Skip to content

Class: LibraryConstruction

The process of constructing a library from input material (such as amplified cDNA or barcoded cell sample) derived from one or more cell samples. cDNA is fragmented into smaller pieces appropriate for sequencing and at the same time a library index barcode is incorporated to enable identification of library origin, allowing libraries to be pooled together for sequencing.

URI: bican:LibraryConstruction

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

Inheritance

Slots

Name Cardinality and Range Description Inheritance
used 0..1
ProvEntity or 
BarcodedCellSample or 
AmplifiedCdna		 The input barcoded cell sample or amplified cDNA from which the library was d... direct
method 0..1
LibraryTechnique		 Standardized nomenclature to describe the specific library method used direct
process_date 0..1
Date		 Date of library construction direct
input_quantity_ng 0..1
Float		 Amount of cDNA going into library construction in nanograms direct
set 0..1
String		 Library set, containing multiple library_names that were processed at the sam... direct
id 1
String		 A unique identifier for an entity Entity, Procedure, NamedThing
iri 0..1
IriType		 An IRI for an entity Entity, Procedure, NamedThing
category *
Curie		 Name of the high level ontology class in which this entity is categorized Entity, Procedure, NamedThing
type *
String		 Entity, Procedure, NamedThing
name 0..1
LabelType		 A human-readable name for an attribute or entity Entity, Procedure, NamedThing
description 0..1
NarrativeText		 a human-readable description of an entity Entity, Procedure, NamedThing
has_attribute *
Attribute		 connects any entity to an attribute Entity, Procedure, NamedThing
deprecated 0..1
Boolean		 A boolean flag indicating that an entity is no longer considered current or v... Entity, Procedure, NamedThing
provided_by *
String		 The value in this node property represents the knowledge provider that create... Procedure, NamedThing
xref *
Uriorcurie		 A database cross reference or alternative identifier for a NamedThing or edge... Procedure, NamedThing
full_name 0..1
LabelType		 a long-form human readable name for a thing Procedure, NamedThing
synonym *
LabelType		 Alternate human-readable names for a thing Procedure, NamedThing

Usages

used by used in type used
Library was_generated_by range LibraryConstruction

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: LibraryConstruction
description: The process of constructing a library from input material (such as amplified
  cDNA or barcoded cell sample) derived from one or more cell samples.  cDNA is fragmented
  into smaller pieces appropriate for sequencing and at the same time a library index
  barcode is incorporated to enable identification of library origin, allowing libraries
  to be pooled together for sequencing.
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 barcoded cell sample or amplified cDNA from which the library
      was derived from.
    domain_of:
    - DissectionRoiDelineation
    - TissueDissection
    - CellDissociation
    - CellEnrichment
    - EnrichedCellSampleSplitting
    - CellBarcoding
    - CdnaAmplification
    - LibraryConstruction
    - LibraryPooling
    - ProvActivity
    any_of:
    - range: BarcodedCellSample
    - range: AmplifiedCdna
attributes:
  method:
    name: method
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_technique
    description: Standardized nomenclature to describe the specific library method
      used.  This specifies the alignment method required for the library.  For example,
      10xV3.1 (for RNASeq single assay), 10xMult-GEX (for RNASeq multiome assay),
      and 10xMult-ATAC (for ATACSeq multiome assay).
    in_subset:
    - analysis
    - tracking
    - alignment
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-AJAJCN35
    slot_uri: bican:7b60d59e-fdd7-4b27-a2d4-cae9b69103a6
    alias: library method
    domain_of:
    - CellBarcoding
    - LibraryConstruction
    range: library_technique
  process_date:
    name: process_date
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_preparation_date
    description: Date of library construction.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-JCJCNM35
    slot_uri: bican:9c2f575d-1b64-451d-894f-656861afe07a
    alias: library creation date
    domain_of:
    - CellDissociation
    - CellEnrichment
    - CellBarcoding
    - CdnaAmplification
    - LibraryConstruction
    - LibraryPooling
    range: date
  input_quantity_ng:
    name: input_quantity_ng
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_input_ng
    description: Amount of cDNA going into library construction in nanograms.
    in_subset:
    - analysis
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-AFAFXP37
    rank: 1000
    slot_uri: bican:e4d31d97-722d-4771-a0e4-e6062190f2c1
    alias: library input ng
    domain_of:
    - LibraryConstruction
    range: float
  set:
    name: set
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_prep_set
    description: Library set, containing multiple library_names that were processed
      at the same time.
    in_subset:
    - analysis
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-PCPCVR50
    slot_uri: bican:b124ffa9-9134-4a61-a30d-bb191b2fc7fa
    alias: library prep set
    domain_of:
    - CdnaAmplification
    - LibraryConstruction
    range: string

