PROV and Real Things

LAND AND WATER

Simon J D Cox & Nicholas J Car 4th December 2015

PROV and real things | Cox & Car

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

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PROV and real things | Cox & Car

Real workflows

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PROV and real things | Cox & Car

Proposal:

1. Describe specimen preparation using a generic process model (i.e. input-process-output)

2. Use W3C PROV as the generic process model

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PROV and real things | Cox & Car

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..*

+relatedSamplingFeature0..*

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ISO 19156:2011 Geographic Information – Observations and measurements (S J D Cox, Ed.)

PROV and real things | Cox & Car

Specimen model in sam-lite

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S J D Cox, Ontology for observations and sampling features, with alignments to existing models, Sem. Web (in press)

PROV and real things | Cox & Car

What is PROV?

Core classes: - Entity

- thing of interest (‘endurant’)

- Activity - transformation event

(‘occurrent’)- Agent

- responsible party or process

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T. Lebo, S. Sahoo, D.L. McGuinness, PROV-O: The PROV Ontology, (2013). http://www.w3.org/TR/prov-o/

PROV and real things | Cox & Car

PROV applications

The entities of interest are usually • Datasets• Publications, papers, reports, products

i.e. information objects

How about the ‘internet of things’?

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PROV and real things | Cox & Car

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!

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PROV and real things | Cox & Car

Example: carbonate analysis

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Entities: specimens, data, reports

Agents: people, machines

Activities: preparation-steps, observations

PROV and real things | Cox & Car

Ontology Design Pattern

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input data

config

plan output dataactivity

machine agent

human agent

This work with real things fits my generic PROV usage design pattern

PROV and real things | Cox & Car

Example: insect taxonomy

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Entities: specimens, data, reports

Agents: people, machines

Activities: preparation-steps, observations

PROV and real things | Cox & Car

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

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PROV and real things | Cox & Car

Elaborations

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These examples use only ‘core’ PROV:

qualifiedInfluence properties enable recording of more detail

PROV and real things | Cox & Car

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 ….?

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* Galleries, Libraries, Archives & Museums

PROV and real things | Cox & Car

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 …

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CSIRO Land and WaterSimon Cox Research Scientistt +61 3 9545 2365e simon.cox@csiro.au

Geoscience AustraliaNicholas CarData Architectt +61 2 6249 9093e nicholas.car@ga.gov.au

LAND AND WATER

Thank you