IBM has made available free Web services tools that automate and streamline searching of National Center for Biotechnology Information (NCBI) databases containing molecular and genetic information used by scientists and researchers.
Available for download at http://alphaworks.ibm.com, the Web services tools are implemented in Java and use a simpler interface than the NCBI's PubMed, GenBank and BLAST (Basic Local Alignment Search Tool) interfaces, said Michael Blocksome, a software engineer in IBM's life sciences development.
PubMed is a database of life sciences journals, while GenBank contains some 25 billion DNA sequences. Using the IBM Web services tools, researchers can query the PubMed database for text of an abstract or search by author name, which "grabs XML (Extensible Markup Language) for articles that satisfy that query" and parses the XML into "session numbers" that identify genetic sequences in GenBank that are related to the PubMed articles, Blocksome said.
After that, researchers can use the BLAST tool to look for other genetic sequences that are similar to the ones found in the GenBank search, leading to a "huge" set of results. "If you had to go to the (NCBI) Web site to do all of that, it would quickly become difficult to organize all of that information, separate in your mind," he said. Instead, the IBM tools enable a workflow that keeps search results together and has the user's computer track them.
"When we started working on it, we saw a lot of manual effort, it was error prone and time consuming to use different tools, different databases," said Doc Dockter, project manager in IBM life sciences.
There is a demo that can be played with online at the alphaworks site so that nothing is downloaded, or there is an example program that can be downloaded that runs through the three available Web services tools hosted on the alphaworks servers. The third way is to download the software for a 90-day period. As with other alphaworks tools, users have to download the software again after the 90-day period expires.
The tools have been available on the alphaworks site since mid-February, but IBM has just begun publicizing them. So far, there have been 452 downloads of the Web services tools, Docktor said.