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Microsoft-led BioIT Alliance to Tackle Biomarker Data Exchange in Second Proof-of-Concept Project

The BioIT Alliance, a network of life science hardware and software providers created to improve biomedical data exchange using Microsoft technologies, kicked off an effort this week to address interoperability challenges in the field of biomarker identification and validation.
The so-called Biomarkers Project is the second proof-of-concept initiative for the BioIT Alliance, which was formed in April [BioInform 04-07-06]. The first project, still ongoing, is a collaboration between Microsoft, the Scripps Research Institute, and software services firm InterKnowlogy to develop a system called the Collaborative Molecular Environment, which enables researchers to more easily share and annotate 3D images.
Don Rule, platform strategy advisor for bioinformatics at Microsoft, told BioInform that the C-ME system is currently deployed at Scripps, and that the company plans to make the code available later this year as “shared source” for software firms who are interested in commercializing it. One firm, IO Informatics, has already expressed interest in commercializing aspects of C-ME, he said.
The goal of the C-ME project was to develop tools that could capture data more effectively within a single lab, Rule said. “But what came out of that was we recognized that even if you can capture it at the lab better, it all needs to be integrated with data that comes off the equipment, with data that occurs in other labs.”
The aim of the next project, therefore, will be to “figure out how to create interfaces that will allow people to share data between and among their applications more effectively,” Rule said.
While biomedical research has plenty of interoperability challenges to choose from, Rule said that biomarker discovery made the most sense for a number of reasons. “When you look at the research that’s going on now – either for theranostics, or pharmacogenetics, or for rescuing drugs, or stratification for clinical trials – every single one of those has an element of trying to determine a biomarker that will describe to you what will be most effective,” he said. “So that was sort of a common thread across many, many companies that we saw, and it really resonates with people as an area to focus on.”
Partners in the Biomarker Project include founding BioIT Alliance members Affymetrix, Accelrys, Amylin Pharmaceuticals, Applied Biosystems, the BioTeam, Digipede Technologies, Discovery Biosciences, Geospiza, Hewlett-Packard, InterKnowlogy, Sun Microsystems, and VizX Labs. In addition, several new members have joined, including Agilent Technologies, Illumina, Strand Life Sciences, and Transenda.
In the Biomarkers Project, Microsoft intends to “specify a web services architecture that will enable companies to push data from one to the other.” This architecture should allow users “to go from the clinic all the way through to the molecular testing lab, and all the way through to gaining some insight on that data,” Rule said.
“The hope here is that we can work with vendors and say this is a consistent way that we are going to represent data, and by doing that, it makes it much easier to build tools on top of it,” he said.
Rule stressed that the effort doesn’t intend to create new data standards or to “homogenize” data from different platforms. “Those systems are evolving very, very quickly and I think we would be doing a disservice if we said everyone has to present data in the same way,” he said. “What’s important is that we have results that are uniform in their comparability, and that we provide the capability to go back to the raw data in all cases.” 
Rather than focus on standards, Rule said, the goal is to focus on the implementation.
The project comprises three stages, Rule said: identifying a “specific scenario” to address, which in this case will likely be gene expression analysis; working with partners to identify “important junctions,” or interfaces for passing data among different entities; and creating a functional specification that “that describes those interfaces.”
Microsoft intends to act as a “catalyst” in the first two steps, but it will play a larger role in the creation of the functional spec, which will work with several Microsoft technologies, including its upcoming Vista operating system, Windows Presentation Foundation, and features of its SharePoint products.
Rule said that the implementation process will draw from his prior experiences in developing internet protocols. “What we used to do after the spec was done was get in a room and plug systems together and try to pass data from one to the other. We used to call them plugfests,” he said. “What we want to do is a virtual plugfest where vendors will expose some interfaces out on the internet and allow them to pass data from one to the other.”
The Biomarkers Project will bring together a number of firms that are usually considered competitors rather than collaborators, but Rule said it wasn’t too difficult to convince companies like ABI, Agilent, and Illumina to work together on the effort.
“I think each one of them recognizes that nobody buys from only one vendor,” he said. “By working together, they believe that the whole market is better off and that they will actually sell more product by enabling it to be useful sooner.”

“What’s important is that we have results that are uniform in their comparability, and that we provide the capability to go back to the raw data in all cases.”

Illumina spokesperson Maurissa Bornstein told BioInform via e-mail that the company is participating in the effort because it sees “potential for platform assay data to be more readily available for integration and analysis throughout the discovery process for end users.”
Francois Mandeville, business manager for bioinformatics marketing/sales and R&D at Agilent, said that the company expects its GeneSpring software package to benefit from the initiative. In an e-mail to BioInform, he said that the utility of the software would be “enhanced by the adoption of interoperability standards.”
Mandeville added that there is “widening recognition across the research community in particular, but also in the vendor marketplace, that the interoperability problem is a bottleneck that must be addressed.”
The industry doesn’t have a good track record with interoperability consortia, and a number of well-intentioned efforts over the past few years, such as the OMG and I3C, never really got off the ground. Nevertheless, Mandeville said, “Vendors can’t let the past get in the way of this important mission.”
Rule added that many of the vendors in the BioIT Alliance aren’t focused on the research market where their tools are currently used, but further downstream, in the clinic. “That’s what’s really important to them. So by making the research side of it go faster, they believe that world is closer at hand,” he said.
Rule said that the initiative should have an initial proof-of-concept biomarker pipeline based on gene expression analysis in place within a few months. “I’m hoping that early next year we’ll have some small collection of vendors that are able to begin talking to each other,” he said.
However, he noted that the “end product” of a generalized system to exchange clinical and biomolecular data “arbitrarily” across systems is “very, very far away.”

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