name 0..1
LabelType		 a long-form human readable name for a thing Genome, BiologicalEntity, NamedThing
synonym *
LabelType		 Alternate human-readable names for a thing Genome, BiologicalEntity, NamedThing
in_taxon *
OrganismTaxon		 connects an entity to its taxonomic classification Genome, BiologicalEntity, ThingWithTaxon
in_taxon_label 0..1
LabelType		 The human readable scientific name for the taxon of the entity Genome, BiologicalEntity, ThingWithTaxon
has_biological_sequence 0..1
BiologicalSequence		 connects a genomic feature to its sequence Genome, GenomicEntity

Usages

used by used in type used
GeneAnnotation referenced_in any_of[range] GenomeAnnotation
AnnotationCollection genome_annotations range GenomeAnnotation

Identifier and Mapping Information

Schema Source

  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema

Mappings

Mapping Type Mapped Value
self bican:GenomeAnnotation
native bican:GenomeAnnotation

LinkML Source

Direct

name: genome annotation
description: Location and nomenclature of genes and all of the coding regions in a
  genome assembly  and the classification of genes and transcripts into types.
from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
is_a: genome
slots:
- version
- digest
- content_url
- authority
attributes:
  reference assembly:
    name: reference assembly
    description: The reference genome assembly that this genome annotation was created
      from.
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    domain_of:
    - genome annotation
    required: true
    inlined: true
    any_of:
    - range: genome assembly
    - range: string

