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Class: Protocol

URI: nmdc:Protocol

classDiagram class Protocol click Protocol href "../Protocol" Protocol : analysis_type Protocol --> "* _recommended_" AnalysisTypeEnum : analysis_type click AnalysisTypeEnum href "../AnalysisTypeEnum" Protocol : description Protocol : name Protocol : protocol_for Protocol --> "0..1" ProtocolForEnum : protocol_for click ProtocolForEnum href "../ProtocolForEnum" Protocol : type Protocol : url

Slots

Name Cardinality and Range Description Inheritance
url 0..1
String		 direct
name 0..1
String		 A human readable label for an entity direct
type 1
Uriorcurie		 the class_uri of the class that has been instantiated direct
description 0..1
String		 a human-readable description of a thing direct
protocol_for 0..1
ProtocolForEnum		 The type of planned process that the protocol describes direct
analysis_type * recommended
AnalysisTypeEnum		 Select all the data types associated or available for this biosample direct

Usages

used by used in type used
NucleotideSequencing protocol_link range Protocol
MassSpectrometry protocol_link range Protocol
Configuration protocol_link range Protocol
MassSpectrometryConfiguration protocol_link range Protocol
ChromatographyConfiguration protocol_link range Protocol
Pooling protocol_link range Protocol
Extraction protocol_link range Protocol
LibraryPreparation protocol_link range Protocol
CollectingBiosamplesFromSite protocol_link range Protocol
SubSamplingProcess protocol_link range Protocol
MixingProcess protocol_link range Protocol
FiltrationProcess protocol_link range Protocol
StorageProcess protocol_link range Protocol
ChromatographicSeparationProcess protocol_link range Protocol
DissolvingProcess protocol_link range Protocol
ProtocolExecution protocol_link range Protocol
MetagenomeSequencing protocol_link range Protocol
ChemicalConversionProcess protocol_link range Protocol
AnnotatingWorkflow protocol_link range Protocol
MetagenomeAnnotation protocol_link range Protocol
MaterialProcessing protocol_link range Protocol
PlannedProcess protocol_link range Protocol
Study protocol_link range Protocol
DataEmitterProcess protocol_link range Protocol
DataGeneration protocol_link range Protocol
WorkflowExecution protocol_link range Protocol
MetagenomeAssembly protocol_link range Protocol
MetatranscriptomeAssembly protocol_link range Protocol
MetatranscriptomeAnnotation protocol_link range Protocol
MetatranscriptomeExpressionAnalysis protocol_link range Protocol
MagsAnalysis protocol_link range Protocol
ReadQcAnalysis protocol_link range Protocol
ReadBasedTaxonomyAnalysis protocol_link range Protocol
MetabolomicsAnalysis protocol_link range Protocol
MetaproteomicsAnalysis protocol_link range Protocol
NomAnalysis protocol_link range Protocol

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value

LinkML Source

Direct

name: Protocol
from_schema: https://w3id.org/nmdc/nmdc
slots:
- url
- name
- type
- description
- protocol_for
- analysis_type
class_uri: nmdc:Protocol

Induced

name: Protocol
from_schema: https://w3id.org/nmdc/nmdc
attributes:
  url:
    name: url
    notes:
    - See issue 207 - this clashes with the mixs field
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: url
    owner: Protocol
    domain_of:
    - ImageValue
    - Protocol
    - DataObject
    range: string
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: Protocol
    domain_of:
    - PersonValue
    - NamedThing
    - Protocol
    range: string
  type:
    name: type
    description: the class_uri of the class that has been instantiated
    notes:
    - 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
    structured_aliases:
      workflow_execution_class:
        literal_form: workflow_execution_class
        predicate: NARROW_SYNONYM
        contexts:
        - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: Protocol
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - PeptideQuantification
    - ProteinQuantification
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
  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: Protocol
    domain_of:
    - ImageValue
    - NamedThing
    - Protocol
    range: string
  protocol_for:
    name: protocol_for
    description: The type of planned process that the protocol describes.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: protocol_for
    owner: Protocol
    domain_of:
    - Protocol
    range: ProtocolForEnum
  analysis_type:
    name: analysis_type
    description: Select all the data types associated or available for this biosample
    title: analysis/data type
    comments:
    - MIxS:investigation_type was included as a `see_also` but that term doesn't resolve
      any more
    examples:
    - value: metagenomics; metabolomics; metaproteomics
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 3
    alias: analysis_type
    owner: Protocol
    domain_of:
    - Biosample
    - Protocol
    slot_group: Sample ID
    range: AnalysisTypeEnum
    recommended: true
    multivalued: true
class_uri: nmdc:Protocol