Feature Conference Report: The ESF programme on ...downloads.hindawi.com/journals/ijg/2003/981532.pdfSteffen Schulze-Kremer (RZPD; Resource Center/Primary Database, Germany) presented

Comparative and Functional GenomicsComp Funct Genom 2003; 4: 68–70.Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.252

Feature

Conference Report: The ESF programme on‘Integrated Approaches to FunctionalGenomics’. Workshop on ‘Ontology forBiology’7–8 November 2002, European Media Laboratory, Villa Bosch,Heidelberg, Germany

Luca Bernardi,1* Isabel Rojas1 and Paul van der Vet21European Media Laboratory, Villa Bosch, Heidelberg, Germany2Centre for Telematics and Information Technology, University of Twente, The Netherlands

*Correspondence to:Luca Bernardi, European MediaLaboratory, Villa Bosch,Heidelberg, Germany.E-mail:[email protected]

Received: 2 December 2002Revised: 4 December 2002

Introduction

Ontologies are finding increasing use in all kinds ofcomputer applications, and applications in biologyare no exception. The main objective of this work-shop was to bring together scientists of variousdisciplines, such as biologists, computer scientists,philosophers and computer linguists, who are work-ing on, or are interested in, the development ofontologies in biology and related fields. We wantedto share experiences, methods, ontologies and tools.The invitation to the speakers mentioned four mainquestions to focus the discussion:

1. Why do we need ontologies? Are ontologiesessential for consistent annotation and indexing?Are they essential for automated processing ofbiological data?

2. How are ontologies built? The teams that buildontologies may comprise domain experts, com-puter scientists and even philosophers in any

combination. What are the experiences in build-ing ontologies? In particular, are there workingpractices that can be shared with other groups?

3. How are ontologies checked for quality? Whatcriteria are relevant? Which tools can be used?

4. How are ontologies used? It is known thatontologies are used for very diverse purposes,and therefore heterogeneity in ontologies isonly to be expected. Additionally, there isthe opportunity to draw attention to novel,unexpected purposes.

The talks

Although the original intent was to organize theworkshop as four sessions, each devoted to oneof the questions above, speakers tended to addressseveral questions in their talks. We will summarizeall talks in an order that, for reasons of exposi-tion, does not reflect the actual order at the work-shop. In this Issue, there are seven reviews and

Copyright European Science Foundation. Published in 2003 by John Wiley & Sons, Ltd.

Conference Report 69

one paper from speakers at the workshop, andthere is also a review by Alexa McCray (NationalLibrary of Medicine, USA), who was invited as aspeaker but was unable to attend. The workshopoffered the opportunity of presenting posters. Atotal of 10 posters presented an interesting com-plement to the series of talks. Abstracts of alltalks and posters, and slides of the talks, can beaccessed via the web page of the workshop athttp://projects.eml.org/sdbv/events/bioontology/.The slides also point to the webpages of the authorsand/or projects.

Two talks were dedicated to the Gene Ontology(GO) project. Midori Harris [European Bioin-formatics Institute (EBI)] gave an introduction toGO, which is arguably the most prominent exampleof a biological ontology in the field of functionalgenomics. She described the classification aspectsconsidered in GO, highlighting its scope, the typeof relations considered and its use, mentioningsome of the tools that use GO. GO is designed pri-marily as a tool for humans: to achieve consistentannotations of data in databases, and as an index-ing aid. Rolf Apweiler (EBI) demonstrated oneparticular use of GO, the Gene Ontology Anno-tation project (GOA), which aims at annotatinggene products using GO terms in a number of EBIdatabases, such as SWISS-PROT + TrEMBL andInterPro. In the old SWISS-PROT data model, anannotation and its source are mentioned in differentfields, so that their relation is broken. GOA reunitesannotation and source.

Although GO is primarily intended to be atool for humans, computer projects involving, forexample, automated text mining, obviously profitfrom consistent annotation. In this sense, GO pre-pares for more automated data processing. How-ever, GO is not intended for automated reason-ing. The annotations produced in the GOA projectwill be regarded by computer scientists as knowl-edge representation, given that they classify andcharacterize the entries in the annotated databases.This ‘knowledge representation language’ is lessexpressive than several other knowledge repre-sentation languages. Typically, the less expressivea knowledge representation language is, the lesspowerful are the capabilities for automated reason-ing. Systems in which the reasoning is partly orwholly automated therefore need a more expres-sive and more formal ontology. Enriching the for-mal semantic content of GO is one of the goals

of the GONG initiative (http://gong.man.ac.uk).Jennifer Williams (Ontology Works, USA) pre-sented an initial work that also moves in this direc-tion. She enriches GO with formalized backgroundknowledge and formalizes the ontology in otherways. The intention is to use the result as a start-ing point for systems that are able to reason aboutbiological data.

Udo Hahn (University of Freiburg, Germany)and Alfonso Valencia (Spanish National Centerof Biotechnology) talked about their experiencesin using ontologies in systems that perform infor-mation extraction from text. Hahn presented hiswork on the partly automatic extraction of an ontol-ogy from the UMLS (Unified Medical LanguageSystem) thesaurus. Valencia presented his work onthe automatic generation of classifications of gene-product functions using bibliographic information.

With respect to methodologies for the con-struction of ontologies, Aldo Gangemi (ItalianNational Research Council) presented a series ofhigh-level conceptual tools for building domainontologies, ontologies for biomedical domainsamong them. He introduced DOLCE, a founda-tional ontology containing an axiomatic charac-terization of basic, domain-independent conceptsand relations. He also introduced the ONIONSmethodology for the transformation of terminolo-gies into ontologies.

Steffen Schulze-Kremer (RZPD; ResourceCenter/Primary Database, Germany) presentedhis experience in the development of ontologiesfor biology. He characterized ontologies in biologyand bioinformatics and described the methodologyand tools he uses.

