Class: CellBarcoding

The process of adding a molecular barcode to individual cells in a sample. The input will be either dissociated cell sample or enriched cell sample. Cell barcodes are only guaranteed to be unique within this one collection. One dissociated cell sample or enriched cell sample can lead to multiple barcoded cell samples.

URI: bican:CellBarcoding

classDiagram class CellBarcoding click CellBarcoding href "../CellBarcoding" ProvActivity <|-- CellBarcoding click ProvActivity href "../ProvActivity" Procedure <|-- CellBarcoding click Procedure href "../Procedure" CellBarcoding : category CellBarcoding : deprecated CellBarcoding : description CellBarcoding : full_name CellBarcoding : has_attribute CellBarcoding --> "*" Attribute : has_attribute click Attribute href "../Attribute" CellBarcoding : id CellBarcoding : input_quantity CellBarcoding : iri CellBarcoding : method CellBarcoding --> "0..1" BarcodedCellSampleTechnique : method click BarcodedCellSampleTechnique href "../BarcodedCellSampleTechnique" CellBarcoding : name CellBarcoding : port_well CellBarcoding : process_date CellBarcoding : provided_by CellBarcoding : synonym CellBarcoding : type CellBarcoding : used CellBarcoding --> "*" ProvEntity : used click ProvEntity href "../ProvEntity" CellBarcoding : xref

Inheritance

Entity
- NamedThing
  - Procedure [ ActivityAndBehavior]
    - CellBarcoding [ ProvActivity]

Slots

Name	Cardinality and Range	Description	Inheritance
used	* ProvEntity or DissociatedCellSample or EnrichedCellSample	The input dissociated or enriched cell sample(s) from which the barcoded cell...	direct
port_well	0..1 String	Specific position of the loaded port of the 10x chip	direct
input_quantity	0..1 Integer	Number of enriched or dissociated cells/nuclei going into the barcoding proce...	direct
process_date	0..1 String	Date of cell barcoding process	direct
method	0..1 BarcodedCellSampleTechnique	Standardized nomenclature to describe the general barcoding method used	direct
id	1 String	A unique identifier for an entity	Entity, Procedure, NamedThing
iri	0..1 IriType	An IRI for an entity	Entity, Procedure, NamedThing
category	* Curie	Name of the high level ontology class in which this entity is categorized	Entity, Procedure, NamedThing
type	* String		Entity, Procedure, NamedThing
name	0..1 LabelType	A human-readable name for an attribute or entity	Entity, Procedure, NamedThing
description	0..1 NarrativeText	a human-readable description of an entity	Entity, Procedure, NamedThing
has_attribute	* Attribute	connects any entity to an attribute	Entity, Procedure, NamedThing
deprecated	0..1 Boolean	A boolean flag indicating that an entity is no longer considered current or v...	Entity, Procedure, NamedThing
provided_by	* String	The value in this node property represents the knowledge provider that create...	Procedure, NamedThing
xref	* Uriorcurie	A database cross reference or alternative identifier for a NamedThing or edge...	Procedure, NamedThing
full_name	0..1 LabelType	a long-form human readable name for a thing	Procedure, NamedThing
synonym	* LabelType	Alternate human-readable names for a thing	Procedure, NamedThing

Usages

used by	used in	type	used
BarcodedCellSample	was_generated_by	range	CellBarcoding

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: CellBarcoding
description: The process of adding a molecular barcode to individual cells in a sample.
  The input will be either dissociated cell sample or enriched cell sample. Cell barcodes
  are only guaranteed to be unique within this one collection. One dissociated cell
  sample or enriched cell sample can lead to multiple barcoded cell samples.
in_subset:
- bican
- library_generation
from_schema: https://identifiers.org/brain-bican/library-generation-schema
is_a: procedure
mixins:
- ProvActivity
slots:
- used
slot_usage:
  used:
    name: used
    description: The input dissociated or enriched cell sample(s) from which the barcoded
      cell sample was derived from.
    domain_of:
    - DissectionRoiDelineation
    - TissueDissection
    - CellDissociation
    - CellEnrichment
    - EnrichedCellSampleSplitting
    - CellBarcoding
    - CdnaAmplification
    - LibraryConstruction
    - LibraryPooling
    - ProvActivity
    multivalued: true
    exactly_one_of:
    - range: DissociatedCellSample
    - range: EnrichedCellSample
attributes:
  port_well:
    name: port_well
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: barcoded_cell_sample_port_well
    description: Specific position of the loaded port of the 10x chip.  An Enriched
      or Dissociated Cell Sample is loaded into a port on a chip (creating a Barcoded
      Cell Sample). Can be left null for non-10x methods.
    in_subset:
    - analysis
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-KJKJZK32
    rank: 1000
    slot_uri: bican:aca38100-d245-4be4-9be3-ba27192779fe
    alias: barcoded cell sample port well
    domain_of:
    - CellBarcoding
    range: string
  input_quantity:
    name: input_quantity
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: barcoded_cell_input_quantity_count
    description: Number of enriched or dissociated cells/nuclei going into the barcoding
      process.
    in_subset:
    - analysis
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-ZZZZWQ40
    rank: 1000
    slot_uri: bican:aa534269-7c9b-4b63-b990-eea8cda56d0e
    alias: barcoded cell input quantity count
    domain_of:
    - CellBarcoding
    range: integer
  process_date:
    name: process_date
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: barcoded_cell_sample_preparation_date
    description: Date of cell barcoding process.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-SHSHZS25
    domain_of:
    - CellDissociation
    - CellEnrichment
    - CellBarcoding
    - CdnaAmplification
    - LibraryConstruction
    - LibraryPooling
  method:
    name: method
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: barcoded_cell_sample_technique
    description: 'Standardized nomenclature to describe the general barcoding method
      used.  For example: Multiome, ATAC Only, GEX Only or snm3C-seq.'
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-TDTDDF25
    rank: 1000
    domain_of:
    - CellBarcoding
    - LibraryConstruction
    range: barcoded_cell_sample_technique

