Skip to content

Class: AmplifiedCdna

A collection of cDNA molecules derived and amplified from an input barcoded cell sample. These cDNA molecules represent the gene expression of each cell, with all cDNA molecules from a given cell retaining that cell's unique barcode from the cell barcoding step. This is a necessary step for GEX methods but is not used for ATAC methods.

URI: bican:AmplifiedCdna

classDiagram class AmplifiedCdna click AmplifiedCdna href "../AmplifiedCdna" ProvEntity <|-- AmplifiedCdna click ProvEntity href "../ProvEntity" MaterialSample <|-- AmplifiedCdna click MaterialSample href "../MaterialSample" AmplifiedCdna : amplified_cDNA_quantity_ng AmplifiedCdna : amplified_cDNA_result AmplifiedCdna --> "0..1" AmplifiedCdnaRnaAmplificationPassFail : amplified_cDNA_result click AmplifiedCdnaRnaAmplificationPassFail href "../AmplifiedCdnaRnaAmplificationPassFail" AmplifiedCdna : category AmplifiedCdna : deprecated AmplifiedCdna : description AmplifiedCdna : equivalent_identifiers AmplifiedCdna : full_name AmplifiedCdna : has_attribute AmplifiedCdna --> "*" Attribute : has_attribute click Attribute href "../Attribute" AmplifiedCdna : id AmplifiedCdna : information_content AmplifiedCdna : iri AmplifiedCdna : name AmplifiedCdna : named_thing_category AmplifiedCdna : percent_cdna_longer_than_400bp AmplifiedCdna : provided_by AmplifiedCdna : synonym AmplifiedCdna : type AmplifiedCdna : was_derived_from AmplifiedCdna --> "0..1" BarcodedCellSample : was_derived_from click BarcodedCellSample href "../BarcodedCellSample" AmplifiedCdna : was_generated_by AmplifiedCdna --> "0..1" CdnaAmplification : was_generated_by click CdnaAmplification href "../CdnaAmplification" AmplifiedCdna : xref

Inheritance

Slots

Name Cardinality and Range Description Inheritance
was_generated_by 0..1
CdnaAmplification		 The cDNA amplification process from which the amplified cDNA was generated by direct
was_derived_from 0..1
BarcodedCellSample		 The input barcoded cell sample from which amplified cDNA was derived from direct
name 0..1
LabelType		 Name of a collection of cDNA molecules derived and amplified from an input ba... direct
amplified_cDNA_quantity_ng 0..1
Float		 Amount of cDNA produced after cDNA amplification measured in nanograms direct
amplified_cDNA_result 0..1
AmplifiedCdnaRnaAmplificationPassFail		 Pass or Fail result based on qualitative assessment of cDNA yield and size direct
percent_cdna_longer_than_400bp 0..1
Float		 QC metric to measure mRNA degradation of cDNA direct
id 1
String		 A unique identifier for an entity PhysicalEntity, Entity, MaterialSample, NamedThing
iri 0..1
IriType		 An IRI for an entity PhysicalEntity, Entity, MaterialSample, NamedThing
type *
String		 PhysicalEntity, Entity, MaterialSample, NamedThing
description 0..1
NarrativeText		 a human-readable description of an entity PhysicalEntity, Entity, MaterialSample, NamedThing
has_attribute *
Attribute		 connects any entity to an attribute PhysicalEntity, Entity, MaterialSample, NamedThing
deprecated 0..1
Boolean		 A boolean flag indicating that an entity is no longer considered current or v... PhysicalEntity, Entity, MaterialSample, NamedThing
provided_by *
String		 The value in this node property represents the knowledge provider that create... PhysicalEntity, MaterialSample, NamedThing
xref *
Uriorcurie		 A database cross reference or alternative identifier for a NamedThing or edge... PhysicalEntity, MaterialSample, NamedThing
full_name 0..1
LabelType		 a long-form human readable name for a thing PhysicalEntity, MaterialSample, NamedThing
synonym *
LabelType		 Alternate human-readable names for a thing PhysicalEntity, MaterialSample, NamedThing
information_content 0..1
Float		 Information content (IC) value for a term, primarily from Automats PhysicalEntity, MaterialSample, NamedThing
equivalent_identifiers *
Uriorcurie		 A set of identifiers that are considered equivalent to the primary identifier... PhysicalEntity, MaterialSample, NamedThing
named_thing_category 1..*
Uriorcurie		 Name of the high level ontology class in which this entity is categorized PhysicalEntity, MaterialSample, NamedThing
category 1..*
Uriorcurie		 Name of the high level ontology class in which this entity is categorized Entity

