Tuesday, November 22, 2005
Friday, October 28, 2005
According to the founder and moderator of the list, Peter Murray-Rust, “The emerging Open Data movement shares many goals with the Open Access and Open Source movements, but encompasses its own distinct issues that are in need of examination by the scientific community. This list is intended to facilitate that important discussion.”
To sign up: send an email to SPARC-OpenDataemail@example.com
For more info: http://www.arl.org/sparc/opendata/index.html
Thursday, October 27, 2005
- "Scientific and technological research is essential for social and economic development.
- Scientific communication is a crucial and inherent part of the activities of research and development. Science advances more effectively when there is unrestricted access to scientific information.
- More broadly, open access enables education and use of scientific information by the public.
- In a world that is increasingly globalized, with science claiming to be universal, exclusion from access to information is not acceptable. It is important that access be considered as a universal right, independent of any region.
- Open Access must facilitate developing countries' active participation in the worldwide exchange of scientific information, including free access to the heritage of scientific knowledge, effective participation in the process of generation and dissemination of knowledge, and strengthening the coverage of topics of direct relevance to developing countries.
- Developing countries already have pioneering initiatives that promote Open Access and therefore they should play an important role in shaping Open Access worldwide."
- requiring that publicly funded research is made available through Open Access;
- considering the cost of publication as part of the cost of research;
- strengthening the local OA journals, repositories and other relevant initiatives;
- promoting integration of developing countries scientific information in the worldwide body of knowledge"
Peter Suber and Subbiah Arunachalam review the situation of open access in the developing world in a paper to be published in the InfoPaper of the World Summit on the Information Society in Tunis in November. They answer the big question "Doesn't the digital divide interfere with these plans? [of providing OA to boost research in developing countries]"with: "Yes and no. First, internet access is improving rapidly in many developing countries and equipment costs and connectivity charges are coming down. Second, we should work now on the content side of the divide in order to take full advantage of every increment of progress on the hardware side. Primarily, this means educating scientists about the benefits of OA and persuading universities, libraries, funding agencies, and governments to adopt OA-friendly policies."
Wednesday, July 20, 2005
Monday, July 18, 2005
Dear Margaret Foti, CEO, American Association of Cancer Research,
According to the SPARC Open Access News of July 13, AACR is one of a group that has signed a letter on July 7 to Senator Arlen Specter, expressing "significant concerns about the National Institutes of Health duplicating private sector on-line publishing".
The banner at the top of your website this morning does not say: defending the interests of the private sector in the publishing industry.
What your banner says is quite different. It is "Saving Lives Through Research".
This is a noble reason for the existence of your association. My request is that AACR review its mission, and reconsider its position on the NIH Public Access Policy. I cannot see how such a review could possibly come to any other conclusion than that your mission compels you to fully support and participate in Public Access.
Change is difficult for anyone, and I have no doubt that the small changes needed for Public Access will be a little bit uncomfortable for your association. I urge you, however, to consider how many families, not only in the U.S. but throughout the world - have asked for donations to cancer research in lieu of flowers. How many have wanted to set aside their own comforts in bereavement to speed the research, so that others would be spared the agony that they and their loved ones went through. When so many are seeing the need to speed the research and placing it above their own comfort, surely your association can, too.
Surely you realize that the best way to "accelerate the dissemination of new research findings" - to borrow a phrase from your mission statement - is for cancer researchers to share their findings as openly as possible, as soon as possible. The ideal is to post the findings openly on the web, just as soon as the quality control process (peer review) is complete - generally before
publication. Imposing any delay, or any restrictions on dissemination, is contrary to your mission statement.
Your mission also says that you will "advance the understanding of cancer etiology, prevention, diagnosis, and treatment throughout the world." Outside the wealthy nations, there are many universities with no journal subscriptions at all; and, many places where lack of funds to purchase resources is a deterring factor to education, period. Participating in the NIH Public Access program clearly advances your mission. Lack of access is a factor in the U.S. too, of course; not all states are equally wealthy, and not all can afford all the journals for their university libraries.
Please share this message with your Board, and your members. If your basic mission has changed from saving lives to private sector profits, your mission statement needs updating. If your mission continues to be to accelerate cancer research, then you need to reverse your stance on the NIH's Public Access Policy, from opposition to enthusiastic support and
To facilitate dissemination and encourage other associations to consider their missions when thinking about open access, this is an open letter, copied to the SPARC Open Access Forum.
