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Hands-On Workshops

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How to Develop Your Application Ontologies Using PMDco and OBO+ODK Best Practices

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Platform MaterialDigital- Semantic Interoperability​ Team

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https://github.com/HosseinBeygiNasrabadi/PMDco-workshop

PMDco workshop repository

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How to Develop Your Application Ontologies Using PMDco and OBO+ODK Best Practices

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Workshop content (10 topics, 4 tutorials):

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1- Ontology development and beginners learning materials

2- Ontology levels

3- Basic Formal Ontology (BFO) classes

4- Platform MaterialDigital Core Ontology (PMDco) classes

Tutorial 1: Structure given classes according to PMDco hierarchy (Miro board)

5- Platform MaterialDigital Core Ontology (PMDco) object properties

Tutorial 2: Using appropriate object properties (Miro board)

6- How to develop your application ontologies using PMDco and OBO+ODK best practices?

7- Ontology Development Kit (ODK)

Tutorial 3: Creating ODK repository for PMDco application ontologies (GitHub)

8- Collaborative ontology development workflow, adding taxonomy and axioms

9- PMDco Ontology Design Patterns (ODPs)

Tutorial 4: Ontology editing; adding classes, annotations and axioms (Protege)

10- Ontology evaluation, release, documentation and maintenance

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1- Ontology development and beginners learning materials

An ontology is an explicit, formal specification of a shared conceptualization.

conceptualization:  abstract model (domain, relevant terms, relations)

explicit:      meaning of all terms is clearly and unambiguously defined

formal:       interpretable by machines

shared:      consensus

Ontology development process:

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1- Ontology development and beginners learning materials

PMDco documentation page

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• Top-Level Ontologies: Define very general concepts that apply across all domains

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• Mid-Level Ontologies: Provide reusable structures shared across several domains

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• Domain-Level Ontologies: Describe concepts specific to a particular field

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• Application-Level Ontologies: Highly specific to individual applications or projects

2- Ontology levels

High Temperature Tensile Testing

Mechanical Testing

Materials Science

General

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• ISO standard top-level ontology
• A small top-level ontology that is designed for use in supporting information retrieval, analysis and integration in scientific and other domains.
• Used by more than 800 ontology-driven endeavors throughout the world.

3- Basic Formal Ontology (BFO)

Enable integration across different domain ontologies

Avoid ambiguity by defining core categories (e.g., object, process, quality)

Logical structure helps automated reasoning and validation

Allow systems and datasets to “speak the same language”

Save time and effort by building on established upper-level concepts

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Continuants

• Persist through time while possibly undergoing change
• Exist wholly at any moment in time
• Example: a book

3- Basic Formal Ontology (BFO) classes: the very top

BFO sits at the very top as a domain-neutral upper ontology

Divides all entities into two fundamental categories:

Occurrents

• Happen or unfold over time
• Have temporal parts and duration
• Examples: reading a book

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• Process: Ongoing event with temporal parts (e.g., a surgery, running)
• Process Boundary: Instant where a process starts or ends (e.g., moment of impact)
• Temporal Region: Span of time itself (e.g., a day, a year)
• Spatiotemporal Region: Combination of space and time (e.g., the area of a concert during its performance)

3- Basic Formal Ontology (BFO) classes: Occurrent

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Specifically Dependent Continuants

• Depend on one specific bearer
• If the bearer ceases to exist, then its quality, function, role ceases to exist
• Examples: the color of this apple, my weight

3- Basic Formal Ontology (BFO) classes: Continuant

Independent Continuants

• Exist on their own
• Do not depend on other entities for their existence
• Examples: a rock, a human body, a tree

Generically Dependent Continuants

• Can be copied or instantiated in different bearers
• Examples: a digital file, a PDF document, a gene sequence

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Immaterial Entity: Has no physical mass but still exists spatially

• Site: location occupied by something (e.g., parking space)
• Spatial Region: abstract space (e.g., 3D coordinates)
• Fiat Boundary: non-physical border (e.g., equator)

3- Basic Formal Ontology (BFO) classes: Independent continuant

Material Entity: Has physical presence and occupies space

• Object: one whole, independent thing (e.g., a car)
• Object Aggregate: group of objects (e.g., a fleet of cars)
• Fiat Object Part: arbitrary part of an object (e.g., front half of a car)

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Quality: Inherent and always present in the bearer, Measurable or observable features

Examples: color of an apple, mass of a rock

• Relational Quality: a quality that depends on another entity (e.g., distance between two objects)

Realizable Entity: Exists as a potential; realized in certain conditions

• Role: A realizable entity that depends on external social or institutional context

Example: A person as a teacher, a molecule as a tracer

• Disposition: A realizable entity that reflects an inherent tendency

Example: Fragility of glass, flammability of gasoline

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3- Basic Formal Ontology (BFO) classes: Specifically Dependent Continuant

BFO Classifier

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A mid-level ontology to support the digital transformation of the Materials Science and Engineering (MSE) domain.

