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The new bioinformatics: integrating ecological data from the gene to the biosphere
Jones, M.B.; Schildhauer, M.P.; Reichman, O.J.; Bowers, S. (2006). The new bioinformatics: integrating ecological data from the gene to the biosphere. Annual Review of Ecology, Evolution, and Systematics 37: 519-544. dx.doi.org/10.1146/annurev.ecolsys.37.091305.110031
In: Annual Review of Ecology, Evolution, and Systematics. Annual Reviews: Palo Alto. ISSN 1543-592X, more
Peer reviewed article  

Available in Authors 

Author keywords
    ecoinformatics; data integration; data sharing; metadata; ontology;scientific workflows; semantics

Authors  Top 
  • Jones, M.B.
  • Schildhauer, M.P.
  • Reichman, O.J.
  • Bowers, S.

Abstract
    Bioinformatics, the application of computational tools to the management and analysis of biological data, has stimulated rapid research advances in genomics through the development of data archives such as GenBank, and similar progress is just beginning within ecology. One reason for the belated adoption of informatics approaches in ecology is the breadth of ecologically pertinent data (from genes to the biosphere) and its highly heterogeneous nature. The variety of formats, logical structures, and sampling methods in ecology create significant challenges. Cultural barriers further impede progress, especially for the creation and adoption of data standards. Here we describe informatics frameworks for ecology, from subject-specific data warehouses, to generic data collections that use detailed metadata descriptions and formal ontologies to catalog and cross-reference information. Combining these approaches with automated data integration techniques and scientific workflow systems will maximize the value of data and open new frontiers for research in ecology.

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