By Salvatore Salamone
August 13, 2002 | Spotfire Inc. and OmniViz Inc. have announced that researchers can now import informatics data -- microarray gene expression data with Spotfire, cheminformatics data with OmniViz -- directly into each company's analytic and visualization tool without writing scripts or reformatting.
Spotfire's new three-year collaboration with bioinformatics vendor Rosetta Biosoftware promises to help integrate two very different types of data analysis in one analytic tool. For instance, Spotfire's DecisionSite can access data from small molecule biological assay databases, such as ActivityBase from ID Business Solutions Inc. And Rosetta's Resolver Gene Expression Data Analysis System provides the capability for storing, accessing, and analyzing microarray experiment results.
"Both [Spotfire's and Rosetta's] software systems deliver excellent value in their respective areas, but it has traditionally been difficult to bring the data from these domains together to enable an effective, integrated drug-discovery operation," says Wolfgang Hoeck, senior project manager for research IT at therapeutics manufacturer Amgen Inc.
"The integration of both systems will enable the correlation of small molecule high- and low-throughput screening results, with gene expression data coming from microarray experiments, in a highly visual decision analytics environment," Hoeck says.
OmniViz' recently released version 2.6 of its OmniViz data visualization and mining software added support for cheminformatics (experimentally derived data about the properties and structure of molecules under investigation). Specifically, Version 2.6 includes frequently used chemical structure analysis algorithms and a cheminformatics data import and analysis wizard. The wizard and the new chemical structure-specific analysis routines let researchers import experimental data into the analysis program without reformatting the data.
OmniViz' support for cheminformatics follows a February announcement about the company's collaboration with Affymetrix Inc. OmniViz's Gene Expression module can analyze and visualize data in Affymetrix Analysis Data Model (AADM)-compliant databases. (AADM is the database format for output from Affymetrix GeneChip microarray products.)
"Users of these tools now have out-of-the-box access to the data produced by commonly used informatics tools," says Raymond Lopez, an independent IT industry consultant.
The new importing capabilities stand in contrast to the less efficient way data are traditionally incorporated into analysis applications. Typically, a scientist would spend time writing small computer programs -- called scripts -- to extract informatics data from the database and use that data in the informatics tool; the researcher would then have to put the extracted data into a format that the analytic tool program could understand.
While the Spotfire and OmniViz moves make it easier to use informatics data, they're merely stopgap measures until common data format standards are widely adopted. "One-to-one analytic tool vendor-to-informatics vendor collaborations are the best life scientists can expect until the industry sets data formats standards for all types of informatics data and all the vendors whose tools produce that data comply with those standards," says Lopez. And that is not likely to happen any time soon, he says.