The National Cancer Institute is stocking up on pathway informatics in an effort to provide its 7,500 researchers with access to a greater range of bioinformatics tools. Last week, GeneGo and Genomatix announced that they had signed institute-wide licenses with NCI for their pathway analysis platforms. The news followed a similar announcement from Ingenuity Systems in April.
"My office had received a number of inquiries from laboratories throughout the Center for Cancer Research about some of these new tools, and it became very clear from some of the comments that our investigators are becoming more and more frustrated with being able to handle the large amounts of data that they're receiving from some of the high-throughput genomics and proteomics studies that they're conducting," said David Goldstein, chief of the Office of Science and Technology Partnerships at NCI's CCR. "So we wanted to make sure they had a toolbox of bioinformatics programs that they could apply to some of these studies and help them make sense of their data."
As a result, all NCI investigators now have web-based access to their choice of the three tools: Ingenuity Pathway Analysis, GeneGo's MetaCore, and Genomatix's BiblioSphere PathwayEdition. Goldstein said that NCI is evaluating several other pathway analysis packages, such as Jubilant's PathArt and Ariadne's Pathway Assist, and will likely negotiate some form of license agreement for one or more additional packages.
"We're trying to be as open as possible," said Goldstein. "We're trying to allow our investigators to access as many tools as possible and give the companies the opportunity to work with our scientists without any barriers."
Financial terms were not provided for any of the license agreements, but a spokesman from Genomatix said that his company's NCI license was in the six-figure range.
Julie Bryant, vice president of business development and sales at GeneGo, declined to provide financial details for GeneGo's license, but said that the agreement "is very important to us." Citing the NCI deal along with another recent agreement that GeneGo signed with the Translational Genomics Institute in mid-May, Bryant said that "these are academic centers of excellence doing cutting-edge research, and it's definitely something we want to be a part of."
NCI's wholesale support of these packages is further evidence that the market for pathway informatics tools remains on the upswing, even as demand for sequence-analysis and microarray-analysis tools remains flat. So far this year, GeneGo has announced licensing agreements for its products with NCI, TGen, Exelixis, Procter & Gamble, Organon, GlaxoSmithKline, Altana Pharma, and TNO. Ingenuity, meanwhile, has entered into agreements with NCI, the Erasmus Medical Center, Pfizer, and Wyeth during 2005. Jubilant has announced 10 agreements in that time.
It's anyone's guess when — or whether — demand may slow. The consensus among industry observers is that the market is still in an exploratory period, and users are picking up multiple pathway analysis platforms — just as NCI has done — in an effort to gauge which fits best with their needs [BioInform 02-07-05]. Many in the field predict that a slowdown — and subsequent shakeout — is likely to occur in a year or two when current licenses expire and customers settle on one or two packages.
But the relatively minimal overlap between competing offerings may set pathway informatics tools apart from previous types of bioinformatics packages — and may help extend the sector's honeymoon phase. Unlike microarray analysis tools, for example, which all pretty much carry out the same set of tasks, commercial pathway informatics tools are each built upon their own proprietary data sets, and their own way of representing that data. Some vendors, like Ingenuity and Jubilant, rely on teams of curators to populate their pathway databases. Others, like Ariadne, use automated text-mining methods to glean pathway information from the scientific literature, while Genomatix uses a combination of hand curation and literature mining.
The result, according to Todd Hardin of NCI's Office of Information Systems and Computer Services, is that researchers are "not just picking one and using one. It's sort of like if you're working on an appliance — you're going to use a screwdriver for the screws, you're going to use a wrench for the bolts, and so on." Hardin estimated that the degree of overlap between the three packages is only around 25-30 percent. Goldstein noted that the "algorithms for the different programs are quite distinct," and that they all have "unique strengths and weaknesses."
One caveat that Goldstein did mention is the degree of training required to get users up to speed. Investigators can be "easily overwhelmed" if they are "snowballed by interactions," he said, "so the training component is absolutely critical." NCI is working with all three pathway vendors to provide adequate training for its researchers, he said.
Goldstein said that it's too soon to really determine the impact of these pathway analysis programs on NCI's research goals. However, he said, his team plans to gather feedback from NCI investigators over the course of the licenses. "As we go into the second year of license agreements, we'll probably need to make some choices as to which are better, but right now, all of them are new," he said.
Hardin noted that any evaluation that NCI undertakes will be based on utility, not price. "It's very science-driven, which is what's going to be the most effective, as opposed to what's going to be the most cost effective or what's the cheapest tool," he said. "The cheapest tool, in putting out money for the tool, might be inexpensive, but if it costs our scientists twice as much time to get their work done, that isn't necessarily the cheapest tool."
— Bernadette Toner ([email protected])