I congratulate the U.S. National Institute of Health and the U.S. Senate for their support for Public Access. This is one policy area where many, myself included, see the United States as providing an example of visionary leadership, which other nations would be well advised to follow.
Heather G. Morrison
Thursday, July 07, 2005
Can companies still make money selling genomic and molecular information?
Celera Genomics made hundreds of millions of dollars by selling access to its proprietary genome sequence information. But this month, Celera discontinued its database subscription service and made its 30 billion base pairs of genomic data of humans, rats, and mice freely available through GenBank, operated by the US National Center for Biotechnology Information.
Some see Celera's decision to exit the sequence business as proof of the adage that information wants to be free, and yet another sign that selling access to data is no longer a viable business model. "The trend is perfectly clear. It would be surprising to find any company setting up a business plan that was based on a subscription database of precompetitive information," says Francis Collins, director of the National Human Genome Research Institute and leader of the Human Genome Project, Celera's publicly funded rival in the race to sequence the human genome.
More (including about PubChem, CAS, et cetera)...
Thursday, June 30, 2005
India is expanding a government-led program to provide free, local language software to all of its citizens, as it tries to broaden computer use in the country.
The project was initiated by India's Ministry of Communications and Information Technology, which aims to take computing to the country's masses in the language they are most familiar with.
The CD contains productivity software such as a browser, e-mail client and word processor, as well as tools such as a dictionary and spell-checker. While many of the productivity applications are open source and run on both Linux and Microsoft's Windows operating system, some of the utilities are closed-source and run only on Windows. The software can also be downloaded at http://www.ildc.in/
On 29 Jun 2005, at 22:55, Terry Carroll wrote:
On Wed, 29 Jun 2005, David Dailey wrote (about IP protected plants):
A wee bit of digging on the net tells me it is really neither copyright nor patent but plant law. Chapter 57 of Title 7 specifically deals with the 1970 Plant Variety Protection Act which provides legal intellectual property rights protection, to developers of new varieties of plants that are sexually reproduced.
Wow. I guess Microsoft could get a patent on an Apple, then.
Oh, wait, see Plant Patent no. PP14,757 at
Apple tree named 'Burchinal Red Delicious'
Abstract: A new and distinct variety of apple tree which originated as
a sport limb mutation of 'Wells and Wade cultivar' Oregon Spur.RTM. of
red delicious apple tree (U.S. Plant Pat. No. 2,816), characterized by
a more uniform deeper red color, developing much earlier than fruit of
other red delicious varieties, and having a thicker stem and longer,
deeper red leaf midvein.
Inventors: Burchinal; Robert (East Wenatchee, WA)
Assignee: Microsoft Corporation (Redmond, WA)
Appl. No.: 313685
Filed: December 6, 2002
(Actually, while this is a real patent and Microsoft *is* listed as assignee, the assignee listing appears to be a clerical error on the part of the office of the patent attorney whose does work for both the inventor Mr. Burchinal and Microsoft. See here... But it's a golden delicious mistake, if you'll pardon the pun.)
Wednesday June 29, 2005
Thousands of British academics in every subject from art history to zoology will soon be required to make their research freely available online, the UK research councils have announced.
The move flies in the face of government reluctance to offend the publishing industry and is a victory for proponents of open access to research findings. By making free access a condition of grants, the research councils, which control billions of pounds worth of funding, hope to give British research more impact worldwide as it is taken up and cited by other researchers.
University libraries will benefit from an easing of the financial pressure to acquire more, and ever more expensive, journals as scholars can consult research for free. Read more...
Monday, June 27, 2005
Thursday, June 23, 2005
Sunday, June 19, 2005
By the way, as far as I can see all this, with the ACS/CAS irrational, unfounded, undocumented, unsubstantiated comments about being put out of business, PubChem would still be pretty much unknown to the chemical community. I think PubChem should give Bob Massie the "2005 PubChem Marketing Award" for all his efforts. Considering that PubChem can't advertise or market, the ACS/CAS efforts really need to be properly acknowledged.
Friday, June 17, 2005
US Congress fails to back ACS
House Appropriations Committee refuses to censure or pull funding plug on NIH PubChem operation
By Bobby Pickering 16 Jun 2005
The American Chemical Society has put a brave face on a snub it has received from the US Congress, which has refused to take its side in a dispute with the National Institutes of Health (NIH).
At the eye of the storm is a freely accessible database of small organic molecules, PubChem, made available as part of the NIH Molecular Libraries Roadmap Initiative.
