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Class: TissueSample

The final intact piece of tissue before cell or nuclei prep. This piece of tissue will be used in dissociation and has an region of interest polygon (ROI) associated with it.

URI: bican:TissueSample

classDiagram class TissueSample click TissueSample href "../TissueSample" ProvEntity <|-- TissueSample click ProvEntity href "../ProvEntity" MaterialSample <|-- TissueSample click MaterialSample href "../MaterialSample" TissueSample : category TissueSample : deprecated TissueSample : description TissueSample : dissection_was_guided_by TissueSample --> "0..1" DissectionRoiPolygon : dissection_was_guided_by click DissectionRoiPolygon href "../DissectionRoiPolygon" TissueSample : full_name TissueSample : has_attribute TissueSample --> "*" Attribute : has_attribute click Attribute href "../Attribute" TissueSample : id TissueSample : iri TissueSample : name TissueSample : provided_by TissueSample : structure TissueSample : synonym TissueSample : type TissueSample : was_derived_from TissueSample --> "0..1" Donor : was_derived_from click Donor href "../Donor" TissueSample : was_generated_by TissueSample --> "0..1" TissueDissection : was_generated_by click TissueDissection href "../TissueDissection" TissueSample : xref

Inheritance

Slots

Name Cardinality and Range Description Inheritance
was_derived_from 0..1
Donor		 The donor or brain slab from which the tissue sample was derived from direct
was_generated_by 0..1
TissueDissection		 The dissection process from which the tissue sample was generated by direct
name 0..1
LabelType		 Identifier name for final intact piece of tissue before cell or nuclei prep direct
dissection_was_guided_by 0..1
DissectionRoiPolygon		 The dissection ROI polygon that was used to guide the dissection direct
structure *
String		 Strucure of tissue sample direct
id 1
String		 A unique identifier for an entity Entity, MaterialSample, NamedThing, PhysicalEntity
iri 0..1
IriType		 An IRI for an entity Entity, MaterialSample, NamedThing, PhysicalEntity
category *
Curie		 Name of the high level ontology class in which this entity is categorized Entity, MaterialSample, NamedThing, PhysicalEntity
type *
String		 Entity, MaterialSample, NamedThing, PhysicalEntity
description 0..1
NarrativeText		 a human-readable description of an entity Entity, MaterialSample, NamedThing, PhysicalEntity
has_attribute *
Attribute		 connects any entity to an attribute Entity, MaterialSample, NamedThing, PhysicalEntity
deprecated 0..1
Boolean		 A boolean flag indicating that an entity is no longer considered current or v... Entity, MaterialSample, NamedThing, PhysicalEntity
provided_by *
String		 The value in this node property represents the knowledge provider that create... MaterialSample, NamedThing, PhysicalEntity
xref *
Uriorcurie		 A database cross reference or alternative identifier for a NamedThing or edge... MaterialSample, NamedThing, PhysicalEntity
full_name 0..1
LabelType		 a long-form human readable name for a thing MaterialSample, NamedThing, PhysicalEntity
synonym *
LabelType		 Alternate human-readable names for a thing MaterialSample, NamedThing, PhysicalEntity

Usages

used by used in type used
DissociatedCellSample was_derived_from range TissueSample
CellDissociation used range TissueSample

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type Mapped Value
self bican:TissueSample
native bican:TissueSample
exact NIMP:Tissue

LinkML Source

Direct

name: TissueSample
description: The final intact piece of tissue before cell or nuclei prep. This piece
  of tissue will be used in dissociation and has an region of interest polygon (ROI)
  associated with it.
in_subset:
- bican
- library_generation
from_schema: https://identifiers.org/brain-bican/library-generation-schema
exact_mappings:
- NIMP:Tissue
is_a: material sample
mixins:
- ProvEntity
slots:
- was_derived_from
- was_generated_by
- name
slot_usage:
  was_derived_from:
    name: was_derived_from
    description: The donor or brain slab from which the tissue sample was derived
      from.
    exact_mappings:
    - NIMP:has_parent
    domain_of:
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DigitalAsset
    - ProvEntity
    range: Donor
  was_generated_by:
    name: was_generated_by
    description: The dissection process from which the tissue sample was generated
      by.
    domain_of:
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryPool
    - DissectionRoiPolygon
    - ProvEntity
    range: TissueDissection
  name:
    name: name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: tissue_sample_local_name
    description: Identifier name for final intact piece of tissue before cell or nuclei
      prep.  This piece of tissue will be used in dissociation and has an ROI associated
      with it.
    exact_mappings:
    - NIMP:PD-LJCRCC35
    slot_uri: bican:2e4ca2fc-2d77-4d19-af45-d0fb7bbc2269
    domain_of:
    - Donor
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DissectionRoiPolygon
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - macromolecular machine mixin
    - gene or gene product
    - gene
    - genome
attributes:
  dissection_was_guided_by:
    name: dissection_was_guided_by
    description: The dissection ROI polygon that was used to guide the dissection.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:has_parent
    rank: 1000
    domain_of:
    - TissueSample
    range: DissectionRoiPolygon
  structure:
    name: structure
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: structure
    description: Strucure of tissue sample.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    rank: 1000
    alias: tissue_sample_structure
    domain_of:
    - TissueSample
    multivalued: true

