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Class: LibraryAliquot

One library in the library pool. 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. The resulting demultiplexed fastq files will include the library aliquot name. A given library may produce multiple library aliquots, which is done in the case of resequencing. Each library aliquot will produce a set of fastq files.

URI: bican:LibraryAliquot

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

Inheritance

Slots

Name Cardinality and Range Description Inheritance
was_derived_from 0..1
Library		 The input library from which the library aliquot was derived from direct
name 0..1
LabelType		 One library in the library pool direct
was_generated_by 0..1
ProvActivity		 Generation is the completion of production of a new entity by an activity ProvEntity
id 1
String		 A unique identifier for an entity MaterialSample, PhysicalEntity, Entity, NamedThing
iri 0..1
IriType		 An IRI for an entity MaterialSample, PhysicalEntity, Entity, NamedThing
category *
Uriorcurie		 Name of the high level ontology class in which this entity is categorized MaterialSample, PhysicalEntity, Entity, NamedThing
type *
String		 MaterialSample, PhysicalEntity, Entity, NamedThing
description 0..1
NarrativeText		 a human-readable description of an entity MaterialSample, PhysicalEntity, Entity, NamedThing
has_attribute *
Attribute		 connects any entity to an attribute MaterialSample, PhysicalEntity, Entity, NamedThing
deprecated 0..1
Boolean		 A boolean flag indicating that an entity is no longer considered current or v... MaterialSample, PhysicalEntity, Entity, NamedThing
provided_by *
String		 The value in this node property represents the knowledge provider that create... MaterialSample, PhysicalEntity, NamedThing
xref *
Uriorcurie		 A database cross reference or alternative identifier for a NamedThing or edge... MaterialSample, PhysicalEntity, NamedThing
full_name 0..1
LabelType		 a long-form human readable name for a thing MaterialSample, PhysicalEntity, NamedThing
synonym *
LabelType		 Alternate human-readable names for a thing MaterialSample, PhysicalEntity, NamedThing

Usages

used by used in type used
LibraryPool was_derived_from range LibraryAliquot
LibraryPooling used range LibraryAliquot

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type Mapped Value
self bican:LibraryAliquot
native bican:LibraryAliquot
exact NIMP:Library%20Aliquot

LinkML Source

Direct

name: LibraryAliquot
description: One library in the library pool. 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.
  The resulting demultiplexed fastq files will include the library aliquot name.  A
  given library may produce multiple library aliquots, which is done in the case of
  resequencing.  Each library aliquot will produce a set of fastq files.
in_subset:
- bican
- library_generation
from_schema: https://identifiers.org/brain-bican/library-generation-schema
exact_mappings:
- NIMP:Library%20Aliquot
is_a: material sample
mixins:
- ProvEntity
slots:
- was_derived_from
- name
slot_usage:
  was_derived_from:
    name: was_derived_from
    description: The input library from which the library aliquot was derived from.
    exact_mappings:
    - NIMP:has_parent
    domain_of:
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DigitalAsset
    - ProvEntity
    range: Library
  name:
    name: name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_aliquot_local_name
    description: One library in the library pool.  Each Library_aliquot_name 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.  The resulting demultiplexed fastq files will
      include the library_aliquot_name.
    exact_mappings:
    - NIMP:PD-XCXCCC35
    slot_uri: bican:34191bad-d167-4335-8224-ade897d3728e
    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
  category:
    name: category
    domain_of:
    - attribute
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    pattern: ^bican:[A-Z][A-Za-z]+$

Induced

name: LibraryAliquot
description: One library in the library pool. 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.
  The resulting demultiplexed fastq files will include the library aliquot name.  A
  given library may produce multiple library aliquots, which is done in the case of
  resequencing.  Each library aliquot will produce a set of fastq files.
in_subset:
- bican
- library_generation
from_schema: https://identifiers.org/brain-bican/library-generation-schema
exact_mappings:
- NIMP:Library%20Aliquot
is_a: material sample
mixins:
- ProvEntity
slot_usage:
  was_derived_from:
    name: was_derived_from
    description: The input library from which the library aliquot was derived from.
    exact_mappings:
    - NIMP:has_parent
    domain_of:
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DigitalAsset
    - ProvEntity
    range: Library
  name:
    name: name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_aliquot_local_name
    description: One library in the library pool.  Each Library_aliquot_name 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.  The resulting demultiplexed fastq files will
      include the library_aliquot_name.
    exact_mappings:
    - NIMP:PD-XCXCCC35
    slot_uri: bican:34191bad-d167-4335-8224-ade897d3728e
    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
  category:
    name: category
    domain_of:
    - attribute
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    pattern: ^bican:[A-Z][A-Za-z]+$
attributes:
  was_derived_from:
    name: was_derived_from
    description: The input library from which the library aliquot 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: LibraryAliquot
    domain_of:
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DigitalAsset
    - ProvEntity
    range: Library
  name:
    name: name
    definition_uri: https://w3id.org/biolink/vocab/name
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_aliquot_local_name
    description: One library in the library pool.  Each Library_aliquot_name 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.  The resulting demultiplexed fastq files will
      include the library_aliquot_name.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-XCXCCC35
    rank: 1000
    domain: entity
    slot_uri: bican:34191bad-d167-4335-8224-ade897d3728e
    alias: name
    owner: LibraryAliquot
    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
  was_generated_by:
    name: was_generated_by
    description: Generation is the completion of production of a new entity by an
      activity. This entity did not exist before generation and becomes available
      for usage after this generation.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    rank: 1000
    slot_uri: prov:wasGeneratedBy
    alias: was_generated_by
    owner: LibraryAliquot
    domain_of:
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryPool
    - DissectionRoiPolygon
    - ProvEntity
    range: ProvActivity
  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: LibraryAliquot
    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: LibraryAliquot
    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}
    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: LibraryAliquot
    domain_of:
    - attribute
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    is_class_field: true
    range: uriorcurie
    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: LibraryAliquot
    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: LibraryAliquot
    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: LibraryAliquot
    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: LibraryAliquot
    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: LibraryAliquot
    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: LibraryAliquot
    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: LibraryAliquot
    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: LibraryAliquot
    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