Class: CellDissociation

name: CellDissociation
description: The process of generating dissociated cells from an input tissue sample.
  This process could also introduce a tissue-source barcode (eg cell hashing), allowing
  mixing of cell dissociation samples at the cell barcoding step.
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 tissue sample(s) from which the dissociated cell sample
      was derived from.
    from_schema: bican_prov
    range: TissueSample
    multivalued: true
attributes:
  cell_dissociation_process_date:
    name: cell_dissociation_process_date
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: dissociated_cell_sample_preparation_date
    description: Date of cell dissociation process.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-BUBUFE27
    rank: 1000
    domain_of:
    - CellDissociation

name: CellDissociation
description: The process of generating dissociated cells from an input tissue sample.
  This process could also introduce a tissue-source barcode (eg cell hashing), allowing
  mixing of cell dissociation samples at the cell barcoding step.
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 tissue sample(s) from which the dissociated cell sample
      was derived from.
    from_schema: bican_prov
    range: TissueSample
    multivalued: true
attributes:
  cell_dissociation_process_date:
    name: cell_dissociation_process_date
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: dissociated_cell_sample_preparation_date
    description: Date of cell dissociation process.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-BUBUFE27
    rank: 1000
    alias: cell_dissociation_process_date
    owner: CellDissociation
    domain_of:
    - CellDissociation
    range: string
  used:
    name: used
    description: The input tissue sample(s) from which the dissociated cell sample
      was derived from.
    from_schema: bican_prov
    rank: 1000
    slot_uri: prov:used
    alias: used
    owner: CellDissociation
    domain_of:
    - DissectionRoiDelineation
    - TissueDissection
    - CellDissociation
    - CellEnrichment
    - EnrichedCellSampleSplitting
    - CellBarcoding
    - CdnaAmplification
    - LibraryConstruction
    - LibraryPooling
    - ProvActivity
    range: TissueSample
    multivalued: true
  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: CellDissociation
    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: CellDissociation
    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: CellDissociation
    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
  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: CellDissociation
    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
  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: CellDissociation
    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: CellDissociation
    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: CellDissociation
    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: CellDissociation
    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: CellDissociation
    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: CellDissociation
    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: CellDissociation
    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: CellDissociation
    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: CellDissociation
    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: CellDissociation
    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: CellDissociation
    domain_of:
    - entity
    is_class_field: true
    range: uriorcurie
    required: true
    multivalued: true