Class: Planned Process (PlannedProcess)

Note

This is an abstract class and should not be instantiated directly.

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

Inheritance

NamedThing
- PlannedProcess

Slots

Name	Cardinality and Range	Description	Inheritance
has_input	* NamedThing	An input to a process	direct
has_output	* NamedThing	An output from a process	direct
processing_institution	0..1 ProcessingInstitutionEnum	The organization that processed the sample	direct
protocol_link	0..1 Protocol		direct
start_date	0..1 String	The date on which any process or activity was started	direct
end_date	0..1 String	The date on which any process or activity was ended	direct
qc_status	0..1 StatusEnum	Stores information about the result of a process (ie the process of sequencin...	direct
qc_comment	0..1 String	Slot to store additional comments about laboratory or workflow output	direct
has_failure_categorization	* FailureCategorization		direct
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
ProtocolExecution	has_process_parts	range	PlannedProcess

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	OBI:0000011
native	nmdc:PlannedProcess

LinkML Source

Direct

name: PlannedProcess
title: Planned Process
from_schema: https://w3id.org/nmdc/nmdc
is_a: NamedThing
abstract: true
slots:
- has_input
- has_output
- processing_institution
- protocol_link
- start_date
- end_date
- qc_status
- qc_comment
- has_failure_categorization
class_uri: OBI:0000011

Induced

name: PlannedProcess
title: Planned Process
from_schema: https://w3id.org/nmdc/nmdc
is_a: NamedThing
abstract: true
attributes:
  has_input:
    name: has_input
    description: An input to a process.
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - input
    rank: 1000
    alias: has_input
    owner: PlannedProcess
    domain_of:
    - PlannedProcess
    range: NamedThing
    multivalued: true
  has_output:
    name: has_output
    description: An output from a process.
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - output
    rank: 1000
    alias: has_output
    owner: PlannedProcess
    domain_of:
    - PlannedProcess
    range: NamedThing
    multivalued: 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: PlannedProcess
    domain_of:
    - PlannedProcess
    range: ProcessingInstitutionEnum
  protocol_link:
    name: protocol_link
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: protocol_link
    owner: PlannedProcess
    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: PlannedProcess
    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: PlannedProcess
    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: PlannedProcess
    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: PlannedProcess
    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: PlannedProcess
    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
    notes:
    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'
    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters
      will be accepted
    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked
      via per-class id slot usage assertions
    - minting authority shoulders should probably be enumerated and checked in the
      pattern
    examples:
    - value: nmdc:mgmag-00-x012.1_7_c1
      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    identifier: true
    alias: id
    owner: PlannedProcess
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: PlannedProcess
    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: PlannedProcess
    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: PlannedProcess
    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: PlannedProcess
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
class_uri: OBI:0000011