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Class: MolecularAssayProtocol

Protocol for molecular biology assays (qRT-PCR, Western blot, ELISA). Captures detection method, normalization, primers, and platform details.

URI: soma:MolecularAssayProtocol

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

      MolecularAssayProtocol : antibodies_used

      MolecularAssayProtocol : description

      MolecularAssayProtocol : detection_method

      MolecularAssayProtocol : equipment_required

      MolecularAssayProtocol : id

      MolecularAssayProtocol : institution

      MolecularAssayProtocol : last_updated

      MolecularAssayProtocol : lysis_buffer

      MolecularAssayProtocol : name

      MolecularAssayProtocol : normalization_method

      MolecularAssayProtocol : platform

      MolecularAssayProtocol : primer_sequences

      MolecularAssayProtocol : protocol_author

      MolecularAssayProtocol : protocol_type

      MolecularAssayProtocol : protocol_version

      MolecularAssayProtocol : publication_reference

      MolecularAssayProtocol : quality_control_criteria

      MolecularAssayProtocol : reference_gene

      MolecularAssayProtocol : replicate_requirements

      MolecularAssayProtocol : sub_protocols





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



      MolecularAssayProtocol : validation_status

Inheritance

Slots

Name Cardinality and Range Description Inheritance
detection_method 0..1
String		 Detection method used (e direct
normalization_method 0..1
String		 Method used for data normalization direct
antibodies_used *
String		 Antibodies used in staining or detection direct
primer_sequences *
String		 Primer sequences used for PCR-based methods direct
reference_gene 0..1
String		 Reference/housekeeping gene used for normalization direct
lysis_buffer 0..1
String		 Lysis buffer used for sample preparation direct
platform 0..1
String		 Assay platform or instrument used (e direct
protocol_type 0..1
String		 The specific type of protocol Protocol
protocol_version 0..1
String		 Version of the protocol Protocol
equipment_required *
String		 Equipment required for this protocol Protocol
sub_protocols *
Protocol		 Other protocols that are part of this protocol's workflow Protocol
quality_control_criteria 0..1
String		 Quality control acceptance criteria Protocol
replicate_requirements 0..1
Integer		 Number of replicates required Protocol
protocol_author 0..1
String		 Author of the protocol Protocol
institution 0..1
String		 Institution where protocol was developed Protocol
publication_reference 0..1
String		 Reference to protocol publication Protocol
last_updated 0..1
Date		 Date protocol was last updated Protocol
validation_status 0..1
String		 Validation status of the protocol Protocol
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

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type Mapped Value
self soma:MolecularAssayProtocol
native soma:MolecularAssayProtocol

LinkML Source

Direct

name: MolecularAssayProtocol
description: Protocol for molecular biology assays (qRT-PCR, Western blot, ELISA).
  Captures detection method, normalization, primers, and platform details.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: Protocol
slots:
- detection_method
- normalization_method
- antibodies_used
- primer_sequences
- reference_gene
- lysis_buffer
- platform

Induced

name: MolecularAssayProtocol
description: Protocol for molecular biology assays (qRT-PCR, Western blot, ELISA).
  Captures detection method, normalization, primers, and platform details.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: Protocol
attributes:
  detection_method:
    name: detection_method
    description: Detection method used (e.g., flow cytometry, plate reader).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: detection_method
    owner: MolecularAssayProtocol
    domain_of:
    - StainingProtocol
    - MolecularAssayProtocol
    range: string
  normalization_method:
    name: normalization_method
    description: Method used for data normalization.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: normalization_method
    owner: MolecularAssayProtocol
    domain_of:
    - StainingProtocol
    - MolecularAssayProtocol
    range: string
  antibodies_used:
    name: antibodies_used
    description: Antibodies used in staining or detection.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: antibodies_used
    owner: MolecularAssayProtocol
    domain_of:
    - StainingProtocol
    - MolecularAssayProtocol
    range: string
    multivalued: true
  primer_sequences:
    name: primer_sequences
    description: Primer sequences used for PCR-based methods.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: primer_sequences
    owner: MolecularAssayProtocol
    domain_of:
    - MolecularAssayProtocol
    range: string
    multivalued: true
  reference_gene:
    name: reference_gene
    description: Reference/housekeeping gene used for normalization.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: reference_gene
    owner: MolecularAssayProtocol
    domain_of:
    - MolecularAssayProtocol
    range: string
  lysis_buffer:
    name: lysis_buffer
    description: Lysis buffer used for sample preparation.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: lysis_buffer
    owner: MolecularAssayProtocol
    domain_of:
    - MolecularAssayProtocol
    range: string
  platform:
    name: platform
    description: Assay platform or instrument used (e.g., QuantStudio, Illumina).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: platform
    owner: MolecularAssayProtocol
    domain_of:
    - MolecularAssayProtocol
    range: string
  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: MolecularAssayProtocol
    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: MolecularAssayProtocol
    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: MolecularAssayProtocol
    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: MolecularAssayProtocol
    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: MolecularAssayProtocol
    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: MolecularAssayProtocol
    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: MolecularAssayProtocol
    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: MolecularAssayProtocol
    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: MolecularAssayProtocol
    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: MolecularAssayProtocol
    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: MolecularAssayProtocol
    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: MolecularAssayProtocol
    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: MolecularAssayProtocol
    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: MolecularAssayProtocol
    domain_of:
    - NamedThing
    range: string