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Ariadne Moves Into New Digs, Snags SBIR to Create Toxicology Database With MedScan NLP

Ariadne Genomics has officially graduated from startup mode — at least according to Maryland’s Montgomery County Economic Development Fund, which last week awarded the company an $80,000 grant to help it move out of the technology incubator where it’s been housed since it was founded in 2002.
In addition, the company this week announced that it has been awarded a $100,000 Small Business Innovation Research grant from the National Institutes of Health that it will use to extend its product portfolio into toxicology.
Stephen Sharp, senior director of marketing and product management at Ariadne, told BioInform that the privately held firm met a number of conditions that allowed it to be “promoted” from the Maryland Technology Development Center — one of which was reaching profitability.
“The incubator environment was very helpful,” Sharp said, noting that the firm likely would not have reached this milestone without it. The $80,000 grant will help the firm to move into and outfit its new offices in Rockville, Md., “with very little down time.”
Ariadne currently employs 39 people in Maryland and is looking to add another four US staffers, including a West Coast salesperson. Sharp said the company hopes to expand its presence in the European market in the coming year as well, and has already added several distributors in Europe.
Just over a year ago, Ariadne’s ability to reach profitability was far from certain. In late 2005, Stratagene backed out as the exclusive distributor for Ariadne’s pathway software, which it sold under the brand name PathwayAssist, following a lengthy dispute over the terms of the distribution agreement [BioInform 12-12-05]. 
The end of the Stratagene agreement left Ariadne in the lurch, since it had no direct sales staff of its own, and could no longer sell its software under the broadly recognized PathwayAssist name, changing it to Pathway Studio.
But it appears that the company weathered the transition successfully. “2006 was our first year of direct sales,” Sharp said. “In that year, we had to put together a sales team and a marketing team.” Prior to that, he said, the company’s marketing team was a single person. “The whole business side of the company needed to be built last year,” he said.
Now, with a year’s worth of product sales under its belt, new offices, and its earnings statement in the black, the company is setting its sights on expanding its product offering.
Learning the Lingo of Toxicology
The new SBIR grant, awarded by the National Center for Research Resources, will help Ariadne develop a database of toxicology, small molecule-enzyme interactions, and human metabolism. The company will also use the cash “to expand the scope” of its MedScan natural-language-processing system “beyond its traditional focus on pathway analysis,” Ariadne said in a statement.
Ariadne developed MedScan to extract protein-interaction information from the scientific literature. The system was used to create the company’s ResNet database, which currently includes more than 1.25 million functional relationships and underlies the Pathway Studio software.
The SBIR grant supports development of a modified version of MedScan that will be able to extract metabolic, toxicological, and clinical information from the literature. This extended version of MedScan will then be used to automatically populate and update the new database.
Sharp described toxicology as “a natural functionality for … pathway analysis because pathway analysis is all about pulling knowledge out of the literature in one way or another that allows the researcher to really look at what are the possible interactions for a small chemical compound.”

“The whole business side of the company needed to be built last year.”

The lion’s share of the development work will be in “identifying the terminology, the grammar, the syntax … and the appropriate sentence content for the way toxicologists talk about biological entities and chemical entities,” Sharp said. “Within MedScan, one needs to build a dictionary that specifically addresses the field of toxicology.”
Once the new version of MedScan is developed, it will be used to glean information from PubMed, ToxLine, and full-text journals in order to create the new database.
Sharp said that the company plans to have “at least a beta version” of the database available before the SBIR grant expires in August. It’s likely that the toxicology database will be a standalone offering rather than an embedded feature of Pathway Studio, although Sharp noted that the company has not yet finalized its plans for the release of the new product.
Ariadne’s foray into toxicology follows on the heels of its competitors in the pathway analysis market — Ingenuity Systems and GeneGo — which both showcased their products’ capabilities in the area of toxicity at the recent Molecular Medicine Tri-Conference [BioInform 03-02-07].   
But Sharp said that the MedScan technology, which comes with Pathway Studio, gives it an edge in the competitive pathway informatics market because “we aren’t biased as to what’s in our database.” MedScan enables users to update their pathways with new information in real time, so pathway analysis “is as rich as the literature allows it to be,” he said.

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