Reference·Classes

Class: Provenance

W3C PROV-O aligned provenance ABOUT the artifact that carries it — reusable on any entity (Network, TimeSeries, Dynamics, …), which is why it holds no identity of its own: the parent supplies that. The identified prov:Entity a standalone provenance record names is ResultEntity, which carries one of these.

Carried by the frozen spec beside a result container, this is the whole record of the run: activities says what was executed and when, environment says on what machine and against which package versions, and digest checksums what came out. None of that is derivable from a recipe, which is why it is recorded — and all of it travels with the artifact it describes rather than in a parallel directory that has to be kept in step.

URI: tvbo:Provenance

 classDiagram
    class Provenance
    click Provenance href "./Provenance.html"
      Provenance : activities
        
          
    
        
        
        Provenance --> "*" Activity : activities
        click Activity href "./Activity.html"
    

        
      Provenance : date_created
        
          
    
        
        
        Provenance --> "0..1" String : date_created
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      Provenance : derived_from
        
          
    
        
        
        Provenance --> "0..1" String : derived_from
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      Provenance : digest
        
          
    
        
        
        Provenance --> "*" Digest : digest
        click Digest href "./Digest.html"
    

        
      Provenance : environment
        
          
    
        
        
        Provenance --> "0..1" SoftwareEnvironment : environment
        click SoftwareEnvironment href "./SoftwareEnvironment.html"
    

        
      Provenance : experiment_yaml_hash
        
          
    
        
        
        Provenance --> "0..1" String : experiment_yaml_hash
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      Provenance : generated_by
        
          
    
        
        
        Provenance --> "0..1" String : generated_by
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      Provenance : inputs
        
          
    
        
        
        Provenance --> "*" ReferenceFingerprint : inputs
        click ReferenceFingerprint href "./ReferenceFingerprint.html"
    

        
      Provenance : license
        
          
    
        
        
        Provenance --> "0..1" String : license
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      Provenance : outputs
        
          
    
        
        
        Provenance --> "*" String : outputs
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      Provenance : references
        
          
    
        
        
        Provenance --> "*" String : references
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      

Class Properties

Property	Value
Class URI	tvbo:Provenance

Slots

Name	Cardinality and Range	Description	Inheritance
derived_from	0..1 xsd:string		direct
references	* xsd:string		direct
environment	0..1 SoftwareEnvironment	The machine and the resolved package set the run actually loaded, carried in …	direct
date_created	0..1 xsd:string	ISO 8601 (prov:generatedAtTime)	direct
outputs	* xsd:string	The data variables the container actually holds, read off it when the record …	direct
license	0..1 xsd:string		direct
generated_by	0..1 xsd:string	Software/agent identifier: the prov:Agent this artifact is attributed to	direct
experiment_yaml_hash	0..1 xsd:string	SHA-256 hex digest of the normalised experiment YAML that produced this artif…	direct
digest	* Digest	Checksums of the artifact itself, keyed by function name	direct
activities	* Activity	The runs that produced this artifact, serialized to BEP028’s activity record	direct
inputs	* ReferenceFingerprint	Per-input fingerprints for cache invalidation	direct

Usages

used by	used in	type	used
Figure	provenance	range	Provenance
ResultEntity	provenance	range	Provenance
ExperimentResultSidecar	provenance	range	Provenance
Phenotype	provenance	range	Provenance
Network	provenance	range	Provenance
SimulationExperiment	provenance	range	Provenance

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/tvbo

Mappings

Mapping Type	Mapped Value
self	tvbo:Provenance
native	tvbo:Provenance

LinkML Source

Direct

name: Provenance
description: 'W3C PROV-O aligned provenance ABOUT the artifact that carries it — reusable
  on any entity (Network, TimeSeries, Dynamics, ...), which is why it holds no identity
  of its own: the parent supplies that. The identified ``prov:Entity`` a standalone
  provenance record names is ``ResultEntity``, which carries one of these.

