The Royal Society London, May 19-21st, 2010Mouse models for human disease Phenotype database interoperability and integration Damian Smedley, EBI

The Royal Society London, May 19-21st, 2010Mouse models for human disease Why do we need data integration and interoperability?

The Royal Society London, May 19-21st, 2010Mouse models for human disease Centralised vs distributed solutions Genomics MGI Ensembl IKMC projects KOMPEUCOMMNorCOMM Eurexpress /GXD etc JaxMice Phenotype/Expression Strains IMSREMMA Europhenome TIGM portal Centralised warehouse v1 Central database Centralised warehouse v2Distributed solution nightly data syncs web services

The Royal Society London, May 19-21st, 2010Mouse models for human disease Centralised solutions Advantages –Better query performance for large datasets –Easier to analyse raw data in one location Disadvantages –Regular data deposition is non-trivial –Designing a single schema to store different types of data is not simple. –Persuading people to “give up” their data/databases/websites –Will still need to make interoperable with other data sources

The Royal Society London, May 19-21st, 2010Mouse models for human disease Distributed solutions Advantages –Domain expertise at production site exploited –Different types of data easily integrated as long as they share something in common such as a gene identifier –No need for nightly data flow to keep data up to date –No need for redundant data in each database –Easier to persuade people to collaborate in a distributed scenario Disadvantages –Technical knowledge required to deploy the web services –Potential query performance problems for large datasets (may need to provide summary level data) –Potential problems performing analysis over all datasets –Problems with services going down

The Royal Society London, May 19-21st, 2010Mouse models for human disease 1000 Genomes - centralisation

The Royal Society London, May 19-21st, 2010Mouse models for human disease International Cancer Genome Consortium Canada Pancreas Australia Pancreas China Stomach Japan Liver (virus related) France Liver (alcohol-related) Breast (HER2+ve) UK Breast (several subtypes) Spain CLL India Oral Cavity

The Royal Society London, May 19-21st, 2010Mouse models for human disease ICGC - distributed

The Royal Society London, May 19-21st, 2010Mouse models for human disease Joint Ensembl and EurExpress query

The Royal Society London, May 19-21st, 2010Mouse models for human disease IKMC portal: knockoutmouse.org GXD EurexpressNorCOMM EUCOMM KOMP TIGM EMMA KOMP rep CMMR IMSR Ensembl CREATE Europhenome

The Royal Society London, May 19-21st, 2010Mouse models for human disease IKMC interoperability strategy IKMC Sanger, UK ES cells + lines EMMA (UK), KOMP (USA), CMMR (Canada) Harwell, UK Phenotype(EuroPhenome etc) JAX, USA MGI Edinburgh, UK EURExpress Sanger, UK Ensembl JAX, USA GXD CREATE EBI, UK BioMart query interface(s) MGI ID

The Royal Society London, May 19-21st, 2010Mouse models for human disease

The Royal Society London, May 19-21st, 2010Mouse models for human disease Europhenome: raw and summary data

The Royal Society London, May 19-21st, 2010Mouse models for human disease Possible strategy for phenotype data BioMart query interface(s) IKMC Sanger, UK ES cells + lines EMMA (UK), KOMP (USA), CMMR (Canada) MGI ID JAX, USA MGI Edinburgh, UK EURExpress Sanger, UK Ensembl MGI ID JAX, USA GXD MGI ID CREATE EBI, UK Central database High thoughput phenotyping centres Presentation of raw results Analysis to assign phenotypes to genes MGI ID High throughput phenotyping

The Royal Society London, May 19-21st, 2010Mouse models for human disease Linking from IKMC portal Phenotyping Phenotype searches

The Royal Society London, May 19-21st, 2010Mouse models for human disease Linking from IKMC portal

The Royal Society London, May 19-21st, 2010Mouse models for human disease

The Royal Society London, May 19-21st, 2010Mouse models for human disease Acknowledgements The whole CASIMIR consortium and in particular: Paul Schofield, Michael Gruenberger, Chao-Kung Chen, George Gkoutos, Ann-Marie Mallon, John Hancock : MouseFinder tool. MartSearch: Vivek Iyer, Darren Oakley, Bill Skarnes BioMart: Arek Kaspryzk, Syed Haider, Edoardo Marcora