What Queries Are Saved and Run Again at a Laterdate One Advantage Is That the Query Uses Themost

Query Builder Overview

QB takes advantage of how the information is stored in FlyBase to let more sophisticated searches relative to QuickSearch or other search tools on FlyBase.

Using QB, you tin can search whatsoever field in a FlyBase report using a QuerySegment, and then combine the resulting hit-listing with searches in other fields, allowing combinatorial searches that bring together QuerySegments with Boolean operators. (Notation that Homo Disease, Cell Line, Gene Grouping, and Strain reports are not currently attainable with QueryBuilder).

A set of results can be exported to QB from other searches on FlyBase, through the 'Export' button at the top of a hit-list, then modified to refine the search past adding additional query segments.

Getting Started

Select one of the 3 options on the QB start page:

1. Select a pre-constructed QueryTemplate
2. Import a previously saved query
3. Build a new query

Select a Pre-constructed Query Template

The commencement option on the QB showtime page allows 1 to cull a query from a big drove of pre-constructed query templates. The available templates are organized by data type. To come across the list of templates related to a given class of information, choose the data grade of interest from the pull downwardly carte at the left. A list of pre-constructed query templates volition announced at the correct and a information class-specific list of "keywords" will appear at the left. The list of templates can be further refined by selecting 1 or more of the keywords. Merely the templates containing the chosen keywords will remain. To return to the complete set of templates for a given information class, only deselect the called keywords.

Example Templates:

1. List the genes associated with a specified cistron ontology term (e.m. transcription factor activity) that are reported to genetically interact with a specified gene (e.thou. bsk).
2. List the balancers for a specific chromosome (eastward.thousand.*3LR*) bachelor in a stock.
3. Listing the lethal insertions for a specified gene (e.g. N).

When you find a template that matches or is similar to your query of interest, click on the template. This volition bring you to a QueryBuilder Page with the specified query prepare and set to run. To modify the parameters to exactly lucifer your own query specifications, employ the green "Edit" tabs present in each segment of the query. Change the search terms as desired, click "Finish Editing", and and then select "Run query".

Import a Saved Query

Any QuerySchema (a collection of QuerySegments combined using Boolean operators) tin can be saved for running over again at a later date using the "Store This Query" option on the QB results page. The QuerySchema is saved to your computer as a minor text file. To run the query again, choose "Import a saved query" from the QB get-go page. Use the "Choose File" option to retrieve the file. The proper name of the chosen file will announced adjacent to the "Choose File" box. Click on the green "Done (activate query in new QueryBuilder session)" button, which volition have y'all to the QueryBuilder folio with your saved query entered. Edit the query if desired (as described below), and then click on "Run query".

Build a New Query

Click the yellow box on the QB start folio titled' 'Build a new query". Follow the instructions below to either build a query using any text string of your choosing, build a query using controlled vocabulary terms, or to do an expression blueprint query.

Below is a the initial Query segment box that you lot will run across that is set up to be filled in.

Building a segment using whatever text string

Step 1: Select the DataClass yous desire to search from the DataClass dropdown bill of fare. This will announced in the "DataClass" line of the query segment.

There are 19 options to choose from. In most cases, choosing a particular DataClass changes the window display to evidence the Querybuilder searchable fields establish in the study for that DataSet. In other cases (Expression Search, Controlled Vocabularies) a defended search interface appears.

Stride 2: Click on the radio push next to the report field yous wish to search. This volition appear in the "Field" line of the query segment.

Step 3: Enter the text string for your search in the QuerySegment's "SearchText" box. The search algorithm will search for occurrences of the text string you entered in the specific field that you selected in step one. In cases where the selected field value may be case sensitive (eastward.g. symbol), you can opt for running a case sensitive search by choosing "yes" in the "example-sensitive" dropdown bill of fare. For some fields, autocomplete will list valid field entries guided past the text you take typed.

Step 4: Click the "Cease editing" push.

Step 5 (optional): Add an additional search segments past clicking the "+" button. A new box will appear and you tin repeat the selection procedure. The additional segment(southward) can be joined to existing segments using standard Boolean operators. The default operator is "AND". To change to "OR" or "Only Non", click on the join box until you reach the desired operator. You tin can remove query segments past clicking on the "x" in the top right corner of the query box.

Step 6: Click on "Run query". (Note that the default search is for D. melanogaster. To search for results in other Drosophila species, choose the species of interest from the "Species filter" drop downwardly menu before you run the query).

Step 7: To see results for the DataClass specified in your search, click on the advisable dark-green button, which indicates the number of hits and takes you to the relevant study or a hitlist. To see results in other cross-referenced DataClasses, click the green results push button for the DataClass of interest.

Building a segment using a Controlled Vocabulary term

Step 1: Select "Controlled Vocabularies (CV)" from the DataClass drop-downwards carte du jour.

Step two: Clicking this option changes the window brandish to show tiptop-level terms from various CVs used in FlyBase for GO ontology, beefcake, developmental stage and phenotype terms. You lot tin either browse through the CVs from these peak-level terms or you tin can search for terms matching what you are looking for, using the search box above the terms. By default, your search will be performed using CV terms from the whole subtree of the term yous've chosen. If you lot wish to search only for the exact CV term y'all take chosen, select "This CV term only" from the "Retrieve records annotated with" drop downwards bill of fare. (Hint: you'll recall more results by searching the whole subtree)

Stride 3: Once you've decided on a term, click on the green box to employ the term in your search. The window returns to the QB query page, where the first QuerySegment has been populated with your chosen CV term.

