CASIMIR WP4 Data Representation John Hancock MRC Harwell

1. CASIMIR WP4 Data Representation John Hancock MRC Harwell

2. 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

3. Networking Meetings & Outreach • 12 Mar 09 – Cambridge – Discussion on phenotype ontologies (Harwell, EBI, Cambridge) [Mamm Genome paper] • 23-24 Mar 09 – Berlin – Discussion of mouse phenotypes and HPO (Hancock, Beck, Robinson) • 25-27 Mar 09 – Brussels – Biobanks • 24-28 Apr 09 – Banff, Canada – FANG • 6-8 May 09 – Geneva – Gen2Phen discussion on phenotype representation • 25-26 Jun 09 – Hinxton – MNBF – discussion of behaviour ontology • 10-14 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

4. 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)

5. 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, 496-510. • 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, 457-461. 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.

6. 4.2 Report to Commission on data representation - 2010 • 4.3 Publication of major findings – IN PROGRESS • 4.4 Network meeting – Early 2010? • 4.5 Report of network meeting - 2010 • 4.6 - Present conclusions at meetings - IN PROGRESS

7. 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

8. 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