Class: LibraryPreparation

URI: nmdc:LibraryPreparation

classDiagram class LibraryPreparation click LibraryPreparation href "../LibraryPreparation" BiosampleProcessing <|-- LibraryPreparation click BiosampleProcessing href "../BiosampleProcessing" LibraryPreparation : alternative_identifiers LibraryPreparation : description LibraryPreparation : designated_class LibraryPreparation : end_date LibraryPreparation : has_failure_categorization LibraryPreparation --> "0..*" FailureCategorization : has_failure_categorization click FailureCategorization href "../FailureCategorization" LibraryPreparation : has_input LibraryPreparation --> "1..*" Biosample : has_input click Biosample href "../Biosample" LibraryPreparation : has_output LibraryPreparation --> "1..*" NamedThing : has_output click NamedThing href "../NamedThing" LibraryPreparation : id LibraryPreparation : instrument_name LibraryPreparation : library_preparation_kit LibraryPreparation : library_type LibraryPreparation --> "0..1" LibraryTypeEnum : library_type click LibraryTypeEnum href "../LibraryTypeEnum" LibraryPreparation : name LibraryPreparation : pcr_cycles LibraryPreparation : processing_institution LibraryPreparation --> "0..1" ProcessingInstitutionEnum : processing_institution click ProcessingInstitutionEnum href "../ProcessingInstitutionEnum" LibraryPreparation : protocol_link LibraryPreparation --> "0..1" Protocol : protocol_link click Protocol href "../Protocol" LibraryPreparation : qc_comment LibraryPreparation : qc_status LibraryPreparation --> "0..1" StatusEnum : qc_status click StatusEnum href "../StatusEnum" LibraryPreparation : start_date

Inheritance

NamedThing
- PlannedProcess
  - BiosampleProcessing
    - LibraryPreparation

Slots

Name	Cardinality and Range	Description	Inheritance
library_preparation_kit	0..1 String		direct
library_type	0..1 LibraryTypeEnum		direct
pcr_cycles	0..1 Integer		direct
has_input	1..* Biosample	An input to a process	BiosampleProcessing, PlannedProcess
designated_class	0..1 Uriorcurie		PlannedProcess
end_date	0..1 String	The date on which any process or activity was ended	PlannedProcess
has_output	1..* NamedThing	An output biosample to a processing step	PlannedProcess
processing_institution	0..1 ProcessingInstitutionEnum	The organization that processed the sample	PlannedProcess
protocol_link	0..1 Protocol		PlannedProcess
start_date	0..1 String	The date on which any process or activity was started	PlannedProcess
instrument_name	0..1 String	The name of the instrument that was used for processing the sample	PlannedProcess
qc_status	0..1 StatusEnum	Stores information about the result of a process (ie the process of sequencin...	PlannedProcess
qc_comment	0..1 String	Slot to store additional comments about laboratory or workflow output	PlannedProcess
has_failure_categorization	0..* FailureCategorization		PlannedProcess
id	1..1 Uriorcurie	A unique identifier for a thing	NamedThing
name	0..1 String	A human readable label for an entity	NamedThing
description	0..1 String	a human-readable description of a thing	NamedThing
alternative_identifiers	0..* Uriorcurie	A list of alternative identifiers for the entity	NamedThing

Usages

used by	used in	type	used
Database	library_preparation_set	range	LibraryPreparation
LibraryPreparation	library_type	domain	LibraryPreparation

Aliases

LibraryConstruction

Comments

OBI:0000711 specifies a DNA input (but not ONLY a DNA input)

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/nmdc/nmdc

Mappings

Mapping Type	Mapped Value
self	nmdc:LibraryPreparation
native	nmdc:LibraryPreparation
close	OBI:0000711

LinkML Source

Direct

name: LibraryPreparation
comments:
- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- LibraryConstruction
close_mappings:
- OBI:0000711
is_a: BiosampleProcessing
slots:
- library_preparation_kit
- library_type
- pcr_cycles
slot_usage:
  has_input:
    name: has_input
    domain_of:
    - BiosampleProcessing
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    required: true
  has_output:
    name: has_output
    domain_of:
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    required: true
  id:
    name: id
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - Activity
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}{id_version}{id_locus}'
      interpolated: true
class_uri: nmdc:LibraryPreparation