Usages

used by used in type used
Library was_derived_from any_of[range] AmplifiedCdna
LibraryConstruction used any_of[range] AmplifiedCdna

Identifier and Mapping Information

Schema Source

  • from schema: https://identifiers.org/brain-bican/library-generation-schema

Mappings

Mapping Type Mapped Value
self bican:AmplifiedCdna
native bican:AmplifiedCdna
exact NIMP:Amplified%20cDNA

LinkML Source

Direct

name: AmplifiedCdna
description: A collection of cDNA molecules derived and amplified from an input barcoded
  cell sample. These cDNA molecules represent the gene expression of each cell, with
  all cDNA molecules from a given cell retaining that cell's unique barcode from the
  cell barcoding step. This is a necessary step for GEX methods but is not used for
  ATAC methods.
in_subset:
- bican
- library_generation
from_schema: https://identifiers.org/brain-bican/library-generation-schema
exact_mappings:
- NIMP:Amplified%20cDNA
is_a: material sample
mixins:
- ProvEntity
slots:
- was_generated_by
- was_derived_from
- name
slot_usage:
  was_generated_by:
    name: was_generated_by
    description: The cDNA amplification process from which the amplified cDNA was
      generated by.
    from_schema: bican_prov
    range: CdnaAmplification
  was_derived_from:
    name: was_derived_from
    description: The input barcoded cell sample from which amplified cDNA was derived
      from.
    from_schema: bican_prov
    exact_mappings:
    - NIMP:has_parent
    range: BarcodedCellSample
  name:
    name: name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: amplified_cdna_local_name
    description: Name of a collection of cDNA molecules derived and amplified from
      an input barcoded_cell_sample.  These cDNA molecules represent the gene expression
      of each cell, with all cDNA molecules from a given cell retaining that cell's
      unique barcode from the cell barcoding step.  This is a necessary step for GEX
      methods but is not used for ATAC methods.
    from_schema: bican_biolink
    exact_mappings:
    - NIMP:PD-YAAGGG39
    slot_uri: bican:e2606a11-114e-472f-9e05-33f9b6fc3089
attributes:
  amplified_cDNA_quantity_ng:
    name: amplified_cDNA_quantity_ng
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: amplified_cdna_amplified_quantity_ng
    description: Amount of cDNA produced after cDNA amplification measured in nanograms.
    in_subset:
    - analysis
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-TITIIC26
    rank: 1000
    slot_uri: bican:0db79d05-8612-4896-b9d3-eb1558841449
    domain_of:
    - AmplifiedCdna
    range: float
  amplified_cDNA_result:
    name: amplified_cDNA_result
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: amplified_cdna_rna_amplification_pass_fail
    description: Pass or Fail result based on qualitative assessment of cDNA yield
      and size.
    in_subset:
    - analysis
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-XXXXFQ31
    rank: 1000
    slot_uri: bican:bc62bdb2-7dc8-4404-bb84-ce0bbcae59e5
    domain_of:
    - AmplifiedCdna
    range: amplified_cdna_rna_amplification_pass_fail
  percent_cdna_longer_than_400bp:
    name: percent_cdna_longer_than_400bp
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: amplified_cdna_percent_cdna_longer_than_400bp
    description: QC metric to measure mRNA degradation of cDNA.  Higher % is higher
      quality starting material.  Over 400bp is used as a universal cutoff for intact
      (full length) vs degraded cDNA and is a common output from Bioanalyzer and Fragment
      Analyzer elecropheragrams.
    in_subset:
    - analysis
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-JJJJWD35
    rank: 1000
    slot_uri: bican:8d150467-f69e-461c-b54c-bcfd22f581e5
    domain_of:
    - AmplifiedCdna
    range: float

