PROV and Real Things

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MODSIM2015 presentation on provenance and real things

Science

PROV and Real Things
LAND AND WATER
Simon J D Cox & Nicholas J Car
4th December 2015

The problem
preparation workflow on a
specimen’s journey from
collection to analysis is complex,
and variable
its description must be available
in order to evaluate or
reproduce observations
this workflow may link in to
other business workflows like
data publication
PROV and real things | Cox & Car2 |

Real workflows
PROV and real things | Cox & Car3 |

Proposal:
1. Describe specimen preparation using a generic process model
(i.e. input-process-output)
2. Use W3C PROV as the generic process model
PROV and real things | Cox & Car4 |

ISO 19156 Specimen model
Specimen is a kind of
Sampling Feature
• [0..*] Preparation Steps
Issues:
• Can’t tie the
predecessor/successor to a
preparation step
• UML/XML only
SF_Specimen
+ currentLocation: Location [0..1]
+ materialClass: GenericName
+ samplingLocation: GM_Object [0..1]
+ samplingMethod: SF_Process [0..1]
+ samplingTime: TM_Object
+ size: Measure [0..1]
+ specimenType: GenericName [0..1]
SF_SamplingFeature
+ lineage: LI_Lineage [0..1]
+ parameter: NamedValue [0..*]
Location
+ geometryLocation: GM_Object
+ nameLocation: EX_GeographicDescription
GFI_Feature
SamplingFeatureComplex
+ role: GenericName
PreparationStep
+ processOperator: CI_ResponsibleParty [0..1]
+ time: TM_Object
SF_Process
+processingDetails
0..*
Intention
+sampledFeature 1..*
0..*
+relatedSamplingFeature
0..*
PROV and real things | Cox & Car5 |
ISO 19156:2011 Geographic Information – Observations and measurements (S J D Cox, Ed.)

Specimen model in sam-lite
PROV and real things | Cox & Car6 |
S J D Cox, Ontology for observations and sampling features, with alignments to existing models, Sem. Web (in press)

What is PROV?
Core classes:
- Entity
- thing of interest
(‘endurant’)
- Activity
- transformation event
(‘occurrent’)
- Agent
- responsible party or
process
PROV and real things | Cox & Car7 |
T. Lebo, S. Sahoo, D.L. McGuinness, PROV-O: The PROV Ontology, (2013). http://www.w3.org/TR/prov-o/

PROV applications
The entities of interest are usually
• Datasets
• Publications, papers, reports, products
i.e. information objects
How about the ‘internet of things’?
PROV and real things | Cox & Car8 |

Specimen  PROV mapping
Specimen sub-class-of prov:Entity .
Process sub-class-of prov:Agent .
Preparation-step sub-class-of prov:Activity .
Specimen is a real thing!
PROV and real things | Cox & Car9 |

Example:
carbonate
analysis
PROV and real things | Cox & Car10 |
Entities:
specimens,
data, reports
Agents:
people,
machines
Activities:
preparation-steps,
observations

Ontology Design Pattern
PROV and real things | Cox & Car11 |
input data
config
plan
output
data
activity
machine
agent
human
agent
This work with real things fits my generic PROV usage design pattern

Example: insect
taxonomy
PROV and real things | Cox & Car12 |
Entities:
specimens,
data, reports
Agents:
people,
machines
Activities:
preparation-steps,
observations

URIs for agents  some ‘vocabularies’ required
• People, including functional positions
(‘the lab technician at the time’)
• Machines, other pieces of kit
• URIs for specimens – see IGSN
PROV and real things | Cox & Car13 |

Elaborations
PROV and real things | Cox & Car14 |
These examples use only ‘core’ PROV:
qualifiedInfluence properties
enable recording of more detail

Provenance vs provenance
Provenance in GLAM* world
= chain-of-custody of non-reproducible things
To verify identity, but also important for assay data, drug-testing, forensics
Provenance in data world
= transformations of reproducible things
Provenance in the world of specimens
= transformations of non-reproducible things ….?
PROV and real things | Cox & Car15 |
* Galleries, Libraries, Archives & Museums

Summary
• Original application of PROV to real things
• Core PROV model capable of capturing specimen prep & analysis
• Specialization might make it stronger, but little needed
• Bringing ‘data’ provenance home to the GLAM application …
PROV and real things | Cox & Car16 |

