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American Chemical Society Expresses Opposition to NIH’s PubChem

The press reports that the American Chemical Society is calling on Congress to shut down the NIH’s PubChem, a freely accessible database that connects chemical information with biomedical research and clinical information, organizing facts in numerous public databases into a unified whole. PubChem is a critical component of the NIH strategic “roadmap” to speed new medical treatments and improve healthcare.

The American Chemical Society and NIH’s PubChem

The American Chemical Society (ACS) is calling on Congress to “refocus” and curtail the NIH’s PubChem, a freely accessible database that connects chemical information with biomedical research and clinical information, organizing facts in numerous public databases into a unified whole.1 It is a critical component of NIH’s Molecular Libraries Initiative, which in turn is a key element of the NIH strategic “roadmap” to speed new medical treatments and improve healthcare.

ACS claims that PubChem competes with its Chemical Abstracts Service (CAS). There are strong arguments that PubChem and the Chemical Abstracts Service databases are complementary, not duplicative.


PubChem is a freely accessible database created by NIH in 2004 to provide information about small organic molecules. It is designed for use as a research tool and as a starting point that may lead to the development of new medications. The database connects chemical information with biomedical research and clinical information, organizing facts in numerous databases into a unified whole.PubChem is a critical part of the Molecular Libraries initiative of the NIH Roadmap for Medical Research. It combines new data generated by NIH with data available from other public sources to create a powerful new research tool. It is part of the powerful family of integrated databases operated by the National Library of Medicine — including GenBank, PubMed and a host of other resources that are utilized millions of times a day by scientists all over the world. The integration of these databases makes the whole much greater than the sum of its parts.PubChem is a critical new tool that will speed the development of new treatments for America’s most important health problems. It brings information about the biological activities of chemical substances to biomedical researchers on a broad scale.A fundamental NIH principle is that medical research information developed with public funds must be made freely and publicly available for the good of advancing medical research to cure disease.As announced in a press release about the Nature Publishing Group’s new journal Nature Chemical Biology, chemical compounds mentioned in that journal’s research articles are linked to the PubChem database so readers can consult more information about its chemical structures and properties, and biological assay results. Concomittantly, data about compounds mentioned in articles is automatically deposited into PubChem, providing new data for the PubChem database.
ACS/CAS has expressed concern that PubChem is a threat to the financial survival of the Chemical Abstracts Service (CAS). PubChem provides free access to its database; CAS charges a fee for researchers to use its database. ACS has demanded that NIH shut down PubChem or substantially alter it so as not to compete with CAS.NIH met with ACS officials to seek a solution that would resolve the society’s concern. Since the initial meeting, there have been multiple communications between NIH and ACS leadership. ACS has effectively broken off discussions, leaving the issues unresolved. NIH is willing to continue discussions with ACS/CAS to benefit the scientific community and biomedical research. For example, NIH has said it is willing to link to the CAS database, essentially providing CAS with access to a new market. Medical researchers infrequently use CAS at this time.Opposition to PubChem is from the ACS leadership. It is not clear if ACS members are aware of the issue and if they would agree with the ACS leadership’s position.NIH staff analysis shows that PubChem and CAS overlap relatively little in terms of content. PubChem and CAS differ widely in scope and resources:

  • Budget — CAS budget is reported to be $260 million; PubChem budget is $3 million.
  • Staffing — CAS staff is reported to be 1,300; PubChem staff is 13.
  • Scope — CAS has information on 25 million unique chemicals; PubChem has information on 850,000 unique chemicals (though this number is expected to grow).
  • Purpose — CAS provides chemical, commercial and patent information to chemists; PubChem integrates medical information for medical researchers.
  • Overlap — PubChem and CAS content are complementary resources aimed at different segments of the scientific community.
Update (7/27/05):
On July 14, 2005 the Senate Appropriations Committee voted to forward the FY 2006 Labor, Health and Human Services, Education, and Related Agencies Appropriations bill to the full Senate. The accompanying report provides comment and guidance to NIH regarding PubChem and its relationship with the private sector. The senate report modified the parallel House report, seeming to provide stronger support for PubChem, notably by highlighting the “primary goal of maximizing progress in science” but goes on to suggest that NIH avoid “unnecessary duplication and competition with private sector databases.” A conference to resolve differences between the House and Senate bills is expected in the Fall.The full language of the report’s clause on PubChem:

PubChem- 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.