Induced

name: AmplifiedCdna
description: A collection of cDNA molecules derived and amplified from an input barcoded
  cell sample. These cDNA molecules represent the gene expression of each cell, with
  all cDNA molecules from a given cell retaining that cell's unique barcode from the
  cell barcoding step. This is a necessary step for GEX methods but is not used for
  ATAC methods.
in_subset:
- bican
- library_generation
from_schema: https://identifiers.org/brain-bican/library-generation-schema
exact_mappings:
- NIMP:Amplified%20cDNA
is_a: material sample
mixins:
- ProvEntity
slot_usage:
  was_generated_by:
    name: was_generated_by
    description: The cDNA amplification process from which the amplified cDNA was
      generated by.
    from_schema: bican_prov
    range: CdnaAmplification
  was_derived_from:
    name: was_derived_from
    description: The input barcoded cell sample from which amplified cDNA was derived
      from.
    from_schema: bican_prov
    exact_mappings:
    - NIMP:has_parent
    range: BarcodedCellSample
  name:
    name: name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: amplified_cdna_local_name
    description: Name of a collection of cDNA molecules derived and amplified from
      an input barcoded_cell_sample.  These cDNA molecules represent the gene expression
      of each cell, with all cDNA molecules from a given cell retaining that cell's
      unique barcode from the cell barcoding step.  This is a necessary step for GEX
      methods but is not used for ATAC methods.
    from_schema: bican_biolink
    exact_mappings:
    - NIMP:PD-YAAGGG39
    slot_uri: bican:e2606a11-114e-472f-9e05-33f9b6fc3089
attributes:
  amplified_cDNA_quantity_ng:
    name: amplified_cDNA_quantity_ng
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: amplified_cdna_amplified_quantity_ng
    description: Amount of cDNA produced after cDNA amplification measured in nanograms.
    in_subset:
    - analysis
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-TITIIC26
    rank: 1000
    slot_uri: bican:0db79d05-8612-4896-b9d3-eb1558841449
    alias: amplified_cDNA_quantity_ng
    owner: AmplifiedCdna
    domain_of:
    - AmplifiedCdna
    range: float
  amplified_cDNA_result:
    name: amplified_cDNA_result
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: amplified_cdna_rna_amplification_pass_fail
    description: Pass or Fail result based on qualitative assessment of cDNA yield
      and size.
    in_subset:
    - analysis
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-XXXXFQ31
    rank: 1000
    slot_uri: bican:bc62bdb2-7dc8-4404-bb84-ce0bbcae59e5
    alias: amplified_cDNA_result
    owner: AmplifiedCdna
    domain_of:
    - AmplifiedCdna
    range: amplified_cdna_rna_amplification_pass_fail
  percent_cdna_longer_than_400bp:
    name: percent_cdna_longer_than_400bp
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: amplified_cdna_percent_cdna_longer_than_400bp
    description: QC metric to measure mRNA degradation of cDNA.  Higher % is higher
      quality starting material.  Over 400bp is used as a universal cutoff for intact
      (full length) vs degraded cDNA and is a common output from Bioanalyzer and Fragment
      Analyzer elecropheragrams.
    in_subset:
    - analysis
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-JJJJWD35
    rank: 1000
    slot_uri: bican:8d150467-f69e-461c-b54c-bcfd22f581e5
    alias: percent_cdna_longer_than_400bp
    owner: AmplifiedCdna
    domain_of:
    - AmplifiedCdna
    range: float
  was_generated_by:
    name: was_generated_by
    description: The cDNA amplification process from which the amplified cDNA was
      generated by.
    from_schema: bican_prov
    rank: 1000
    slot_uri: prov:wasGeneratedBy
    alias: was_generated_by
    owner: AmplifiedCdna
    domain_of:
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryPool
    - DissectionRoiPolygon
    - ProvEntity
    range: CdnaAmplification
  was_derived_from:
    name: was_derived_from
    description: The input barcoded cell sample from which amplified cDNA was derived
      from.
    from_schema: bican_prov
    exact_mappings:
    - NIMP:has_parent
    rank: 1000
    slot_uri: prov:wasDerivedFrom
    alias: was_derived_from
    owner: AmplifiedCdna
    domain_of:
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DigitalAsset
    - ProvEntity
    range: BarcodedCellSample
  name:
    name: name
    definition_uri: https://w3id.org/biolink/vocab/name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: amplified_cdna_local_name
    description: Name of a collection of cDNA molecules derived and amplified from
      an input barcoded_cell_sample.  These cDNA molecules represent the gene expression
      of each cell, with all cDNA molecules from a given cell retaining that cell's
      unique barcode from the cell barcoding step.  This is a necessary step for GEX
      methods but is not used for ATAC methods.
    in_subset:
    - translator_minimal
    - samples
    from_schema: bican_biolink
    aliases:
    - label
    - display name
    - title
    mappings:
    - rdfs:label
    exact_mappings:
    - NIMP:PD-YAAGGG39
    narrow_mappings:
    - dct:title
    - WIKIDATA_PROPERTY:P1476
    rank: 1000
    domain: entity
    slot_uri: bican:e2606a11-114e-472f-9e05-33f9b6fc3089
    alias: name
    owner: AmplifiedCdna
    domain_of:
    - attribute
    - entity
    - macromolecular machine mixin
    - Donor
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DissectionRoiPolygon
    - named thing
    - organism taxon
    - study result
    - relative frequency analysis result
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: label type
  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/library-generation-schema
    exact_mappings:
    - AGRKB:primaryId
    - gff3:ID
    - gpi:DB_Object_ID
    rank: 1000
    domain: entity
    slot_uri: biolink:id
    identifier: true
    alias: id
    owner: AmplifiedCdna
    domain_of:
