YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit

Abstract

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) provides high-quality curated genomic, genetic, and molecular information on the genes and their products of the budding yeast Saccharomyces cerevisiae. To accommodate the increasingly complex, diverse needs of researchers for searching and comparing data, SGD has implemented InterMine (http://www.InterMine.org), an open source data warehouse system with a sophisticated querying interface, to create YeastMine (http://yeastmine.yeastgenome.org). YeastMine is a multifaceted search and retrieval environment that provides access to diverse data types. Searches can be initiated with a list of genes, a list of Gene Ontology terms, or lists of many other data types. The results from queries can be combined for further analysis and saved or downloaded in customizable file formats. Queries themselves can be customized by modifying predefined templates or by creating a new template to access a combination of specific data types. YeastMine offers multiple scenarios in which it can be used such as a powerful search interface, a discovery tool, a curation aid and also a complex database presentation format. DATABASE URL: http://yeastmine.yeastgenome.org.

Figure 1.

Example of a template search of expression data: screenshot of the ‘SpellDataSet→SpellScore→Genes’ template showing the SpellExpression Score constrained to be between ≥3 and ≤−3, and the SpellDatasetCondition name constrained to be ‘=*sorbitol*’. Switching ON the other parameters such as ‘SpellDataSet author’ or ‘SpellDataset pubmedID’ will allow constraint of those values. The ‘Show Results’ button runs the query. This template is prepopulated with certain constraints, but clicking on the ‘Edit Query’ button will bring up the Model browser, which offers more options for query constraints and output formats.

Figure 2.

An example of editing a template using the Query Builder. The Model Browser (on the left) displays the attributes for the GOAnnotation object in the Gene→GO Terms template. Clicking on the ‘CONSTRAIN→’ button next to the namespace box allows one to constrain on the ontology namespace. The Query Overview (on the right) shows the ontology namespace being restricted to the value ‘Biological Process’.