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Surreal Life VII - What PubChem?

What follows is the background on the attempt of the American Chemical Society to remove taxpayer-funded content from the public domain. PubScience has already bitten the dust. If PubChem goes, you can be sure PubMed (the only reliable, free medical information on the web) will be gone too. The irony? I polled our SciEng staff and got the same responses as everyone else I know: that the ACS databases fill their needs already - no one's going to cancel their subscriptions simply b/c PubChem exists.

To say that that the ACS can only survive in the total absence of other databases is just pure, unadulterated greediness and it's anti-democratic to boot - it's a move to remove completely from the public domain that which was already paid for by the public and is statutorily in the public doman by default. Instead of offering a product people clearly will buy b/c of its many additional features, the ACS wants to require people to buy its product b/c there'll be no alternative. I'm so sure that will make everything better.

The American Chemical Society is calling on Congress to shut down the NIH's PubChem, a freely accessible database on small organic molecules. PubChem is an important component of NIH's Molecular Libraries Initiative, which is a key element of the NIH "road map" for medical research.

ACS claims that PubChem competes with Chemical Abstracts Service (CAS). In reality, PubChem and the Chemical Abstracts Service databases are complementary, not duplicative.

ACS is currently targeting the Ohio delegation to Congress, Rep. Ralph Regula (OH), Chairman of the House Appropriations Subcommittee on Labor, Health and Human Services, Education, and Related Agencies, and Senator Arlen Specter (PA), Chairman of the Senate Appropriations Subcommittee on Labor, Health and Human Services, Education and Related Agencies.

What is PubChem?
In 2004, as part of the NIH's Roadmap Initiative to speed new medical treatments and improved health care to all Americans, NIH launched an on-line database called PubChem as part of a suite of databases supporting the New Pathways to Discovery component of the roadmap effort. New Pathways focuses on very basic biomedical research, and especially focuses on understanding the molecular biology of health and illnesses. Bioinformatics is a critical component of that effort.

Drawing from many public sources, PubChem organizes information about the biological activities of chemical compounds into a comprehensive biomedical database. All of this supports the part of the Roadmap called the Molecular Libraries initiative. PubChem is the informatics backbone for virtually all of these components, and is intended to empower the scientific community to use small molecule chemical compounds in their research.

What is the issue?
A bedrock 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.

The American Chemical Society (ACS) has expressed concern that a new NIH database called PubChem, which was created to support the NIH Roadmap initiative, and especially the Molecular Libraries Initiative, 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.

o ACS/CAS claims that a federally supported database that is freely available to all users and is supported by federal tax dollars has an unfair advantage over the CAS service, which charges a fee for access to its database.
o ACS claims that PubChem will cripple CAS, sapping both it and the ACS's economic foundation, resulting in the loss of jobs in Columbus, Ohio.
o ACS/CAS appears to want NIH to either shut down the PubChem database or severely limit its content so that it does not overlap with ACS/CAS in any way.
o ACS/CAS also appears to want to provide some of the information contained in PubChem, but at a cost to researchers who would use this information.

This is much the same argument that the information industry made with regard to PubScience which they managed to get shut down.

PubChem is a free, publicly available database created by NIH in 2004 to provide information about small molecules for use as research tools and as potential starting points that may lead to the development of new medications. The database connects chemical information with biomedical research and clinical information in a connect-the-dots fashion, organizing facts in numerous public databases into a unified whole. PubChem is a critical part of the Molecular Libraries initiative of the NIH Roadmap for Medical Research. It will combine new data generated by this initiative with data available from other public sources to create a powerful new research tool. PubChem is the latest member of the powerful family of integrated databases operated by the National Library of Medicine, including GenBank, PubMed, GEO, OMIM, 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.

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.
Chemicals: 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.
PubChem and CAS content are complementary resources tailored to the needs of different segments of the scientific community.

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, PubChem management is willing to link to the CAS database, essentially bringing CAS a new, untapped market of customers. Medical researchers infrequently use CAS at this time.