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FlyBase: integration and improvements to query tools.

Wilson RJ, Goodman JL, Strelets VB, FlyBase Consorti - Nucleic Acids Res. (2007)

Bottom Line: The database serves researchers of diverse backgrounds and interests, and offers several different query tools to provide efficient access to the data available and facilitate the discovery of significant relationships within the database.Recently, FlyBase has developed Interactions Browser and enhanced GBrowse, which are graphical query tools, and made improvements to the search tools QuickSearch and QueryBuilder.Furthermore, these search tools have been integrated with Batch Download and new analysis tools through a more flexible search results list, providing powerful ways of exploring the data in FlyBase.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Indiana University 1001 E 3rd Street, Bloomington, IN 47405, USA.

ABSTRACT
FlyBase (http://flybase.org) is the primary resource for molecular and genetic information on the Drosophilidae. The database serves researchers of diverse backgrounds and interests, and offers several different query tools to provide efficient access to the data available and facilitate the discovery of significant relationships within the database. Recently, FlyBase has developed Interactions Browser and enhanced GBrowse, which are graphical query tools, and made improvements to the search tools QuickSearch and QueryBuilder. Furthermore, these search tools have been integrated with Batch Download and new analysis tools through a more flexible search results list, providing powerful ways of exploring the data in FlyBase.

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Interactions Browser. The options at the top of the page of the Interactions Browser permit the selection of different types of interaction data and adjustment of the scan depth, which refers to the number of interaction steps shown from the query. The ‘auto’ value set for the scan depth by default chooses a number based on the complexity of the data. In the diagram, the alleles or genes that interact directly with the query allele or gene are shown in dark blue, and alleles or genes that interact with them are shown in light blue if the scan depth is set to 2. The program uses different colored lines to indicate the type of interaction and arrows to denote the direction in which the interaction was recorded. In some interaction diagrams that have many alleles or genes, the symbols can overlap making it hard to identify them. To view this data the picture can be redrawn in another orientation by choosing a different rotation factor.
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Figure 3: Interactions Browser. The options at the top of the page of the Interactions Browser permit the selection of different types of interaction data and adjustment of the scan depth, which refers to the number of interaction steps shown from the query. The ‘auto’ value set for the scan depth by default chooses a number based on the complexity of the data. In the diagram, the alleles or genes that interact directly with the query allele or gene are shown in dark blue, and alleles or genes that interact with them are shown in light blue if the scan depth is set to 2. The program uses different colored lines to indicate the type of interaction and arrows to denote the direction in which the interaction was recorded. In some interaction diagrams that have many alleles or genes, the symbols can overlap making it hard to identify them. To view this data the picture can be redrawn in another orientation by choosing a different rotation factor.

Mentions: The Interactions Browser is a new program available under the ‘Tools’ menu that provides a graphical way of exploring the genetic interactions reported in the allele reports. The browser works in two modes: you can either search for the interactions of an allele (Figure 3), or the interactions of a gene. The latter will show the interactions of all alleles of the gene. Each node of an interaction diagram is a hyperlink, which enables you to navigate and browse the complex web of known genetic interactions. Placing your cursor over the center of a node activates a pop-up window that in the case of a network of gene interactions contains a summary of the function of that particular gene, while in the case of interactions between alleles shows the context in which the interactions of that allele have been reported.Figure 3.


FlyBase: integration and improvements to query tools.

Wilson RJ, Goodman JL, Strelets VB, FlyBase Consorti - Nucleic Acids Res. (2007)

Interactions Browser. The options at the top of the page of the Interactions Browser permit the selection of different types of interaction data and adjustment of the scan depth, which refers to the number of interaction steps shown from the query. The ‘auto’ value set for the scan depth by default chooses a number based on the complexity of the data. In the diagram, the alleles or genes that interact directly with the query allele or gene are shown in dark blue, and alleles or genes that interact with them are shown in light blue if the scan depth is set to 2. The program uses different colored lines to indicate the type of interaction and arrows to denote the direction in which the interaction was recorded. In some interaction diagrams that have many alleles or genes, the symbols can overlap making it hard to identify them. To view this data the picture can be redrawn in another orientation by choosing a different rotation factor.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238994&req=5

Figure 3: Interactions Browser. The options at the top of the page of the Interactions Browser permit the selection of different types of interaction data and adjustment of the scan depth, which refers to the number of interaction steps shown from the query. The ‘auto’ value set for the scan depth by default chooses a number based on the complexity of the data. In the diagram, the alleles or genes that interact directly with the query allele or gene are shown in dark blue, and alleles or genes that interact with them are shown in light blue if the scan depth is set to 2. The program uses different colored lines to indicate the type of interaction and arrows to denote the direction in which the interaction was recorded. In some interaction diagrams that have many alleles or genes, the symbols can overlap making it hard to identify them. To view this data the picture can be redrawn in another orientation by choosing a different rotation factor.
Mentions: The Interactions Browser is a new program available under the ‘Tools’ menu that provides a graphical way of exploring the genetic interactions reported in the allele reports. The browser works in two modes: you can either search for the interactions of an allele (Figure 3), or the interactions of a gene. The latter will show the interactions of all alleles of the gene. Each node of an interaction diagram is a hyperlink, which enables you to navigate and browse the complex web of known genetic interactions. Placing your cursor over the center of a node activates a pop-up window that in the case of a network of gene interactions contains a summary of the function of that particular gene, while in the case of interactions between alleles shows the context in which the interactions of that allele have been reported.Figure 3.

Bottom Line: The database serves researchers of diverse backgrounds and interests, and offers several different query tools to provide efficient access to the data available and facilitate the discovery of significant relationships within the database.Recently, FlyBase has developed Interactions Browser and enhanced GBrowse, which are graphical query tools, and made improvements to the search tools QuickSearch and QueryBuilder.Furthermore, these search tools have been integrated with Batch Download and new analysis tools through a more flexible search results list, providing powerful ways of exploring the data in FlyBase.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Indiana University 1001 E 3rd Street, Bloomington, IN 47405, USA.

ABSTRACT
FlyBase (http://flybase.org) is the primary resource for molecular and genetic information on the Drosophilidae. The database serves researchers of diverse backgrounds and interests, and offers several different query tools to provide efficient access to the data available and facilitate the discovery of significant relationships within the database. Recently, FlyBase has developed Interactions Browser and enhanced GBrowse, which are graphical query tools, and made improvements to the search tools QuickSearch and QueryBuilder. Furthermore, these search tools have been integrated with Batch Download and new analysis tools through a more flexible search results list, providing powerful ways of exploring the data in FlyBase.

Show MeSH