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.
Organisations
People |
ORCID iD |
| Andrew Law (Principal Investigator) | |
| Alan Archibald (Co-Investigator) |
Publications
Aerts J
(2009)
An introduction to scripting in Ruby for biologists.
in BMC bioinformatics
Aerts, J
(2008)
MIQAS - Minimal Information For QTL And Association Studies
in Plant & Animal Genomes XVI Conference
Bailey L
(2009)
01-P020 MicroRNA regulation of ES cell differentiation
in Mechanisms of Development
Baxter R
(2008)
A rapid and robust sequence-based genotyping method for BoLA-DRB3 alleles in large numbers of heterozygous cattle.
in Animal genetics
Burt DW
(2009)
The Chicken Gene Nomenclature Committee report.
in BMC genomics
Carre, W
(2008)
Chicken Gene-Nomenclature / Ortholog Database
in Plant & Animal Genomes XVI Conference
Connelley T
(2009)
Genomic and cDNA analysis of the bovine TCRß gene repertoire
in Veterinary Immunology and Immunopathology
Connelley T
(2009)
Genomic analysis reveals extensive gene duplication within the bovine TRB locus.
in BMC genomics
Hocking PM
(2012)
Many quantitative trait loci for feather growth in an F(2) broiler × layer cross collocate with body weight loci.
in British poultry science
McBride D
(2009)
01-P012 The role of micro-RNAs in the development of the chick gonads
in Mechanisms of Development
| 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/ |