CSIRO Land and Water
Simon Cox
Research Scientist
t +61 3 9545 2365
e simon.cox@csiro.au
Geoscience Australia
Nicholas Car
Data Architect
t +61 2 6249 9093
e nicholas.car@ga.gov.au
LAND AND WATER
Thank you

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PROV and Real Things

1. PROV and Real Things LAND AND WATER Simon J D Cox & Nicholas J Car 4th December 2015

2. The problem preparation workflow on a specimen’s journey from collection to analysis is complex, and variable its description must be available in order to evaluate or reproduce observations this workflow may link in to other business workflows like data publication PROV and real things | Cox & Car2 |

3. Real workflows PROV and real things | Cox & Car3 |

4. Proposal: 1. Describe specimen preparation using a generic process model (i.e. input-process-output) 2. Use W3C PROV as the generic process model PROV and real things | Cox & Car4 |

5. ISO 19156 Specimen model Specimen is a kind of Sampling Feature • [0..*] Preparation Steps Issues: • Can’t tie the predecessor/successor to a preparation step • UML/XML only SF_Specimen + currentLocation: Location [0..1] + materialClass: GenericName + samplingLocation: GM_Object [0..1] + samplingMethod: SF_Process [0..1] + samplingTime: TM_Object + size: Measure [0..1] + specimenType: GenericName [0..1] SF_SamplingFeature + lineage: LI_Lineage [0..1] + parameter: NamedValue [0..*] Location + geometryLocation: GM_Object + nameLocation: EX_GeographicDescription GFI_Feature SamplingFeatureComplex + role: GenericName PreparationStep + processOperator: CI_ResponsibleParty [0..1] + time: TM_Object SF_Process +processingDetails 0..* Intention +sampledFeature 1..* 0..* +relatedSamplingFeature 0..* PROV and real things | Cox & Car5 | ISO 19156:2011 Geographic Information – Observations and measurements (S J D Cox, Ed.)

6. Specimen model in sam-lite PROV and real things | Cox & Car6 | S J D Cox, Ontology for observations and sampling features, with alignments to existing models, Sem. Web (in press)

7. What is PROV? Core classes: - Entity - thing of interest (‘endurant’) - Activity - transformation event (‘occurrent’) - Agent - responsible party or process PROV and real things | Cox & Car7 | T. Lebo, S. Sahoo, D.L. McGuinness, PROV-O: The PROV Ontology, (2013). http://www.w3.org/TR/prov-o/

8. PROV applications The entities of interest are usually • Datasets • Publications, papers, reports, products i.e. information objects How about the ‘internet of things’? PROV and real things | Cox & Car8 |

9. Specimen  PROV mapping Specimen sub-class-of prov:Entity . Process sub-class-of prov:Agent . Preparation-step sub-class-of prov:Activity . Specimen is a real thing! PROV and real things | Cox & Car9 |

10. Example: carbonate analysis PROV and real things | Cox & Car10 | Entities: specimens, data, reports Agents: people, machines Activities: preparation-steps, observations

11. Ontology Design Pattern PROV and real things | Cox & Car11 | input data config plan output data activity machine agent human agent This work with real things fits my generic PROV usage design pattern

12. Example: insect taxonomy PROV and real things | Cox & Car12 | Entities: specimens, data, reports Agents: people, machines Activities: preparation-steps, observations

13. URIs for agents  some ‘vocabularies’ required • People, including functional positions (‘the lab technician at the time’) • Machines, other pieces of kit • URIs for specimens – see IGSN PROV and real things | Cox & Car13 |

14. Elaborations PROV and real things | Cox & Car14 | These examples use only ‘core’ PROV: qualifiedInfluence properties enable recording of more detail

15. Provenance vs provenance Provenance in GLAM* world = chain-of-custody of non-reproducible things To verify identity, but also important for assay data, drug-testing, forensics Provenance in data world = transformations of reproducible things Provenance in the world of specimens = transformations of non-reproducible things ….? PROV and real things | Cox & Car15 | * Galleries, Libraries, Archives & Museums

16. Summary • Original application of PROV to real things • Core PROV model capable of capturing specimen prep & analysis • Specialization might make it stronger, but little needed • Bringing ‘data’ provenance home to the GLAM application … PROV and real things | Cox & Car16 |

17. CSIRO Land and Water Simon Cox Research Scientist t +61 3 9545 2365 e simon.cox@csiro.au Geoscience Australia Nicholas Car Data Architect t +61 2 6249 9093 e nicholas.car@ga.gov.au LAND AND WATER Thank you

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