  Carried by the frozen spec beside a result container, this is the whole record of
  the run: ``activities`` says what was executed and when, ``environment`` says on
  what machine and against which package versions, and ``digest`` checksums what came
  out. None of that is derivable from a recipe, which is why it is recorded — and
  all of it travels with the artifact it describes rather than in a parallel directory
  that has to be kept in step.'
from_schema: https://w3id.org/tvbo
slots:
- derived_from
- references
- environment
slot_usage:
  environment:
    name: environment
    description: 'The machine and the resolved package set the run actually loaded,
      carried in full rather than by name: this record travels with one container''s
      sidecar, so a reference to an environment defined elsewhere would point outside
      the only file a reader has.'
    inlined: true
attributes:
  date_created:
    name: date_created
    description: ISO 8601 (prov:generatedAtTime)
    from_schema: https://w3id.org/tvbo
    domain_of:
    - SimulationTool
    - Provenance
    range: string
  outputs:
    name: outputs
    description: The data variables the container actually holds, read off it when
      the record is written rather than predicted from the spec, so a run that recorded
      less than it declared is visible here. The one fact in this record that the
      recipe beside it cannot supply.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Provenance
    - ResultEntity
    range: string
    multivalued: true
  license:
    name: license
    from_schema: https://w3id.org/tvbo
    domain_of:
    - CommonCoordinateSpace
    - SoftwarePackage
    - SoftwareRequirement
    - Provenance
    range: string
  generated_by:
    name: generated_by
    description: 'Software/agent identifier: the prov:Agent this artifact is attributed
      to.'
    from_schema: https://w3id.org/tvbo
    close_mappings:
    - prov:wasAttributedTo
    rank: 1000
    domain_of:
    - Provenance
    range: string
  experiment_yaml_hash:
    name: experiment_yaml_hash
    description: SHA-256 hex digest of the normalised experiment YAML that produced
      this artifact. Used by the cross-experiment cache (see :class:`SimulationStudy.from_file`)
      to detect when a cached upstream result has gone stale because the experiment's
      spec was edited. Computed as ``hashlib.sha256(yaml.safe_dump(normalized_yaml).encode()).hexdigest()``
      over the fully resolved (post-``!include``) experiment block.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Provenance
    range: string
  digest:
    name: digest
    description: Checksums of the artifact itself, keyed by function name. BEP028's
      ``Digest``, and distinct from ``experiment_yaml_hash``, which digests the spec
      that produced the artifact rather than the artifact.
    from_schema: https://w3id.org/tvbo
    exact_mappings:
    - prov:value
    rank: 1000
    domain_of:
    - Provenance
    range: Digest
    multivalued: true
    inlined: true
  activities:
    name: activities
    description: The runs that produced this artifact, serialized to BEP028's activity
      record. Each names the command, the software that carried it out and what it
      consumed.
    from_schema: https://w3id.org/tvbo
    exact_mappings:
    - prov:wasGeneratedBy
    rank: 1000
    domain_of:
    - Provenance
    range: Activity
    multivalued: true
    inlined: true
    inlined_as_list: true
  inputs:
    name: inputs
    description: Per-input fingerprints for cache invalidation. Each entry records
      the IRI + dotted-field path of an ``aux_data`` reference plus the (mtime, size,
      sha256) of the underlying file at the time the artifact was produced. A downstream
      cache hit requires every fingerprint to match the current file state.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Provenance
    range: ReferenceFingerprint
    multivalued: true
    inlined_as_list: true
class_uri: tvbo:Provenance

Induced

name: Provenance
description: 'W3C PROV-O aligned provenance ABOUT the artifact that carries it — reusable
  on any entity (Network, TimeSeries, Dynamics, ...), which is why it holds no identity
  of its own: the parent supplies that. The identified ``prov:Entity`` a standalone
  provenance record names is ``ResultEntity``, which carries one of these.

