Class: ExecutableProtocol

A concrete, orderable protocol at a named provider that would execute some or all of a proposed experiment, together with what it needs as input and which pathograph nodes it would return a measurement on.

URI: dismech:class/ExecutableProtocol

 classDiagram
    class ExecutableProtocol
    click ExecutableProtocol href "../../classes/ExecutableProtocol/"
      ExecutableProtocol : description

      ExecutableProtocol : evidence





        ExecutableProtocol --> "*" EvidenceItem : evidence
        click EvidenceItem href "../../classes/EvidenceItem/"



      ExecutableProtocol : inputs_required

      ExecutableProtocol : measures

      ExecutableProtocol : name

      ExecutableProtocol : notes

      ExecutableProtocol : protocol_id

      ExecutableProtocol : protocol_url

      ExecutableProtocol : provider

      ExecutableProtocol : retrieved_date

      ExecutableProtocol : venue_type





        ExecutableProtocol --> "0..1" ExecutionVenueEnum : venue_type
        click ExecutionVenueEnum href "../../enums/ExecutionVenueEnum/"

Slots

Name	Cardinality and Range	Description	Inheritance
name	1 String	The protocol's name as the provider publishes it, copied exactly	direct
description	0..1 String	What this protocol would contribute to the experiment, and why it is the righ...	direct
provider	1 String	The organisation that would execute the protocol, named as that organisation ...	direct
venue_type	0..1 ExecutionVenueEnum	Broad kind of facility that would execute the protocol	direct
protocol_id	0..1 String	The provider's own stable identifier for the protocol — a catalogue handle, s...	direct
protocol_url	0..1 Uri	The provider's own page for this protocol	direct
measures	* String	Entity references for the pathograph nodes, phenotypes, or other modeled obje...	direct
inputs_required	0..1 String	What the requester must supply for the protocol to run — DNA sequences as a C...	direct
retrieved_date	0..1 Date	Date the provider's catalogue was read for the identifier recorded here	direct
evidence	* EvidenceItem	Literature or provider documentation supporting the protocol's suitability or...	direct
notes	0..1 String		direct

Usages

used by	used in	type	used
Experiment	executable_protocols	range	ExecutableProtocol

Comments

• Reached from Experiment.executable_protocols. A proposed experiment in a KNOWLEDGE_GAP discussion states what should be measured; this records that a service exists which would measure it, so the feasibility of a gap is readable from the entry rather than re-researched each time somebody asks what it would take to close it.
• Recording a protocol is a feasibility note, not a plan. It does not propose, authorise, fund, or commit to running anything, and it is not evidence about the disease: nothing here asserts a result.
• provider plus protocol_id is the identity of the service and venue_type is the durable classification. Deliberately records no price, turnaround, or throughput: those are commercial terms that go out of date without any signal that they have, and reproducing a vendor's price list is not this knowledge base's job. Cost and scheduling are settled with the provider at the point of ordering.

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/monarch-initiative/dismech

Mappings

Mapping Type	Mapped Value
self	dismech:ExecutableProtocol
native	dismech:ExecutableProtocol

LinkML Source

Direct

name: ExecutableProtocol
description: A concrete, orderable protocol at a named provider that would execute
  some or all of a proposed experiment, together with what it needs as input and which
  pathograph nodes it would return a measurement on.
comments:
- Reached from `Experiment.executable_protocols`. A proposed experiment in a `KNOWLEDGE_GAP`
  discussion states what *should* be measured; this records that a service exists
  which would measure it, so the feasibility of a gap is readable from the entry rather
  than re-researched each time somebody asks what it would take to close it.
- 'Recording a protocol is a feasibility note, not a plan. It does not propose, authorise,
  fund, or commit to running anything, and it is not evidence about the disease: nothing
  here asserts a result.'
- '`provider` plus `protocol_id` is the identity of the service and `venue_type` is
  the durable classification. Deliberately records no price, turnaround, or throughput:
  those are commercial terms that go out of date without any signal that they have,
  and reproducing a vendor''s price list is not this knowledge base''s job. Cost and
  scheduling are settled with the provider at the point of ordering.'
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- description
- provider
- venue_type
- protocol_id
- protocol_url
- measures
- inputs_required
- retrieved_date
- evidence
- notes
slot_usage:
  name:
    name: name
    description: The protocol's name as the provider publishes it, copied exactly.
      A summary of what it would be used for belongs in `description`.
    required: true
  provider:
    name: provider
    required: true
  description:
    name: description
    description: What this protocol would contribute to the experiment, and why it
      is the right one — the curator's reasoning, not the provider's marketing copy.
  retrieved_date:
    name: retrieved_date
    description: 'Date the provider''s catalogue was read for the identifier recorded
      here. Record it alongside `protocol_id` or `protocol_url`, because a provider''s
      catalogue changes without notice and without a version, so an identifier with
      no retrieval date cannot be aged: a reader has no way to tell a current handle
      from one that was renamed two years ago.'
  evidence:
    name: evidence
    description: 'Literature or provider documentation supporting the protocol''s
      suitability or its precedent for this measurement. Not a place for results:
      this object describes a protocol that has not been run.'
    recommended: false

