Representing the ChEBI ontology in OWL

•

2 j'aime•1,163 vues

Janna Hastings

Presented at the EBI Industry Programme Ontology tutorial.

Technologie

The ChEBI ontology and OWL Industry Programme Ontology Tutorial European Bioinformatics Institute 13 October 2010 Janna Hastings EBI Chemoinformatics and Metabolism

Overview ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10

Introduction to ChEBI ,[object Object],[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10

ChEBI ontology 4/26/2010 A ChEBI entry page

ChEBI ontology ChEBI ontology 20.10.10 ,[object Object],[object Object],[object Object],[object Object],( R ) -adrenaline

ChEBI ontology 20.10.10 Molecular structure ontology

ChEBI internal ontology architecture ChEBI ontology 20.10.10 Oracle database

A ChEBI entity in OBO format ,[object Object],ChEBI ontology 20.10.10

Expressing ChEBI in OWL ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10

ChEBI in OWL: Relationship patterns ,[object Object],[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10

ChEBI in OWL: Metadata ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10

A ChEBI entity in OWL format ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10

ChEBI in OWL: Editing and reasoning ,[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10

Chemical structures and OWL ,[object Object],ChEBI ontology 20.10.10 caffeine Molecules consist of atoms connected by bonds single bond double bond Carbon atom Hydrogen atom Nitrogen atom Oxygen atom

Structure-based classification ,[object Object],carboxylic acid cyclic molecule if molecule has part some carboxy group if molecule has property cyclic, i.e. a self-connected cyclic path exists through the molecule’s atoms

OWL representation Without internal structure, all parts must be explicitly asserted (which leads to a combinatorial explosion for larger molecules) But the internal structure of complex molecules cannot be encoded in OWL ontology axioms due to their cycles does not have a model in the shape of a tree

Description Graphs ,[object Object],[object Object],[object Object],[object Object]

Rules ,[object Object],[object Object],[object Object],[object Object],[object Object]

Chemical description graphs + Rules defined to detect cycles and parts Reasoning results: able to perform classification (but scalability a concern)

Acknowledgements ,[object Object],[object Object],[object Object],[object Object],ChEBI ontology 20.10.10

Recommandé

We’re all SMILES! Building Chemical Semantic Web Services with SADI, ChEBI, a...Michel Dumontier

Owl web ontology languagehassco2011

Web ontology language (owl)Ameer Sameer

Ontology engineering Aliabbas Petiwala

Automatic classification in ChEBIJanna Hastings

Representing chemicals using OWL, Description Graphs and RulesMichel Dumontier

OWL and OBODuncan Hull

Formalization and implementation of BFO 2 with a focus on the OWL implementationgolpedegato2

Recommandé

We’re all SMILES! Building Chemical Semantic Web Services with SADI, ChEBI, a...Michel Dumontier

Owl web ontology languagehassco2011

Web ontology language (owl)Ameer Sameer

Ontology engineering Aliabbas Petiwala

Automatic classification in ChEBIJanna Hastings

Representing chemicals using OWL, Description Graphs and RulesMichel Dumontier

OWL and OBODuncan Hull

Formalization and implementation of BFO 2 with a focus on the OWL implementationgolpedegato2

Obo and common logicChris Mungall

Real World Applications of OWLMichel Dumontier

Formal representation of models in systems biologyMichel Dumontier

Sw owl rules-proposalokeee

2011 ebi industry workshopMichel Dumontier

Towards ubiquitous OWL computing: Simplifying programmatic authoring of and q...Hilmar Lapp

2009 CSBB LAB 新生訓練 Abner Huang

The Subliminal Toolbox: automating steps in the reconstruction of metabolic n...Neil Swainston

MIREOTMelanie Courtot

Experiences in the biosciences with the open biological ontologies foundry an...Chris Mungall

Macromolecules or Big Small Molecules? Handling biopolymers in a chemical reg...NextMove Software

Improving the quality of chemical databases with community-developed tools (a...baoilleach

20090511 Manchester BiochemistryMichel Dumontier

Tutorial OWL and drug discovery ICBO 2013Samuel Croset

Ontology Development Kit: Bio-Ontologies 2019Chris Mungall

Protein structure classification/domain prediction: SCOP and CATH (Bioinforma...SELF-EXPLANATORY

