A year ago, Ariadne Genomics might have named GeneGo one of its biggest competitors — and vice versa. But growing demand for pathway analysis software has fostered a spirit of collaboration among vendors in the space, a trend illustrated by a recent integration partnership between the two firms.
Announced last week, the agreement will make Ariadne’s MedScan TextMiner literature-mining software a plug-in module for GeneGo’s MetaCore pathway database platform. The integrated offering, expected to be available before the end of the year, will add natural-language-processing capabilities to MetaCore so that users can mine the scientific literature and other documents to update the database in real time.
The algorithm behind MedScan TextMiner is the same as that available in PathwayAssist, Ariadne’s desktop pathway analysis software, which is marketed by Stratagene. Ilya Mazo, president of Ariadne, said that the primary difference between the firms’ pathway products is one of scale.
“GeneGo has a conceptually similar system, but it’s an enterprise-level solution,” he said. “So for us, as we don’t have an enterprise-level product at this point, we decided to go ahead and use GeneGo as a vehicle for some of our tools to get a chance at the pharmaceutical market.”
MetaCore customers who use the upcoming plug-in will be able to make data from their text-mining available on the enterprise level.
“In some areas we compete, and in some areas we’re going to leverage each other’s skills,” said Julie Bryant, vice president of business development and marketing at GeneGo.
She said the collaboration made sense because customers were asking for literature-extraction capabilities to augment the manually curated information in MetaCore. “In some circumstances, our customers want to have access to absolutely everything that’s available, and you can do that through natural-language processing,” she told BioInform last week.
Of course, the partnership does have its competitive aspects as well, according to Mazo:
“To some extent, both [we] and GeneGo see Ingenuity as our major competitor, so we believe we’re going to gain more by joining our forces, because together we have more to offer than Ingenuity does.”
More Partnerships, More Customers
Ariadne currently considers itself a text-mining software company and a pathway analysis company — a model that fits well with its partnership strategy. “Our philosophy is that we’re trying to make our software tools as open as possible,” said Mazo. “People are welcome to integrate our [text-mining] software with their data, or other software providers can offer import for our data. Our goal is to deliver our tools to as many scientists as possible.”
GeneGo is not Ariadne’s first partner in the pathway analysis market. In February, the company entered into a co-marketing agreement with Jubilant Biosys that would allow PathwayAssist users to access Jubilant’s PathArt database for an additional fee, and the companies are also working together in a pathway-based research collaboration with Genstruct. Ariadne is also partnering with Integrated Genomics to add pathway information from Integrated Genomics’ ERGO collection of curated microbial and eukaryotic genomes to PathwayAssist.
GeneGo, meanwhile, has signed a licensing agreement with Invitrogen, which markets the Vector PathBlazer software from the former Informax. Bryant said she was unable to disclose further details of that partnership at this time. GeneGo is also “talking to many companies in multiple areas” about future partnership possibilities. Like Ariadne, she said, “We have an integration philosophy and strategy.”
On the customer front, GeneGo announced a licensing agreement for MetaCore with Bristol-Myers Squibb in August. Bryant said that the company is also “working with all the major pharmaceutical companies.” but is unable to disclose who they are.
Other pathway software firms are also making inroads into pharma. Ariadne announced a licensing agreement for PathwayAssist with AstraZeneca; Ingenuity claims Millennium, GlaxoSmithKline, Wyeth, SurroMed, and Aventis among its customer base, and Jubilant Biosys said it has 19 licenses with pharmaceutical companies worldwide. Sreenivas Devidas, Jubilant’s vice president of business development and strategy, said that 90 percent of its sales are for enterprise-wide licenses.
And it’s not just software companies who claim they are seeing greater demand for pathway analysis tools. Affymetrix last week hosted a webcast to introduce its GeneChip customers to a range of pathway analysis products on the market, including PathwayAssist, MetaCore, PathArt, and Vector PathBlazer. In January, Affy hosted a similar webcast for microarray analysis software [BioInform 02-09-04], but the company is aware that the analytical process doesn’t stop at GeneSpring and its ilk, according to Steve Lincoln, vice president of bioinformatics at Affymetrix.
“Our customers really want to use the results of these initial analyses to go further and understand biologically what is going on within the cell,” Lincoln wrote in an e-mail to BioInform. “Pathway tools bring these next steps in the process within their reach, and they do so in a more scalable and powerful way than can be done, say, by reading journals alone.”
Something for Everyone?
The Affy webcast highlighted a defining characteristic of the pathway informatics sector: the broad spectrum of capabilities offered by different systems. Unlike microarray software, which all tends to perform the same analytical and visualization tasks, pathway informatics systems can range from primarily visualization tools, such as Vector PathBlazer, to more content-focused platforms, like MetaCore.
“The space remains relatively new and diverse,” said Lincoln. “The webcast series is not designed to have the products compete with each other head-to-head, but instead to deliberately highlight examples of different kinds of tools and different capabilities available.” In addition, he said, different users have different sets of requirements: Some want to integrate the content into a third-party statistical tool, others are looking for “the consistency” of manual data curation, while others want visualization capabilities to display their own data or public pathway databases in a single view.
It is these differences in content and presentation that fosters partnerships between seemingly competitive firms, such as the one between Ariadne and GeneGo. With little overlap in terms of features or content, pathway informatics vendors can benefit by working together to provide tailored systems to meet specific customer demands.
Additionally, it appears that there is plenty of room in this growing market for all these players — at least for now. “This year, I see that customers are looking at all the options that are out there,” Bryant said, but “over the next 12 months they’re going to decide which ones they actually need, and they’ll understand … what the really important things are and what the nuances are.” As long as vendors continue to differentiate their products to meet the wide range of user requirements, the pathway informatics market may be able to avoid the shakeouts that occurred in the genome database and microarray analysis markets.
Ariadne is already preparing for a future in which “the [pathway] content will be in abundance, so the value of the content might decrease as a result.” In that scenario, he said, “There will still be a need [for MedScan] because in addition to being able to generate content, you can also use it just to stay up to date.”
Bryant said she expects the sector to get a bit more competitive as customers grow out of their experimental phase and settle on one or two pathway informatics platforms, and as more informatics vendors identify pathway analysis as a growth market and jump into the market. However, she said, companies like GeneGo and its peers are likely to have a first-mover advantage over latecomers.
“I think the leaders are already in there … they’re coming out with good products, and their customers seem to be pretty happy, so I’m not sure how many more companies could come into the market and succeed,” she said.