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Welcome to bioquery.org
The official website of the BioQuery Project.

What is BioQuery?

BioQuery is a bioinformatics software program that provides a single, powerful user interface for building search strategies for numerous different biomedical databases. BioQuery is also a full update service, allowing you to save your searches on our server, and to receive periodic updates when new data is found matching your search criteria. BioQuery helps researchers maintain a COMPLETE set of the available data on their area of interest.


The BioQuery project is officially closed.

After ten years of service, the BioQuery project has been shut down in favor of the current services offered through the National Center for Biotechnology Information (NCBI). If you would like to create and submit queries to NCBI-hosted biomedical databases, please visit NCBI and PubMed for an overview of tools. This site will remain up for purely historical purposes. Please feel free to look around, but you will be unable to download or use the BioQuery application.


Databases from the National Center for Biotechnology Information (NCBI) currently accessible through BioQuery:

  • PubMed (Medline)
  • Nucleotide (GenBank+)
  • Protein (Swiss-Prot+)
  • PopSet
  • Structure
  • Genome
  • OMIM
  • Taxonomy

Who is BioQuery for?

  • Researchers who want to search multiple biomedical databases from a single interface.
  • Researchers who need an update service to alert them when new data is added to biomedical databases, or when existing data is modified or annotated.
  • Developers who want to add database searching capability to their programs. Check out the Developer's Guide for more details.

How much does BioQuery cost?

Nothing! It is 100% free. The source code has been released under the GNU Lesser General Public License.


What can I do with BioQuery?

You can create and submit searches to several different BioMedical databases. With the BioQuery interface, you can create large, complex searches that precisely target the information you want to extract. You can save these searches for later use, and edit any part of an existing query to continue to fine-tune your search strategy. You can also save the results returned by your queries in your own private directory on our server. Most importantly, you can activate the BioQuery update service to notify you when new material is added to the database, and email you the latest results of your search.



BioQuery is a free service and has been supported by the following organizations:
  • Synaptocode Software, maker of TrialWare4J, a software licensing, copy protection, and anti-piracy tool specifically for Java desktop applications.
  • Proteome Software, a maker of proteomics software tools to help scientists make confident protein identifications from their mass spectrometry data.
  • Oregon Health & Science University (OHSU)
  • National Center for Biotechnology Information (NCBI)

The BioQuery servers are hosted by Kattare Internet Services. Kattare provides the best open-source and Java-based web hosting we have encountered, and has kept BioQuery up and running 24/7 since 2001. Thanks Kattare!


Send feedback to: support@bioquery.org