An International Centre for Mouse Genetics

CASIMIR WP4Data Representation

John HancockMRC 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]

• 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

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, 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.

An International Centre for Mouse Genetics

• 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

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

An International Centre for Mouse Genetics