Senate Report 109-103 – DEPARTMENTS OF LABOR, HEALTH AND HUMAN SERVICES, AND EDUCATION, AND RELATED AGENCIES APPROPRIATION BILL, 2006. http://thomas.loc.gov/cgi-bin/cpquery/?&db_id=cp109&sid=cp109LH9vq&r_n=sr103.109&item=&sel=TOC_509159&

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PubChem Supporters:
Library and public interest organizationsAssociation of American Medical CollegesAssociation of Academic Health Science LibrariesUK ScientistsRichard J. Roberts, 1993 Nobel prize recipient for Physiology or MedicineUC’s Systemwide Academic Council

Statement from the ACS regarding PubChem.Reply to Nobel Laureate Roberts (see above) from Madeleine Jacobs, ACS Executive Director and Chief Executive Officer.Open letter from ACS President Dr. William F. Carroll, Jr.

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The American Chemical Society was founded in 1876. It is a U.S. not-for-profit corporation whose national charter was approved by the U.S. Congress on August 25, 1937, for the purposes of encouraging the advancement of chemistry; promoting research in chemical science and industry; increasing and diffusing chemical knowledge; and promoting scientific interests and inquiry through its meetings, reports, papers, and publications. The Society has more than 159,000 members.At December 31, 2004, the American Chemical Society had over $1 billion in assets and annual operating revenues of almost $410 million. The table below shows revenue sources and expenses (emphasis added).

ACS Revenues and Expenses
Unrestricted revenues – $410 million Total expenses $404 million
Electronic services 62% Salaries and fringe benefits 46%
Printed services 16% Professional services 10%
Petroleum Research Fund 7% Advertising, marketing, sales promotion 6%
Advertising 4% Grants & awards 6%
Member insurance 3% Electronic data processing 5%
Dues 3% Building operations 5%
Investment income 2% Depreciation & amortization 5%
Other 4% Publication & distribution 5%
Member insurance premiums 3%
Travel 2%
Database fees & royalties 1%
Interest & financing 1%
Other 6%
Source: ACS (http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html?DOC=committees%5Cbandf%5Cindex.html)

Total compensation for the ACS executive director was $1.025 million in 2003 and its president of publications received over $670,000 that year. Scholars’ concern about ACS executive salaries was reported in the Chronicle of Higher Education on August 18, 2004.

According to the ACS website “the principle sources of funding for the Society’s activities include net revenues generated by the Publications Division and the Chemical Abstracts Service Division.”

ACS publishes approximately 30 scholarly journals. Average annual subscription price increases for those journals from 2003-2005 is 9%.

