Introduction to Mammalian Genome special issue: Informatics and Integrative Genomics—Part 2

Introduction to Mammalian Genome special issue: Informatics and Integrative Genomics—Part 2 Mamm Genome (2015) 26:365 DOI 10.1007/s00335-015-9604-9 Introduction to Mammalian Genome special issue: Informatics and Integrative Genomics—Part 2 Ann-Marie Mallon Published online: 28 September 2015 Springer Science+Business Media New York 2015 In Part 1 of this special issue, we focused on the infor- on the International Knockout Mouse Consortium (IKMC). matics developments from the Mouse Genome Informatics Underpinning many global resources are the worldwide (MGI) resource at the Jackson Laboratory to celebrate their mouse clinics who require 24/7 laboratory information 25 year anniversary. As highlighted in Part 1, informatics management systems (LIMS) to ensure data accuracy and and integrative genomics is a large field, driving forward standardisation. The paper by Maier et al. gives a review of new areas of insight in many aspects of mouse genetics and the current LIMS systems in use across the world. A key functional genomics. In this second issue, we are focusing element of LIMS systems is the ability to acquire data on on a breadth of work from genome annotation, platforms animal welfare, and the next review by Bussell and Wells for data dissemination, and mouse resources, to methods describes efforts to implement a common language for for integrating mouse functional data with human disease. mouse welfare. The first group of papers in this issue by Mudge and Simon et al. and Wiles et al. describe the underpinning Harrow, McGarvey et al. and de Hoon et al. review the informatics approaches that are being developed for muta- current picture of annotating the mouse reference genome tion detection and genome editing with CRISPR-Cas9. Two and the mouse transcriptome. The reviews of the Mouse papers follow on the collaborative cross and diversity out- Genomes Project by Adams et al. and the International bred projects by Bogue et al. and Morgan and Welsh. The Mouse Phenotyping Consortium portal by Ring et al. final section of this special issue begins with a review by describe two large-scale resources of use to the biomedical Gkoutos et al. on the current ontologies for describing mouse and mouse genetics community. The following three behaviour, a key ontology required for integration with papers review an ever-growing field of big data generation human disease descriptors. This leads on to papers describ- in mouse genetics, and the generation and analysis of 2D ing methods for cross-species comparisons and functional and 3D image data. The first paper by Hayamizu et al. genomics by Haendel et al. and Bubier et al. functional gives an overview of the ontologies required for describing analysis and comparative biology in the gene ontology (GO) anatomy, with the next two papers by Armit et al. and by Richardson and Bult and Drabkin et al. and a concluding Burel et al. describing two image resources: eMouseAtlas paper by Schriml and Mitraka on disease ontologies. and OMERO. This special issue on Informatics and Integrative Portals which enable users to gain access to mouse Genomics exhorts the importance of informatics in mouse models are a key informatics resource for the community. genetics. The collection of articles in Parts 1 and 2 Two papers by Eppig et al. and Rosen et al. describe the demonstrates the breadth and depth of extraordinary International Mouse Strain Resource (IMSR) and a review developments in data capture, dissemination, analysis and integration of mouse data. In addition, they highlight the anticipated growth in data, we can expect as mouse func- & Ann-Marie Mallon tional genomics contributes to the ‘big data’ era. This rapid growth in data provides numerous opportunities to seek novel and translational insights into the genome and gene MRC Mammalian Genetics Unit, MRC Harwell, Harwell function. Science and Innovation Campus, Harwell OX11 0RD, UK Mammalian Genome Springer Journals

Introduction to Mammalian Genome special issue: Informatics and Integrative Genomics—Part 2

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Copyright © 2015 by Springer Science+Business Media New York
Life Sciences; Cell Biology; Animal Genetics and Genomics; Human Genetics
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