If you simply want to search a database right now, you must Create a New Search.
If you want to create and save a search, or have automatic updates sent to you when new data is added to a database, you must first Create a New Search.
If you want to modify or submit a search you previously created or saved, see Opening Saved Files.
There are 3 ways to begin creating a new search:
Once a Search has been created, the Search View should be visible.
To define your Search, you need to enter search terms that indicate what you are looking for in the database. Enter your search terms in the box labeled: 'Enter Search Terms'. Type any words you wish to search for here. (You can also paste text that was copied from somewhere else. Try pressing 'ctrl-V' on the keyboard or right-clicking (or control-click) on the text box).
Most databases break each entry into multiple fields such as "Author", "Name", "Keyword", "Organism", etc. To tell the Search which field to look in when searching for a word to this:
For most databases you can enter multiple search terms separated by boolean operators such as "AND", "OR", and "NOT". Whether a particular operator is supported depends on the database, so see the help pages for that database if you're not sure. You can simply type the boolean operators in between your search terms. Important: make sure that there is a space before and after each boolean operator, or the database will give you incorrect results.
To return every item in the database that has ANY of the terms you entered, separate the terms with "OR".
To return only items that contain ALL of the terms you entered, separate them with "AND".
If you are using the "NOT" operator, or are mixing "AND" and "OR" operators, the order that terms are entered is important. This makes it difficult to figure out exactly what will be returned. Most databases accept parentheses (), which determine the order in which the operators are applied.
When using parentheses, make sure all these things are true:
For example:
This is a good search line:
( (dunwiddie tv[AUTH] AND brundege jm[AUTH]) OR (hippocampus[TITLE] AND electrophysiology[ALL]) )
This is a bad search line:
( (dunwiddie tv[AUTH] AND) brundege jm[AUTH])
Once you have created a Search for a particular database, you can view the help page for that database. The help page should give details about the search fields and boolean operators supported by that database.
To view the help page, make sure you have a Search View for that database visible.
Press the 'Database Help' button that is to the right of the database name at the top of the View.
Once you have typed the terms you're interested in into the Enter Search Terms text box, press the 'Search' button to the right of the box. The search is sent to the database and the results are returned (this may take a few seconds). The results appear in the box at the bottom of the screen. Please note that not all of the Results are displayed. To change the number of results displayed see Changing the number of items returned. The terms you entered have now moved up to the top of the screen to the Search History section. For a simple search, go ahead and review the results at the bottom (see Editing Results for details). You can also build a more complex search by adding multiple lines to the search history.
The Search History is the section at the top of the Search View just below the database name. It contains each line you have submitted to the database. Each line shows 4 things:
If you change any of the Search settings and want to redisplay the results, simply press the 'View Results' button again.
The Search History gives you useful feedback on what you have already done by showing you the total number of items returned for each line (this may be much larger than the number of items that are displayed in the Results Box, because this is limited by the # of Items to Display setting). You can also use the Search History to build multiline Searches.
One of the easiest ways to build a complex search is to add one or a few terms to each line, and then combine several different lines using boolean operators.
Here's a brief example:
Let's say you have created a new NCBI PubMed search, and you want to extract this:
articles that examine the role of dopamine in the accumbens brain region in drug abuse. Here's one strategy:
You can add line numbers to any part of a search, but these 2 things MUST be true:
You can only submit a single line to the database at any one time. Hence, to search the database for all of the things you have added, add a line that combines all the others. This is simplified with the Combine all lines function.
Search settings can be adjusted in the 'Adjust Search Settings' roll-up box. When you start the program, this box is closed, as shown below:
To open the box, press the down arrow button on the right side. You can also double-click anywhere on the title near the top of the box. This will open the box, revealing several controls.
Press the top right button again to close the box, or double-click on the title at the top. The controls in the Adjust Search Settings box are described below.
When building a multiline search, you may want to quickly add lines to the Search History without submitting each line. You will still be able to see how many items that line returns, but will not have to wait for the actual results to appear at the bottom of the screen.
To add lines to the Search History without submitting them, open the Adjust Search Settings box. The top item in the box is labled 'View results every time we add new terms?'. It is 'Yes' by default. Click on 'No'. The button next to the 'Enter Search Terms' text box should changed from 'Search' to 'Add Terms'. When it is pressed, the line will be added to the Search History but the results will not appear at the bottom of the screen in the Results Box. To view the results, just press the 'View Results' button next to the line in the Search History. These buttons will still work the same.
Multiline searches can be constructed by combining lines from the Search History as described in Multiline Searches (Adding line numbers to your Search). You can automatically combine ALL of the line in the Search History, which may make it easier to summarize a large search without having to type in many line numbers. To combine all lines:
Note that if there are not at least 2 lines in the Search History, the 'Combine Lines' button will be grey and inactive. There must be at least 2 lines in the history to combine.
Most databases support several different formats for their results. Some are short, some are detail rich, and some are designed for machines to read if you want to download the results into another database.
To change the format of the results:
The formats available depend on which database you are searching. The easiest way to see what a given format looks like is to select and press 'View Results', or read the Help pages for that database.
The 3rd column in the Search History labeled 'Number Returned' shows the actual number of items in the database that match a given Search line. The number of results that are displayed in the Results Box is usually less than this number, and is limited to prevent an excessive drain on the database server.
To change the number of items shown in the Results Box:
You can edit or modify search lines after they have been added to the Search History. There are 3 things you can do:
To insert or delete a search line:
In the Search History right-click (or control-click) on the text of the line. In the pop-up menu there should be an item labeled 'Tools' with a small arrow pointing to the right. Click the 'Tools' item. Another pop-up menu should appear to the side with 4 more options:
When a line is inserted or deleted, all of the other line numbers that are listed in the Search History will automatically adjust to point to the correct place. Any references to a deleted line will be removed. Please note that if a line is deleted and another line does nothing other than point to it, both lines will be removed.
When the 'Search' or 'View Results' buttons have been pressed, the items found in the database are displayed in the Results Box at the bottom of the screen. Inside the Results Box, just above the text of the Results on the right side there are 3 buttons: 'Clear Results', 'Edit Results', 'Save Results'.
If you want to edit the results, or preserve them just during this session, press the 'Edit Results' button. The results are pulled out of the Search View and appear in their own View (the 'Results View'). This means they get their own tab and name, and you can switch back and forth between the Search View and the Results by clicking on the tabs at the top of the screen. Once the Results are moved to their own View they are no longer affected by anything you do in the Search View, so you can change the search and resubmit it, collecting several different sets of results. There is no limit to how many sets of results you can have open at one time.
Once you have a set of results open in a Results View, you can edit it and save it whenever you like. The results are simply text files, so you can type your own notes into them, delete unwanted items, and cut, copy, and paste between the Results View and any other program on your computer. You can save the results to the BioQuery server at any time (see Saving and Opening files).
BioQuery can save files to the BioQuery server. If you want to save a file to your computer, copy the text and paste it into your text editor or word processor (this may change in the future).
There are two ways to save results. One is to save them directly from the Search View by pressing the 'Save Results' button. This will open a Window allowing you to enter a filename and location on the BioQuery server. Press 'OK' and the file will be saved. The results are also moved to their own Results View in a new tab, and can be further edited and resaved. See Editing Results.
The second way to save results is to first display them in a Results View (see Editing Results), and then save the View as a file (see Saving and Opening files). This has the same effect as just pressing the 'Save Results' button.
Next Help topic: Automating a Search (getting updates)