ACS Journal Data: Price, Impact, and Use

Title List Price 2005 ISI Impact Factor 2003 UC Online Uses 2004 Avg Annual Price Increase ’03-’05
Accounts of Chemical Research $526 15 10,767 9%
Analytical Chemistry $1,374 5.25 24,909 9%
Biochemistry $3,427 3.922 48,359 9%
Bioconjugate Chemistry $835 3.547 7,217 9%
Biomacromolecules $905 2.824 3,856 9%
Biotechnology Progress $924 1.488 3,224 9%
Chemical Research in Toxicology $974 3.332 3,262 9%
Chemical Reviews $970 21.036 18,841 9%
Chemistry of Materials $1,394 4.374 14,746 9%
Crystal Growth & Design $2,185 2.742 1,460 9%
Energy & Fuels $1,097 1.303 867 9%
Environmental Science & Technology $1,507 3.592 17,454 9%
Industrial & Engineering Chemistry Research $1,704 1.317 2,923 9%
Inorganic Chemistry $2,604 3.389 15,598 13%
Journal of Agricultural and Food Chemistry $1,169 2.102 13,351 9%
Journal of the American Chemical Society $3,165 6.516 158,535 9%
Journal of Chemical & Engineering Data $908 0.95 594 9%
Journal of Chemical Information and Modeling $621 3.078 2,070 8%
Journal of Chemical Theory and Computation $975 (new) (new) (new)
Journal of Combinatorial Chemistry $1,060 4.2 2,853 9%
Journal of Medicinal Chemistry $1,828 4.82 22,812 9%
Journal of Natural Products $758 1.849 17,174 9%
The Journal of Organic Chemistry $2,139 3.297 40,726 9%
The Journal of Physical Chemistry A $1,979 2.792 14,527 9%
The Journal of Physical Chemistry B $1,979 3.679 32,929 9%
Journal of Proteome Research $915 5.611 2,896 9%
Langmuir $2,912 3.098 26,267 9%
Macromolecules $2,611 3.621 14,750 9%
Molecular Pharmaceutics $1,185 (new) 478 (new)
Nano Letters $1,256 6.144 32,199 9%
Organic Letters $3,361 4.092 45,958 9%
Organic Process Research & Development $766 1.041 2,031 9%
Organometallics $2,454 3.375 14,577 9%
Total $52,714 4.17 700,598 9%
UC and ACS:
UC scholars published over 2,300 articles in ACS journals from 2003 to 2005.More than 70 UC scholars serve as editors or editorial board members on ACS journals.Through a systemwide license coordinated by the California Digital Library, all of UC has access to SciFinder Scholar which includes the CAS databases: Chemical Abstracts, Registry, CASREACT, CHEMCATS, and CHEMLIST. The CDL also manages a systemwide license providing access to the online editions of ACS journals, their online backfiles and Chemical and Engineering News.After consultation with its Special Committee on Scholarly Communication, on June 7, 2005 UC’s Academic Council expressed its concern via letters to principals at ACS and to members of congress.

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Talk about publishing issues with your society:
University of California faculty serve on 67% of the editorial boards of ACS journals and about 15% of all top-tier journals. They wield enormous influence with publishers.Ask for clarification and justification of the ACS’s arguments against PubChem.Discuss the possibilities for open access resources, such as PubChem, to complement high-quality but expensive subscription-based resources such as CAS.Discuss ways to support society activities from creative sources other than escalating subscription prices, which become unsustainable.Encourage your scholarly society to maintain reasonable prices for its journals.
Consult with your library:
The libraries stand ready to assist you and are eager to discuss their responses to the overall economic challenges in scholarly communication and their reaction to this specific issue. A list of UC’s library scholarly communication officers is maintained at http://libraries.universityofcalifornia.edu/scholarly/.
Contact legislators:
The ACS lobbying efforts are targeting Rep. Ralph Regula (OH), Chairman of the House Appropriations Subcommittee on Labor, Health and Human Services, Education, and Related Agencies (tel. 202-225-3876, fax 202-225-3059>; andSenator Arlen Specter (PA), Chairman of the Senate Appropriations Subcommittee on Labor, Health and Human Services, Education and Related Agencies (tel. 202-224-4254, fax 202-228-1229).Other legislator contact information is available at http://www.senate.gov/ and http://www.house.gov/.

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[In chronological order. Web addresses are provided where possible but access may require a personal or institutional subscription to the source. Excerpts from many of these items are available from Peter Suber’s Open Access News.]

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1Based on statements from ACS principals Madeleine Jacobs, and Dr. William F. Carroll (reported above under Position Statements), this characterization of ACS actions was changed on June 27th, 2005 to “‘refocus” and curtail PubChem” from the original use of “shut down.”

2Most background information presented in this section is from the Scholarly Publishing and Academic Resources Coalition (SPARC); communiqué from Director Rick Johnson to SPARC members; May 19, 2005.

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