hyperontology for the biomedical ontologist

Hyperontology for the Biomedical OntologistA Sketch and Some Examples

Oliver Kutz 1

Till Mossakowski 1, 2

Janna Hastings 3,4

Alexander Garcia Castro 5

Aleksandra Sojic 6

1 Research Center on Spatial Cognition, University of Bremen, Germany2 DFKI GmbH Bremen and University of Bremen, Germany

3 Chemoinformatics and Metabolism, European Bioinformatics Institute, UK4 Swiss Centre for Affective Sciences, University of Geneva, Switzerland

5 University of Arkansas for Medical Sciences, USA6 European School of Molecular Medicine, Milan; and University of Milan, Italy

ICBO, Buffalo, July 2011

Wednesday, April 12, 2023 2

Heterogeneous Formalisms

Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

OWL

OBOHOL

CL RDF

RulesFrames

OWL-EL

OWL-RL

Modal logic Temporal logic

Fuzzy logicNon-monotonic

logic

Wednesday, April 12, 2023 3Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

Wednesday, April 12, 2023 4

Heterogeneous Content

Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

Patient information

agefamily history

Disease information

social status

Physiological information

diet

blood pressuremetabolic profile

genotype

cell type

pathways

etiology

symptomsGranularity

Time Qualitative /Quantative

Pathological / Canonical

Wednesday, April 12, 2023 5Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

Modularity as desiderataSmall modules:• human understandable, re-usable, one level at

a time, etc.• Proving-in-the-small

Large programs constructed from modules:• Composition, Linkage, etc.• Proving-in-the-large

Idea of a Module Interconnection Language

Wednesday, April 12, 2023 6Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

Modularity at design-time

Subject-specific modules

Logic-specific modules (extensions)

“Minimal” expressivity for a given topic

Imports and complex interrelationships

Wednesday, April 12, 2023 7

Hyperontology is a framework for interrelating

heterogeneous ontologymodules

Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

Logical translation

Modular connections

Integrated tools and reasoners

Wednesday, April 12, 2023 8Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

Systematically linking ontology modules defined in different formalisms requires:

A logic graph

Fixed logic translations

Wednesday, April 12, 2023 9Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

Common Algebraic Specification Language

Standardised many-sorted first-order specification language

Various extensions and sublanguages, including higher-order dialects, modal logic, OWL-DL;

Supports structured specifications including: imports, hiding, renaming, union, extensions.

Wednesday, April 12, 2023 10Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

Semantics of structured specifications

Wednesday, April 12, 2023 11Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

HETCASL

Extension of CASL for seamless combination of different logics

Provides syntactic “sugar”

Wednesday, April 12, 2023 12Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

HETS – The Heterogeneous Tool SetStructured representations

Reuse/independent development of modules

Library of logics/formalisms supported, incl. OWL-DL

Various provers connected: incl. OWLDL, first-order, higher-order, model checker

Wednesday, April 12, 2023 13

Wednesday, April 12, 2023 14Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

Applications

A sketch of some scenarios

from bio-ontologies

Wednesday, April 12, 2023 15Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

HOL as constraintBoth the Sequence Ontology (SO) and the RNAO

provide axiomatizations in first-order and higher-order logic

to further constrain the semantics of the relationships that they use in OWL

(not explicitly linked to the OWL version)

Wednesday, April 12, 2023 16Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

SIMULATION

ANATOMY

Wednesday, April 12, 2023 17Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

Biochemical Structures

Wednesday, April 12, 2023 18Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

FullerenesCubic, 3-connected, planar graphs in which all faces are either pentagons or hexagons (5 or 6 atoms).

Can be defined with Monadic Second Order Logic (MSOL)

Cubic

3-connected

Planar (Kuratowski)

Wednesday, April 12, 2023 19Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

Interrelating Ontologies

Wednesday, April 12, 2023 20Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

Wednesday, April 12, 2023 21Hyperontology for Bio-ontologists (WoMBO @ ICBO 2011)

Conclusions

Biomedical ontologies are highly complex

and need diverse formalisms for proper treatment

The Hyperontology framework provides the “plumbing” to seamlessly integrate such

formalisms

Wednesday, April 12, 2023 22

Acknowledgements

FundingDFG-funded collaborative research centre

SFB/TR 8 `Spatial Cognition' The German Federal Ministry of Education and

Research (Project 01 IW 07002 FormalSafe).