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NIH Rejects ACS Offer to Host PubChem, Forms Group to Advise NCBI on Private-Sector Issues


The American Chemical Society and the National Institutes of Health took steps last month to settle an ongoing dispute over the PubChem small-molecule database hosted by the National Center for Biotechnology Information, but both sides are still chewing over the terms of a possible resolution.

In May, ACS first contended that the freely available PubChem database duplicates its own fee-based CAS Registry, and presents unfair competition for the non-profit organization's primary source of revenue [BioInform 05-16-05]. After several months of discussions between the two organizations — and the involvement of the US House of Representatives and Senate, both of which addressed the issue as part of their 2006 federal appropriations recommendations [BioInform 7-25-05] — ACS in early August offered to develop and support a freely available database that would include data from NIH screening centers as well as other compounds with associated bioassay data. ACS pledged $10 million and 15 staff members over five years to support the project.

NIH rejected the offer, however. In an Aug. 22 letter to ACS President William Carroll, NIH Director Elias Zerhouni said that his staff gave the "generous" proposal "very serious consideration," but ultimately determined that the "most critical aspects of PubChem would be lost in such a model."

"Obviously ACS is one stakeholder in all of this, but there are a number of others as well, and we didn't want to continue any of these discussions much longer without broadening it to a wider set of stakeholders."

In particular, Zerhouni cited "the integration of PubChem with other public biomedical databases," which places NCBI in "an ideal and unique position to create this integrated view," unlike CAS, which "quite appropriately focuses on chemistry." Zerhouni also pointed out that even if NIH were to hand over the reins of PubChem to the private sector, it would have to do so through a competitive bidding process. (The full text of the letter is available from the NIH reading room at

In a move to put the squabble to rest, Zerhouni proposed a six-part "alternative structure" that includes a collaboration between CAS and NIH to assign registry numbers for PubChem structures and a promise that PubChem "will not disseminate information on chemical reactions, measured properties, methods, patents and applications, markush structures, or conference information."

A key component of the proposal — and one that NIH has already taken steps to implement — is the creation of a working group comprising private-sector participants that will advise NCBI on issues of interest to commercial providers of chemical information. One key responsibility of this group will be to evaluate the "biomedical relevance" of compounds in PubChem — a key sticking point in the wrangling between ACS and NIH.

ACS has claimed that PubChem includes a number of compounds that are not directly related to medical research, but NIH contends that many of these are of interest for toxicology purposes, while others may have undiscovered therapeutic value. The proposed working group could serve as a referee of sorts in this debate, and would have the authority to retrospectively remove compounds from PubChem that are deemed to not have biomedical relevance.

On Sept. 1, NIH issued a request for nominations for potential members of the working group, which will advise NCBI on a number of issues, including "avoiding unnecessary duplication with commercial information providers." (The request is available at

"We hope that the American Chemical Society will send a representative to participate in this working group," Zerhouni noted in his Aug. 22 letter.

Jeremy Berg, director of the National Institute of General Medical Sciences, told BioInform that NIH views the private-sector working group as a key step in resolving the ongoing dispute. "That's been a major concern that we've had all along in the discussions. Obviously ACS is one stakeholder in all of this, but there are a number of others as well, and we didn't want to continue any of these discussions much longer without broadening it to a wider set of stakeholders."

When asked if other stakeholders had expressed concerns similar to those of ACS, Berg said, "We've certainly heard from other people, but it hasn't been so much in the nature of concern. I think other groups are interested in interacting with PubChem." One example he cited is the journal Nature Chemical Biology, which is now depositing compounds in PubChem once they are published.

Brian Dougherty, director of the office of legislative government affairs at ACS, told BioInform that the organization is "considering" Zerhouni's proposal, but has not yet had time to discuss it fully due to the national ACS meeting, which was held Aug. 28 — Sept. 1.

ACS President William Carroll posted an open letter on the ACS website on Aug. 23 ( that said ACS officials are "studying" the proposed structure, but still argued in favor of NIH "taking advantage of the CAS Registry."

Carroll also criticized the recent growth of PubChem from 600,000 compounds to 3 million compounds, "most of which have no particular biomedical focus or affiliated data." The bulk of these new compounds, however, come from the ZINC virtual screening project at the University of California, San Francisco — an NIH-funded project.

Dougherty said that Carroll's letter was prepared ahead of time in order to update ACS members on the status of the PubChem issue before the start of the annual meeting. While it was updated to account for the NIH proposal of the day before, it was not intended as an official response to Zerhouni's letter.

In the meantime, NIH continues to stand by its view that PubChem and CAS are "complementary" resources, Berg said. "You can go to the CAS resources to get chemical information, and then go to PubChem to get access to biomedical information. We've been working to try to find ways to work more synergistically with the resources that are out there, including CAS," he said.

— Bernadette Toner ([email protected])

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