the industry ontologies foundry ontology foundry – academia •inp-enit, university of toulouse...

The Industry Ontologies FoundryBarry Smith

National Center for Ontological Research (NCOR) Buffalo, NY

EMMC, November 7, 2017

The problem of interoperability in digital manufacturingWhy interoperability always fails• Clients, vendors, … use different software• Hardware changes• Software changes• Personnel changesThis makes it impossible to answer digitally questions whose answers turn on accessing bodies of data sourced from different organizations

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Companies routinely pay consultants to build custom systems to integrate legacy data.

Such custom systems:• represent significant investment for large

companies, and• are out of reach to small companies.But they fail even for large companies

Ontologies: A partial solution

• A common terminological framework• High flexibility and easy extensibility• Ontology-driven software

Unfortunately• many, many examples of ontology failure

Typical reasons for ontology failure• Too many ontologies (everybody wants one; everybody thinks they are

easy to build)• So they are built in ad hoc ways – do not promote interoperability• No common methodology• Short half life (often EU funded)• No definitions • Few axioms• No commonly accepted quality control standards• Poor training• Poor documentationetc., etc.

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Consequence: no real-world examples of industrial use• The industrial IT world has been burned too often by bad experiences

with ontologies

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The Gene Ontology (GO, 1998–)

Uses of ‘ontology’ in PubMed abstracts

for consistent tagging of genomics data and literature, now used across all of the life sciences

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Why was the GO so successful?

Uses of ‘ontology’ in PubMed abstracts

it was the only game in town, and so it did indeed help to solve the problem of interoperability; has received huge amounts of funding; still has no competitors

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part_of

is_a

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GO’s three sub-ontologies

is_a

biological molecular cellular process function component

2004–: GO extended with new ontology modules for:

cell typesproteinssequencesmetabolismdevelopmentdiseases anatomy

…

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Anatomy Ontology(FMA*, CARO)

Environment Ontology(EnvO)

Infectious Disease

Ontology(IDO*)

Biological Process

Ontology (GO)

Cell Ontology

(CL)

CellularComponent

Ontology(FMA*, GO*) Phenotypic

QualityOntology

(PaTO)Subcellular Anatomy Ontology (SAO)

Sequence Ontology(SO*) Molecular

Function(GO*)Protein Ontology

(PRO*) 11

top-level

mid-level

domain-level

Information Artifact Ontology

(IAO)

Ontology for Biomedical

Investigations(OBI)

Spatial Ontology(BSPO)

Basic Formal Ontology (BFO)

Common top level

RELATIONTO TIME

GRANULARITY

CONTINUANT OCCURRENT

INDEPENDENT DEPENDENT

ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)

Anatomical Entity(FMA, CARO)

OrganFunction

(FMP, CPRO) Phenotypic Quality(PaTO)

Biological Process

(GO)CELL AND CELLULAR

COMPONENT

Cell(CL)

Cellular Component(FMA, GO)

Cellular Function

(GO)

MOLECULEMolecule

(ChEBI, SO,RnaO, PrO)

Molecular Function(GO)

Molecular Process(GO)

Open Biomedical Ontologies (OBO) Foundry (ca. 2004) (Gene Ontology in yellow)

Coordinated evolution of ontologies

Basic Formal Ontology

Continuant Occurrent(Process, Event)

IndependentContinuant

(Thing)

DependentContinuant(Attribute)

http://basic-formal-ontology.org13

Basic Formal Ontology = reverse engineering top level of GO



(Thing)

DependentContinuant(Attribute)

http://basic-formal-ontology.org14

GO: cellular component

GO: biological process

GO: molecularfunction



ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)


OrganFunction


Organism-Level Process

(GO)

CELL AND CELLULAR

COMPONENT

Cell(CL)


Cellular Function

(GO)

Cellular Process(GO)

MOLECULEMolecule

(ChEBI, SO,RNAO, PRO)


Molecular Process

(GO)

rationale of OBO Foundry coverage (http://obofoundry.org)

GRANULARITY

RELATION TO TIME

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OBO Foundry growing to encompass further domains

Environments and Environmental Systems (ENVO) Populations, Communities (PCO)Information Artifacts (IAO)Experiments (OBI)

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(Thing)

Specifically DependentContinuant

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QualityDispositionFunctionRole …

Basic Formal Ontology 2.0 = adds capability to deal with information artifacts



(Thing)

Specifically DependentContinuant

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QualityDispositionFunctionRole …

Generically DependentContinuant

Information Entity

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~ 300 ontologies re-using BFO

http://ontology.buffalo.edu/BOBFO20

modular hub and spokes strategy

Examples of ontology suites with top-level ontology hubsOntology suite Domain URL

