Bio-ontologies SIG in conjunction with ISMB July Boston, USA

General Info 94 participants – mainly from USA and moslty Stanford University. Online proceedings will be published – the authors who are interested must prepare a camera-ready according to special requirements, if they want they paper to be in a referred edition. All PPT presentations are available on the SIG website.

Interesting Presentations The Bioportal – facilities ISA Software Suit – annotation of experimental data (assays), annotation according to ontologies Knowledge Blog Journal of Biomedical Semantics Other conferences OBML, ICBO, SMBM

Interesting Presentations Ciccarese & Clark – Metadata is kept separately from the data and can be used to find crossing points with other documents Ghazvinian et al. How Orthogonal are the OBO Foundry Ontologies? – Numbers 53 ontologies in total 93% overlap 13 ontologies reuse terms only 3 ontologies are fully orthogonal – Reasons terms representing the same entity with same name terms representing related but different entities with the same name terms represent different entities with the same name

OpenTox related Issues Definition of ontologies [Rzhetsky, A.]: – Tool for structuring, organising, mathematical theory – Walking shoes – Esperanto – common language Referencing ontologies – MIREOT - Minimum information to reference an external ontology terms Upload to Bioportal –

OpenTox related Issues Available ontologies – E-Lico project eProPlan (e-Lico Protégé-based Planning) & Data Mining Work Flow Ontology Data Mining Ontology for Workflow Optimization (DMOP) through Meta- Mining – OntoDM: An Ontology of Data Mining – Exposé – DDI - An Ontology for Drug Discovery Investigations Web Protégé = Collaborative Protégé Different partners can use one of those for editing the same ontology Soon compatibility between Protégé 3 and 4 is expected

Important Contacts Dr. Larisa N. Soldatova – SIG co-organiser RC UK Fellow, Computer Science Department, The University of Wales, Aberystwyth, UK Prof. Ross King – with previous experience in predictive toxicology Group Coordinator Computational Biology Group Department of Computer Science Aberystwyth University Julia Kozlovsky (AstraZeneca) Pistoia Alliance (open standards) - Innovative Medicines Initiative - James Malone a mailing list where one could ask related questions