Induced

name: CellBarcoding
description: The process of adding a molecular barcode to individual cells in a sample.
  The input will be either dissociated cell sample or enriched cell sample. Cell barcodes
  are only guaranteed to be unique within this one collection. One dissociated cell
  sample or enriched cell sample can lead to multiple barcoded cell samples.
in_subset:
- bican
- library_generation
from_schema: https://identifiers.org/brain-bican/library-generation-schema
is_a: procedure
mixins:
- ProvActivity
slot_usage:
  used:
    name: used
    description: The input dissociated or enriched cell sample(s) from which the barcoded
      cell sample was derived from.
    domain_of:
    - DissectionRoiDelineation
    - TissueDissection
    - CellDissociation
    - CellEnrichment
    - EnrichedCellSampleSplitting
    - CellBarcoding
    - CdnaAmplification
    - LibraryConstruction
    - LibraryPooling
    - ProvActivity
    multivalued: true
    exactly_one_of:
    - range: DissociatedCellSample
    - range: EnrichedCellSample
attributes:
  port_well:
    name: port_well
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: barcoded_cell_sample_port_well
    description: Specific position of the loaded port of the 10x chip.  An Enriched
      or Dissociated Cell Sample is loaded into a port on a chip (creating a Barcoded
      Cell Sample). Can be left null for non-10x methods.
    in_subset:
    - analysis
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-KJKJZK32
    rank: 1000
    slot_uri: bican:aca38100-d245-4be4-9be3-ba27192779fe
    alias: barcoded cell sample port well
    owner: CellBarcoding
    domain_of:
    - CellBarcoding
    range: string
  input_quantity:
    name: input_quantity
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: barcoded_cell_input_quantity_count
    description: Number of enriched or dissociated cells/nuclei going into the barcoding
      process.
    in_subset:
    - analysis
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-ZZZZWQ40
    rank: 1000
    slot_uri: bican:aa534269-7c9b-4b63-b990-eea8cda56d0e
    alias: barcoded cell input quantity count
    owner: CellBarcoding
    domain_of:
    - CellBarcoding
    range: integer
  process_date:
    name: process_date
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: barcoded_cell_sample_preparation_date
    description: Date of cell barcoding process.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-SHSHZS25
    alias: process_date
    owner: CellBarcoding
    domain_of:
    - CellDissociation
    - CellEnrichment
    - CellBarcoding
    - CdnaAmplification
    - LibraryConstruction
    - LibraryPooling
    range: string
  method:
    name: method
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: barcoded_cell_sample_technique
    description: 'Standardized nomenclature to describe the general barcoding method
      used.  For example: Multiome, ATAC Only, GEX Only or snm3C-seq.'
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-TDTDDF25
    rank: 1000
    alias: method
    owner: CellBarcoding
    domain_of:
    - CellBarcoding
    - LibraryConstruction
    range: barcoded_cell_sample_technique
  used:
    name: used
    description: The input dissociated or enriched cell sample(s) from which the barcoded
      cell sample was derived from.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    rank: 1000
    slot_uri: prov:used
    alias: used
    owner: CellBarcoding
    domain_of:
    - DissectionRoiDelineation
    - TissueDissection
    - CellDissociation
    - CellEnrichment
    - EnrichedCellSampleSplitting
    - CellBarcoding
    - CdnaAmplification
    - LibraryConstruction
    - LibraryPooling
    - ProvActivity
    range: ProvEntity
    multivalued: true
    exactly_one_of:
    - range: DissociatedCellSample
    - range: EnrichedCellSample
  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: CellBarcoding
    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/library-generation-schema
    exact_mappings:
    - WIKIDATA_PROPERTY:P854
    rank: 1000
    slot_uri: biolink:iri
    alias: iri
    owner: CellBarcoding
    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/library-generation-schema
    rank: 1000
    is_a: type
    domain: entity
    slot_uri: biolink:category
    designates_type: true
    alias: category
    owner: CellBarcoding
    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/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: CellBarcoding
    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/library-generation-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: CellBarcoding
    domain_of:
    - attribute
    - entity
    - macromolecular machine mixin
    - Donor
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DissectionRoiPolygon
    - 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/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: CellBarcoding
    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/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
    - 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: CellBarcoding
    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/library-generation-schema
    exact_mappings:
    - oboInOwl:ObsoleteClass
    rank: 1000
    slot_uri: biolink:deprecated
    alias: deprecated
    owner: CellBarcoding
    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/library-generation-schema
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:provided_by
    alias: provided_by
    owner: CellBarcoding
    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/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: CellBarcoding
    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/library-generation-schema
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:full_name
    alias: full_name
    owner: CellBarcoding
    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/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: CellBarcoding
    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