An International Centre for Mouse Genetics CASIMIR WP4 Data Representation John Hancock MRC Harwell

An International Centre for Mouse Genetics WP Objectives Assessment of technical aspects of database interoperability as a barrier to scientific and financial sustainability Assessment of the variability of practice in the semantics of biological data representation, e.g. genotype, gene expression Assessment of emerging standards and current practice for data representation, annotation and ontologies

An International Centre for Mouse Genetics Networking Meetings & Outreach 12 Mar 09 – Cambridge – Discussion on phenotype ontologies (Harwell, EBI, Cambridge) [Mamm Genome paper] Mar 09 – Berlin – Discussion of mouse phenotypes and HPO (Hancock, Beck, Robinson) Mar 09 – Brussels – Biobanks Apr 09 – Banff, Canada – FANG 6-8 May 09 – Geneva – Gen2Phen discussion on phenotype representation Jun 09 – Hinxton – MNBF – discussion of behaviour ontology Jul 09 – Kyoto – discussion of standards for exchange of phenotype data 22 Jul 09 – Joint workshop with ENFIN at DILS09 on database registries 2-6 Sep 09 – WT/CSH meeting on Mouse Genetics & Genomics – discussion session including discussion of data availability 28 Oct 09 – London – ontologies discussion meeting (Harwell, Sanger, EBI, Cambridge) 31 Oct-6 Nov 09 – IMGC, La Jolla – Interphenome meeting to discuss open release of phenotype data 4 Dec 09 – ELIXIR Community Event, London 9 Dec 09 – Data standards for systems biology

An International Centre for Mouse Genetics Funding “Spin-Outs” VBO - A tool for bridging vertebrate anatomy ontologies Vertebrate anatomy Bridging Ontology Using Most Recent Common Ancestor as a concept to link homologous anatomical terms BBSRC (under consideration) PIs: Hancock, Schofield, Ashburner, Brazma (Parkinson) IMPC (International Mouse Phenotyping Consortium) Close involvement in planning of IT infrastructure (La Jolla, Harwell)

An International Centre for Mouse Genetics Publications months 25-present Kaput, J. Cotton, R. G. H. Hardman, L. Al Aqeel, A. I. Al-Aama, J. Y. Al-Mulla, F. Aretz, S. Auerbach, A. D. Axton, M. Bapat, B. et al. (2009). Planning the Human Variome Project: The Spain Report. Human Mutation 30, Hancock, J. M., Mallon, A. M., Beck, T., Gkoutos, G. V., Mungall, C. and Schofield, P. N. (2009). Mouse, man, and meaning: bridging the semantics of mouse phenotype and human disease. Mamm Genome 20, Submitted: Smedley, D., Schofield, P., Chen, C.-K., Aidinis, V., Ainali, C., Ashburner, M., Bard, J., Balling, R., Birney, E., Blake, A., et al. Does it do what it says on the tin? The CASIMIR Database Description Framework; metadata for interoperability. Submitted to Nature Biotechnology Schofield, P.N., Gkoutos, G.V., Gruenberger, M., Sundberg, J.P. & Hancock, J.M. Phenotype ontologies for mouse and man; bridging the semantic gap. Submitted to Disease Models & Mechanisms.

An International Centre for Mouse Genetics 4.2 Report to Commission on data representation Publication of major findings – IN PROGRESS 4.4 Network meeting – Early 2010? 4.5 Report of network meeting Present conclusions at meetings - IN PROGRESS

An International Centre for Mouse Genetics WP4 Achievements Furthered Interphenome objectives Harmonisation of ontologies (EQ & MP) for mouse phenotype description Fostered links between mouse phenotype description and human disease description Links to HPO Disease decomposition a priority Stockholm meeting; Attendance at other “human” meetings DDF – new standards for database interoperability

An International Centre for Mouse Genetics Next Steps for WP4? Final Networking Meeting To be held in early 2010 Concept: Behaviour ontology? IMPC IT planning meeting Phenotype to disease Location? Written reports DMM and Mammalian Genome papers Written report for Commission

An International Centre for Mouse Genetics