  Carried by the frozen spec beside a result container, this is the whole record of
  the run: ``activities`` says what was executed and when, ``environment`` says on
  what machine and against which package versions, and ``digest`` checksums what came
  out. None of that is derivable from a recipe, which is why it is recorded — and
  all of it travels with the artifact it describes rather than in a parallel directory
  that has to be kept in step.'
from_schema: https://w3id.org/tvbo
slot_usage:
  environment:
    name: environment
    description: 'The machine and the resolved package set the run actually loaded,
      carried in full rather than by name: this record travels with one container''s
      sidecar, so a reference to an environment defined elsewhere would point outside
      the only file a reader has.'
    inlined: true
attributes:
  date_created:
    name: date_created
    description: ISO 8601 (prov:generatedAtTime)
    from_schema: https://w3id.org/tvbo
    owner: Provenance
    domain_of:
    - SimulationTool
    - Provenance
    range: string
  outputs:
    name: outputs
    description: The data variables the container actually holds, read off it when
      the record is written rather than predicted from the spec, so a run that recorded
      less than it declared is visible here. The one fact in this record that the
      recipe beside it cannot supply.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Provenance
    domain_of:
    - Provenance
    - ResultEntity
    range: string
    multivalued: true
  license:
    name: license
    from_schema: https://w3id.org/tvbo
    owner: Provenance
    domain_of:
    - CommonCoordinateSpace
    - SoftwarePackage
    - SoftwareRequirement
    - Provenance
    range: string
  generated_by:
    name: generated_by
    description: 'Software/agent identifier: the prov:Agent this artifact is attributed
      to.'
    from_schema: https://w3id.org/tvbo
    close_mappings:
    - prov:wasAttributedTo
    rank: 1000
    owner: Provenance
    domain_of:
    - Provenance
    range: string
  experiment_yaml_hash:
    name: experiment_yaml_hash
    description: SHA-256 hex digest of the normalised experiment YAML that produced
      this artifact. Used by the cross-experiment cache (see :class:`SimulationStudy.from_file`)
      to detect when a cached upstream result has gone stale because the experiment's
      spec was edited. Computed as ``hashlib.sha256(yaml.safe_dump(normalized_yaml).encode()).hexdigest()``
      over the fully resolved (post-``!include``) experiment block.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Provenance
    domain_of:
    - Provenance
    range: string
  digest:
    name: digest
    description: Checksums of the artifact itself, keyed by function name. BEP028's
      ``Digest``, and distinct from ``experiment_yaml_hash``, which digests the spec
      that produced the artifact rather than the artifact.
    from_schema: https://w3id.org/tvbo
    exact_mappings:
    - prov:value
    rank: 1000
    owner: Provenance
    domain_of:
    - Provenance
    range: Digest
    multivalued: true
    inlined: true
  activities:
    name: activities
    description: The runs that produced this artifact, serialized to BEP028's activity
      record. Each names the command, the software that carried it out and what it
      consumed.
    from_schema: https://w3id.org/tvbo
    exact_mappings:
    - prov:wasGeneratedBy
    rank: 1000
    owner: Provenance
    domain_of:
    - Provenance
    range: Activity
    multivalued: true
    inlined: true
    inlined_as_list: true
  inputs:
    name: inputs
    description: Per-input fingerprints for cache invalidation. Each entry records
      the IRI + dotted-field path of an ``aux_data`` reference plus the (mtime, size,
      sha256) of the underlying file at the time the artifact was produced. A downstream
      cache hit requires every fingerprint to match the current file state.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Provenance
    domain_of:
    - Provenance
    range: ReferenceFingerprint
    multivalued: true
    inlined: true
    inlined_as_list: true
  derived_from:
    name: derived_from
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: prov:wasDerivedFrom
    owner: Provenance
    domain_of:
    - Provenance
    - SimulationStudy
    range: string
  references:
    name: references
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:references
    owner: Provenance
    domain_of:
    - Provenance
    - Observation
    - Dynamics
    - SimulationExperiment
    - SimulationStudy
    range: string
    multivalued: true
  environment:
    name: environment
    description: 'The machine and the resolved package set the run actually loaded,
      carried in full rather than by name: this record travels with one container''s
      sidecar, so a reference to an environment defined elsewhere would point outside
      the only file a reader has.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Provenance
    domain_of:
    - Provenance
    - Observation
    - SimulationExperiment
    - PDESolver
    range: SoftwareEnvironment
    inlined: true
class_uri: tvbo:Provenance