Open Biomedical Ontologies Foundry life sciences http://obofoundry.org

VIVO-Integrated Semantic Framework (VIVO-ISF)

scientific research (persons, works, relations of authorship)

https://bioportal.bioontology.org/ontologies/VIVO-ISF

Planteome Ontologies plant science / genomics http://www.plantontology.org/

Common Core Ontologies (CCO) military and related domains https://github.com/CommonCoreOntology/

Common IC Ontology intelligence community

Infectious Disease Ontologies (ISO)

Infectious diseases, vaccines http://infectiousdiseaseontology.org/page/

UNEP SDGIO UN Sustainable Development Interface Ontology

http://pre-uneplive.unep.org/portal

Industry Ontologies Foundry (IOF)

Industry Ontology Foundry (IOF) initiativeto create a suite of interoperable high quality ontologies covering the domain of industrial (especially manufacturing) engineering

• ontologies should be developed in tandem to ensure that they promote interoperability

• ontologies should be small but easily extensible for different companies, products, …

Industry Ontology Foundry – GOVERNMENT

NIST• Nenad Ivezic• Boonserm Kulvatunyou• KC Morris• Vijay Srinivasan• Ram Sriram• Paul Witherell• Evan Wallace• …

Air Force Research Lab• Clare Paul• …

Industry Ontology Foundry – INDUSTRY

• Airbus • Autodesk• Cambridge Semantics • CIMData• CUBRC • Dassault Industries…

Industry Ontology Foundry – ACADEMIA

• INP-ENIT, University of Toulouse (Hedi Karray)• Clemson University (Venkat Krovi)• École polytechnique fédérale de Lausanne (Dimitris Kiritsis)• Loughborough University, UK (Bob Young)• National Center for Ontological Research (Kemper Lewis, Rahul

Rai, Barry Smith)• Penn State (Timothy Simpson)• Texas State (Farhad Ameri)• UMass Amherst (Ian Grosse)• University of Toronto (Michael Grüninger)• …

IOF testbeds 1. DMDII Process Workflow / Ontoview2. Product Life Cycle Ontology3. MatOnto Materials Ontology

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IOF testbeds 1. DMDII2. MatOnto Materials Ontology3. Product Life Cycle Ontology

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Digital Manufacturing and Design Innovation Institute (DMDII)

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http://dmdii.uilabs.org/projects/calls/completing-the-model-based-definition

Buffalo initiative: Coordinated Holistic Alignment of Manufacturing Processes

create a flexible extensible suite of interoperable generic public-domain ontologies covering the domain of manufacturing engineering

test the utility of these ontologies in the day to day work flows of a local manufacturing enterprise


The Common Core Ontologies

Time Agent Artifact Event Unit Geospatial

InfoQuality

https://github.com/CommonCoreOntology/https://www.youtube.com/watch?v=SDUyUdLY43g: Ontoview

https://www.youtube.com/watch?v=SDUyUdLY43g


Act of Radiographic

Exam

Act of Lot Acceptance

Testing

Nominal Measurement

Information Content Entity

xsd: “Pass”

Information Content Entity

Bearer

Inflation Device

Particulars

Universals

CHAMP: Act of Production

CCO: Intention Act

BFO:ProcessBFO: Generically

Dependent continuant

BFO: Object

PLC: Product

CCO: Artifact

CCO: Information Content Entity

BFO: continuant BFO: occurrentis a

is a

is a

is a

is a

is a

is a

is a

instance of

instance of

instance of

instance of

instance ofparticipates in

participates in

has output

inheres in

has text value

Coordinated Holistic Alignment of Manufacturing Processes (CHAMP)

Process Workflow and OntoviewRon Rudnicki (CUBRC)

Industry Ontologies Foundry (IOF) PresentationOctober 20, 2017


IOF testbeds 1. DMDII2. Product Life Cycle Ontology3. MatOnto Materials Ontology

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IOF testbeds 1. DMDII2. Product Life Cycle Ontology (NCOR Buffalo and EPFL

Lausanne)3. MatOnto Materials Ontology

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Top-level organization of BFO (simplified)

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ProcessInformation EntityMaterial Entity

BFO: Continuant BFO: Occurrent

Temporal Region

occupies

Spatial Region

occupies


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Portion of MaterialPart/Component

SwitchBoilerFurnaceTank

FactoryAccess roadDelivery vehicle


Product Model (output of CAD system)

