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ACS Lauds Congress for Addressing PubChem Duplication in Budget; Next Steps Uncertain

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The American Chemical Society 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 said in a statement last week.

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 [BioInform 05-16-05].

PubChem Language from House
Appropriations Committee Report
(June 21, 2005):

"The Committee understands that the stated mission of the PubChem database, which is part of the NIH Roadmap Initiative, is to create a new and comprehensive database of chemical structures and their biological activities, and will house both compound information from the scientific literature as well as screening and probe data from the new NIH molecular libraries screening center network. The Committee is concerned that NIH is replicating scientific information services that already exist in the private sector. In order to properly focus PubChem, the Committee urges NIH to work with private sector providers to avoid unnecessary duplication and competition with private sector chemical databases."

PubChem Language from Senate
Appropriations Committee Report
(July 14, 2005):

"The Committee is aware of the development of PubChem, the informatics component of the Molecular Libraries project of the NIH Roadmap for Medical Research. The Committee understands that the purpose of PubChem is to create a database of chemical structures and their biological activities. PubChem will house both data from the new NIH molecular libraries screening center network and compound information from the scientific literature. The Committee 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."

ACS issued the statement following a July 15 report accompanying the Senate's 2006 budget recommendations for the departments of labor, health and human services, education, and related agencies. 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." (See sidebar for complete text of the passage)

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." [BioInform 06-20-05]

The Senate's statement "is another significant step toward a resolution that will supplement and not supplant private scientific information services," ACS said in the statement. "We look forward to NIH's response in light of House and Senate actions, as ACS continues discussions with NIH toward a resolution that appropriately leverages longstanding private efforts and best serves the scientific community."

An NIH spokesman told BioInform last week that ACS and NIH are "continuing to have discussions," but was unable to provide details on the current status of negotiations. He noted 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.

An official NIH statement notes that officials from NIH and ACS met on June 24 "for productive discussions regarding the PubChem database and its potential impact on private chemical databases." The organizations "agreed to continue to work together to seek an equitable solution that advances the NIH Roadmap and scientific research overall without unnecessary duplication of existing private services," according to the statement.

Brian Dougherty, director of the office of legislative government affairs at ACS, told BioInform that the organization is still "waiting to hear back from NIH" following the June 24 meeting. "They said that they would work with us on an appropriate focus for PubChem," he said, adding that ACS is "optimistic that we will hear something that will move us in the direction of a collaboration."

Nevertheless, he said, "it's still not clear when our next communication will be."

Dougherty was also cautious regarding the significance of Congress's statements on the matter. "It's certainly not clear cut," he said.

Indeed, 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.


The Senate's statement "is another significant step toward a resolution that will supplement and not supplant private scientific information services. We look forward to NIH's response in light of House and Senate actions."

The NIH spokesman acknowledged that the phrase "unnecessary duplication" is open for interpretation, and has "caused some head-scratching" among NIH officials.

Christopher Austin, senior advisor for translational research at NHGRI and a principal leader for the Molecular Libraries implementation group, told BioInform in May that NIH had intended to provide links to the CAS Registry in PubChem in a similar way that PubMed links out to subscription-based journals. "We would like to … make those links available, but we can only make those links if CAS gives us the information to allow the links to be made," he said at the time. He also noted that the move should actually help expand the CAS Registry customer base rather then cut into it.

When asked whether such a linking mechanism was on the negotiating table, Dougherty said that ACS is "open to any type of integration that makes sense for both of our missions and for the scientific community."

For ACS, "the question is not whether NIH advances the Molecular Libraries initiative but how, and there is a way to rely on existing, long-standing private services," Dougherty said. "If we got to that, I think there are rich opportunities for linking and cross-linking. It's just difficult to talk about the specifics without getting some type of agreement on the focus and how NIH is going to leverage the private sector.

— Bernadette Toner ([email protected])

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