Chemical publisher goes after NIH

The American Chemical Society (ACS) is lobbying Congress to rein in a new National Institutes of Health database of biomedical research because, the society argues, the government-run database infringes on the private sector.

NIH launched the database, PubChem, in 2004 as part of NIH's Roadmap Initiatives to speed new medical treatments and improved health care to Americans. PubChem catalogs the names and structures of 850,000 chemicals. This number is expected to grow.

ACS fears that PubChem will duplicate its Chemical Abstracts Service (CAS). Officials at the two organizations have exchanged letters, meetings and phone calls since 2004.

At an impasse, ACS is now urging policy-makers and Congress to refocus PubChem.

”ACS believes strongly that the federal government should not seek to become a taxpayer-supported, competitive scientific publisher," ACS said in a statement. "By collecting, organizing and disseminating small-molecule information whose creation it has not funded and which duplicates CAS services, NIH has started, rather ominously, down the path to unfettered scientific publishing.”

“NIH does amazing things as far as funding basic research, but we’re getting into a little bit of mission creep here...the site will come at the expense of NIH basic research,” said Brian Dougherty, senior adviser to the chief strategy officer at ACS.

ACS officials worry that NIH will find biological relevance in any small molecule.

Dougherty said ACS suggested a technical working group to set parameters for PubChem to focus on only the small molecules that relate to bioassay data, information collected about the strength or biological activity of a substance, such as a drug, by comparing its effects with those of a standard preparation on living cells. “NIH has been unwilling to put anything in writing,” he said. “We think this is going to put us out of business if it keeps growing and no parameters are set.”

NIH officials said they are confused as to why ACS insists PubChem will affect the organization's business when the two organizations' missions and audiences are different.

“What is in common is a relatively small number of compound structures and names," said Christopher Austin, senior adviser to the translational research director at the NIH Chemical Genomics Center at the National Human Genome Research Institute. "ACS has gotten hung up on this. They have taken this, frankly, rather disingenuously, to implicate that PubChem duplicates CAS. CAS has 25 million structures. PubChem has about 850,000. PubChem is a subset. Not everything that is in CAS is relevant to biomedical research.”

NIH maintains that its fundamental mission is biomedical research, not petroleum or the chemicals of companies such as DuPont and Dow Chemical. “This list of names will get bigger, but will fill out the biological space...not the chemical space," Austin said.

NIH officials understand that refocusing PubChem will slow medical progress. “It would have profoundly negative effects on this new paradigm of making medical discoveries, right at the time that it is just getting started.... Unfettered access to a large number of different types of information is what allows fundamental new discoveries to be made," Austin said. "To kill this thing when it’s still in the cradle would have a dramatically negative effect on medical discovery."

The rational arguments that NIH has made to ACS have had virtually no effect, he said. “They are fundamentally not understanding that PubChem deals with an entire intellectual area that they know nothing about," he said.

And NIH officials said that many of ACS’ arguments are untrue.

“PubChem does not come at the expense of basic research; it empowers basic research,” said Larry Thompson, chief of the Communications and Public Liaison Branch at the National Human Genome Research Institute.

“It is entirely plausible that NIH might find biological relevance in any small molecule," Thompson said. "That’s why it’s called research. No one knows what molecule will be the next blockbuster drug. An unknown small molecule may one day prove to the cure for cancer.... Today’s medicine cabinet is filled with improbable chemicals that proved to be powerful treatments for disease. Warfarin, an ingredient in rat poison, is also used as an anticoagulant to thin blood to treat venous thrombosis, blood clots in the lung and heart disease. Mustard gas, that lethal cloud that covered the battle fields of World War I to fatally sear the lungs of enemy soldiers, is used to treat psoriasis and has been used to treat a form of leukemia, a cancer of white blood cells.”

NIH sought a technical working group with ACS so that the two organizations could find the most effective way to get value out of both databases. NIH officials said the organization has no desire to undercut CAS, but would rather work with the society to ensure the viability of both information services. By linking to PubChem, CAS could have access to an entirely new market of biological and medical researchers for its products and services, but ACS has not shown an interest in pursuing that opportunity, Thompson said.

Thompson added that accusations that NIH has been unwilling to meet with ACS to discuss parameters for PubChem or anything else are wrong.

"Clearly there would be no purpose to establishing a working group to further discuss our fundamental disagreement," wrote Madeleine Jacobs, executive director of ACS, in her last letter to NIH April 13.

ACS has cut off the conversation, in favor of seeking a political solution.

Rick Johnson, director of the Scholarly Publishing and Academic Resources Coalition, said, unlike ACS, NIH researchers are not hiring chemists to pore through patents to extract chemical names and structures.

“They’re taking on something that is not any threat to them and they are precluding an activity that will be key to returning on the NIH investment [in the human genome] drugs and better health care," he said. “What they want to do is neuter [PubChem] so it’s useless to anyone.”

"It's all about protecting the CAS franchise, not about what's best for biomedicine,” Johnson added.


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