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ACS, Congress Point to PubChem Duplication


The American Chemical Society says it is “delighted” that a pair of US House and Senate oversight committees has included “cautionary language” addressing the NIH PubChem database as part of their respective 2006 federal appropriations recommendations.

ACS has accused the publicly funded small-molecule database of posing unfair competition for its CAS Registry, a subscription-based resource that provides the bulk of the non-profit organization’s annual revenues.

ACS issued its statement following a July 15 report accompanying the Senate’s 2006 budget recommendations. In a section of the report discussing the National Library of Medicine’s budget, a Senate committee said it “expects the NIH to work with private sector chemical information providers, with a primary goal of maximizing progress in science while avoiding unnecessary duplication and competition with private sector databases.”

In June, a House of Representatives committee included similar — albeit slightly harsher — language in its own appropriations report, noting that it was “concerned that NIH is replicating scientific information services that already exist in the private sector,” and urging NIH to work with private-sector database providers “to avoid unnecessary duplication and competition.”

The Senate’s statement “is another significant step toward a resolution that will supplement and not supplant private scientific information services,” ACS says.

An NIH spokesman says that ACS and NIH are “continuing to have discussions,” but was unable to provide details on the current status of negotiations. He says that NIH is “grateful for Congress’s support for PubChem, and we certainly intend to follow” the governing body’s recommendation to avoid duplication of outside resources.

Still, the use of the phrase “unnecessary duplication” is likely to be a matter of debate, since NIH contends that PubChem, which contains just over a million molecules, does not come close to duplicating the content of the CAS Registry, which contains around 25 million compounds.

— Bernadette Toner


Bristol-Myers Squibb has taken a multi-year license to Ingenuity’s Pathways Analysis and Pathways Knowledge Base applications, making the tools available to all BMS scientists.


Sanofi Pasteur, a Toronto-based division of Sanofi-Aventis, is using informatics software from Biomax in its vaccine research. Biomax says the deal includes its BioRS data integration system as well as its Pedant-Pro sequence-analysis pipeline.


The Blueprint Initiative will add data from pre-publication manuscripts in Sage Publications’ Journal of Biomolecular Screening into BIND, the Biomolecular Interaction Network Database. Sage, which will incorporate BIND IDs into its manuscripts, joins a number of other journal publishers — including AAAS/Science, Blackwell Publishing, Cell Press, and the Nature Publishing Group — working with Blueprint.


Rosetta Biosoftware and GeneGo have agreed to establish interoperability between Rosetta Biosoftware’s Resolver gene expression analysis system and GeneGo’s MetaCore pathway analysis platform, allowing researchers to exchange data between the systems in order to analyze gene expression data and perform pathway analysis.


The French National Genomic Research Consortium, or CNRG, has secured a global license to Genomatix Software’s pathway analysis platform. This is the third large-scale deal with a government institution for the bioinformatics company.



US Patent 6,922,638. System and method for transacting and manipulating a multi-sequence search using biological data repositories. Inventors: James Wallace; Kai Wang; John Liljeberg. Assignee: PhenoGenomics. Issued: July 26, 2005.

This patent covers a method for multi-sequence searching using “a set of search query parameters specifying a plurality of sequence sets” which are then loaded into a database query.


US Patent 6,909,970. Fast microarray expression data analysis method for network exploration. Inventors: Valery Kanevsky; Aditya Vailaya. Assignee: Agilent Technologies. Issued: June 21, 2005.

This approach to network reconstruction “includes the steps of selecting a predictor set of features, adding a complement to the predictor set based on a quality of prediction, checking to see if all of the features of the predictor set are repeated, and then removing one feature from the predictor set. … If the features of the predictor set are repeated, the algorithm and method terminate.”



Amount of a six-month Phase I Small Business Innovation Research grant awarded by the National Heart, Lung, and Blood Institute to Gene Network Sciences to help the company continue developing its cardiac modeling efforts with improved protocols and a new software tool for data integration in cardiac electrical activity simulations.


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