Objectives

• Semantic Interoperability
• FAIR Data Principles
• Workflow Modeling

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Applications

• Material Specifications
• Process Chains
• Data Integration and Analysis
• Device and Function Modeling

4- Platform MaterialDigital Core Ontology (PMDco) classes

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4- Platform MaterialDigital Core Ontology (PMDco) classes

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Manufacturing module

Material characterization module

Data transformation module

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4- Platform MaterialDigital Core Ontology (PMDco) classes

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Materials module

Devices module

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4- Platform MaterialDigital Core Ontology (PMDco) classes

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Qualities module

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4- Platform MaterialDigital Core Ontology (PMDco) classes

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Your application ontology classes

4- Platform MaterialDigital Core Ontology (PMDco) classes

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Miro Board

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Workshop example:

"High temperature tensile testing ontology” by reusing PMDco

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Tutorial 1: Structure given classes according to PMDco hierarchy (Miro board)

* This tutorial designed based on PMDco v3.0.0.rc1

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Tutorial 1: Structure given classes according to PMDco hierarchy

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Tutorial 1: Answer

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How to Develop Your Application Ontologies Using PMDco and OBO+ODK Best Practices

​

Workshop content (10 topics, 4 tutorials):

​

1- Ontology development and beginners learning materials

2- Ontology levels

3- Basic Formal Ontology (BFO) classes

4- Platform MaterialDigital Core Ontology (PMDco) classes

Tutorial 1: Structure given classes according to PMDco hierarchy (Miro board)

5- Platform MaterialDigital Core Ontology (PMDco) object properties

Tutorial 2: Using appropriate object properties (Miro board)

6- How to develop your application ontologies using PMDco and OBO+ODK best practices?

7- Ontology Development Kit (ODK)

Tutorial 3: Creating ODK repository for PMDco application ontologies (GitHub)

8- Collaborative ontology development workflow, adding taxonomy and axioms

9- PMDco Ontology Design Patterns (ODPs)

Tutorial 4: Ontology editing; adding classes, annotations and axioms (Protege)

10- Ontology evaluation, release, documentation and maintenance

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5- Platform MaterialDigital Core Ontology (PMDco) object properties

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5- Platform MaterialDigital Core Ontology (PMDco) object properties

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Workshop example:

"High temperature tensile testing ontology” by reusing PMDco

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Tutorial 2: Using appropriate object properties (Miro board)

* This tutorial designed based on PMDco v3.0.0.rc1

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Miro Board

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Tutorial 2: Using appropriate object properties

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Tutorial 2: Answer

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How to Develop Your Application Ontologies Using PMDco and OBO+ODK Best Practices

​

Workshop content (10 topics, 4 tutorials):

​

1- Ontology development and beginners learning materials

2- Ontology levels

3- Basic Formal Ontology (BFO) classes

4- Platform MaterialDigital Core Ontology (PMDco) classes

Tutorial 1: Structure given classes according to PMDco hierarchy (Miro board)

5- Platform MaterialDigital Core Ontology (PMDco) object properties

Tutorial 2: Using appropriate object properties (Miro board)

6- How to develop your application ontologies using PMDco and OBO+ODK best practices?

7- Ontology Development Kit (ODK)

Tutorial 3: Creating ODK repository for PMDco application ontologies (GitHub)

8- Collaborative ontology development workflow, adding taxonomy and axioms

9- PMDco Ontology Design Patterns (ODPs)

Tutorial 4: Ontology editing; adding classes, annotations and axioms (Protege)

10- Ontology evaluation, release, documentation and maintenance

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6- How to develop your application ontologies using pmdco and OBO+ODK best practices?

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7- Ontology Development Kit (ODK)

• Open-source toolkit and ontology life cycle management system for a standardized and transparent ontology development process.
• Automation of tasks like: import and release management, consistency checks, reasoning, and quality assurance.
• Supports us to comply to the best-practices of ontology development and avoid errors in imports and inconsistencies.
• Modularized approach through clearly separable components and modules.
• Uses technologies like ROBOT, Docker, GitHub Actions.
• Community-based tool with regular updates

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Workshop example:

"High temperature tensile testing ontology” by reusing PMDco

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Tutorial 3: Creating ODK repository for PMDco application ontologies (GitHub)

GitHub ODK template

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How to participate:

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Case A) I plan developing professional AO:

We recommend learning ODK and use it for creating your repo. Now you can just watch how an ODK is looking like.

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Case B) I want to test ODK, I may use it:

Participate in this tutorial and make your first ODK repo.

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Case C) I don’t plan developing AO and use ODK:

You can just watch how an ODK is looking like.

