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Inpharmatica Breaks Biopendium Platform into Four Modules to Target Mass Market for Informatics

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UK-based informatics firm Inpharmatica has decided that the best way to extend the market for its flagship Biopendium protein-annotation database is to break it apart.

The company has released four web-based components derived from Biopendium as part of a new product line dubbed Annotation Express. One of these modules, a microarray probe annotation database called Blu-Chip, made its debut at IBC's Chips to Hits conference earlier in the month.

Imad Yassin, director of business development at Inpharmatica, told BioInform that Biopendium has grown over time to become a "huge product" that is simply too large and too expensive for many potential customers, particularly academic and government labs — a market that the company has not addressed in the past, but one that it is targeting more aggressively with the new product line.

Privately held Inpharmatica, founded in 1998, has built its business around the Biopendium platform, which it uses primarily in collaborative agreements with large pharmaceutical firms. Yassin said that the company intends to continue along this track, but is now broadening its focus to reach the lower-end market with the line of user-friendly modular tools.

"We found that certain customers are interested in certain parts of this product, so we modularized Biopendium, and at the same time built in new modules that are suitable for the single user," he said. Biopendium has proven "popular" with bioinformaticians, he said, "but recently there has been a dramatic increase in the number of researchers who want to interpret their own experiments, for example, microarray users."


"We found that certain customers are interested in certain parts of this product, so we modularized Biopendium, and at the same time built in new modules that are suitable for the single user."

Development of the new system has been an "ongoing project," he said, driven by customer requests. "We basically started talking to our customers and saying, 'Which modules do you use most?' and we found out what makes sense to be grouped together, and then we came up with these modules."

In its discussions with customers, Inpharmatica also found that many users viewed Biopendium as a product for the bioinformatics specialist, not the bench biologist — a perception that limited the potential market for its technology. Annotation Express was developed in part to bring the same capability of Biopendium to this wider user base, Yassin said. "Annotation Express could be a method whereby biologists who want validation or backing for their experimental data don't need to ask the bioinformatics group every time they have a question," he said.

The goal, he added, "was to build up a system that allows us to take this product to the mass market."

Pricing for Biopendium varies, but it starts at $40,000 per user per year for academic users, while the new Annotation Express modules start at $5,000 per user per year. Inpharmatica released a lower-priced online version of Biopendium, called Biopendium Online, in 2003, but Yassin said that the price of the system was still too high for many of the customers that the company is targeting with the new offering.

In addition to Blu-Chip, a database that assigns proteins to Affymetrix probes, the other modules in Annotation Express include Domain Professor, which includes protein domain annotation from Biopendium along with several new interface options; InGOt, a database of Gene Ontology annotations and additional proprietary data; and Bio-Clip, which includes summary annotations of the other modules for bulk annotations.

So far, Yassin said, Inpharmatica has seen the most interest in the Blu-Chip module, which the company claims offers higher-quality probe-to-protein assignments than other resources.

Because the product line is still new, Inpharmatica has not yet secured any paying customers for the Annotation Express modules, but Yassin said that the company has signed up several non-profit and commercial users for free online trials.

Organizationally, Inpharmatica has rolled Biopendium, Annotation Express, and its bioinformatics services offering into a single business unit that it calls Biogensa — in line with its Chematica line of chemogenomics products and Admensa suite of ADME-tox tools.

In January, Inpharmatica CEO John Lisle told BioInform that market interest for the company's tools was "slightly more weighted towards the chemistry space than the biological," but added at the time that "Biopendium continues to do well." [BioInform 01-31-05].

Yassin echoed that assertion, noting that Inpharmatica signed an agreement earlier in the month with Schering for access to Biopendium.

In addition, a new version of Biopendium, version 21, is slated for release this week. Yassin said that the new release will include 6.5 million protein sequences, of which 2.6 million are unique, from more than 6,000 different organisms. The company used 20,000 protein structures containing more than 4,000 different ligands to produce around 20 billion sequence-to-sequence relationships and 350 million structure-to-structure relationships, he said.

— Bernadette Toner ([email protected])

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