The ACS claims the database competes with its Chemical Abstracts Service (CAS) publishing operation, from which it made the majority of its $410m revenues last year.
In a statement, the ACS said: "The NIH has created a mini-replica of the CAS Registry, and a replica poised to expand. That replica will, over time, pose an insurmountable threat to CAS' survival for the very reason that it is a taxpayer-supported resource."
But critics were quick to point out that the ACS, as a not-for-profit organization, has itself benefited from substantial tax concessions over the years, as well as an establishment grant from the National Science Foundation, awarded in the late 60s/early 70s.
However, the ACS maintained in a published statement that "the fact that NSF turned to CAS to develop the Registry in no way justifies NIH replicating it today".
Supporters of PubChem insist that the two resources are entirely of different scale, with a CAS Registry budget at around $260m compared to PubChem's $3m annual budget, and CAS staff numbering 1,300, while PubChem has a mere 13.
The ACS had hoped to put pressure on the NIH through Congressional supporters, but last week the House of Representatives' Appropriations Committee approved the annual NIH budget with only the slightest admonishment that both parties work together. The committee said it "urges NIH to work with private sector providers to avoid unnecessary duplication and competition with private sector chemical databases."
The ACS declined the opportunity to speak to IWR this week, but issued a statement that it is "very pleased that the House Appropriations Subcommittee expressed concern about PubChem replicating private scientific information services. We will continue to work diligently with NIH toward a collaborative model and solution."
Yet it is now difficult to see how it can develop a dialogue with the NIH and work towards a compromise solution, having already adopted such heavy-handed tactics.
The ACS is noted for taking a bullish stance over the threat to its revenues from open access publishing. In December 2004, it filed a complaint in the US District Court of DC against Google for alleged trademark infringement of the CAS SciFinder Scholar brand and for "unfair competition".
The US organisation is also under fire from some parts of the academic community for the levels of remuneration it awards employees. The not-for-profit organisation paid out 46% of its total expenses of $404m in salaries and fringe benefits last year, with its executive director receiving a total compensation package of over $1m.
Thursday, June 16, 2005
Quote (from Francis S. Collins, director of the National Human Genome Research Institute at the NIH): "Precompetitive data, data of fundamental significance that doesn't justify strong intellectual-property protection or secrecy, this is data that wants to be public," he said. Scientists have reached a "pretty strong" consensus about this issue."
(For a limited time, the full article is accessible to non-subscribers)
Tuesday, June 14, 2005
The Honorable Ralph Regula
Chairman, Subcommittee on Labor, Health and Human Services,
Education, and Related Agencies
Committee on Appropriations
United States House of Representatives
Rayburn House Office Building, Room 2358
Washington, DC 20515-6024
Dear Chairman Regula:
I am writing on behalf of the University of California’s Academic Council and its Special
Committee on Scholarly Communication. We want to express our enthusiastic support for
continuation of PubChem, an immensely useful project underway at the National Center for
Biotechnology Information (NCBI) in the National Institutes of Health (NIH). It has come to
our attention that during the markup of the FY 2006 Labor-HHS Appropriations bill the
Subcommittee may consider language that would restrict PubChem.
In discussion with colleagues at the University of California and elsewhere we have come to
understand that PubChem represents a vital next step for NIH in leveraging its investment in the human genome project, filling in the picture of small molecules. It is a powerful tool that enables medical researchers to harness NIH-funded and other public resources about chemical structures so that they can advance development of new medications. By simply clicking on links, researchers navigate through the range of information resources—for example, searching on a chemical name, viewing its structure in PubChem, and finding articles that refer to it in PubMed Central. By ensuring that publicly financed knowledge is broadly accessible on the Internet in this way, NIH is enhancing the return on public investment in research and stimulating further innovation by public and private scientific enterprises. As you may know Nobelist Richard Roberts and other renowned chemists have spoken in detail about these benefits of PubChem
Equally important, we believe that PubChem is an important initiative in the NIH’s program to
provide broad access to scholarship. The NIH is providing much needed leadership to accelerate the advancement of knowledge through experiments in the rapid delivery of the results of science and scholarship to the widest audience at the lowest cost possible.
It is our understanding from press reports that the American Chemical Society (ACS) has called for NIH to unreasonably restrict PubChem. ACS claims that PubChem competes with its Chemical Abstracts Service (CAS), a well-known, high-quality, and expensive database, to which only about 1,000 U.S. universities can afford to subscribe. However, there is evidence that PubChem and the CAS databases are, and can continue to be, complementary, not duplicative.
