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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.

Show MeSH
Results Analysis/Refinement Tool. The Results Analysis/Refinement Tool has been used to display the distribution of Biological Process controlled vocabulary terms applied to a list of the components of the Notch signaling pathway. The second column displays the term for which the distribution was created. The next three columns show a graphical display, the raw size, and the relative size of the term in the distribution. Clicking on the number in the ‘Related records’ column will return a hit list containing the individual records that make up that bin.
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Figure 2: Results Analysis/Refinement Tool. The Results Analysis/Refinement Tool has been used to display the distribution of Biological Process controlled vocabulary terms applied to a list of the components of the Notch signaling pathway. The second column displays the term for which the distribution was created. The next three columns show a graphical display, the raw size, and the relative size of the term in the distribution. Clicking on the number in the ‘Related records’ column will return a hit list containing the individual records that make up that bin.

Mentions: The search results page, the hit list, is presented when you perform any search that returns multiple hits (Figure 1). By default, all records are selected for inclusion in subsequent manipulations, but the checkboxes allow user-defined subsets to be created. The first data column links directly to the report for each record that matched your search. Other columns link to GBrowse or to searches that return hits directly related to that record. In addition to these links, the hit list provides a set of powerful tools for query refinement or batch processing. The ‘Show related’ drop-down menu enables you to see all objects of a particular class that are related to the hits selected in your list. For example, selecting ‘Clones’ from the ‘Show related’ menu of a genes search will return a list of clones that are related to the selected genes. The ‘Results Analysis/Refinement’ button provides the frequency of values within your selected hits for a predefined list of fields. Selecting ‘Biological Process’, for example, from the Results Analysis/Refinement tool for a list of genes involved in the Notch signaling pathway will result in a page listing the distribution of the different Biological Process controlled vocabulary terms associated with the list (Figure 2). Clicking on the number in the ‘Related records’ column will return the genes that make up that distribution bin. Lastly, the ‘HitList Conversion Tools’ button allows you to send the selected hits to the Batch Download tool or to a new QueryBuilder session for further advanced queries, to download IDs to a local file on your computer, or to view HTML tables of various third-party data sources linked to the hits in your result list.Figure 2.


FlyBase: integration and improvements to query tools.

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

Results Analysis/Refinement Tool. The Results Analysis/Refinement Tool has been used to display the distribution of Biological Process controlled vocabulary terms applied to a list of the components of the Notch signaling pathway. The second column displays the term for which the distribution was created. The next three columns show a graphical display, the raw size, and the relative size of the term in the distribution. Clicking on the number in the ‘Related records’ column will return a hit list containing the individual records that make up that bin.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Results Analysis/Refinement Tool. The Results Analysis/Refinement Tool has been used to display the distribution of Biological Process controlled vocabulary terms applied to a list of the components of the Notch signaling pathway. The second column displays the term for which the distribution was created. The next three columns show a graphical display, the raw size, and the relative size of the term in the distribution. Clicking on the number in the ‘Related records’ column will return a hit list containing the individual records that make up that bin.
Mentions: The search results page, the hit list, is presented when you perform any search that returns multiple hits (Figure 1). By default, all records are selected for inclusion in subsequent manipulations, but the checkboxes allow user-defined subsets to be created. The first data column links directly to the report for each record that matched your search. Other columns link to GBrowse or to searches that return hits directly related to that record. In addition to these links, the hit list provides a set of powerful tools for query refinement or batch processing. The ‘Show related’ drop-down menu enables you to see all objects of a particular class that are related to the hits selected in your list. For example, selecting ‘Clones’ from the ‘Show related’ menu of a genes search will return a list of clones that are related to the selected genes. The ‘Results Analysis/Refinement’ button provides the frequency of values within your selected hits for a predefined list of fields. Selecting ‘Biological Process’, for example, from the Results Analysis/Refinement tool for a list of genes involved in the Notch signaling pathway will result in a page listing the distribution of the different Biological Process controlled vocabulary terms associated with the list (Figure 2). Clicking on the number in the ‘Related records’ column will return the genes that make up that distribution bin. Lastly, the ‘HitList Conversion Tools’ button allows you to send the selected hits to the Batch Download tool or to a new QueryBuilder session for further advanced queries, to download IDs to a local file on your computer, or to view HTML tables of various third-party data sources linked to the hits in your result list.Figure 2.

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