Induced

name: genome annotation
description: Location and nomenclature of genes and all of the coding regions in a
  genome assembly  and the classification of genes and transcripts into types.
from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
is_a: genome
attributes:
  reference assembly:
    name: reference assembly
    description: The reference genome assembly that this genome annotation was created
      from.
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    alias: reference_assembly
    owner: genome annotation
    domain_of:
    - genome annotation
    range: string
    required: true
    inlined: true
    any_of:
    - range: genome assembly
    - range: string
  version:
    name: version
    definition_uri: https://w3id.org/biolink/vocab/version
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    broad_mappings:
    - pav:version
    - owl:versionInfo
    rank: 1000
    is_a: node property
    domain: dataset
    slot_uri: biolink:version
    alias: version
    owner: genome annotation
    domain_of:
    - genome annotation
    - genome assembly
    range: string
  digest:
    name: digest
    description: Stores checksum information.
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    alias: digest
    owner: genome annotation
    domain_of:
    - genome annotation
    range: string
    multivalued: true
    inlined: true
    inlined_as_list: true
    any_of:
    - range: checksum
    - range: string
  content_url:
    name: content_url
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    slot_uri: schema:url
    alias: content_url
    owner: genome annotation
    domain_of:
    - genome annotation
    range: string
    multivalued: true
  authority:
    name: authority
    description: The organization responsible for publishing the data.
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    alias: authority
    owner: genome annotation
    domain_of:
    - genome annotation
    range: AuthorityType
  id:
    name: id
    definition_uri: https://w3id.org/biolink/vocab/id
    description: A unique identifier for an entity. Must be either a CURIE shorthand
      for a URI or a complete URI
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    exact_mappings:
    - AGRKB:primaryId
    - gff3:ID
    - gpi:DB_Object_ID
    rank: 1000
    domain: entity
    slot_uri: biolink:id
    identifier: true
    alias: id
    owner: genome annotation
    domain_of:
    - ontology class
    - entity
    - attribute
    - named thing
    - taxonomic rank
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    required: true
  iri:
    name: iri
    definition_uri: https://w3id.org/biolink/vocab/iri
    description: An IRI for an entity. This is determined by the id using expansion
      rules.
    in_subset:
    - translator_minimal
    - samples
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    exact_mappings:
    - WIKIDATA_PROPERTY:P854
    rank: 1000
    slot_uri: biolink:iri
    alias: iri
    owner: genome annotation
    domain_of:
    - attribute
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: iri type
  category:
    name: category
    definition_uri: https://w3id.org/biolink/vocab/category
    description: 'Name of the high level ontology class in which this entity is categorized.
      Corresponds to the label for the biolink entity type class. In a neo4j database
      this MAY correspond to the neo4j label tag. In an RDF database it should be
      a biolink model class URI. This field is multi-valued. It should include values
      for ancestors of the biolink class; for example, a protein such as Shh would
      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
      In an RDF database, nodes will typically have an rdf:type triples. This can
      be to the most specific biolink class, or potentially to a class more specific
      than something in biolink. For example, a sequence feature `f` may have a rdf:type
      assertion to a SO class such as TF_binding_site, which is more specific than
      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
      biolink:NamedThing}. NOTE: The category slot was modified to have a curie range
      and a pattern for bican categories.'
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    is_a: type
    domain: entity
    slot_uri: biolink:category
    designates_type: true
    alias: category
    owner: genome annotation
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    is_class_field: true
    range: curie
    multivalued: true
    pattern: ^bican:[A-Z][A-Za-z]+$
  type:
    name: type
    definition_uri: https://w3id.org/biolink/vocab/type
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    mappings:
    - rdf:type
    exact_mappings:
    - gff3:type
    - gpi:DB_Object_Type
    rank: 1000
    domain: entity
    slot_uri: rdf:type
    alias: type
    owner: genome annotation
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    multivalued: true
  name:
    name: name
    definition_uri: https://w3id.org/biolink/vocab/name
    description: A human-readable name for an attribute or entity.
    in_subset:
    - translator_minimal
    - samples
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    aliases:
    - label
    - display name
    - title
    mappings:
    - rdfs:label
    exact_mappings:
    - gff3:Name
    - gpi:DB_Object_Name
    narrow_mappings:
    - dct:title
    - WIKIDATA_PROPERTY:P1476
    rank: 1000
    domain: entity
    slot_uri: rdfs:label
    alias: name
    owner: genome annotation
    domain_of:
    - attribute
    - entity
    - macromolecular machine mixin
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene or gene product
    - gene
    - genome
    range: label type
  description:
    name: description
    definition_uri: https://w3id.org/biolink/vocab/description
    description: a human-readable description of an entity
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    aliases:
    - definition
    mappings:
    - dct:description
    exact_mappings:
    - IAO:0000115
    - skos:definitions
    narrow_mappings:
    - gff3:Description
    rank: 1000
    slot_uri: dct:description
    alias: description
    owner: genome annotation
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: narrative text
  has attribute:
    name: has attribute
    definition_uri: https://w3id.org/biolink/vocab/has_attribute
    description: connects any entity to an attribute
    in_subset:
    - samples
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    exact_mappings:
    - SIO:000008
    close_mappings:
    - OBI:0001927
    narrow_mappings:
    - OBAN:association_has_subject_property
    - OBAN:association_has_object_property
    - CPT:has_possibly_included_panel_element
    - DRUGBANK:category
    - EFO:is_executed_in
    - HANCESTRO:0301
    - LOINC:has_action_guidance
    - LOINC:has_adjustment
    - LOINC:has_aggregation_view
    - LOINC:has_approach_guidance
    - LOINC:has_divisor
    - LOINC:has_exam
    - LOINC:has_method
    - LOINC:has_modality_subtype