As you know, PubChem is a critical component of NIH's Molecular Libraries initiative, which in turn is a lynchpin of the NIH strategic Roadmap to enhance health care and speed delivery of new medical treatments. Indeed, the directors of the NIH institutes unanimously rank the Molecular Libraries initiative as the highest priority of the NIH Roadmap. It is a mistake to endanger the promise of the Roadmap by imposing restrictions on PubChem that fundamentally undermine its utility. There is simply too much at stake.
We also are worried about the chilling effect that the ACS campaign might have on creative
attempts to increase access to science. We wonder whether the Society’s position has been
thoroughly vetted with its membership. A number of eminent library and public interest
organizations have expressed their belief that science and the American public are well served by continued development and maintenance of PubChem. University of California faculty members have authored or co-authored over 2,300 articles in ACS publications in the last 2 ½ years alone. Seventy-two UC faculty hold ACS journal editorial positions and a number serve on ACS committees and sections. We are encouraging these faculty members to discover the facts, discuss the issue with colleagues, and let ACS know their preference.
Meanwhile, we are grateful for your leadership on the recent NIH Public Access Policy, which
offers immense potential to advance science. In the same vein, we encourage you to support
PubChem and the broader Molecular Libraries initiative at NIH.
Thank you for the opportunity to share our perspectives with you.
George R. Blumenthal, Chair
UC Academic Council
Publishers make appeal to lawmakers in NIH dispute
BY Aliya Sternstein
Published on Jun. 13, 2005
American Chemical Society officials are asking lawmakers to rein in those responsible for a federal database of molecular structures because they say it will cut into the society's income from the sale of similar information.
The National Institutes of Health created PubChem in 2004 as part of NIH's Roadmap for Medical Research initiative to speed the discovery of new medical treatments. PubChem has a list of names and structures of 850,000 chemicals.
ACS officials fear that PubChem will duplicate the society's Chemical Abstracts Service (CAS). NIH and ACS officials have exchanged letters, meetings and phone calls since 2004. Now because of an impasse in those discussions, ACS officials are urging lawmakers to put restrictions on NIH's development of PubChem.
"ACS believes strongly that the federal government should not seek to become a taxpayer-supported, competitive scientific publisher," ACS said in a statement last month. "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."
Brian Dougherty, senior adviser to the chief strategy officer at ACS, said the society suggested forming a technical working group to set parameters for PubChem. "NIH has been unwilling to put anything in writing," Dougherty 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 about why ACS insists that PubChem will harm the society's business interests. "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," he said. "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 officials said narrowing PubChem's focus could slow medical progress. "It would have profoundly negative effects on this new paradigm of making medical discoveries," Austin said.
Larry Thompson, chief of the communications and public liaison branch at the National Human Genome Research Institute, said biomedical researchers could discover biological relevance in any small molecule. "That's why it's called research," he said. "No one knows what molecule will be the next blockbuster drug."
Thompson said NIH officials have no desire to undercut CAS, and they are willing to work with the society to ensure the viability of both information services.
Thursday, June 09, 2005
Monday, June 06, 2005
I presume that NIH would like to associate CAS Registry Numbers with the substances in this database and that CAS not only has refused to provide them, but views PubChem as a turf incursion.
The world has changed since CAS was the best source for abstracts of the chemical literature. We no longer require leagues of abstract writers, since most journals require submissions to include an abstract. Even interpreters, although still essential, have a diminished role with the advent of language-conversion software.
Our library has dropped its subscription to hard-copy Chemical Abstracts and funnels requests for literature searches through a single subscriber. For most purposes (in a health department), services from other search providers such as Ovid and ISI overlap what would be provided by CAS, and the expense is one we can do without.
In general, the American Chemical Society has done an admirable job of adapting the literature under its control with the advent of the Internet. Most, if not all, issues of the society's journals are accessible to subscribers under terms that compare favorably with those offered by other publishers.
This enlightened use of the Internet is not entirely true of CAS, which jealously guards every bit of information under its control. It could be argued that the CAS number is the most important unique descriptor of a substance and is thereby public currency which should be granted freely. It is a datum that can provide a link to all scientific literature for a substance and thus will bring people (not just chemists) to the ACS publications pertinent to their needs; these people could purchase that information for a small fee.
CAS has the ability to provide a database, not unlike PubChem, and the question becomes not one of NIH overstepping its function, but of CAS failing to adapt to potential new markets for its information. I pose this question: Why won't CAS provide me, a dues-paying chemist, with the information that PubChem is offering to the public? A follow-up question is this: Why won't CAS open to every person that portion of its database which would increase the accessibility of the chemical literature? This would not only benefit the public, but also the publishers of that information.
