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Data and ontology integration issues in the biosciences. Marijke Keet Napier University, 10 Colinton Road, Edinburgh EH10 5DT [email protected] / [email protected] Presentation at the Micro-Array Department, University of Amsterdam 23-8-2004. Overview presentation.

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data and ontology integration issues in the biosciences

Data and ontology integration issues in the biosciences

Marijke Keet

Napier University, 10 Colinton Road, Edinburgh EH10 5DT [email protected] / [email protected]

Presentation at the Micro-Array Department, University of Amsterdam


overview presentation
Overview presentation
  • Data integration ontology
  • Ontologies

kinds, formalisation, bias & bioscience [after the break]

  • Ontology integration

categorisation, some challenges

overview presentation3
Overview presentation
  • Data integration ontology
  • Ontologies

kinds, formalisation, bias & bioscience [after the break]

  • Ontology integration

categorisation, some challenges

data heterogeneity
Data heterogeneity
  • Schematic

data type, labelling, aggregation, generalisation

  • Semantic

naming, scaling and units, confounding

  • Intensional

domain, integrity constraints

Based on Goh (1996)

integrating data
Integrating data

e.g. DB1has attribute name colour and value green and DB2 with color and 2DE60E

Data is different, but the conceptualisation is the same. Capture this agreement in an ontology.

Shorthand: “specification of a shared conceptualisation” (Gruber), but better: “An ontology is a logical theory accounting for the intended meaning of a formal vocabulary, i.e. its ontological commitment to a particular conceptualisation of the world. The intended models of a logical language using such a vocabulary are constrained by its ontological commitment. An ontology indirectly reflects this commitment (and the underlying conceptualisation) by approximating these intended models.” (Guarino, 1998).

Overview presentation
  • Data integration ontology
  • Ontologies

kinds, formalisation, bias & bioscience [after the break]

  • Ontology integration

categorisation, some challenges

kinds of ontologies
Kinds of ontologies
  • Representation ontologies:conceptualisations that underlie knowledge representation formalisms.
  • Top-levelontologies: generic and intermediate ontology concepts. This can be on top of a domain ontology or as stand-alone effort; main aspect is domain independence.
  • Genericontologies consist of the general, foundational aspects of a conceptualisation (a lower branch in a top-level)
  • Intermediateontologiesare slightly more tailored towards a conceptualisation of a specific domain. There may not be references to generic ontologies.
  • Domainontologiesspecialize in a subset of generic ontologies in a domain or sub-domain.
  • Applicationontologies (…):the UoD is even narrower than a domain ontology.
levels of formalisation 1 2
Levels of formalisation (1-2)

Catalogue of normalised terms: is a simple list without inclusion order, axioms or glosses.

Glossed catalogue: a catalogue with natural language glossary entries, e.g. a dictionary of medicine.

Prototype-based ontology: types and subtype are distinguished by prototypes rather than definitions and axioms in a formal language

Taxonomy: is a collection of concepts having a partial order induced by inclusion.

Axiomatised taxonomy: as taxonomy, but then with axioms and stated in a formal language.

Context library / axiomatised ontology: a set of axiomatised taxonomies with relations among them, like the inclusion of one context into another one, or the use of a concept from one in the other one.

Lightweight ontologies

Informal ontology

Semi-formal ontology?

Heavyweight ontologies

Formal ontology

formalisations 2 2
Formalisations (2-2)


athletic game

court game


outdoor game

field game


game(x)  activity(x)

athletic game(x)  game(x)

court game(x)  athletic game(x)  y. played_in(x,y)  court(y)

tennis(x)  court game(x)

double fault(x)  fault(x)  y. part_of(x,y)  tennis(y)




field game

court game

athletic game

outdoor game

Axiomatized theory



NT athletic game

NT court game

RT court

NT tennis

RT double fault


DB/OO scheme



Ontological precision

precision: the ability to catch all and only the intended meaning

(for a logical theory, to be satisfied by intended models)

Gangemi (2004)

