How do you find reports containing the information that you want? Most often, the search tool QuickSearch will be the best place to start a search (). This section describes the updated version of ‘QuickSearch’ while the following section, ‘Alternatives to QuickSearch’, details some of the other tools available on FlyBase.
The QuickSearch tool on the FlyBase home page has recently been updated with extended capabilities. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. This tabbed organization has allowed us to make each search form clearer, and in most tabs we have been able to add extra functionality. Several of the tabs contain entirely new search tools, such as a new ‘Simple’ search form, an easy-to-use tool with access to all the data types in FlyBase (see ).
The ‘Simple’ tab performs a global search of FlyBase data ( top). The form has a very clean interface, with only a textbox and a ‘Search’ button for input. When a single word or phrase is entered, this search combs all the FlyBase data records that can be text-searched and returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a table of individual matches in that data type. Alternatively, you can edit the phrase directly and search again, without having to start over.
There are several tabs on QuickSearch that allow searches using controlled vocabulary terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on GO terms, anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes and anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs
The ‘References’ tab offers a search of the extensive FlyBase bibliography. Searches can be filtered by title/abstract text, journal name, publication type and reference IDs (PubMed or FlyBase), in addition to the author and date filters. Appropriate fields also allow the use of Boolean operators, so you can search for papers authored by e.g. ‘Smith NOT Johnson’ or published ‘>2006’ (after 2006).
The ‘Data Type’ tab contains a trimmed-down version of the previous QuickSearch form. The lengthy drop-down menu of data classes has been shortened considerably, with many of the data classes now having their own tabs, but the behavior of the search in this tab is otherwise largely unchanged. Here you can search specific data classes in the FlyBase database, such as stocks, gene associations, sequence features or aberrations. When you search any one of the FlyBase data classes, your results will be restricted to only those hits from within that data class. If you are unsure how FlyBase classifies the item you are looking for (e.g., a gene, allele, insertion or clone), you can select the ‘All data types’ option to have QuickSearch search every class of data in FlyBase (or use the ‘Simple’ tab to search all report data in FlyBase).
Many of the tabs make use of our FlyBase-specific auto-complete feature. Auto-completion is probably familiar to Google™ (or similar) web search page users, and most browsers now have a mechanism like this to provide hints when users are filling out forms. The textboxes in auto-complete-enabled QuickSearch tabs suggest search phrases that are specific to FlyBase data reports. This auto-complete feature overrides your browser's auto-complete function.
An advanced coordinated auto-complete has been active in the QuickSearch tool for some time. Here is an example of how it works in the ‘Expression’ tab:
When the ‘expression pattern (lit. curated)’ data class is selected, text box fields for Stage, Tissue and Cell Loc. (cell location) are displayed. The auto-complete for these three fields is coordinated in the following sense: Suppose you enter ‘fertilized egg stage’ in the Stage text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; ‘egg’, ‘female pronucleus’, ‘fertilized egg’ and ‘male pronucleus’. This is because, out of the multitude of CV terms available for the Tissue field, only these four terms have actually been used in combination with ‘fertilized egg stage’ by curators in an annotation captured in the FlyBase database. If you enter any other term in the Tissue text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.
Using the terms suggested by the auto-complete feature ensures that you do not enter terms that would be mutually exclusive (or have simply not been used by curators). Terms suggested by the auto-complete should always return results. If the coordinated auto-complete does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case, you should try another combination.
Many will find that the search capabilities of QuickSearch meet your needs and we recommend the tool as the first entry point to FlyBase data. More complex tools have a steeper learning curve, but ultimately allow for very powerful searches across all of FlyBase. To become familiar with the tools’ capabilities and to learn how best to use them may require some investment of time, but these tools allow very efficient filtering of the vast amounts of Drosophila
data. A list of all the tools, with descriptions of the data they search, can be found in the tools overview section (http://flybase.org/static_pages/docs/tools_overview.html
), found under the tools menu in the FlyBase navigation bar.
Alternatives to QuickSearch
While QuickSearch offers rapid, intuitive methods to search FlyBase, some users will want to delve more deeply or obtain a more focused result set than QuickSearch can achieve. For those users FlyBase provides more robust search tools, such as BLAST, QueryBuilder, or TermLink.
The FlyBase ‘BLAST
’ tool (http://flybase.org/blast/
) is an ideal entry point for researchers interested in the fly homolog of their favorite non-Drosophila
gene. It will retrieve Drosophila
genes with sequences similar to the submitted sequence.
) is a web-based tool to build powerful queries across the many data types in FlyBase. With experience, one can construct queries to obtain hit lists of genes and other data types matching almost any set of criteria. In addition, there are a number of pre-defined QueryBuilder templates available to guide the less-experienced user through the use of combinatorial searches between and within report pages.
The ‘TermLink’ (http://flybase.org/static_pages/termlink/termlink.html
) tool enables browsing of the CVs used by FlyBase curators and the retrieval of CV term reports. These reports contain a definition for the term (when available), a relationship tree showing similar terms, as well as links to curated data (phenotypes, expression patterns etc.) described using the term.
You may wish to export or download a list of genes or other items generated using one of the search methods described above. FlyBase offers several means to do this.
When using QuickSearch, a result ‘hit list’ page will have two buttons at the top: a ‘Results Analysis/Refinement’ button and a ‘Hitlist Conversion Tools’ button. The first button displays an assortment of ways to summarize and analyze the result list. The second displays a similar variety of ways to export or download the list. For example, one can download a text document containing the FlyBase ID numbers (e.g. FBgn0261526) for every item in your list, or export a hit list to the Batch Download tool.
The ‘Batch Download’ tool (http://flybase.org/static_pages/downloads/ID.html
) allows you to save a file containing information about each item in the list. The tool provides options that depend on the type of data in the list. For instance, if you have obtained a list of gene reports, the Batch Download tool will give you the option to download a FASTA file with each gene sequence. Likewise, if you have a list of references from the FlyBase bibliography, the Batch Download tool will let you download the references in one of several tabular formats.
The FlyBase site also provides many precomputed bulk data files for simple download. Data files that have been requested frequently by FlyBase users are compiled at each release, using the current release data, and links to these have been collected in the Precomputed Files page. Using the navigation bar, go to Files -> Files Overview for a description of the available files or to Files -> Precomputed files (http://flybase.org/static_pages/downloads/bulkdata7.html
) for direct access.