    - LOINC:has_object_guidance
    - LOINC:has_scale
    - LOINC:has_suffix
    - LOINC:has_time_aspect
    - LOINC:has_time_modifier
    - LOINC:has_timing_of
    - NCIT:R88
    - NCIT:eo_disease_has_property_or_attribute
    - NCIT:has_data_element
    - NCIT:has_pharmaceutical_administration_method
    - NCIT:has_pharmaceutical_basic_dose_form
    - NCIT:has_pharmaceutical_intended_site
    - NCIT:has_pharmaceutical_release_characteristics
    - NCIT:has_pharmaceutical_state_of_matter
    - NCIT:has_pharmaceutical_transformation
    - NCIT:is_qualified_by
    - NCIT:qualifier_applies_to
    - NCIT:role_has_domain
    - NCIT:role_has_range
    - INO:0000154
    - HANCESTRO:0308
    - OMIM:has_inheritance_type
    - orphanet:C016
    - orphanet:C017
    - RO:0000053
    - RO:0000086
    - RO:0000087
    - SNOMED:has_access
    - SNOMED:has_clinical_course
    - SNOMED:has_count_of_base_of_active_ingredient
    - SNOMED:has_dose_form_administration_method
    - SNOMED:has_dose_form_release_characteristic
    - SNOMED:has_dose_form_transformation
    - SNOMED:has_finding_context
    - SNOMED:has_finding_informer
    - SNOMED:has_inherent_attribute
    - SNOMED:has_intent
    - SNOMED:has_interpretation
    - SNOMED:has_laterality
    - SNOMED:has_measurement_method
    - SNOMED:has_method
    - SNOMED:has_priority
    - SNOMED:has_procedure_context
    - SNOMED:has_process_duration
    - SNOMED:has_property
    - SNOMED:has_revision_status
    - SNOMED:has_scale_type
    - SNOMED:has_severity
    - SNOMED:has_specimen
    - SNOMED:has_state_of_matter
    - SNOMED:has_subject_relationship_context
    - SNOMED:has_surgical_approach
    - SNOMED:has_technique
    - SNOMED:has_temporal_context
    - SNOMED:has_time_aspect
    - SNOMED:has_units
    - UMLS:has_structural_class
    - UMLS:has_supported_concept_property
    - UMLS:has_supported_concept_relationship
    - UMLS:may_be_qualified_by
    rank: 1000
    domain: entity
    slot_uri: biolink:has_attribute
    alias: has_attribute
    owner: genome annotation
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: attribute
    multivalued: true
  deprecated:
    name: deprecated
    definition_uri: https://w3id.org/biolink/vocab/deprecated
    description: A boolean flag indicating that an entity is no longer considered
      current or valid.
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    exact_mappings:
    - oboInOwl:ObsoleteClass
    rank: 1000
    slot_uri: biolink:deprecated
    alias: deprecated
    owner: genome annotation
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: boolean
  provided by:
    name: provided by
    definition_uri: https://w3id.org/biolink/vocab/provided_by
    description: The value in this node property represents the knowledge provider
      that created or assembled the node and all of its attributes.  Used internally
      to represent how a particular node made its way into a knowledge provider or
      graph.
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:provided_by
    alias: provided_by
    owner: genome annotation
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    multivalued: true
  xref:
    name: xref
    definition_uri: https://w3id.org/biolink/vocab/xref
    description: A database cross reference or alternative identifier for a NamedThing
      or edge between two NamedThings.  This property should point to a database record
      or webpage that supports the existence of the edge, or gives more detail about
      the edge. This property can be used on a node or edge to provide multiple URIs
      or CURIE cross references.
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    aliases:
    - dbxref
    - Dbxref
    - DbXref
    - record_url
    - source_record_urls
    narrow_mappings:
    - gff3:Dbxref
    - gpi:DB_Xrefs
    rank: 1000
    domain: named thing
    slot_uri: biolink:xref
    alias: xref
    owner: genome annotation
    domain_of:
    - named thing
    - gene
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - genome
    range: uriorcurie
    multivalued: true
  full name:
    name: full name
    definition_uri: https://w3id.org/biolink/vocab/full_name
    description: a long-form human readable name for a thing
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:full_name
    alias: full_name
    owner: genome annotation
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: label type
  synonym:
    name: synonym
    definition_uri: https://w3id.org/biolink/vocab/synonym
    description: Alternate human-readable names for a thing
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    aliases:
    - alias
    narrow_mappings:
    - skos:altLabel
    - gff3:Alias
    - AGRKB:synonyms
    - gpi:DB_Object_Synonyms
    - HANCESTRO:0330
    - IAO:0000136
    - RXNORM:has_tradename
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:synonym
    alias: synonym
    owner: genome annotation
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: label type
    multivalued: true
  in taxon:
    name: in taxon
    definition_uri: https://w3id.org/biolink/vocab/in_taxon
    annotations:
      canonical_predicate:
        tag: canonical_predicate
        value: true
    description: connects an entity to its taxonomic classification. Only certain
      kinds of entities can be taxonomically classified; see 'thing with taxon'
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    aliases:
    - instance of
    - is organism source of gene product
    - organism has gene
    - gene found in organism
    - gene product has organism source
    exact_mappings:
    - RO:0002162
    - WIKIDATA_PROPERTY:P703
    narrow_mappings:
    - RO:0002160
    rank: 1000
    is_a: related to at instance level
    domain: thing with taxon
    slot_uri: biolink:in_taxon
    inherited: true
    alias: in_taxon
    owner: genome annotation
    domain_of:
    - thing with taxon
    - biological entity
    - gene
    - genome
    range: organism taxon
    multivalued: true
  in taxon label:
    name: in taxon label
    definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
    annotations:
      denormalized:
        tag: denormalized
        value: true
    description: The human readable scientific name for the taxon of the entity.
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    exact_mappings:
    - WIKIDATA_PROPERTY:P225
    rank: 1000
    is_a: node property
    domain: thing with taxon
    slot_uri: biolink:in_taxon_label
    alias: in_taxon_label
    owner: genome annotation
    domain_of:
    - thing with taxon
    - biological entity
    - gene
    - genome
    range: label type
  has biological sequence:
    name: has biological sequence
    definition_uri: https://w3id.org/biolink/vocab/has_biological_sequence
    description: connects a genomic feature to its sequence
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:has_biological_sequence
    alias: has_biological_sequence
    owner: genome annotation
    domain_of:
    - genomic entity
    - gene
    - genome
    range: biological sequence