GeneCards acts like a sophisticated encyclopedia, integrating a vast and comprehensive range of information about human genes and their encoded proteins from dozens of major data sources, both public and proprietary.A US-Israeli start-up is now offering pharmaceutical and biotechnology companies an innovative data mining tool that can help speed up the process of gene research enabling them to bring new life saving drugs and treatments to market quicker.

Xennex, which was founded in 2003 and is now based in Cambridge, Massachusetts, offers commercial life science companies access to a new database, called GeneCards, which was developed by a team of scientists at the Weizmann Institute of Science in Rehovot.

The database acts like a sophisticated encyclopedia, integrating a vast and comprehensive range of information about human genes and their encoded proteins from dozens of major data sources, both public and proprietary. It then brings these together in one Web-accessible knowledge base.

Users can access this web site, and simply by pressing the relevant key words into a search field, can extract and integrate concise and thorough details about any aspect of gene exploration. Data is divided into different fields such as aliases, chromosomal location, ontologies, diseases, pathways, and expression, all searchable by keywords. The emphasis is on medical aspects and roles in disease. Information is presented in a user-friendly interface, offering clear and comprehensive links to all gene-related biological and medical information.

The need for such a tool in the life sciences field is vital. Today there are huge amounts of information available about the human genome, and this information is stored in countless different libraries, all of which specialize in different things. Researchers can easily get dragged into a lengthy and time-consuming search as they look for the relevant data.

“Drug discovery is a long, difficult and expensive process,” says David Warshawsky, 39, the CEO of Xennex. “GeneCards saves our customers a great deal of time and money because they can build up a complete picture of a gene in a very short time.”

Commercial users license the technology either on a per use or a per user basis, though academics can still use the data mining tool for free through 20 or so university web sites. Xennex offers the technology either through its own web site, or clients can add it to their own server.

GeneCards was the brainchild of Professor Doron Lancet, head of the Weizmann Institute’s Crown Human Genome Center, who began developing the product in 1987 with a team of experts in bioinformatics. Originally it was only available to universities and research institutes, but gradually an increasing number of commercial companies began to show interest in the product.

In 2003, Warshawsky, the former director of worldwide business development at Compugen, and entrepreneur Adam Kaplan, who is now VP of Xennex, applied for a license to develop the product for commercial use. The company was founded with a small injection of capital from the founders, and from other angel investors. No investment was needed in R&D as the database was already operating. “The main tool was already built, we just had to make it available to commercial customers,” Warshawsky told ISRAEL21c.

“Normally R&D costs millions of dollars. We were able to use the small amount of capital we invested in building relationships, rather than spending on R&D.”

Xennex also began work with another major advantage – the tool was already popular and widely used. “When we started selling the product, there were already a large number of people who had used the product and were interested in using it further,” Warshawsky explains.

Sales grew rapidly as a result, and today Xennex is already profitable, and has thousands of users across the world. The company licenses GeneCards to between 20 to 30 of the world’s leading pharmaceutical and biotechnology players in North America, Europe, and Japan. The database is also used regularly by dozens of smaller pharmaceutical and biotech companies.

In recent months, a new area of business has emerged for Xennex – patent law. Patent lawyers need a tool like GeneCards to speed up their work in reviewing and approving patent applications in the life sciences area. Lahive & Cockfield, a Boston based intellectual property law firm that specializes in biotechnology patents, has been using GeneCards for some time. A spokesman at the US office said: “GeneCards is extremely helpful, the biggest plus being that GeneCards provides a central place for accessing all information about a specific gene which translates into a more efficient use of time, and decreased frustration with other more traditionally used databases.”

In March, Xennex signed a significant licensing deal with the European Patent Office (EPO). Patent examiners at the EPO access GeneCards to carry out research, retrieve relevant information supporting patent-related activities, and determine whether new inventions can be patented.

The agreement means that GeneCards becomes a key component in the process of approving relevant biotech patent applications at the EPO. The product will be used at EPO sites throughout Europe, including those in Germany, the Netherlands, and Austria.

“The information [from GeneCards] provides immediate insight into current knowledge about the respective gene, including a focus on its cellular functions, and its involvement in diseases. This is valuable information for us,” said Gerard Giroud, Principal Director Documentation/Tools of the European Patent Office.

Warshawsky believes that GeneCards is a unique tool in the market, and that competition is very unlikely in the near future. “This is an innovative approach to sharing information,” he explains. “It is very user-friendly and provides clear and comprehensive information for users. It may be that another company will decide to generate their own machinery to fill their own needs, but they will have to spend millions of dollars developing it, and it will take many years. GeneCards is already out there, and people have been using it for over eight years – that means eight years of development and improvement. We capitalize on that past. Anyone who tries to redo our technology from scratch, will have a long development ahead of them. It is not a straightforward thing to do. You don’t need to generate a second GeneCards, there is already one that works very well.”

In return for receiving the license to sell GeneCards commercially, Xennex has agreed to continue supporting and overseeing R&D work carried out by the 12-man research group at the Weizmann Institute. “The interaction between Xennex and the researchers at the Weizmann Institute is the key to the success of our company,” admits Warshawsky.

Part of that work includes four new data mining products that Xennex hopes to introduce to the commercial market sometime later this year, or early next year. Warshawsky said these new database products will enhance the GeneCards offering.

In addition, Xennex is looking for possibilities for collaboration. In February, Xennex and German company, Lion Bioscience announced that they will deliver an integrated solution to the life sciences market, which allows Lion’s SRS users to view GeneCards data within SRS. SRS is a data integration platform used by pharmaceutical companies such as Eli Lilly, and Johnson & Johnson, that provides fast access to diverse life sciences data from public and proprietary sources. By integrating the two technologies, scientists will be able to deploy the power of data integration offered by SRS with the gene-centered knowledge of GeneCards to advance their research.

The company’s goals now are to increase its expansion into IP law firms, to continue collaborating with other companies, and to improve the GeneCards offering. In July, for instance, Xennex signed an agreement with Californian company, Applied Biosystems Group. Under the terms of this, Applied Biosystems, an Applera Corporation business, is to provide GeneCards’ customers with direct access to its entire collection of nearly three million genomic assays. This, says Warshawsky, will offer users innovative tools to help them follow promising database search leads with real-world lab experiments.

“We believe in GeneCards,” says Warshawsky. “It is our dream to help life science companies with their research efforts. We are not a company that is going to make billions of dollars, but our goal is to provide GeneCards to as many companies as possible. We already have a solid customer base, and this is growing fast.”