The Industry Ontologies Foundry Ontology Foundry – ACADEMIA •INP-ENIT, University of Toulouse...
Transcript of 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
Continuant Occurrent(Process, Event)
IndependentContinuant
(Thing)
DependentContinuant(Attribute)
http://basic-formal-ontology.org14
GO: cellular component
GO: biological process
GO: molecularfunction
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic Quality(PaTO)
Organism-Level Process
(GO)
CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Component(FMA, GO)
Cellular Function
(GO)
Cellular Process(GO)
MOLECULEMolecule
(ChEBI, SO,RNAO, PRO)
Molecular Function(GO)
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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Basic Formal Ontology
Continuant Occurrent(Process, Event)
IndependentContinuant
(Thing)
Specifically DependentContinuant
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QualityDispositionFunctionRole …
Basic Formal Ontology 2.0 = adds capability to deal with information artifacts
Continuant Occurrent(Process, Event)
IndependentContinuant
(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
Basic Formal Ontology
The Common Core Ontologies
Time Agent Artifact Event Unit Geospatial
InfoQuality
https://github.com/CommonCoreOntology/https://www.youtube.com/watch?v=SDUyUdLY43g: Ontoview
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
https://www.youtube.com/watch?v=SDUyUdLY43g
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
ProcessInformation EntityMaterial Entity
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Portion of MaterialPart/Component
SwitchBoilerFurnaceTank
FactoryAccess roadDelivery vehicle
ProcessInformation EntityMaterial Entity
Product Model (output of CAD system)
Requirement Specification
Process PlanProduction PlanPart/Component List
Maintenance PlanMaintenance ReportMaintenance History 38
ProcessInformation EntityMaterial Entity
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
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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
Product Life Cycle (PLC)
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
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Follows
Proc
ess
Process
Planned Process
Product Life Cycle (PLC)
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
Product Life Cycle (PLC)
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
Product Life Cycle (PLC)
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)
Basic Formal Ontology
The Common Core Ontologies
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
Basic Formal Ontology
Machine and Tool Ontology
Manufacturing Process Ontology
The Common Core Ontologies
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
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic Quality(PaTO)
Organism-Level Process
(GO)
CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Component(FMA, GO)
Cellular Function
(GO)
Cellular Process(GO)
MOLECULEMolecule
(ChEBI, SO,RNAO, PRO)
Molecular Function(GO)
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