Bioinformatics to underpin genome analyses in farm animals

Lead Research Organisation: University of Edinburgh
Department Name: College of Medicine and Veterinary Medic

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Technical Summary

Bioinformatics is the cornerstone on which large-scale genome analyses can be built. In this application, we propose to continue to develop resource databases and systems developed as part of previous BBSRC-funded work and integrate them fully with other data types (e.g. genome sequence) in order to enable hypothesis-driven and hypothesis-generating analyses to be performed in the context of as wide a body of data and knowledge as possible.

Publications

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Aerts J (2009) An introduction to scripting in Ruby for biologists. in BMC bioinformatics

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Aerts, J (2008) MIQAS - Minimal Information For QTL And Association Studies in Plant & Animal Genomes XVI Conference

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Bailey L (2009) 01-P020 MicroRNA regulation of ES cell differentiation in Mechanisms of Development

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Burt D (2009) The chicken gene nomenclature committee report in BMC Genomics

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Carre, W (2008) Chicken Gene-Nomenclature / Ortholog Database in Plant & Animal Genomes XVI Conference

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Connelley T (2009) Genomic and cDNA analysis of the bovine TCRß gene repertoire in Veterinary Immunology and Immunopathology

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McBride D (2009) 01-P012 The role of micro-RNAs in the development of the chick gonads in Mechanisms of Development

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Paterson, T (2010) A prototype Java API for the Ensembl database system in Tenth Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics

 
Title ArkDB database and data model 
Description ArkDB is a generic, species-independent database built to store genetic linkage and other genome mapping data for a given species. It stores details of references, markers and loci and genetic linkage and cytogenetic maps which can be drawn using the online map-drawing application. Data from linkage maps held within the ArkDB system can be drawn alongside their corresponding genome sequence maps. It uses a common underlying data model that permits all mapping data to be stored and compared in a single schema 
Type Of Material Database/Collection of data 
Year Produced 2008 
Provided To Others? Yes  
Impact Comparative genomics is a lot simpler and more graphical for farmed animal species than it was previously. 
URL http://www.thearkdb.org/
 
Title resSpecies Database model 
Description Database to handle pedigree populations, genotypes and phenotypes for genetic linkage mapping and quantitative trait linkage mapping studies. Common central data model permits reformatting of data in readiness for import into common analysis programs. 
Type Of Material Database/Collection of data 
Year Produced 2008 
Provided To Others? Yes  
Impact Non computer-literate scientists can manipulate data - error free - within minutes rather than days 
URL http://www.resspecies.org
 
Title ArkDB 
Description ArkDB is a generic, species-independent database and associated web interface built to capture the (then) state of published information on genome mapping in a given species. It stores details of references, markers and loci and genetic linkage and cytogenetic maps which can be drawn using the online map-drawing application. Data from linkage maps held within the ArkDB system can be drawn alongside their corresponding genome sequence maps 
Type Of Technology Webtool/Application 
Year Produced 2008 
Impact Comparative genomics got a whole lot easier. Comparing the genetic architecture of multiple species is now possible in an interactive graphical environment 
URL http://www.thearkdb.org/
 
Title ArkMAP 
Description Draws genetic linkage, radiation hybrid or other genomic/genetic linkage mapping representations 
Type Of Technology Webtool/Application 
Year Produced 2010 
Impact Several studies/papers facilitated, particularly in the area of fish comparative genomics 
URL http://www.bioinformatics.roslin.ed.ac.uk/arkmap/
 
Title GMD data format 
Description We have developed a simple generic XML schema (GenomicMappingData.xsd - GMD) to allow export and exchange of mapping data in a common lightweight XML document format. This schema represents the various types of data objects commonly described across mapping datasources and provides a mechanism for recording relationships between data objects. The schema is sufficiently generic to allow representation of any map type (for example genetic linkage maps, radiation hybrid maps, sequence maps and physical maps). It also provides mechanisms for recording data provenance and for cross referencing external datasources (including for example ENSEMBL, PubMed and Genbank.). The schema is extensible via the inclusion of additional datatypes, which can be achieved by importing further schemas, e.g. a schema defining relationship types. We have built demonstration web services that export data from our ArkDB database according to the GMD schema, facilitating the integration of data retrieval into Taverna workflows. 
Type Of Technology Webtool/Application 
Year Produced 2009 
Impact We can use a consistent and standardised data exchange format between our different data systems. That simplifies code development 
URL http://bioinformatics.roslin.ed.ac.uk/gmd/
 
Title Genotype Checker 
Description GenotypeChecker is a desktop tool for identifying likely data errors in pedigree/genotype datasets and to assist data cleansing. Datapoint errors in pedigree genotype datasets are difficult to identify and adversely affect downstream genetic analyses. Errors that are inconsistent with the rules of Mendelian inheritance typically invalidate linkage analysis algorithms, and cause such analyses to fail. Genotype errors may arise from a variety of systematic or sporadic errors in either the genotyping assay, or in recording the pedigree or genotype information. By applying an inheritance-checking algorithm for markers across the pedigree and visualising the inheritance data in an exploratory user interface, GenotypeChecker allows the sources of data inconsistency can be resolved. 
Type Of Technology Webtool/Application 
Year Produced 2009 
Impact Allowed us to clean data from complex pedigree experiments and thus permit the analysis of data that would otherwise have remained unusable. Provided the basis of the subsequent VIPER project which further developed the code and the ideas within it. 
URL http://bioinformatics.roslin.ed.ac.uk/genotypechecker/
 
Title resSpecies 
Description Database and associated web interface to handle pedigree populations, genotypes and phenotypes for genetic linkage mapping and quantitative trait linkage mapping studies. System checks inheritance of markers and formats/reformats data in readiness for import into common analysis programs. 
Type Of Technology Webtool/Application 
Year Produced 2008 
Impact Non computer-literate scientists can manipulate data - error free - within minutes rather than days 
URL http://www.resspecies.org/