Induced

name: LibraryPreparation
comments:
- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- LibraryConstruction
close_mappings:
- OBI:0000711
is_a: BiosampleProcessing
slot_usage:
  has_input:
    name: has_input
    domain_of:
    - BiosampleProcessing
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    required: true
  has_output:
    name: has_output
    domain_of:
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    required: true
  id:
    name: id
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - Activity
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}{id_version}{id_locus}'
      interpolated: true
attributes:
  library_preparation_kit:
    name: library_preparation_kit
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: library_preparation_kit
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: string
  library_type:
    name: library_type
    title: library type
    examples:
    - value: DNA
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: LibraryPreparation
    alias: library_type
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: LibraryTypeEnum
  pcr_cycles:
    name: pcr_cycles
    from_schema: https://w3id.org/nmdc/nmdc
    exact_mappings:
    - OBI:0002475
    rank: 1000
    alias: pcr_cycles
    owner: LibraryPreparation
    domain_of:
    - LibraryPreparation
    range: integer
  has_input:
    name: has_input
    description: An input to a process.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: NamedThing
    multivalued: true
    alias: has_input
    owner: LibraryPreparation
    domain_of:
    - BiosampleProcessing
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    range: Biosample
    required: true
  designated_class:
    name: designated_class
    comments:
    - required on all instances in a polymorphic Database slot like planned_process_set
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    designates_type: true
    alias: designated_class
    owner: LibraryPreparation
    domain_of:
    - PlannedProcess
    range: uriorcurie
  end_date:
    name: end_date
    description: The date on which any process or activity was ended
    todos:
    - add date string validation pattern
    comments:
    - We are using string representations of dates until all components of our ecosystem
      can handle ISO 8610 dates
    - The date should be formatted as YYYY-MM-DD
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: end_date
    owner: LibraryPreparation
    domain_of:
    - PlannedProcess
    range: string
  has_output:
    name: has_output
    description: An output biosample to a processing step
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: NamedThing
    multivalued: true
    alias: has_output
    owner: LibraryPreparation
    domain_of:
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    range: NamedThing
    required: true
  processing_institution:
    name: processing_institution
    description: The organization that processed the sample.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: PlannedProcess
    alias: processing_institution
    owner: LibraryPreparation
    domain_of:
    - OmicsProcessing
    - PlannedProcess
    range: processing_institution_enum
  protocol_link:
    name: protocol_link
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: PlannedProcess
    alias: protocol_link
    owner: LibraryPreparation
    domain_of:
    - PlannedProcess
    range: Protocol
  start_date:
    name: start_date
    description: The date on which any process or activity was started
    todos:
    - add date string validation pattern
    comments:
    - We are using string representations of dates until all components of our ecosystem
      can handle ISO 8610 dates
    - The date should be formatted as YYYY-MM-DD
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: start_date
    owner: LibraryPreparation
    domain_of:
    - PlannedProcess
    range: string
  instrument_name:
    name: instrument_name
    description: The name of the instrument that was used for processing the sample.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: PlannedProcess
    alias: instrument_name
    owner: LibraryPreparation
    domain_of:
    - OmicsProcessing
    - PlannedProcess
    range: string
  qc_status:
    name: qc_status
    description: Stores information about the result of a process (ie the process
      of sequencing a library may have for qc_status of 'fail' if not enough data
      was generated)
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: qc_status
    owner: LibraryPreparation
    domain_of:
    - PlannedProcess
    - WorkflowExecutionActivity
    range: StatusEnum
  qc_comment:
    name: qc_comment
    description: Slot to store additional comments about laboratory or workflow output.
      For workflow output it may describe the particular workflow stage that failed.
      (ie Failed at call-stage due to a malformed fastq file).
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: qc_comment
    owner: LibraryPreparation
    domain_of:
    - PlannedProcess
    - WorkflowExecutionActivity
    range: string
  has_failure_categorization:
    name: has_failure_categorization
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: has_failure_categorization
    owner: LibraryPreparation
    domain_of:
    - PlannedProcess
    - WorkflowExecutionActivity
    range: FailureCategorization
  id:
    name: id
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    identifier: true
    alias: id
    owner: LibraryPreparation
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - Activity
    range: uriorcurie
    required: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
    structured_pattern:
      syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}{id_version}{id_locus}'
      interpolated: true
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: LibraryPreparation
    domain_of:
    - Protocol
    - NamedThing
    - PersonValue
    - Activity
    range: string
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: LibraryPreparation
    domain_of:
    - Study
    - NamedThing
    - ImageValue
    range: string
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: alternative_identifiers
    owner: LibraryPreparation
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - MetaboliteQuantification
    range: uriorcurie
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
class_uri: nmdc:LibraryPreparation