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Class: Collecting Biosamples From Site (CollectingBiosamplesFromSite)

URI: nmdc:CollectingBiosamplesFromSite

classDiagram class CollectingBiosamplesFromSite click CollectingBiosamplesFromSite href "../CollectingBiosamplesFromSite" PlannedProcess <|-- CollectingBiosamplesFromSite click PlannedProcess href "../PlannedProcess" CollectingBiosamplesFromSite : alternative_identifiers CollectingBiosamplesFromSite : description CollectingBiosamplesFromSite : end_date CollectingBiosamplesFromSite : has_failure_categorization CollectingBiosamplesFromSite --> "*" FailureCategorization : has_failure_categorization click FailureCategorization href "../FailureCategorization" CollectingBiosamplesFromSite : has_input CollectingBiosamplesFromSite --> "1..*" Site : has_input click Site href "../Site" CollectingBiosamplesFromSite : has_output CollectingBiosamplesFromSite --> "1..*" Biosample : has_output click Biosample href "../Biosample" CollectingBiosamplesFromSite : id CollectingBiosamplesFromSite : name CollectingBiosamplesFromSite : processing_institution CollectingBiosamplesFromSite --> "0..1" ProcessingInstitutionEnum : processing_institution click ProcessingInstitutionEnum href "../ProcessingInstitutionEnum" CollectingBiosamplesFromSite : protocol_link CollectingBiosamplesFromSite --> "0..1" Protocol : protocol_link click Protocol href "../Protocol" CollectingBiosamplesFromSite : qc_comment CollectingBiosamplesFromSite : qc_status CollectingBiosamplesFromSite --> "0..1" StatusEnum : qc_status click StatusEnum href "../StatusEnum" CollectingBiosamplesFromSite : start_date CollectingBiosamplesFromSite : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
has_input 1..*
Site		 An input to a process PlannedProcess
has_output 1..*
Biosample		 An output from a process 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
end_date 0..1
String		 The date on which any process or activity was ended 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 *
FailureCategorization		 PlannedProcess
id 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 *
Uriorcurie		 A list of alternative identifiers for the entity NamedThing
type 1
Uriorcurie		 the class_uri of the class that has been instantiated NamedThing

Usages

used by used in type used
Database collecting_biosamples_from_site_set range CollectingBiosamplesFromSite

Comments

  • this illustrates implementing a Biosample relation with a process class

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self nmdc:CollectingBiosamplesFromSite
native nmdc:CollectingBiosamplesFromSite
close OBI:0000744

LinkML Source

Direct

name: CollectingBiosamplesFromSite
title: Collecting Biosamples From Site
comments:
- this illustrates implementing a Biosample relation with a process class
from_schema: https://w3id.org/nmdc/nmdc
close_mappings:
- OBI:0000744
is_a: PlannedProcess
slot_usage:
  has_input:
    name: has_input
    domain_of:
    - PlannedProcess
    range: Site
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$'
      interpolated: true
  has_output:
    name: has_output
    domain_of:
    - PlannedProcess
    range: Biosample
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'
      interpolated: true
  id:
    name: id
    domain_of:
    - NamedThing
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$'
      interpolated: true
class_uri: nmdc:CollectingBiosamplesFromSite

Induced

name: CollectingBiosamplesFromSite
title: Collecting Biosamples From Site
comments:
- this illustrates implementing a Biosample relation with a process class
from_schema: https://w3id.org/nmdc/nmdc
close_mappings:
- OBI:0000744
is_a: PlannedProcess
slot_usage:
  has_input:
    name: has_input
    domain_of:
    - PlannedProcess
    range: Site
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$'
      interpolated: true
  has_output:
    name: has_output
    domain_of:
    - PlannedProcess
    range: Biosample
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'
      interpolated: true
  id:
    name: id
    domain_of:
    - NamedThing
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$'
      interpolated: true
attributes:
  has_input:
    name: has_input
    description: An input to a process.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: has_input
    owner: CollectingBiosamplesFromSite
    domain_of:
    - PlannedProcess
    range: Site
    required: true
    multivalued: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$'
      interpolated: true
  has_output:
    name: has_output
    description: An output from a process.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: has_output
    owner: CollectingBiosamplesFromSite
    domain_of:
    - PlannedProcess
    range: Biosample
    required: true
    multivalued: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'
      interpolated: true
  processing_institution:
    name: processing_institution
    description: The organization that processed the sample.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: processing_institution
    owner: CollectingBiosamplesFromSite
    domain_of:
    - PlannedProcess
    range: ProcessingInstitutionEnum
  protocol_link:
    name: protocol_link
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: protocol_link
    owner: CollectingBiosamplesFromSite
    domain_of:
    - PlannedProcess
    - Study
    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: CollectingBiosamplesFromSite
    domain_of:
    - PlannedProcess
    range: string
  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: CollectingBiosamplesFromSite
    domain_of:
    - 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: CollectingBiosamplesFromSite
    domain_of:
    - PlannedProcess
    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: CollectingBiosamplesFromSite
    domain_of:
    - PlannedProcess
    range: string
  has_failure_categorization:
    name: has_failure_categorization
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: has_failure_categorization
    owner: CollectingBiosamplesFromSite
    domain_of:
    - PlannedProcess
    range: FailureCategorization
    multivalued: true
    inlined: true
    inlined_as_list: true
  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: CollectingBiosamplesFromSite
    domain_of:
    - NamedThing
    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}:clsite-{id_shoulder}-{id_blade}$'
      interpolated: true
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: CollectingBiosamplesFromSite
    domain_of:
    - PersonValue
    - NamedThing
    - Protocol
    range: string
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: CollectingBiosamplesFromSite
    domain_of:
    - ImageValue
    - NamedThing
    range: string
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: alternative_identifiers
    owner: CollectingBiosamplesFromSite
    domain_of:
    - MetaboliteIdentification
    - NamedThing
    range: uriorcurie
    multivalued: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  type:
    name: type
    description: the class_uri of the class that has been instantiated
    notes:
    - replaces legacy nmdc:type slot
    - makes it easier to read example data files
    - required for polymorphic MongoDB collections
    examples:
    - value: nmdc:Biosample
    - value: nmdc:Study
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://github.com/microbiomedata/nmdc-schema/issues/1048
    - https://github.com/microbiomedata/nmdc-schema/issues/1233
    - https://github.com/microbiomedata/nmdc-schema/issues/248
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: CollectingBiosamplesFromSite
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
class_uri: nmdc:CollectingBiosamplesFromSite