U.S. Database Coordination ActivitiesSupported by Allotments of Regional Research Funds, Hatch Act For the Period 1/1/11-12/31/11January 14, 2012 | |||
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OVERVIEW:
Coordination of the CSREES National Animal Genome Research
Program’s (NAGRP) Bioinformatics is primarily based at, and led from,
Iowa State University (ISU), with additional activities at Mississippi
State University (MSU) and is supported by NRSP-8. The NAGRP is made up
of the membership of the Animal Genome Technical Committee, including the
Bioinformatic Subcommittee.
FACILITIES AND PERSONNEL: James Reecy, Department of Animal Science, ISU, serves as Coordinator with Susan J. Lamont (ISU), Max Rothschild (ISU), Chris Tuggle (ISU), and Fiona McCarthy (MSU) as Co-Coordinators. Iowa State University and Mississippi State University provide facilities and support. OBJECTIVES: The NRSP-8 project was renewed as of 10/01/08, with the following objectives: 1. Create shared genomic tools and reagents and sequence information to enhance the understanding and discovery of genetic mechanisms affecting traits of interest; 2. Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes; and 3. Develop, integrate and implement bioinformatic resources to support the discovery of genetic mechanisms that underlie traits of interest. PROGRESS TOWARD OBJECTIVE 1: Create shared genomic tools and reagents and sequence information to enhance the understanding and discovery of genetic mechanisms affecting traits of interest. See activities listed below. PROGRESS TOWARD OBJECTIVE 2. Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes. Over the past year, partnered with researchers at Kansas State University, Michigan State University, Iowa State University and U.S. Department of Agriculture, we have further developed and improved the web interfaced relational databases to store and disseminate phenotypic and genotypic information from large genomic studies in farm animals and better serve the needs by the researchers. For example, we are working with the PRRS CAP Host Genome consortium to develop a relational database to house individual animal genotype and phenotype data (http://www.animalgenome.org/lunney/index.php). This will help the consortium, whose individual research labs lack expertise with relational databases, share information among consortium members and thereby facilitate data analysis. PROGRESS TOWARD OBJECTIVE 3: Develop, integrate and implement bioinformatic resources to support the discovery of genetic mechanisms that underlie traits of interest. The following describes the project's activities over this past year.
Poultry NRSP-8 funds were used to support the development of BirdBase resources. Specifically, Chicken Gene Nomenclature Committee (CGNC) database was developed, updating records from the Roslin GeneNames effort and providing access to chicken gene nomenclature. It is now possible for biocurators and community experts to add nomenclature, download current nomenclature. In addition this resource is now linked the NCBI Entrez Gene chicken gene pages (with thanks to Janet Weber). During 2012, we expect to link in with Ensembl Genes and with the HGNC. Via BirdBase, a bird comparative genome browser is being developed. This will initially include the chicken, turkey and zebra finch genomes and will then be expanded to include all bird genomes (including bird genomes sequences as part of the BGI-10K Genomes project). Currently we have accessed funds for this comparative browser (and its set up) and are in the process of buying the server. We expect the bird comparative genome browser to be online during 2012.
Cattle
Sheep
Aquaculture
Multi-species
Ontology development Via AgBase, we were recruited by the Phenotype Ontology Research Coordination Network (NSF DBI 0956049) to develop an avian anatomy ontology with the goal of integrating this with other, existing ontologies to describe phenotypes. Using MSU and AgBase funds we have about 650 terms that cover avian musculoskeletal and integument systems. The information for these terms includes relationships, synonyms, definitions, and comments (homologies to mammalian structures; species differences). The development of this ontology is done in collaboration with Duncan Davidson (UK Medical Research Council) and in conjunction with the larger Phenotype RCN Vertebrate Working group. This work will continue with BirdBase collaborators during 2012 (as funding permits) and will enable poultry researchers to describe phenotype in a standard way that promotes data sharing.
Software development As a result of collaborations between Iowa State University, the Medical College of Wisconsin, and University of Iowa, the Virtual Comparative Map (VCMap) tool has passed its initial development stage and now transferred to the AnimalGenome.ORG (http://www.animalgenome.org/VCmap/). More application development will be expected. To improve links between AgBase and the NRSP-8 website, AgBase now also provides a link to the Virtual Comparative Map (VCMap). Please feel free to try things out, and send any feedback to: vcmap@animalgenome.org. Genome2Seq, an online tool that rapidly retrieves a fasta file of sequences based on genome co-ordinates generated from RNA-Seq data, was developed. Users specify either bovine, horse, chicken or pig genomes. The input file is a tab-delimited text file containing a unique ID, chromosome number, start location, and stop location in that order. The output is (a) a list of matching genes and their associated GO annotation; and (b) a fasta file of sequences for any co-ordinates that do not match any annotated genes. Genome2Seq is available via AgBase and the NRSP-8 website. The web site and user forum listserv for CRI-MAP user interactions in improving the CRIMAP software (http://www.animalgenome.org/tools/share/crimap/) has been actively used.
Minimal standards development
Expanded Animal QTLdb functionality In addition, The QTLdb has been revamped to accommodate genome map (map unit: bp) based QTL and association data (e.g. GWAS data). The map view and QTL details view have updated to integrate these new data types. A new user option allows one to view "QTL", "eQTL", "Associations", or combinations of these data. Some minor but useful improvements continue to be made. For example users can see a list of references for the QTL within any chromosomal view window.
Facilitating research OBJECTIVE 2: Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes. We will seek to partner with any NRSP-8 members wishing to warehouse phenotypic and genotypic data in customized relational databases. This will help consortia/researchers whose individual research labs lack expertise with relational databases to warehouse and share information. OBJECTIVE 3: Develop, integrate and implement bioinformatic resources to support the discovery of genetic mechanisms that underlie traits of interest. We will continue to work with bovine, mouse, rat, and human QTL database curators to develop minimal information for publication standards. We will also work with these same database groups to improve phenotype and measurement ontologies, which will facilitate transfer of QTL information across species. We will continue working with U.S. colleagues, as well as throughout Europe to develop a Bioinformatics Blueprint, similar to the Animal Genomics Blueprint recently published by USDA-CSREES, to help direct future livestock-oriented bioinformatic/database efforts. Publications:
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