Robert G. Briggs
Friday, June 03, 2005
The action related to CAS' Chemical Registry Structure Database, and followed the withdrawal by CAS of the full Registry Structure File from Dialog on 1st January 1990, thereby denying Dialog the ability to offer graphical substructure searching on its service (a feature available on a competing online service jointly operated by CAS).
Dialog argued that CRSD "has no substitutes and thus constitutes a separate and distinct market" which CAS was monopolising in contravention of anti-trust laws.
Amongst the 10 claims made by Dialog were five alleging monopoly practices, one alleging unfair competition, and one relating to a subsidy of $15 million plus that had been provided by the National Science Foundation at the time the CAS database was being created, and which Dialog claimed obliged ACS to license all data at a fair price. This obligation had been
breached by CAS, alleged Dialog, both by its withdrawal of connection table data essential for graphical structure searching, and because CAS had for some years refused to licence its abstracts of the chemical literature.
The Dialog lawsuit also claimed that its revenues from the CAS database had fallen 45% between 1984 and 1988, partly due to steep rises in CAS licence fees and royalties, and partly because of data being withheld.
ACS responded to the lawsuit by countersuing on issues of accounting. As I recall the case was eventually settled out court.
Thursday, June 02, 2005
"Using taxpayer money to fund the same work that is performed by CAS
and offering it at no charge is both a wasteful use of public funds and one
that threatens nearly 1,300 jobs at CAS and the viability of that entire
To which Steve Heller responded:
"Give me a break - who can really take you seriously when you say 12 NLM employees can/will put 1,300 CAS employees out of work? It is an insult to most every CAS employee to imply they do so little that 1 NLM staff member can put 100 of them out of work."
These gems are from the following exchange:
You write below:
"I also know that, by your own admission, you are hardly
a disinterested party in the matter of PubChem."
And what are you ??
As for disinformation, you are way ahead of us all. You can add untruths, distortions, and misleading statements to that as well.
As for what happened in 1970, I was there. I was one of the leaders of the project. Whatever version of what happened that Mary Good may have put in an ACS memo is just her opinion. As for the sky falling in, the NIH/EPA CIS was not designed to put CAS out of business - and as you may notice - it did not. CAS thrived in spite of the CIS running for over a decade. And it was people at NLM who were happy to support the ACS when they went to senior NIH officials about the CIS.
You also say you were told:
"the CAS business model is outdated and outmoded."
In my opinion and that of most others who have done and continue to do work and research in the field is that we have been saying this for years and no one at the ACS or CAS listens.
You need to work on getting your facts straight. The sky is still not falling in - no matter how often you and Chicken Little say so. And this e-mail will be a record of my prediction that CAS will still be in business in 5/10 years from now.
There is essentially no duplication of information, let alone an effort to do so. All PubChem submissions come from outside sources. So if you want to stop outsiders from sending things to NIH go after them.
How dare you use the total NIH budget of somewhat less than $30 billion to say the $3 million of PubChem funds (most of which has nothing to do with chemicals) are competition or will put CAS out of business.
And give me a break - who can really take you seriously when you say 12 NLM employees can/will put 1300 CAS employees out of work? It is an insult to most every CAS employee to imply they do so little that 1 NLM satff member can put 100 of them out of work.
And speaking of Google, the useless waste of ACS funds to sue them, is just another example of misguided management who can't seem to think of anything positive to do with all the ACS money they control, other than keeping their rather high salaries and bonuses going on and on and on. And a search on Google of "acs and pubchem" will produce thousands of hits of American organizations and those outside the USA who disagree 100% with you and your management. You have unleashed a massive protest against the ACS, which has already damaged its image and reputation and will continue to do so, since I am sure you plan to go down with the ship and not work with the community which has been so vocal against the ACS position. As an ACS staff member told me in San Diego after a full day of ACS bashing at a CINF symposium, "I am sad to see that the ACS has replaced Elsevier as the evil empire." Minds, like parachutes only work when they are open. I may be a disgruntled member (and will continue to be a member), but I now see there are hundreds of others and lots of organizations in the USA and abroad who realize that while they need CAS for patents and abstracts they don't need the ACS or CAS for their biomedical data. The real question at hand is not "if" PubChem data will be available, but "where".