These talks were well complemented by thoseof Esther Ratsch (European Media Labora-tory, Germany) and Alain Viari (INRIA Rhone-Alpes). Ratsch presented work on the creation ofan ontology for the domain of protein interactions.The ontology is developed by an interdisciplinarygroup that comprises researchers in biology, com-puter science and computer linguistics. Viari intro-duced Genostar, a software platform for genomicdata integration and analysis. Genostar is based onan ontology of the ‘genomic world’, represented asa large network of biological entities and their rela-tionships. Viari also presented the work of AnneMorgat (INRIA Rhone-Alpes) — who unfortu-nately was not able to attend — on the Panoramixproject. Panoramix aims at federating knowledge

Copyright European Science Foundation. Published in 2003 by John Wiley & Sons, Ltd. Comp Funct Genom 2003; 4: 68–70.

70 Conference Report

bases in the fields of relational annotation of micro-bial genomes. The system is based on a formaland explicit representation of the biological entitiesinvolved in genome analysis.

Steffen Staab (University of Karlsruhe,Germany) discussed the set of tools, languages andservices that are collectively known as the ‘seman-tic web’. The semantic web aims at interoperableweb services. The semantic web is designed to relyon many, decentralized ontologies that have beenmade available by their owners, rather than on cen-tralized, monolithic ontologies.

Daniel von Wachter (University of Leipzig,Germany) offered a more philosophical touch tothe workshop. He demonstrated how philosophicalviewpoints influence the building of ontologies bymeans of an example from his own work, whichdeals with a theory of causality and an ontology ofa part of the medical domain. The claim is that byusing that theory, the construction of the domainontology is facilitated.

Conclusions and future aims

The workshop was the theatre of many discussions,both after talks and in the long intervals betweensessions. They reflected how the field is far fromestablished and that even terminological issuesplay a role. The differences between perspectives(use, objective and even definition of ontology) areclosely correlated with the purpose to which theontology is put. Although this is in itself not a sur-prising conclusion, it pays to emphasize it becausejust mentioning the term ‘ontology’ still suffices togenerate a heated debate. Mutual misunderstandingstands in the way of interdisciplinary work, and allagreed that the functional genomics research pro-gram is only feasible if researchers from a numberof disciplines cooperate. Researchers from differentbackgrounds should then come to terms with eachother, recognizing different use contexts and needs,and different ways to approach the subject. Bio-logical subject matter is quite foreign to computer

scientists. Computer scientists cannot reasonablyexpect biologists to be aware of, or even inter-ested in, how particular applications are built. Fora biologist, a computer application is just a tool. Itshould fulfil the requirements every tool has to ful-fil: ease of use, transparency, efficiency and effec-tiveness. Bioinformaticians fall midway betweenthese two professions. They also approach com-puter applications as tools but they put their toolsto very advanced uses. Bioinformaticians tend tobuild their software partly, or wholly, themselves,and they can thus function as two-way interpreters.

On the second day, there was a discussion abouta possible sequel to this workshop. Interdisciplinarycooperation is best practised in concrete projects,where the benefits of cooperation are visible to allfrom the outset. It was therefore proposed to orga-nize a hands-on, summer school-like event where awell-defined biological ontology topic is addressedin such a way that biologists, bioinformaticians andcomputer scientists are all involved. One of thekey issues is to define the end-user role for thedeliverable of this event, because the end user isthe ultimate arbiter on system functionality. Thesethoughts have to mature before they can be com-municated to the community.

Acknowledgements

The workshop committee would like to thank the EuropeanScience Foundation for its generous grant and support. Wewould also like to thank the other sponsors of the work-shop: the Klaus Tschira Foundation (KTS), the EuropeanMedia Laboratory (EML) and Ace Bioscience. The organi-zational support of the University of Twente is gratefullyacknowledged. Special thanks go to Annette Martin, forher constant and kind support, and her patience in answer-ing our questions regarding the workshop organization. Theorganizers would like to acknowledge the help of the fol-lowing persons from the EML and KTS: Andreas Reuter,Barbel Mack, Kornelia Gorisch, Silke Peters, Peter Thoma,Ursula Kummer, Holger Buckel, Peter Saueressig, Rein-hold Weinmann and Alexandra Martin. Last, but not least,thanks to the reviewers and of course to the participants,who made the workshop a very interesting one.

Copyright European Science Foundation. Published in 2003 by John Wiley & Sons, Ltd. Comp Funct Genom 2003; 4: 68–70.

Submit your manuscripts athttp://www.hindawi.com

Hindawi Publishing Corporationhttp://www.hindawi.com Volume 2014

Anatomy Research International

PeptidesInternational Journal of


Hindawi Publishing Corporation http://www.hindawi.com

International Journal of

Volume 2014

Zoology


Molecular Biology International

GenomicsInternational Journal of


The Scientific World JournalHindawi Publishing Corporation http://www.hindawi.com Volume 2014


BioinformaticsAdvances in

Marine BiologyJournal of



Signal TransductionJournal of


BioMed Research International

Evolutionary BiologyInternational Journal of



Biochemistry Research International

ArchaeaHindawi Publishing Corporationhttp://www.hindawi.com Volume 2014


Genetics Research International


Advances in

Virolog y

Hindawi Publishing Corporationhttp://www.hindawi.com

Nucleic AcidsJournal of

Volume 2014

Stem CellsInternational



Enzyme Research


International Journal of

Microbiology

Documents

Feature Conference Report: The ESF programme on ...downloads.hindawi.com/journals/ijg/2003/981532.pdfSteffen Schulze-Kremer (RZPD; Resource Center/Primary Database, Germany) presented