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Tutorial 3: Creating ODK repository for PMDco application ontologies (GitHub)

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How to Develop Your Application Ontologies Using PMDco and OBO+ODK Best Practices

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Workshop content (10 topics, 4 tutorials):

​

1- Ontology development and beginners learning materials

2- Ontology levels

3- Basic Formal Ontology (BFO) classes

4- Platform MaterialDigital Core Ontology (PMDco) classes

Tutorial 1: Structure given classes according to PMDco hierarchy (Miro board)

5- Platform MaterialDigital Core Ontology (PMDco) object properties

Tutorial 2: Using appropriate object properties (Miro board)

6- How to develop your application ontologies using PMDco and OBO+ODK best practices?

7- Ontology Development Kit (ODK)

Tutorial 3: Creating ODK repository for PMDco application ontologies (GitHub)

8- Collaborative ontology development workflow, adding taxonomy and axioms

9- PMDco Ontology Design Patterns (ODPs)

Tutorial 4: Ontology editing; adding classes, annotations and axioms (Protege)

10- Ontology evaluation, release, documentation and maintenance

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8- Collaborative ontology development workflow, adding taxonomy and axioms

1- GitHub desktop: clone the repository

2- Protege:

src/ontology/httto-edit.owl

Edit Ontology

3- GitHub desktop: commit and push

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8- Collaborative ontology development workflow, adding taxonomy and axioms

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https://github.com/materialdigital/core-ontology/tree/main/patterns

9- PMDco Ontology Design Patterns (ODPs)

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Workshop example:

"High temperature tensile testing ontology” by reusing PMDco

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Tutorial 4: Ontology editing; adding classes, annotations and axioms (Protege)

Option A (commit and push possibility):

1- GitHub desktop: clone the “PMDco Workshop” repository (QR code link below)

2- Protégé: open file> src/ontology/httto-edit.owl

Option B (faster, just for participating in tutorial):

1- Protégé: open from URL> QR code link below)

How to participate:

httto.ttl

GitHub PMDco Workshop

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Tutorial 4: Ontology editing; adding classes, annotations and axioms (Protege)

1- Add ao classes (yellow ones) in their designed hierarchy

2- Create annotations (at least definitions) for your created classes

3- Create axioms (as shown in the graph) for your created classes

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Tutorial 4: Example adding classes, annotations, and axioms

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How to Develop Your Application Ontologies Using PMDco and OBO+ODK Best Practices

​

Workshop content (10 topics, 4 tutorials):

​

1- Ontology development and beginners learning materials

2- Ontology levels

3- Basic Formal Ontology (BFO) classes

4- Platform MaterialDigital Core Ontology (PMDco) classes

Tutorial 1: Structure given classes according to PMDco hierarchy (Miro board)

5- Platform MaterialDigital Core Ontology (PMDco) object properties

Tutorial 2: Using appropriate object properties (Miro board)

6- How to develop your application ontologies using PMDco and OBO+ODK best practices?

7- Ontology Development Kit (ODK)

Tutorial 3: Creating ODK repository for PMDco application ontologies (GitHub)

8- Collaborative ontology development workflow, adding taxonomy and axioms

9- PMDco Ontology Design Patterns (ODPs)

Tutorial 4: Ontology editing; adding classes, annotations and axioms (Protege)

10- Ontology evaluation, release, documentation and maintenance

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10- Ontology evaluation, release, documentation and maintenance

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10- Ontology evaluation, release, documentation and maintenance

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How to Develop Your Application Ontologies Using PMDco and OBO+ODK Best Practices

​

Workshop content (10 topics, 4 tutorials):

​

1- Ontology development and beginners learning materials

2- Ontology levels

3- Basic Formal Ontology (BFO) classes

4- Platform MaterialDigital Core Ontology (PMDco) classes

Tutorial 1: Structure given classes according to PMDco hierarchy (Miro board)

5- Platform MaterialDigital Core Ontology (PMDco) object properties

Tutorial 2: Using appropriate object properties (Miro board)

6- How to develop your application ontologies using PMDco and OBO+ODK best practices?

7- Ontology Development Kit (ODK)

Tutorial 3: Creating ODK repository for PMDco application ontologies (GitHub)

8- Collaborative ontology development workflow, adding taxonomy and axioms

9- PMDco Ontology Design Patterns (ODPs)

Tutorial 4: Ontology editing; adding classes, annotations and axioms (Protege)

10- Ontology evaluation, release, documentation and maintenance

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Bi-weekly public sessions�Fridays, 1-2 pm��Audience�Ontology practitioners & MSE domain experts

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Key activities

• Knowledge transfer
• Experience exchange
•  Modeling challenges – User insights
•  Collaborative PMDco enhancement

Check out our YouTube channel

Invitation to PMD Ontology Playground Meetings

Participate in our PMD Playground Meetings

Please register via our mailing list.

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PMDco workshop materials have been prepared by Platform MaterialDigital- Semantic Interoperability​ Team.

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For more information, please contact us via

 hossein.beygi_nasrabadi@fiz-karlsruhe.de.