Overview presentation
  • Data integration ontology
  • Ontologies

kinds, formalisation, bias & bioscience [after the break]

  • Ontology integration

categorisation, some challenges

ontology integration 1 4
Ontology integration (1-4)
  • Combining different conceptualisations (‘views on reality’)… somehow.
  • System, language/syntax, structure, and semantic integration. Latter most difficult.
  • Structure and/versus semantic integration example
  • Anarchy of terminology, definitions and methodologies (now at least 24 terms and 48 definitions & methodologies)
  • Organise into levels of integration. Develop taxonomy of ontology integration?
ontology integration 2 4
Ontology integration (2-4)

Example structure/semantics


ontology integration 3 4
Ontology integration (3-4)

Initial categorisation

Increase in (perceived) difficulty of operation

Unification, total compatibility, merging [similar subject domains]

Merging [different subject domains], partial compatibility

Mapping, approximations, helper model, alignment, intersection ontology

Extending, incremental loading

Use in/for applications

Queried ontologies, hybrid ontologies

Increase in level of integration

ontology integration 4 4
Ontology integration (4-4)

Some challenges

  • (In)formal ontologies
  • (In)consistencies in ontology design decisions during development (relationships) detail
  • Top-down versus/combined with bottom-up

Using foundational aspects in ontology development decreases the chance of design inconsistencies and facilitates integration

  • Subject domain heterogeneity example
  • Conflicting goals
  • More conflicts and mismatches here
in consistencies in ontology design decisions 1 2
(In)consistencies in ontology design decisions (1-2)
  • Subsumption versus instantiation: if A isA B, then all instances of A are also instances of B. The latter says ainstanceOfA, i.e. a is an individual (particular, instance) and not a subtype of A.
  • Desiderata to create the hierarchy. Like keeping function, structure, process separate.

E.g. the OBO phenotype ontology does not:

%attribute\:excretory_function ; PATO:00300204

%attribute\:urination ; PATO:00305204

%attribute\:urine_composition ; PATO:00301204

in consistencies in ontology design decisions 2 2
(In)consistencies in ontology design decisions (2-2)
  • E.g. aseptate hypha isa hypha [aseptate = hypha without cross walls] and hypha in mycelium isa hypha. Former is about a special kind of hypha, the latter takes topology as distinction for subtyping -> are distinct factors though treated as a same kind of isA where in the FAO hypha subsumes both.

Allow multiple inheritance - or not?

  • partOf: such as parthood, proper parthood, connection, external connection, tangential parthood, interior parthood, partial coincidence and located-in (see e.g. Smith and Rosse, 2004; Donnelly, 2004)
  • Properties and meta properties (see Guarino and Welty (2000) for details)


conflicts and mismatches
Conflicts and mismatches
  • Factors affecting ontology combination tasks
  • Practical problems: finding matchings, diagnosis repeatability, software usability, social factors of cooperation, goals
  • Mismatches between ontologies
  • - language level
  • syntax, logical representation, semantics of primitives, language expressivity, precision
  • - ontology level
  • - conceptualisation
  • content/UoD, concept scope, relationship scope, context, aggregation, accuracy
  • - explication
  • terminological: hyper-/hyponyms (generalization), homonyms, synonyms
  • modelling style: paradigm, entity/concept description
  • encoding
  • Versioning: identification, traceability, translation
Overview presentation
  • Data integration ontology
  • Ontologies

kinds, formalisation, bias & bioscience

  • Ontology integration

categorisation, some challenges

ontologies for bioscience 1 3
Ontologies for bioscience (1-3)



Formation of a theory

Formation of hypothesis



New empirical axioms/laws (universal)


Empirical axioms/laws (universal)




Induction, confirmation


Facts with an empirical basis


ontologies for bioscience 2 3
Ontologies for bioscience (2-3)
  • Ontologies as engineering artefacts

- Facilitate knowledge reuse, interoperability

Modelling practice

Another item in the problem-solver’s toolbox

Part of a new/improved software system

- SW tools for ontology development, maintenance, integration

  • Ontologies embedded in science

- Top-level ontologies

Attempt to understand, what/why

- W.r.t. bioscience

‘Co-defining’ concepts?