Induced

name: ExecutableProtocol
description: A concrete, orderable protocol at a named provider that would execute
  some or all of a proposed experiment, together with what it needs as input and which
  pathograph nodes it would return a measurement on.
comments:
- Reached from `Experiment.executable_protocols`. A proposed experiment in a `KNOWLEDGE_GAP`
  discussion states what *should* be measured; this records that a service exists
  which would measure it, so the feasibility of a gap is readable from the entry rather
  than re-researched each time somebody asks what it would take to close it.
- 'Recording a protocol is a feasibility note, not a plan. It does not propose, authorise,
  fund, or commit to running anything, and it is not evidence about the disease: nothing
  here asserts a result.'
- '`provider` plus `protocol_id` is the identity of the service and `venue_type` is
  the durable classification. Deliberately records no price, turnaround, or throughput:
  those are commercial terms that go out of date without any signal that they have,
  and reproducing a vendor''s price list is not this knowledge base''s job. Cost and
  scheduling are settled with the provider at the point of ordering.'
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  name:
    name: name
    description: The protocol's name as the provider publishes it, copied exactly.
      A summary of what it would be used for belongs in `description`.
    required: true
  provider:
    name: provider
    required: true
  description:
    name: description
    description: What this protocol would contribute to the experiment, and why it
      is the right one — the curator's reasoning, not the provider's marketing copy.
  retrieved_date:
    name: retrieved_date
    description: 'Date the provider''s catalogue was read for the identifier recorded
      here. Record it alongside `protocol_id` or `protocol_url`, because a provider''s
      catalogue changes without notice and without a version, so an identifier with
      no retrieval date cannot be aged: a reader has no way to tell a current handle
      from one that was renamed two years ago.'
  evidence:
    name: evidence
    description: 'Literature or provider documentation supporting the protocol''s
      suitability or its precedent for this measurement. Not a place for results:
      this object describes a protocol that has not been run.'
    recommended: false
attributes:
  name:
    name: name
    description: The protocol's name as the provider publishes it, copied exactly.
      A summary of what it would be used for belongs in `description`.
    examples:
    - value: Adolescent Nephronophthisis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: ExecutableProtocol
    domain_of:
    - GenomicRegion
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - SeverityTier
    - DifferentialDiagnosis
    - Subtype
    - ReferenceRangeBand
    - SurrogateEndpointCollection
    - GeneClassificationCollection
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ComorbidityAssociation
    - Grouping
    - ModuleCollection
    range: string
    required: true
  description:
    name: description
    description: What this protocol would contribute to the experiment, and why it
      is the right one — the curator's reasoning, not the provider's marketing copy.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: ExecutableProtocol
    domain_of:
    - Descriptor
    - DietaryModification
    - GenomicRegion
    - GeneticContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - EnvironmentalMechanismTarget
    - ModelDivergence
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - SurrogateEndpointCollection
    - GeneClassificationCollection
    - ProteinStructure
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - HistopathologyFinding
    - ImagingFinding
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - TreatmentEffectModifier
    - DeliverySystem
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - VariantPopulationEffect
    - FunctionalEffect
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ConditionDescriptor
    - GOEnrichment
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    - Grouping
    - GroupingCriteria
    - LogicalCriterion
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: string
  provider:
    name: provider
    description: 'The organisation that would execute the protocol, named as that
      organisation names itself (for example `Ginkgo Cloud Lab`, `Emerald Cloud Lab`,
      `UNC Lineberger High-Throughput Screening Facility`). Deliberately free text
      rather than an enum: the set of providers is open and changes without warning,
      so an enum would need a schema PR per new laboratory. The durable classification
      is `venue_type`.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: provider
    owner: ExecutableProtocol
    domain_of:
    - ExecutableProtocol
    range: string
    required: true
  venue_type:
    name: venue_type
    description: Broad kind of facility that would execute the protocol.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: venue_type
