Von Mäusen und Menschen Datenbrücken verbessern den Zugang zu Forschungsdaten in INFRAFRONTIER

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1 Von Mäusen und Menschen Datenbrücken verbessern den Zugang zu Forschungsdaten in INFRAFRONTIER Michael Raess & Philipp Gormanns, Helmholtz Zentrum München Helmholtz Open Access Webinars 16 and 24 July 2013

2 The INFRAFRONTIER Research Infrastructure INFRAFRONTIER Systemic Phenotyping INFRAFRONTIER Mouse Clinics Archiving / Distribution Access to scientific platforms, data and mouse models

3 The INFRAFRONTIER partner network Canada 15 European countries + Canada a Mouse clinics EMMA archiving and distribution nodes Bioinformatics ormatics Coordinated at HMGU Israel

4 Systemic Phenotyping

5 Archiving & distribution European Mouse Mutant Archive Lines in archive

6 The scientific scope of INFRAFRONTIER

7 INFRAFRONTIER users worldwide

8 International Mouse Phenotyping Consortium

9 International Mouse Phenotyping Consortium Systemic Phenotypic analysis of ~ mammalian protein coding genes

10 Functional annotation how much is known? All protein coding genes with GO annotations (n = 22823) Source: MGI At least one GO annotation for biological or molecular function (n = 15509) Biological function unknown (n = 6169) Molecular function unknown (n = 6102) 5% 22% 5%

11 INFRAFRONTIER European activities INFRAFRONTIER Legal Entity INFRAFRONTIER-I3 BioMedBridges InfraCoMP INFRAFRONTIER Preparatory Phase J F M A M J J A S O N D J F M A M J J A S O N D J F M A M J J A S O N D J F M A M J J A S O N D J F M A M J J A S O N D J F M A M J J A S O N D J F M A M J J A S O N D J F M A M J J A S O N D J F M A M J J A S O N D

12 BioMedBridges ( Building data bridges among the biomedical research infrastructures

13 BioMedBridges Three construction work packages to build the technical bridges Secure Access and Standards will facilitate the effective sharing of data Technical integration will construct the e-infrastructure Five inter-related use cases To test the technical and data developments of the construction work packages Each use case focusses on a particular ESFRI Research Infrastructure Training participants to ensure common understanding Training the user community on the standards and tools developed Training Standards description & harmonisation Technical integration Interoperability of large scale image data sets Improving the link between mouse models and human data Personalized Medicine Integrating structural data Technology watch Capturing the expertise from e- infrastructure providers Ensuring BioMedBridges adopts the state of the art Secure access Integrating disease-related data and terminology

14 BioMedBridges WP7 PhenoBridge Bridging the gap between mouse and human datasets, using diabetes as an example Dataset t A Annotations & Ontologies Annotations & Ontologies Dataset A Dataset t B Dataset t C PhenoBridge Dataset B Dataset C

15 BioMedBridges WP7 PhenoBridge I know the human phenotype. What s matching? I know the matching mouse phenotype, and much more... Ontologies, data services Available mice, genes, pathways, experimental data, publications,...

16 Ontology introduction Ontology An ontology is an approach to structure knowledge.

17 PhenoBridge ontologies MP Mammalian Phenotype Ontology HPO Human Phenotype Ontology Smith et al.; Genome Biology 2005 Robinson et al.; Am J Hum Genet 2008

18 Ontology introduction Ontology structure enables subphenotype mapping PAX6 mutation Mouse: Decreased eyesize Human: Opaque cornea Zebrafish: Malformed retina Drosophila: Eyeless Eye abnormalities Washington et al.; PLoS Biol. 2009

19 Ontology mapping Logical definition (EQ Model) Washington et al.; PLoS Biol Washington et al.; PLoS Biol. 2009

20 Semantic Comparison (OWLSim) Washington et al.; PLoS Biol. 2009

21 PhenoBridge Determining the phenotype similarity of two entities, e.g. mouse model and a disease. Smedley et al. Database 2013;2013:bat25

22 Current tasks in BioMedBridges Improving descriptions of diabetes and obesity in the Human Phenotype Ontology Co-annotation of human-mouse datasets related to diabetes and obesity Technical (semantic) integration of systemic phenotyped mouse models

23 Outlook Web service Analysis of systemic phenotyped KO mice with other resources Find potential mouse models for a human disease

24 To sum up: The INFRAFRONTIER Research Infrastructure provides access to mouse models to study human diseases The INFRAFRONTIER Research Infrastructure also provides access to scientific platforms and services linked to the mouse models In the BioMedBridges Project INFRAFRONTIER and other biomedical research infrastructures work on the interoperability of data and services. The BioMedBridges Work Package PhenoBridge aims to bridge the species gap between mouse and human phenotypes in the fields of obesity and diabetes Ontologies are necessary for sophisticated mapping of annotated datasets between different species. Semantic integration of phenotyped mouse models enables research infrastructure bridging. If you have further questions, please contact Michael Raess or Philipp Gormanns