Part of falsification paradigm and steps 2, 3 of standard view

-> synergy, mutually beneficial process, but…

ontologies for bioscience 3 3
Ontologies for bioscience (3-3)
  • The very essence of scientific progress is change, redefinition and creation of new concepts.

-> ontology subject to (extensive) modification. Complicates integration

  • Concepts underspecified, hypotheses and theories exist simultaneously.

-> accommodate this in an ontology? E.g. a library of ‘alternative views ontologies’, with loose coupling instead of integration?

-> capture what is, what can be, (and what might be?)

  • Biological data is more complicated than technological and practice data.

-> more here

  • Systems Thinking, integrative concepts, holism and process-orientation contradict with ‘objectifying’ knowledge in ontologies

-> interdisciplinary work of ontologists with scientists

  • Empiricism and the theoretical methodology in life sciences.

-> bottom-up resp. top-down procedures for ontology development

formalising biological knowledge
Formalising biological knowledge
  • Challenging biological data characteristics detail

Are these aspects real challenges, or due to limited expressiveness of non-formal approaches and software modelling paradigms (ER, OO, …), or maybe due to limited knowledge of both the domain expert and ontologist?

  • Applied sciences within ‘bio’ (medicine, ecology, environmental sciences), contexts detail



main biological data characteristics

No legacy, no full knowledge of UoD.

-> Former might be alleviated over time; double curriculum, but

still difference in ‘science’ and ‘engineering’ approaches


radations/non-discrete data, occasional relationships, conditionality.

-> Separate layer of sw, or semantics intricate part of bio data?

Uncertainties, ‘postulations’, importance of parameters, properties.

-> characteristic of conducting scientific research; lack vs

abundance of data can be argued as design decision, not

characteristic of the data/concepts; ‘upgrading’ of concepts

Definitional problems and lack of standardisation in nomenclature.

-> Is the surface layer of next point; overabundance of ‘semi-

standards’; can be in itself interdisciplinary within bioscience


isagreements between and within research groups, ‘alternative’

hypotheses and theories coexist.

-> There is not one ‘what is’; development of multiple theories,

concepts before agreement is part of doing scientific

research; library of models, aliases

Main biological data characteristics


applied bioscience
Applied bioscience

Emphasis core sciences:

‘All-inclusive’ comprehensive models

Emphasis applied bioscience:

Conceptually representing the integration

of various core disciplines,

Only what is relevant in limited context



references and more info 1 2
References and more info (1-2)
  • Donnelly, M. (2004). On parts and holes: the spatial structure of the human body. MEDINFO 2004, San Francisco, USA.
  • Gangemi, A. (2004). Some design patterns for domain ontology building and analysis. Manchester 15-16 January.
  • Goh, C.H. (1996). Representing and reasoning about semantic conflicts in heterogeneous information sources. PhD, MIT.
  • Guarino, N. (1998). Formal Ontology and Information Systems. In: Formal Ontology in Information Systems, Proceedings of FIOS'98, Trento, Italy, Amsterdam: IOS Press.
  • Guarino, N. and Welty, C. (2000). A formal ontology of properties. Proceedings of 12th Int. Conf. on Knowledge Engineering and Knowledge Management, Lecture Notes on Computer Science, Springer Verlag.
  • Keet, C.M. (2004). Ontology development and integration for the biosciences. Technical Report, Napier University, Edinburgh, UK.
  • Smith, B. and Rosse, C. (2004). The role of foundational relations in the alignment of biomedical ontologies. Proceedings of MEDINFO, San Francisco, USA.
references and more info 2 2
References and more info (2-2)
  • Some websites with different perspectives/aims/information on ontologies




Formal Ontology

RE Kent

WonderWeb project

JF Sowa


AAAI page

  • Links to a few of groups developing tools

KAON, Protégé, VU, STARLab