USDA Stakeholder Workshop on Animal Bioinformatics: summary and recommendations

Abstract

An electronic workshop was conducted on 4 November–13 December 2002 to discuss current issues and needs in animal bioinformatics. The electronic (e-mail listserver) format was chosen to provide a relatively speedy process that is broad in scope, cost-efficient and easily accessible to all participants. Approximately 40 panelists with diverse species and discipline expertise communicated through the panel e-mail listserver. The panel included scientists from academia, industry and government, in the USA, Australia and the UK. A second ‘stakeholder’ e-mail listserver was used to obtain input from a broad audience with general interests in animal genomics. The objectives of the electronic workshop were: (a) to define priorities for animal genome database development; and (b) to recommend ways in which the USDA could provide leadership in the area of animal genome database development. E-mail messages from panelists and stakeholders are archived at http://genome.cvm.umn.edu/bioinfo/. Priorities defined for animal genome database development included: (a) data repository; (b) tools for genome analysis; (c) annotation; (d) practical application of genomic data; and (e) a biological framework for DNA sequence. A stable source of funding, such as the USDA Agricultural Research Service (ARS), was recommended to support maintenance of data repositories and data curation. Continued support for competitive grants programs within the USDA Cooperative State Research, Education and Extension Service (CSREES) was recommended for tool development and hypothesis-driven research projects in genome analysis. Additional stakeholder input will be required to continuously refine priorities and maximize the use of limited resources for animal bioinformatics within the USDA.

A Vision for Development and Utilization of High-Throughput Phenotyping and Big Data Analytics in Livestock

“…It is long-recognized that understanding phenotype, or the display or expression of the genotype in measurable traits, is key to understanding biological systems (Houle et al, 2010) to advance animal agriculture by understanding how to maintain animal health, productivity, and economic sustainability (Hamernik and Adelson, 2003). With the advent of next-generation sequencing (NGS) techniques, the onslaught of genomic sequence data will need to be balanced with increased, high-quality phenotypic data.…”

Chicken genome sequence: a centennial gift to poultry genetics

“…Interest in providing bioinformatics support for the chicken genome sequence has already been expressed by the EN-SEMBL (http://www.ensembl.org) consortium of the European Bioinformatics Institute (Burt and Pourquie, 2003) and by NCBI (http://www.ncbi.nlm.nih.gov; see Hamernik and Adelson, 2003). It seems likely that one or both of these highly qualified groups will provide the basic support necessary for general use of the chicken genome sequence.…”

“…edu/), among others, will continue to provide special purpose data and services. For a more detailed discussion of the needs for future bioinformatics support, see Hamernik and Adelson (2003).…”