BioQuery is an all-in-one tool that helps users search numerous public biomedical databases. BioQuery is:
Primarily biomedical researchers who need access to public biomedical databases (such as Medline, GenBank, Swiss-prot, etc.), but who want more power and flexibility than they get from the web interfaces to those databases.
BioQuery can help you extract a very precise subset of data from a public biomedical database, and then help you keep that subset of data up-to-date with new database entries.
Typical use may look like this:
A researcher wants to know about all entires in NCBI's Protein database that match her area of investigation. The researcher starts up BioQuery and creates a new Search. She enters search terms individually at first and reviews which protein entries are returned. After some experimentation, she begins to combine numberous terms using boolean operators to refine her search. Soon she finds she has made a complex Search that extracts a very precise subset of protein data that is a close match to her interests. She then runs this Search and gets all of the database entries that currently match her criteria. She saves these Results as a file on the BioQuery server, and possibly extracts the data to download into a local database of her own. She then automates the Search to check the database once per week, and send her any entries that match her search and have been modified or added. She now knows that the subset of data she is keeping will always be up-to-date.
When starting BioQuery you are given access to your own private folder on our server's hard drive. There are three things you can do once BioQuery is open:
To search a database create a new Search or open an existing Search file. A Search View will open in a new Tab on the right. Enter some words in the text box labeled 'Enter search terms'. Press the 'Search' button. The Search is added as a line to the 'Search History' section at top, and the results appear at the bottom.
A BioQuery Search supports Boolean Searching, limiting by field or date, and building complex searches by combining multiple lines. Here's some examples from Entrez PubMed:
The simplest Search is a single word, which usually searches the database for all entries that have that word listed as a keyword:
'atpase' returns 73770 entries
We can be more specific by telling the database what field we want to Search in:
'atpase[TITLE]' returns 17568 entries
We can use a Boolean operator to be more specific:
'atpase[TITLE] AND calmodulin[ALL]' returns 719 entries
We can use parentheses to create even more precise Searches:
'( atpase[TITLE] OR gtpase[TITLE] ) AND ( calmodulin AND calcium )[ALL]' returns 493
Finally, we can reference other line numbers to let us build complex, multi-line Searches:
See Searching the Databases for more info.
Once a Search is created, you can submit it to a database and get back all or some of the items in the database that match your criteria. These are your results. The results initally appear at the bottom of your Search. This is so you can preview them, and see if this was what you wanted, or if you need to further modify your Search to extract the right data from the database.
If you want to keep the Results, you can use the 'Edit Results' or 'Save Results' button to open the results in a new Tab. These results are no longer associated with the Search file, but are now a separate file that can be independently saved and modified. You can type your own notes into a Results file, cut out items that are not of interest, or copy the whole thing from the Results View and paste it into another application or database on your local computer.
See Editing Results for more info.
The most powerful feature of BioQuery is the ability to receive Periodic Updates for any of your Searches. This feature lets you customize exactly what type of Search is submitted to a database and how often it is sent. Items in the database matching your criteria that have been added or modified since the last automatic Search are found and saved for you. You can have these results E-mailed to you, saved to your account on the BioQuery server, or both.
See Automating a Search (getting updates). for more info.
Using these features a researcher can incrementally create a very large, complex, and precise Search strategy for any database they desire. They can slowly add terms, experimenting with the output until they have found combinations of terms that extract exactly what they want from the database. The ability to go back and modify the Search History is a power feature not found in most web-based databases. When the researcher has perfected their Search strategy, they can run the Search and extract all of the items in the database that match their criteria up to the present time. They can then automate the Search to send them any new updates that match their criteria. In this way, the researcher will be assurred that they have a complete set of items that match their search strategy, and that their personal subset of the database entries will always be up-to-date.
Next Help topic: Getting Started