FlyBase QueryBuilder

Query Schema

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Query Builder Help
QueryBuilder Help
  QueryBuilder (QB) provides one-stop shopping for information in FlyBase. QB presents a simple user interface that supports powerful searches by offering access to every DataSet|Field pair (for example, Genes|CV:GO:Molecular Function) in FlyBase along with the ability to include any combination of datasets in the same search. QB automatically creates sets of records that are cross-referenced to the records that match your query, providing links to all related records in FlyBase from a single page. Both simple and complex queries can be built in a few steps:  
  • Select a data class or dataset to search
  • Select a field to search, or use Any field to search full records
  • Provide the information you want to find
  • Select the class of records for results display (optional)
  • Run the search or repeat steps one and two to add additional criteria to your query
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      Features  
      Calculations Calculations can be incorporated into searches of fields that contain numbers.  
          The options are greater than (>), less than (<), plus or minus (+/-) and range (-).  
      Any value, no value Search for the presence or absence of information in a field, rather than a specific value.  
          The options are IS NULL and IS NOT NULL (this query is case sensitive).  
      Logical operators Combine multiple query legs with logical operators.  
          The options are and, or, and but not.  
      Phrases Multiple words are treated as a phrase.  
          Only records that include the search words in the order you specify will be matched.  
      Batch queries Upload a list of FlyBase IDs, search for all related records.  
          Standard Batch download is also available for query results.  
      Hierarchical CV queries Full support for GO and Anatomy/Development term relationships.  
          Searches of CV fields within standard data classes (e.g., Genes) find only records that contain the individual term you specify. The GO/Anatomy CV database associates each term in these CVs with all of the terms below it in the hierarchy, allowing a single search to find records that contain a term or any child of that term.  
      Field type tags Five field type tags help organize and identify search options.  
         
  • CV - Controlled Vocabulary, terms are consistent across records
  • Flag - Flags records with the presence of links of specified type (any search of flag field will be performed as "IS NOT NULL", ignoring user-supplied context)
  • Map - Genetic, cytogenetic, or genomic map data
  • Symbol - Symbols are the only, or predominant, datatype
  • Text - Data is free text, usage may not be consistent from record to record
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      Field content dictionaries Preview the information in a field, or select dictionary entries to use in a search.  
          The field dictionary lists up to 100 most-commonly-used symbols, terms, numbers or words from the data in the selected field.  
      Alternative results Related records in other FlyBase data classes are a click away via the green buttons.  
          QB creates a set of cross-references for the records that match your search criteria. An itemized results list (of Genes records, for example) is displayed for the data class that is selected when a search is run. A series of green buttons at the top of the results page provide links to related records in other data classes (Insertions, for example). With QB you do not need to open each report and click through layers of links to find related information. This feature can also be used to find information that may be difficult to search for directly because of unfamiliar nomenclature (such as Insertion Symbols). Only References are excluded from automatic generation of alternative results (because of the large size of this dataset).  
      Linkouts Related information from other databases is a click away via the yellow buttons.  
          If the records identified by your search include links to external databases, these links are available from the yellow button or buttons in the Linkout section of the results page.  
      Other Points of Information and Examples  
     
    • Asterisk is wild. An asterisk (*) on either end of your search string is interpreted as "any character".
      • Stocks|Symbol mam*
      • Alleles|CV:Phenotype Class *maternal*
      • Insertions|Symbol *ptc*
    • Wild cards are not automatically added to QB searches. If a query is unproductive, try it again with * on one or both ends.
    • Search Flag fields with * or any string of letters.
      • Genes|Flag:InteractiveFly default
      • Polypeptides|Flag:Antibody URL (DSHB Hybridoma) *
    • Case-insensitive searches are standard. There are two exceptions:
      • A case-sensitive Symbol search is available for most data classes.
      • The reserved phrases IS NULL and IS NOT NULL are case sensitive.
    • Multiple words are treated as a phrase.
      • Genes|Text:Other information tissue culture cells
    • Cytological location searches are redirected to the GBrowse dataset, which uses estimated sequence ranges of cytological locations.
    • Join query segments with AND or OR.
    • When using two or more query segments, QB gives precedence to the previous segments.
      • haltere AND wing OR leg is interpreted as (haltere AND wing) OR (leg)
    • Calculation query examples:
      • GBrowse Data|Exact Number of exons > 2   
      • Polypeptides|Protein size (kD) < 50  
      • Annotations|Map:Sequence range 3L:5,787,637..5,819,561 +/- 5000 (commas are optional)
      • Insertions|Map:Cytogenetic location 67B-D
    • References record sets are created only when the References dataset is searched.
      • References|Author Wakimoto (creates a References dataset)
      • Alleles|Text: Discoverer Wakimoto (does not create a References dataset)

     

     
      Notes, known problems and features yet to come  
     
    • Data in the MySQL tables were extracted from acode files. If data are not in the acode files they will not be in the MySQL tables. Data will be extracted directly from chado when available.
    • A check box for 'case-sensitive match' is planned, allowing all field-specific searches to be case sensitive without a special case-sensitive field option.
    • All CV fields will be handled in the same way once data are available via chado.
    • Evidence codes in GO fields (and anything else with similar format) are handled as phrases just as the term is; use flanking wild cards to search based on one word of a phrase. For example, you can find genes annotated with molecular functions "inferred from sequence similarity" by searching Genes|CV:GO:Molecular Function [ENZ] for *sequence*.
    • Cross-references to stocks and images are generated, but those from these data types are blocked. This is because these records may include tangentially related objects, such as the set of genes that are mutant in a multiply marked mapping stock.
    • People data are not included in QB.
    • The CG Symbol field present in some gene reports is not available here. Use Annotation | Symbol: Annotation ID for CG/CR numbers.
    • Data in FlyBase Date fields are in a variety of formats. This needs to be corrected or patched for Date fields to work properly here.
    • All of the menus and dictionary files are produced automatically. Dictionary files remain on the server for 2 hours. If an index dictionary for a given field isn't already present on the server, it will take a bit of time to generate it.