    - ontology class
    - entity
    - attribute
    - named thing
    - taxonomic rank
    - organism taxon
    - study result
    - relative frequency analysis result
    - 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/library-generation-schema
    exact_mappings:
    - WIKIDATA_PROPERTY:P854
    rank: 1000
    slot_uri: biolink:iri
    alias: iri
    owner: AmplifiedCdna
    domain_of:
    - attribute
    - entity
    - named thing
    - organism taxon
    - study result
    - relative frequency analysis result
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: iri type
  type:
    name: type
    definition_uri: https://w3id.org/biolink/vocab/type
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    mappings:
    - rdf:type
    exact_mappings:
    - gff3:type
    - gpi:DB_Object_Type
    rank: 1000
    domain: entity
    slot_uri: rdf:type
    alias: type
    owner: AmplifiedCdna
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - study result
    - relative frequency analysis result
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    multivalued: true
  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/library-generation-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: AmplifiedCdna
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - study result
    - relative frequency analysis result
    - 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/library-generation-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
    - 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: AmplifiedCdna
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - study result
    - relative frequency analysis result
    - 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/library-generation-schema
    exact_mappings:
    - oboInOwl:ObsoleteClass
    rank: 1000
    slot_uri: biolink:deprecated
    alias: deprecated
    owner: AmplifiedCdna
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - study result
    - relative frequency analysis result
    - 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/library-generation-schema
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:provided_by
    alias: provided_by
    owner: AmplifiedCdna
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - study result
    - relative frequency analysis result
    - 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/library-generation-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: AmplifiedCdna
    domain_of:
    - named thing
    - gene
    - attribute
    - organism taxon
    - study result
    - relative frequency analysis result
    - 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/library-generation-schema
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:full_name
    alias: full_name
    owner: AmplifiedCdna
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - study result
    - relative frequency analysis result
    - 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/library-generation-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: AmplifiedCdna
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - study result
    - relative frequency analysis result
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: label type
    multivalued: true
  information content:
    name: information content
    definition_uri: https://w3id.org/biolink/vocab/information_content
    description: Information content (IC) value for a term, primarily from Automats.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:information_content
    alias: information_content
    owner: AmplifiedCdna
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - study result
    - relative frequency analysis result
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: float
  equivalent identifiers:
    name: equivalent identifiers
    definition_uri: https://w3id.org/biolink/vocab/equivalent_identifiers
    description: A set of identifiers that are considered equivalent to the primary
      identifier of the entity. This attribute is used to represent a collection of
      identifiers that are considered equivalent to the primary identifier of an entity.
      These equivalent identifiers may come from different databases, ontologies,
      or naming conventions, but they all refer to the same underlying concept or
      entity. This attribute is particularly useful in data integration and interoperability
      scenarios, where it is important to recognize and link different representations
      of the same entity across various sources.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    see_also:
    - biolink:xref
    - biolink:synonyms
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:equivalent_identifiers
    alias: equivalent_identifiers
    owner: AmplifiedCdna
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - study result
    - relative frequency analysis result
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: uriorcurie
    multivalued: true
  named thing_category:
    name: named thing_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}
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    rank: 1000
    is_a: category
    domain: named thing
    slot_uri: biolink:category
    designates_type: true
    alias: category
    owner: AmplifiedCdna
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - study result
    - relative frequency analysis result
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    is_class_field: true
    is_usage_slot: true
    usage_slot_name: category
    range: uriorcurie
    required: true
    multivalued: true
  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}
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    rank: 1000
    is_a: type
    domain: entity
    slot_uri: biolink:category
    designates_type: true
    alias: category
    owner: AmplifiedCdna
    domain_of:
    - entity
    is_class_field: true
    range: uriorcurie
    required: true
    multivalued: true