All together now: piecing together the knowledge graph of lifeChris Mungall

Systems Biology Model Semantics and IntegrationAllyson Lister

Adapt OWL as a Modular Ontology LanguageJie Bao

Pipeline for automated structure-based classification in the ChEBI ontologyJanna Hastings

Ontology-based Data IntegrationJanna Hastings

Contenu connexe

Similaire à Representing the ChEBI ontology in OWL

Obo and common logicChris Mungall

Real World Applications of OWLMichel Dumontier

Formal representation of models in systems biologyMichel Dumontier

Sw owl rules-proposalokeee

2011 ebi industry workshopMichel Dumontier

Towards ubiquitous OWL computing: Simplifying programmatic authoring of and q...Hilmar Lapp

2009 CSBB LAB 新生訓練 Abner Huang

The Subliminal Toolbox: automating steps in the reconstruction of metabolic n...Neil Swainston

MIREOTMelanie Courtot

Experiences in the biosciences with the open biological ontologies foundry an...Chris Mungall

Macromolecules or Big Small Molecules? Handling biopolymers in a chemical reg...NextMove Software

Improving the quality of chemical databases with community-developed tools (a...baoilleach

20090511 Manchester BiochemistryMichel Dumontier

Tutorial OWL and drug discovery ICBO 2013Samuel Croset

Ontology Development Kit: Bio-Ontologies 2019Chris Mungall

Protein structure classification/domain prediction: SCOP and CATH (Bioinforma...SELF-EXPLANATORY

All together now: piecing together the knowledge graph of lifeChris Mungall

Systems Biology Model Semantics and IntegrationAllyson Lister

Adapt OWL as a Modular Ontology LanguageJie Bao

Similaire à Representing the ChEBI ontology in OWL (20)

Obo and common logic

Real World Applications of OWL

Formal representation of models in systems biology

Sw owl rules-proposal

2011 ebi industry workshop

Towards ubiquitous OWL computing: Simplifying programmatic authoring of and q...

2009 CSBB LAB 新生訓練

The Subliminal Toolbox: automating steps in the reconstruction of metabolic n...

MIREOT

Experiences in the biosciences with the open biological ontologies foundry an...

Macromolecules or Big Small Molecules? Handling biopolymers in a chemical reg...

Improving the quality of chemical databases with community-developed tools (a...

20090511 Manchester Biochemistry

Tutorial OWL and drug discovery ICBO 2013

Ontology Development Kit: Bio-Ontologies 2019

Protein structure classification/domain prediction: SCOP and CATH (Bioinforma...

All together now: piecing together the knowledge graph of life

Systems Biology Model Semantics and Integration

Adapt OWL as a Modular Ontology Language

Plus de Janna Hastings

Pipeline for automated structure-based classification in the ChEBI ontologyJanna Hastings

Ontology-based Data IntegrationJanna Hastings

Using ChEBI to explore the underlying biology in metabolomics studiesJanna Hastings

Chemical classification for the Semantic WebJanna Hastings

Emotion Ontology and Affective NeuroscienceJanna Hastings

Ontologies for Mental Health and DiseaseJanna Hastings

Waves and fields in bio-ontologiesJanna Hastings

Representing addiction in Mental Functioning and Disease ontologiesJanna Hastings

Bio-ontologies in bioinformatics: Growing up challengesJanna Hastings

Mental functioning ontology for interdisciplinary research into mental diseas...Janna Hastings

From chemicals to minds: Integrated ontologies in the search for scientific u...Janna Hastings

Modularity requirements in bio-ontologies: a case study of ChEBIJanna Hastings

The SHAPES workshop, and Holes in living beings Janna Hastings

A chemical view into biological systemsJanna Hastings

Chemical diagrams and the IAOJanna Hastings

The emotion ontology: enabling interdisciplinary research in the affective sc...Janna Hastings

Hyperontology for the biomedical ontologistJanna Hastings

Using multiple ontologies to characterise the bioactivity of small moleculesJanna Hastings

Processes and PropertiesJanna Hastings

Representing sequences of parts in processes using OWLJanna Hastings

Plus de Janna Hastings (20)

Pipeline for automated structure-based classification in the ChEBI ontology

Ontology-based Data Integration

Using ChEBI to explore the underlying biology in metabolomics studies

Chemical classification for the Semantic Web

Emotion Ontology and Affective Neuroscience

Ontologies for Mental Health and Disease

Waves and fields in bio-ontologies

Representing addiction in Mental Functioning and Disease ontologies

Bio-ontologies in bioinformatics: Growing up challenges

Mental functioning ontology for interdisciplinary research into mental diseas...

