1. Bio-ontologies SIG in conjunction with ISMB 2010 9-10 July Boston, USA http://www.bio-ontologies.org.uk

2. 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.

3. Interesting Presentations The Bioportal – facilities http://bioportal.bioontology.org/ http://bioportal.bioontology.org/ ISA Software Suit – annotation of experimental data (assays), annotation according to ontologies http://isatab.sourceforge.net/ http://isatab.sourceforge.net/ Knowledge Blog http://ontologies.knowledgeblog.org http://ontologies.knowledgeblog.org Journal of Biomedical Semantics http://www.jbiomedsem.com http://www.jbiomedsem.com Other conferences OBML, ICBO, SMBM

4. 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

5. 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 http://obi-ontology.org/page/MIREOT http://obi-ontology.org/page/MIREOT Upload to Bioportal – info@bioportal.org info@bioportal.org

6. OpenTox related Issues Available ontologies – E-Lico project http://www.e-lico.eu/?q=node/155 http://www.e-lico.eu/?q=node/155 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 - 2008 http://portal.acm.org/citation.cfm?id=1490755 http://portal.acm.org/citation.cfm?id=1490755 – Exposé – DDI - An Ontology for Drug Discovery Investigations http://users.aber.ac.uk/ddq/ddi/wiki/index.php?title=Main_Page http://users.aber.ac.uk/ddq/ddi/wiki/index.php?title=Main_Page 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

7. Important Contacts Dr. Larisa N. Soldatova – SIG co-organiser RC UK Fellow, Computer Science Department, The University of Wales, Aberystwyth, UK lss@aber.ac.uk Prof. Ross King – with previous experience in predictive toxicology Group Coordinator Computational Biology Group Department of Computer Science Aberystwyth University rdk@aber.ac.uk Julia Kozlovsky (AstraZeneca) Pistoia Alliance (open standards) - http://www.pistoiaalliance.org/ Innovative Medicines Initiative - http://imi.europa.eu/http://www.pistoiaalliance.org/http://imi.europa.eu/ James Malone http://www.ebi.ac.uk/~malone/ http://www.ebi.ac.uk/~malone/ bioontologies@gmail.com a mailing list where one could ask related questions bioontologies@gmail.com