Induced

name: TissueSample
description: The final intact piece of tissue before cell or nuclei prep. This piece
  of tissue will be used in dissociation and has an region of interest polygon (ROI)
  associated with it.
in_subset:
- bican
- library_generation
from_schema: https://identifiers.org/brain-bican/library-generation-schema
exact_mappings:
- NIMP:Tissue
is_a: material sample
mixins:
- ProvEntity
slot_usage:
  was_derived_from:
    name: was_derived_from
    description: The donor or brain slab from which the tissue sample was derived
      from.
    exact_mappings:
    - NIMP:has_parent
    domain_of:
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DigitalAsset
    - ProvEntity
    range: Donor
  was_generated_by:
    name: was_generated_by
    description: The dissection process from which the tissue sample was generated
      by.
    domain_of:
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryPool
    - DissectionRoiPolygon
    - ProvEntity
    range: TissueDissection
  name:
    name: name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: tissue_sample_local_name
    description: Identifier name for final intact piece of tissue before cell or nuclei
      prep.  This piece of tissue will be used in dissociation and has an ROI associated
      with it.
    exact_mappings:
    - NIMP:PD-LJCRCC35
    slot_uri: bican:2e4ca2fc-2d77-4d19-af45-d0fb7bbc2269
    domain_of:
    - Donor
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DissectionRoiPolygon
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - macromolecular machine mixin
    - gene or gene product
    - gene
    - genome
attributes:
  dissection_was_guided_by:
    name: dissection_was_guided_by
    description: The dissection ROI polygon that was used to guide the dissection.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:has_parent
    rank: 1000
    alias: dissection_was_guided_by
    owner: TissueSample
    domain_of:
    - TissueSample
    range: DissectionRoiPolygon
  structure:
    name: structure
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: structure
    description: Strucure of tissue sample.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    rank: 1000
    alias: tissue_sample_structure
    owner: TissueSample
    domain_of:
    - TissueSample
    range: string
    multivalued: true
  was_derived_from:
    name: was_derived_from
    description: The donor or brain slab from which the tissue sample was derived
      from.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:has_parent
    rank: 1000
    slot_uri: prov:wasDerivedFrom
    alias: was_derived_from
    owner: TissueSample
    domain_of:
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DigitalAsset
    - ProvEntity
    range: Donor
  was_generated_by:
    name: was_generated_by
    description: The dissection process from which the tissue sample was generated
      by.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    rank: 1000
    slot_uri: prov:wasGeneratedBy
    alias: was_generated_by
    owner: TissueSample
    domain_of:
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryPool
    - DissectionRoiPolygon
    - ProvEntity
    range: TissueDissection
  name:
    name: name
    definition_uri: https://w3id.org/biolink/vocab/name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: tissue_sample_local_name
    description: Identifier name for final intact piece of tissue before cell or nuclei
      prep.  This piece of tissue will be used in dissociation and has an ROI associated
      with it.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-LJCRCC35
    rank: 1000
    domain: entity
    slot_uri: bican:2e4ca2fc-2d77-4d19-af45-d0fb7bbc2269
    alias: name
    owner: TissueSample
    domain_of:
    - Donor
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DissectionRoiPolygon
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - macromolecular machine mixin
    - gene or gene product
    - 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: TissueSample
    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: TissueSample
    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: TissueSample
    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: TissueSample
    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
  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: TissueSample
    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: TissueSample
    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: TissueSample
    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: TissueSample
    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: TissueSample
    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: TissueSample
    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: TissueSample
    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