CASIMIR WP4 Data Representation John Hancock MRC Harwell
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Transcript of CASIMIR WP4 Data Representation John Hancock MRC Harwell
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