    owner: ExecutableProtocol
    domain_of:
    - ExecutableProtocol
    range: ExecutionVenueEnum
  protocol_id:
    name: protocol_id
    description: The provider's own stable identifier for the protocol — a catalogue
      handle, service code, or SKU — copied exactly as the provider publishes it,
      never composed or tidied. This is what an order would name, so a reworded value
      is not an identifier.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: protocol_id
    owner: ExecutableProtocol
    domain_of:
    - ExecutableProtocol
    range: string
  protocol_url:
    name: protocol_url
    description: The provider's own page for this protocol.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: protocol_url
    owner: ExecutableProtocol
    domain_of:
    - ExecutableProtocol
    range: uri
  measures:
    name: measures
    description: 'Entity references for the pathograph nodes, phenotypes, or other
      modeled objects this protocol would return a measurement on. Uses the same hash-anchor
      grammar as `attaches_to`, and every value must use it. This records *what the
      protocol can observe*, which is a weaker claim than `would_support` / `would_refute`:
      a protocol can measure a node without any one result adjudicating the hypothesis
      attached to it.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: measures
    owner: ExecutableProtocol
    domain_of:
    - ExecutableProtocol
    range: string
    multivalued: true
  inputs_required:
    name: inputs_required
    description: What the requester must supply for the protocol to run — DNA sequences
      as a CSV, a purified antigen, a cell line, a compound plate. Records the input
      that is the requester's problem rather than the provider's, since that is usually
      what decides whether a proposal is actually reachable.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: inputs_required
    owner: ExecutableProtocol
    domain_of:
    - ExecutableProtocol
    range: string
  retrieved_date:
    name: retrieved_date
    description: 'Date the provider''s catalogue was read for the identifier recorded
      here. Record it alongside `protocol_id` or `protocol_url`, because a provider''s
      catalogue changes without notice and without a version, so an identifier with
      no retrieval date cannot be aged: a reader has no way to tell a current handle
      from one that was renamed two years ago.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: retrieved_date
    owner: ExecutableProtocol
    domain_of:
    - ExecutableProtocol
    - SurrogateEndpoint
    - SurrogateEndpointCollection
    - GeneClassificationCollection
    range: date
  evidence:
    name: evidence
    description: 'Literature or provider documentation supporting the protocol''s
      suitability or its precedent for this measurement. Not a place for results:
      this object describes a protocol that has not been run.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: ExecutableProtocol
    domain_of:
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - EnvironmentalMechanismTarget
    - ModelDivergence
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - ReferenceRange
    - SurrogateEndpoint
    - ExternalAssertion
    - Finding
    - Prevalence
    - GeneCaseFraction
    - GeneDiseaseValidityAssertion
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - TreatmentEffectModifier
    - DeliverySystem
    - InfectiousAgent
    - Transmission
    - Diagnosis
    - Inheritance
    - Variant
    - VariantPopulationEffect
    - ModelingConsideration
    - ClassificationAssignment
    - Definition
    - AlgorithmValidationStatus
    - CriteriaSet
    - AssociationSignal
    - AssociationStatistics
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    - Discussion
    - GroupingCriteria
    - GroupingMember
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: EvidenceItem
    recommended: false
    multivalued: true
    inlined: true
    inlined_as_list: true
  notes:
    name: notes
    examples:
    - value: Contagious stage where symptoms appear and the bacteria can be spread
        to others.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: notes
    owner: ExecutableProtocol
    domain_of:
    - GeneticContext
    - OnsetDescriptor
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - ReferenceRange
    - SurrogateEndpoint
    - SurrogateEndpointCollection
    - GeneClassification
    - GeneClassificationCollection
    - ExternalAssertion
    - TrackedIssue
    - Prevalence
    - GeneCaseFraction
    - GeneDiseaseValidityAssertion
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - TreatmentEffectModifier
    - DeliverySystem
    - Transmission
    - Diagnosis
    - VariantPopulationEffect
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - TermMapping
    - MappingConsistency
    - ComorbidityAssociation
    - AssociationSignal
    - AssociationMetric
    - AssociationStatistics
    - MechanisticHypothesis
    - Discussion
    - Grouping
    - GroupingCriteria
    - GroupingMember
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: string