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Title: Advantages for the use of standardized phenotyping in databases

item Volk, Gayle

Submitted to: HortScience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/5/2010
Publication Date: 9/7/2010
Citation: Volk, G.M. 2010. Advantages for the use of standardized phenotyping in databases. HortScience 45:1310-1313.

Interpretive Summary: Large biological repositories maintain databases to record critical information about the items in their collections. Well-documented data, either qualitative or quantitative, that describes the physical attributes or origin of materials increases the value of the collection. This report describes the advantages of using standardized ontologies, or vocabularies, for trait classifications and georeferencing information. Examples of databases that have developed standardized phenotyping methods within medical, animal and plant research programs are provided. Improved standardization and interoperability within national plant databases will allow researchers to better identify plant materials that have the potential to improve yield, quality, and stress tolerance in breeding programs.

Technical Abstract: Genomic sequence data is becoming prevalent in databases; however, associated phenotypic data is much more expensive and difficult to obtain. Standardized ontologies for trait classification provide a mechanism by which searches can be efficiently performed. Through standardization efforts, results can be compared across years, researchers, and locations. Examples of databases that have developed standardized ontologies within medical, animal, and plant research programs demonstrate that standardization is both possible and desirable. With standardization, genotypic and phenotypic data can be analyzed to materials for improved yield, quality, and stress tolerance.