Induced

name: LibraryConstruction
description: The process of constructing a library from input material (such as amplified
  cDNA or barcoded cell sample) derived from one or more cell samples.  cDNA is fragmented
  into smaller pieces appropriate for sequencing and at the same time a library index
  barcode is incorporated to enable identification of library origin, allowing libraries
  to be pooled together for sequencing.
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 barcoded cell sample or amplified cDNA from which the library
      was derived from.
    domain_of:
    - DissectionRoiDelineation
    - TissueDissection
    - CellDissociation
    - CellEnrichment
    - EnrichedCellSampleSplitting
    - CellBarcoding
    - CdnaAmplification
    - LibraryConstruction
    - LibraryPooling
    - ProvActivity
    any_of:
    - range: BarcodedCellSample
    - range: AmplifiedCdna
attributes:
  method:
    name: method
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_technique
    description: Standardized nomenclature to describe the specific library method
      used.  This specifies the alignment method required for the library.  For example,
      10xV3.1 (for RNASeq single assay), 10xMult-GEX (for RNASeq multiome assay),
      and 10xMult-ATAC (for ATACSeq multiome assay).
    in_subset:
    - analysis
    - tracking
    - alignment
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-AJAJCN35
    slot_uri: bican:7b60d59e-fdd7-4b27-a2d4-cae9b69103a6
    alias: library method
    owner: LibraryConstruction
    domain_of:
    - CellBarcoding
    - LibraryConstruction
    range: library_technique
  process_date:
    name: process_date
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_preparation_date
    description: Date of library construction.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-JCJCNM35
    slot_uri: bican:9c2f575d-1b64-451d-894f-656861afe07a
    alias: library creation date
    owner: LibraryConstruction
    domain_of:
    - CellDissociation
    - CellEnrichment
    - CellBarcoding
    - CdnaAmplification
    - LibraryConstruction
    - LibraryPooling
    range: date
  input_quantity_ng:
    name: input_quantity_ng
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_input_ng
    description: Amount of cDNA going into library construction in nanograms.
    in_subset:
    - analysis
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-AFAFXP37
    rank: 1000
    slot_uri: bican:e4d31d97-722d-4771-a0e4-e6062190f2c1
    alias: library input ng
    owner: LibraryConstruction
    domain_of:
    - LibraryConstruction
    range: float
  set:
    name: set
    local_names:
      NIMP:
        local_name_source: NIMP
        local_name_value: library_prep_set
    description: Library set, containing multiple library_names that were processed
      at the same time.
    in_subset:
    - analysis
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    exact_mappings:
    - NIMP:PD-PCPCVR50
    slot_uri: bican:b124ffa9-9134-4a61-a30d-bb191b2fc7fa
    alias: library prep set
    owner: LibraryConstruction
    domain_of:
    - CdnaAmplification
    - LibraryConstruction
    range: string
  used:
    name: used
    description: The input barcoded cell sample or amplified cDNA from which the library
      was derived from.
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    rank: 1000
    slot_uri: prov:used
    alias: used
    owner: LibraryConstruction
    domain_of:
    - DissectionRoiDelineation
    - TissueDissection
    - CellDissociation
    - CellEnrichment
    - EnrichedCellSampleSplitting
    - CellBarcoding
    - CdnaAmplification
    - LibraryConstruction
    - LibraryPooling
    - ProvActivity
    range: ProvEntity
    any_of:
    - range: BarcodedCellSample
    - range: AmplifiedCdna
  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: LibraryConstruction
    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: LibraryConstruction
    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: LibraryConstruction
    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: LibraryConstruction
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    multivalued: true
  name:
    name: name
    definition_uri: https://w3id.org/biolink/vocab/name
    description: A human-readable name for an attribute or entity.
    in_subset:
    - translator_minimal
    - samples
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    aliases:
    - label
    - display name
    - title
    mappings:
    - rdfs:label
    exact_mappings:
    - gff3:Name
    - gpi:DB_Object_Name
    narrow_mappings:
    - dct:title
    - WIKIDATA_PROPERTY:P1476
    rank: 1000
    domain: entity
    slot_uri: rdfs:label
    alias: name
    owner: LibraryConstruction
    domain_of:
    - attribute
    - entity
    - macromolecular machine mixin
    - Donor
    - BrainSlab
    - TissueSample
    - DissociatedCellSample
    - EnrichedCellSample
    - BarcodedCellSample
    - AmplifiedCdna
    - Library
    - LibraryAliquot
    - LibraryPool
    - DissectionRoiPolygon
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene or gene product
    - gene
    - genome
    range: label type
  description:
    name: description
    definition_uri: https://w3id.org/biolink/vocab/description
    description: a human-readable description of an entity
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/library-generation-schema
    aliases:
    - definition
    mappings:
    - dct:description
    exact_mappings:
    - IAO:0000115
    - skos:definitions
    narrow_mappings:
    - gff3:Description
    rank: 1000
    slot_uri: dct:description
    alias: description
    owner: LibraryConstruction
    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: LibraryConstruction
    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: LibraryConstruction
    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: LibraryConstruction
    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: LibraryConstruction
    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: LibraryConstruction
    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: LibraryConstruction
    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