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Class: Protocol

A detailed set of steps for how to perform a specific assay. Protocols ensure reproducibility across laboratories. Contains universal slots; domain-specific details are in protocol subclasses (ImagingProtocol, StainingProtocol, etc.). Protocols can reference other protocols via sub_protocols to represent composite workflows (e.g., sample preparation, wash steps, or post-processing protocols that are shared across assays).

URI: OBI:0000272

 classDiagram
    class Protocol
    click Protocol href "../Protocol/"
      NamedThing <|-- Protocol
        click NamedThing href "../NamedThing/"


      Protocol <|-- ImagingProtocol
        click ImagingProtocol href "../ImagingProtocol/"
      Protocol <|-- StainingProtocol
        click StainingProtocol href "../StainingProtocol/"
      Protocol <|-- SpirometryProtocol
        click SpirometryProtocol href "../SpirometryProtocol/"
      Protocol <|-- MolecularAssayProtocol
        click MolecularAssayProtocol href "../MolecularAssayProtocol/"


      Protocol : description

      Protocol : equipment_required

      Protocol : id

      Protocol : institution

      Protocol : last_updated

      Protocol : name

      Protocol : protocol_author

      Protocol : protocol_type

      Protocol : protocol_version

      Protocol : publication_reference

      Protocol : quality_control_criteria

      Protocol : replicate_requirements

      Protocol : sub_protocols





        Protocol --> "*" Protocol : sub_protocols
        click Protocol href "../Protocol/"



      Protocol : validation_status

Inheritance

Slots

Name Cardinality and Range Description Inheritance
protocol_type 0..1
String		 The specific type of protocol direct
protocol_version 0..1
String		 Version of the protocol direct
equipment_required *
String		 Equipment required for this protocol direct
sub_protocols *
Protocol		 Other protocols that are part of this protocol's workflow direct
quality_control_criteria 0..1
String		 Quality control acceptance criteria direct
replicate_requirements 0..1
Integer		 Number of replicates required direct
protocol_author 0..1
String		 Author of the protocol direct
institution 0..1
String		 Institution where protocol was developed direct
publication_reference 0..1
String		 Reference to protocol publication direct
last_updated 0..1
Date		 Date protocol was last updated direct
validation_status 0..1
String		 Validation status of the protocol direct
id 1
Uriorcurie		 A unique identifier for the entity NamedThing
name 0..1
String		 A human-readable name for the entity NamedThing
description 0..1
String		 A detailed description of the entity NamedThing

Usages

used by used in type used
Container protocols range Protocol
Assay follows_protocols range Protocol
Protocol sub_protocols range Protocol
ImagingProtocol sub_protocols range Protocol
StainingProtocol sub_protocols range Protocol
SpirometryProtocol sub_protocols range Protocol
MolecularAssayProtocol sub_protocols range Protocol
CiliaryFunctionAssay follows_protocols range Protocol
ASLAssay follows_protocols range Protocol
MucociliaryClearanceAssay follows_protocols range Protocol
OxidativeStressAssay follows_protocols range Protocol
CFTRFunctionAssay follows_protocols range Protocol
EGFRSignalingAssay follows_protocols range Protocol
GobletCellAssay follows_protocols range Protocol
BALFSputumAssay follows_protocols range Protocol
LungFunctionAssay follows_protocols range Protocol
FoxJExpressionAssay follows_protocols range Protocol
GeneExpressionAssay follows_protocols range Protocol

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/EHS-Data-Standards/soma

Mappings

Mapping Type Mapped Value
self OBI:0000272
native soma:Protocol

LinkML Source

Direct

name: Protocol
description: A detailed set of steps for how to perform a specific assay. Protocols
  ensure reproducibility across laboratories. Contains universal slots; domain-specific
  details are in protocol subclasses (ImagingProtocol, StainingProtocol, etc.). Protocols
  can reference other protocols via sub_protocols to represent composite workflows
  (e.g., sample preparation, wash steps, or post-processing protocols that are shared
  across assays).
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: NamedThing
slots:
- protocol_type
- protocol_version
- equipment_required
- sub_protocols
- quality_control_criteria
- replicate_requirements
- protocol_author
- institution
- publication_reference
- last_updated
- validation_status
class_uri: OBI:0000272

Induced

name: Protocol
description: A detailed set of steps for how to perform a specific assay. Protocols
  ensure reproducibility across laboratories. Contains universal slots; domain-specific
  details are in protocol subclasses (ImagingProtocol, StainingProtocol, etc.). Protocols
  can reference other protocols via sub_protocols to represent composite workflows
  (e.g., sample preparation, wash steps, or post-processing protocols that are shared
  across assays).
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: NamedThing
attributes:
  protocol_type:
    name: protocol_type
    description: The specific type of protocol. Used to designate which concrete class
      (e.g., ImagingProtocol, StainingProtocol, SpirometryProtocol, MolecularAssayProtocol)
      is instantiated for polymorphic protocol slots.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    designates_type: true
    alias: protocol_type
    owner: Protocol
    domain_of:
    - Protocol
    range: string
  protocol_version:
    name: protocol_version
    description: Version of the protocol.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: protocol_version
    owner: Protocol
    domain_of:
    - Protocol
    range: string
  equipment_required:
    name: equipment_required
    description: Equipment required for this protocol.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: equipment_required
    owner: Protocol
    domain_of:
    - Protocol
    range: string
    multivalued: true
  sub_protocols:
    name: sub_protocols
    description: Other protocols that are part of this protocol's workflow. Use this
      to compose protocols from reusable steps (e.g., sample preparation, wash steps,
      fixation, post-processing). Any Protocol or Protocol subclass is valid.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: sub_protocols
    owner: Protocol
    domain_of:
    - Protocol
    range: Protocol
    multivalued: true
    inlined: true
    inlined_as_list: true
  quality_control_criteria:
    name: quality_control_criteria
    description: Quality control acceptance criteria.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: quality_control_criteria
    owner: Protocol
    domain_of:
    - Protocol
    range: string
  replicate_requirements:
    name: replicate_requirements
    description: Number of replicates required.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: replicate_requirements
    owner: Protocol
    domain_of:
    - Protocol
    range: integer
  protocol_author:
    name: protocol_author
    description: Author of the protocol.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: protocol_author
    owner: Protocol
    domain_of:
    - Protocol
    range: string
  institution:
    name: institution
    description: Institution where protocol was developed.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: institution
    owner: Protocol
    domain_of:
    - Protocol
    range: string
  publication_reference:
    name: publication_reference
    description: Reference to protocol publication.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: publication_reference
    owner: Protocol
    domain_of:
    - Protocol
    range: string
  last_updated:
    name: last_updated
    description: Date protocol was last updated.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: last_updated
    owner: Protocol
    domain_of:
    - Protocol
    range: date
  validation_status:
    name: validation_status
    description: Validation status of the protocol.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: validation_status
    owner: Protocol
    domain_of:
    - Protocol
    range: string
  id:
    name: id
    description: A unique identifier for the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    identifier: true
    alias: id
    owner: Protocol
    domain_of:
    - NamedThing
    - Unit
    - NamedEntity
    range: uriorcurie
    required: true
  name:
    name: name
    description: A human-readable name for the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    slot_uri: schema:name
    alias: name
    owner: Protocol
    domain_of:
    - NamedThing
    - Unit
    - NamedEntity
    range: string
  description:
    name: description
    description: A detailed description of the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    slot_uri: schema:description
    alias: description
    owner: Protocol
    domain_of:
    - NamedThing
    range: string
class_uri: OBI:0000272