Class: LibraryPool

A library pool is made up of library aliquots from multiple libraries. Each library aliquot in a library pool will have a unique R1/R2 index to allow for sequencing together then separating the sequencing output by originating library aliquot through the process of demultiplexing.

URI: bican:LibraryPool

classDiagram class LibraryPool click LibraryPool href "../LibraryPool" ProvEntity <|-- LibraryPool click ProvEntity href "../ProvEntity" MaterialSample <|-- LibraryPool click MaterialSample href "../MaterialSample" LibraryPool : category LibraryPool : deprecated LibraryPool : description LibraryPool : full_name LibraryPool : has_attribute LibraryPool --> "*" Attribute : has_attribute click Attribute href "../Attribute" LibraryPool : id LibraryPool : iri LibraryPool : local_tube_id LibraryPool : name LibraryPool : provided_by LibraryPool : synonym LibraryPool : type LibraryPool : was_derived_from LibraryPool --> "*" LibraryAliquot : was_derived_from click LibraryAliquot href "../LibraryAliquot" LibraryPool : was_generated_by LibraryPool --> "0..1" LibraryPooling : was_generated_by click LibraryPooling href "../LibraryPooling" LibraryPool : xref

Inheritance

Entity
- NamedThing
  - PhysicalEntity [ PhysicalEssence]
    - MaterialSample [ SubjectOfInvestigation]
      - LibraryPool [ ProvEntity]

Slots

Name	Cardinality and Range	Description	Inheritance
was_generated_by	0..1 LibraryPooling	The pooling process from which the library pool was generated by	direct
was_derived_from	* LibraryAliquot	The input aliquot(s) from which the library pool was derived from	direct
name	0..1 LabelType	Library lab's library pool name	direct
local_tube_id	0..1 String	Library Pool Tube local name	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
DigitalAsset	was_derived_from	range	LibraryPool

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	bican:LibraryPool
native	bican:LibraryPool
exact	NIMP:Library%20Pool

LinkML Source

Direct

name: LibraryPool
description: A library pool is made up of library aliquots from multiple libraries.
  Each library aliquot in a library pool will have a unique R1/R2 index to allow for
  sequencing together then separating the sequencing output by originating library
  aliquot through the process of demultiplexing.
in_subset:
- bican
- library_generation
from_schema: https://identifiers.org/brain-bican/library-generation-schema
exact_mappings:
- NIMP:Library%20Pool
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 pooling process from which the library pool was generated by.
    domain_of:
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryPool
    - DissectionRoiPolygon
    - ProvEntity
    range: LibraryPooling
  was_derived_from:
    name: was_derived_from
    description: The input aliquot(s) from which the library pool was derived from.
    exact_mappings:
    - NIMP:has_parent
    domain_of:
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DigitalAsset
    - ProvEntity
    range: LibraryAliquot
    multivalued: true
  name:
    name: name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_pool_local_name
    description: Library lab's library pool name.  For some labs this may be the same
      as "Libray pool tube local name".   Other labs distinguish between the local
      tube label of the library pool and the library pool name provided to SeqCore
      for tracking.  Local Pool Name is used to communicate sequencing status between
      SeqCore and Library Labs.
    exact_mappings:
    - NIMP:PD-KKIAPA48
    slot_uri: bican:29e0578b-6427-4c93-b29b-bde27fbadeec
    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:
  local_tube_id:
    name: local_tube_id
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_pool_local_tube_id
    description: Library Pool Tube local name.  Label of the tube containing the library
      pool, which is made up of multiple library_aliquots.  This is a Library Lab
      local tube name, before the pool is aliquoted to the Seq Core provided tube
      'Library Pool Tube Name'.
    in_subset:
    - analysis
    - tracking
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-WNYWPA48
    rank: 1000
    slot_uri: bican:f1fdea98-7849-4def-a62f-a04cbbf98922
    alias: library_pool_tube_internal_label
    domain_of:
    - LibraryPool
    range: string

Induced

name: LibraryPool
description: A library pool is made up of library aliquots from multiple libraries.
  Each library aliquot in a library pool will have a unique R1/R2 index to allow for
  sequencing together then separating the sequencing output by originating library
  aliquot through the process of demultiplexing.
in_subset:
- bican
- library_generation
from_schema: https://identifiers.org/brain-bican/library-generation-schema
exact_mappings:
- NIMP:Library%20Pool
is_a: material sample
mixins:
- ProvEntity
slot_usage:
  was_generated_by:
    name: was_generated_by
    description: The pooling process from which the library pool was generated by.
    domain_of:
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryPool
    - DissectionRoiPolygon
    - ProvEntity
    range: LibraryPooling
  was_derived_from:
    name: was_derived_from
    description: The input aliquot(s) from which the library pool was derived from.
    exact_mappings:
    - NIMP:has_parent
    domain_of:
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DigitalAsset
    - ProvEntity
    range: LibraryAliquot
    multivalued: true
  name:
    name: name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_pool_local_name
    description: Library lab's library pool name.  For some labs this may be the same
      as "Libray pool tube local name".   Other labs distinguish between the local
      tube label of the library pool and the library pool name provided to SeqCore
      for tracking.  Local Pool Name is used to communicate sequencing status between
      SeqCore and Library Labs.
    exact_mappings:
    - NIMP:PD-KKIAPA48
    slot_uri: bican:29e0578b-6427-4c93-b29b-bde27fbadeec
    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:
  local_tube_id:
    name: local_tube_id
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_pool_local_tube_id
    description: Library Pool Tube local name.  Label of the tube containing the library
      pool, which is made up of multiple library_aliquots.  This is a Library Lab
      local tube name, before the pool is aliquoted to the Seq Core provided tube
      'Library Pool Tube Name'.
    in_subset:
    - analysis
    - tracking
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-WNYWPA48
    rank: 1000
    slot_uri: bican:f1fdea98-7849-4def-a62f-a04cbbf98922
    alias: library_pool_tube_internal_label
    owner: LibraryPool
    domain_of:
    - LibraryPool
    range: string
  was_generated_by:
    name: was_generated_by
    description: The pooling process from which the library pool was generated by.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    rank: 1000
    slot_uri: prov:wasGeneratedBy
    alias: was_generated_by
    owner: LibraryPool
    domain_of:
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryPool
    - DissectionRoiPolygon
    - ProvEntity
    range: LibraryPooling
  was_derived_from:
    name: was_derived_from
    description: The input aliquot(s) from which the library pool 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: LibraryPool
    domain_of:
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DigitalAsset
    - ProvEntity
    range: LibraryAliquot
    multivalued: true
  name:
    name: name
    definition_uri: https://w3id.org/biolink/vocab/name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_pool_local_name
    description: Library lab's library pool name.  For some labs this may be the same
      as "Libray pool tube local name".   Other labs distinguish between the local
      tube label of the library pool and the library pool name provided to SeqCore
      for tracking.  Local Pool Name is used to communicate sequencing status between
      SeqCore and Library Labs.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-KKIAPA48
    rank: 1000
    domain: entity
    slot_uri: bican:29e0578b-6427-4c93-b29b-bde27fbadeec
    alias: name
    owner: LibraryPool
    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: LibraryPool
    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: LibraryPool
    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: LibraryPool
    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: LibraryPool
    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: LibraryPool
    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: LibraryPool
    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: LibraryPool
    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: LibraryPool
    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: LibraryPool
    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: LibraryPool
    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: LibraryPool
    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