Step 4: Add additional query segments as described in a higher place (optional).

Step five: Click on "Run query".

Searching Gene Expression Data

Step 1: Select "Expression Patterns" from the DataClass menu.

Footstep 2: Build your query past entering CV terms in the Developmental Phase, trunk Part/Tissue, and Subcellular Location text fields. The auto-complete feature will help you choose valid CV terms to build an expression statement (see Hints and Tips).

Step 3: Click on the greenish 'Finish editing' push button. You can edit your query before running information technology by clicking the green 'Edit' push, which will take yous back to step 2.

Footstep 4: Add new clauses to your search if desired past clicking on the xanthous plus sign button as described to a higher place.

Pace 5: Click on the greenish 'Run query' push.

Step 6: Click on one of the light-green "Genes", "Insertions" and "Recombinant Constructs" crossreference links to get a hitlist of reports that listing expression pattern data matching the search criteria for the chosen information form.

Hints and Tips for searching expression patterns:

• Note that the Expression or GAL4, etc. QuickSearch tabs provide alternative mechanisms for searching expression patterns but they do not offering the combinatorial search options of QB. In addition, the "Vocabularies" search tool (accessible from a button on the FlyBase home folio) is a powerful tool for identifying CV terms of interest past providing links to vocabulary term reports that include term definitions, hierarchical CV term tree structures, and other useful data.

• The input fields in the QB expression pattern grade use a sophisticated auto-consummate characteristic. When you begin typing in (or fifty-fifty just click inside) a field, a listing of suggested CV terms will announced. For the get-go field you fill in, all advisable CV terms for that category are bachelor.

• Each filled search field further constrains the auto-complete function for the remaining fields. For example, if you take entered "gastrula stage" in the Developmental Stage field, the auto-complete function for the Body Part/Tissue search field will include the CV term "parasegment 10", merely will exclude the CV term "leg". Likewise, if you lot have entered the CV term "prothoracic leg" in the Trunk Part/Tissue seach field, the machine-complete function for the Developmental Phase search field will include "adult phase" but exclude "embryonic stage four".

• If you select only terms suggested past the auto-complete characteristic, your expression statement query should e'er lucifer some results. To avoid running queries which produce no hits, it is highly recommended that you use terms suggested by the machine-consummate feature.

• Below each search field is a Qualifier field, in which you tin enter a qualifier, such as "early" for Developmental Phase, or "apical" for Subcellular Location. Each of the qualifier search fields as well has an motorcar-complete office, and will only offer qualifiers that accept been used in curation with the term entered in the search field higher up it.

• The motorcar-consummate cannot take into business relationship that an expression statement may only exist in, e.thousand., the "Insertions" dataset, when you are currently searching the "Genes" dataset. In these cases, your search will return no direct hits, but the light-green "Cross references" buttons that appear when y'all run the query bespeak that there are hits in another dataset

Additional QB Features

Wild Cards

The Asterisk is wild. An asterisk (*) on either end of your search string, or embedded in the middle of the string, is interpreted equally "any character". Wild cards are not automatically added to QB searches. If a query is unproductive, endeavor it again with * on one or both ends.

Stocks | FlyBase Genotype mam*

Alleles | Phenotypic Form *maternal*

Insertions | Symbol *ptc*

Any value, no value

Search for the presence or absence of information in a field, rather than a specific value.

The options are IS Nothing and IS NOT Zero (this query is instance sensitive).

Logical operators

Combine multiple query legs with logical operators.

The options are AND, OR, and BUT NOT.

When using ii or more query segments, QB gives precedence to the previous segments.

haltere AND wing OR leg is interpreted as (haltere AND fly) OR (leg)

Phrases

Multiple words are treated every bit a phrase.

But records that include the search words in the lodge y'all specify will be matched.

Calculations

Calculations can be incorporated into searches of some fields that contain numbers.

The options are greater than (>), less than (<), plus or minus (+/-) and range (-).

Polypeptides | Length (aa) | <fifty

Polypeptides | Predicted MW | <25

Transcripts | Length (nt) | 100-200

Genes | Number of transcripts | >ten

Hierarchical CV queries

The Get and Anatomy/Development term relationships are fully supported in QueryBuilder.

Searches of CV fields within standard data classes (e.k., Genes) observe only records that contain the individual term y'all specify. The GO/Anatomy CV database associates each term in these CVs with all of the terms below information technology in the hierarchy, allowing a single search to find records that contain a term or any child of that term.

Case Sensitivity

Case-insensitive searches are standard. There are two exceptions:

A case-sensitive Symbol search is bachelor for well-nigh data classes.

The reserved phrases IS Nix and IS Not NULL are case sensitive.

Cytological Location Searches

Cytological Location Searches are redirected to the GBrowse dataset, which uses estimated sequence ranges of cytological locations.

Controlled Vocabularies

To access all of the Gene Ontology, Anatomy, Developmental stage, and Phenotype Controlled Vocabularies (CVs) used in FlyBase, go to Vocabularies.

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-ordinarily-used symbols, terms, numbers or words from the data in the selected field. Admission the lexicon by clicking on the yellowish box in the upper right labelled "select search text from dictionary". Cull the term of involvement and click on "employ selected content".

suttonunden1940.blogspot.com

Source: https://wiki.flybase.org/wiki/FlyBase:QueryBuilder_Help