Requirement Specification

Process PlanProduction PlanPart/Component List

Maintenance PlanMaintenance ReportMaintenance History 38


Design ProcessProduction Process

Production Plan Generation Process

Product Use ProcessProduct Maintenance ProcessProduct Inspection Process

End Of Life Process

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Proc

ess

Info

rmat

ion

Entit

yM

ater

ialE

ntity

time

40

Proc

ess

Info

rmat

ion

Entit

yM

ater

ialE

ntity

Process

Planned Process

Product Life Cycle (PLC)

BFO: Process

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Proc

ess

Process

Planned Process


BFO: Process

ProductionPlan

GenerationProcess

DesignProcess

Follows Mainten-ance

Process

UseProcess

End of Life

Process

Part of Part of Part of Part of Part of

Follows Follows Inter-sperses Follows

Part of

ProductionProcess

Info

rmat

ion

Entit

yM

ater

ialE

ntity

42

Follows

Proc

ess

Process

Planned Process


BFO: Process

Production PlanGeneration Process

DesignProcess

Part of

FollowsProductionProcess

Info

rmat

ion

Entit

y

Part of

Maintenance Process

Part of

Follows

Part of

ProductionPlan

Has outputGuides

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Follows

Proc

ess

Process

Planned Process


BFO: Process

Production PlanGeneration Process

DesignProcess

Part of

FollowsProductionProcess

Info

rmat

ion

Entit

y

Part of

Maintenance Process

Part of

Follows

Part of

ProductionPlan

Has outputGuided-by

Mat

eria

lEn

tity

Has-output

Product45

Planned Process


Production PlanGeneration

Process

Designprocess

FollowsProduction

ProcessPossession,

StorageEnd of Life

Process

Requirements Specification

Guides

Product Model (Drawing, …)

ProductionPlan

Maintenance PlanGeneration

Process MaintenanceProcess

Has output Is input for

Is input for

Maintenance Plan

Guides

Product

Has output Guides

Is input for

Part of Part of Part of Part of Part of

Part of

Has output

Is input for

Is input for

Portion of Waste Material

Has output

Portion of RawMaterial

Factory (Machine, Bulding, …)

Human being (Designer, Manager, Machinist, Maintenance Engineer, User, … )

Utility Supply System (Energy, Water, Data … )

TechnicalDocumentation

Has output

Proc

ess

Info

rmat

ion

Entit

yM

ater

ialE

ntity

BFO: Process

User Documentation

Follows Follows Follows Follows

Has output

Part of

UseProcess

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Has output

Maintenance Report

IOF testbeds

1. DMDII2. Product Life Cycle Ontology3. MatOnto Materials Ontology

MatOnto (background)

Materials Genome InitiativeAFRL-managed ontology (‘MatOnto’)

MatOnto software tool: http://matonto.org/(~ Protégé for ontology suites)Now marketed as ‘Mobi’

IOF MatOnto ontology initiative under direction of Clare Paul (Air Force Research Lab)

http://matonto.org/



Time Agent Artifact Event Unit Geospatial

InfoQuality

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small generic ontologies for aggressive reuse and extension by multiple enterprises

Materials Ontology

CHEBIFunctionally Graded Materials Ontology

Addictive Manufacturing

Ontology


Machine and Tool Ontology

Manufacturing Process Ontology


Time Agent Artifact Event

Product Life Cycle Ontology

Unit Geospatial

InfoQuality

SLACKS

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MatOnto: A suite of ontology modules for materials science based on BFOExisting ontologies in process of being re-engineered to be BFO-conformant:

for Laminated Composites: SLACKS (UMass)for Functionally Graded Materials: FGMO (NCOR, Milan Polytechnic)

Existing ontologies already BFO-conformant:for Polymers: CHEBI (EBI)

See: http://ncorwiki.buffalo.edu/index.php/MatOnto_Ontology_Meetings



ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)


OrganFunction


Organism-Level Process

(GO)

CELL AND CELLULAR

COMPONENT

Cell(CL)


Cellular Function

(GO)

Cellular Process(GO)

MOLECULEMolecule

(ChEBI, SO,RNAO, PRO)


Molecular Process

(GO)

rationale of OBO Foundry coverage (http://obofoundry.org)

GRANULARITY

RELATION TO TIME

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BFO-based treatment of granular levels of material entities

Microbiome is a systemMicrobiota is population of micro-organisms

BFOENVOPCO

‘is a’ relationsThe Environment Ontology

*

* to be created

BFOENVOPCO

‘is a’ relationsThe Environment Ontology

‘determined by’ =def. A system is determined by an entity if the removal of that entity would cause the collapse of that system.

(e.g. removing the corals from a coral reef ecosystem would cause that ecosystem to collapse)

BFOENVOPCO

‘is a’ relations

BFOENVOPCO

‘is a’ relationsIncorporating microbiome

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