From chemicals to minds: Integrated ontologies in the search for scientific u...

Modularity requirements in bio-ontologies: a case study of ChEBI

The SHAPES workshop, and Holes in living beings

A chemical view into biological systems

Chemical diagrams and the IAO

The emotion ontology: enabling interdisciplinary research in the affective sc...

Hyperontology for the biomedical ontologist

Using multiple ontologies to characterise the bioactivity of small molecules

Processes and Properties

Representing sequences of parts in processes using OWL

Dernier

Developer Data Modeling Mistakes: From Postgres to NoSQLScyllaDB

My Hashitalk Indonesia April 2024 PresentationRidwan Fadjar

Powerpoint exploring the locations used in television show Time Clashcharlottematthew16

Are Multi-Cloud and Serverless Good or Bad?Mattias Andersson

What's New in Teams Calling, Meetings and Devices March 2024Stephanie Beckett

"LLMs for Python Engineers: Advanced Data Analysis and Semantic Kernel",Oleks...Fwdays

"ML in Production",Oleksandr BaganFwdays

Gen AI in Business - Global Trends Report 2024.pdfAddepto

Vector Databases 101 - An introduction to the world of Vector DatabasesZilliz

My INSURER PTE LTD - Insurtech Innovation Award 2024The Digital Insurer

Human Factors of XR: Using Human Factors to Design XR SystemsMark Billinghurst

WordPress Websites for Engineers: Elevate Your Brandgvaughan

Training state-of-the-art general text embeddingZilliz

CloudStudio User manual (basic edition):comworks

Story boards and shot lists for my a level piececharlottematthew16

"Subclassing and Composition – A Pythonic Tour of Trade-Offs", Hynek SchlawackFwdays

E-Vehicle_Hacking_by_Parul Sharma_null_owasp.pptxnull - The Open Security Community

Ensuring Technical Readiness For Copilot in Microsoft 3652toLead Limited

Artificial intelligence in cctv survelliance.pptxhariprasad279825

Commit 2024 - Secret Management made easyAlfredo García Lavilla

Dernier (20)

Developer Data Modeling Mistakes: From Postgres to NoSQL

My Hashitalk Indonesia April 2024 Presentation

Powerpoint exploring the locations used in television show Time Clash

Are Multi-Cloud and Serverless Good or Bad?

What's New in Teams Calling, Meetings and Devices March 2024

"LLMs for Python Engineers: Advanced Data Analysis and Semantic Kernel",Oleks...

"ML in Production",Oleksandr Bagan

Gen AI in Business - Global Trends Report 2024.pdf

Vector Databases 101 - An introduction to the world of Vector Databases

My INSURER PTE LTD - Insurtech Innovation Award 2024

Human Factors of XR: Using Human Factors to Design XR Systems

WordPress Websites for Engineers: Elevate Your Brand

Training state-of-the-art general text embedding

CloudStudio User manual (basic edition):

Story boards and shot lists for my a level piece

"Subclassing and Composition – A Pythonic Tour of Trade-Offs", Hynek Schlawack

E-Vehicle_Hacking_by_Parul Sharma_null_owasp.pptx

Ensuring Technical Readiness For Copilot in Microsoft 365

Artificial intelligence in cctv survelliance.pptx

Commit 2024 - Secret Management made easy

Representing the ChEBI ontology in OWL

1. The ChEBI ontology and OWL Industry Programme Ontology Tutorial European Bioinformatics Institute 13 October 2010 Janna Hastings EBI Chemoinformatics and Metabolism

4. ChEBI ontology 4/26/2010 A ChEBI entry page

6. ChEBI ontology 20.10.10 Molecular structure ontology

7. ChEBI ontology 20.10.10 Role ontology

8. ChEBI internal ontology architecture ChEBI ontology 20.10.10 Oracle database

10.

11.

12.

13.

14.

15.

16.

17. OWL representation Without internal structure, all parts must be explicitly asserted (which leads to a combinatorial explosion for larger molecules) But the internal structure of complex molecules cannot be encoded in OWL ontology axioms due to their cycles does not have a model in the shape of a tree

18.

19.

20. Chemical description graphs + Rules defined to detect cycles and parts Reasoning results: able to perform classification (but scalability a concern)

21.

22. Thank you for your attention