There is a Chinese expression for the blindness brought on by inside perspective: jing di zhi wa, "frog in the bottom of a well." The frog looks up and sees only a single circle of the sky; he thinks he sees
clearly, but "he doesn't know how big heaven really is."
Foreign Babes in Beijing, 2005
On Wed, 1 Jun 2005, Madeleine Jacobs wrote:
Dear Dr. Roberts:
I deeply regret that you are pulling out of the ACS-CSIR conference in India
in January. You will deeply disappoint your Indian colleagues who have been
looking forward to hearing from you. I am not sure why you want to punish
your global colleagues because you disagree with some policies of ACS.
Through my editorship of Chemical & Engineering News, I was well aware that
for some time you have been openly in favor of open access journals and free
information. Indeed, as Editor-in-Chief, I gave you space and time to
present your views. I also know that, by your own admission, you are hardly
a disinterested party in the matter of PubChem. I can look at your
distribution list and see that you have sent your notice to many people at
NIH who have nothing to do with the India conference. What are your motives
for sending your letter to this group?
I am glad you're giving me the chance to set the record straight and correct
the misinformation on the subjects that you bring up. I realize that I will
not change your mind since you've stated that you're an advisor to PubChem
and are quoting verbatim in your letter the arguments that one disgruntled
ACS member, who is also an advisor to PubChem, has been putting on various
listservs and feeding to the media. Much of that information is wrong and
So let me provide some additional context and to correct the misinformation
that has been deliberately propagated by NIH staff and its consultants. I
also hope to explain why ACS believes the circumstances are alarming and
could threaten the very existence of Chemical Abstracts Service and many of
the excellent programs we provide to the nearly 158,000 members of the
American Chemical Society and to the profession at large. This is, after
all, a controversy about science.
The short summary is this: NIH has created a database called PubChem that
has the stated purpose of publishing data generated by NIH grantees for the
Molecular Library Initiative and the NIH Roadmap. Such information is to be
linked to bioassay data for use in designing new drugs or other medical
research. The data will be made available free of charge. Contrary to
anything you may have read, we do not now and never have opposed this
concept. Indeed, we do not oppose PubChem. We want it to stay with its
stated mission, as described to us by Dushanka Kleinman in a letter of
January 21: "PubChem's purpose is to archive and make publicly available
for search and retrieval chemical structure and bioassay data generated by
the Molecular Libraries Screening Center Network." I sure you will have
noticed that not one molecule currently in PubChem has been generated by
ACS is not against NIH or PubChem. ACS worked long and hard for years to
mobilize its members to advocate for a doubling of the NIH budget. Our
presidents, our Board of Directors, and our members supported this doubling
because we thought the money would be used to advance research through
research grants. We succeeded in helping NIH.
Now, what we are seeing is something that goes far beyond what NIH first
proposed. PubChem duplicates the CAS Registry, the world's hallmark database
for identifying all chemical substances encountered in the scientific
literature and patents since 1907. The Registry is also the underpinning for
many of the related information tools that CAS has developed since 1907.
Together, these tools have compressed what would formerly take weeks or
months of research time into minutes or seconds-literally fast-forwarding
scientific progress. Following on some starter grants from the National
Science Foundation, ACS has invested $500 million in developing,
maintaining, and enhancing this database.
It appears that there are individuals in the Library of Medicine who, for 25
years, have wanted to own the CAS Registry, and now that ACS, along with
sister organizations, helped get NIH's budget doubled, they finally have the
money to simply replicate the Registry. This is not speculation. We have
strong evidence in the minutes from the ACS Board of Directors meetings in
the 1979-80 timeframe, in the clear recollection of Dr. Mary Good (chair of
the Board of Directors at that time), and in current information from people
inside the Library. So there is much more going on than would first appear.
Why are we concerned about PubChem?
· This duplication of effort constitutes unnecessary, unfair, improper
competition from the government, with a proven service that has been
operating successfully for nearly 100 years.
· Using taxpayer money to fund the same work that is performed by CAS
and offering it at no charge is both a wasteful use of public funds and one
that threatens nearly 1,300 jobs at CAS and the viability of that entire
operation. In contrast, ACS has used its own financial resources and the
skills of thousands of highly skilled scientists to create the world-renown
Registry. The costs are borne by the users, which is an effective and
appropriate business model.
· If Registry subscribers turn to the "free" services of PubChem, it's
not only the Registry that is threatened. Also at risk are the many other
CAS information products that are essential to the research community and
which are not likely to be duplicated by PubChem.
· More than half of the Society's net revenues are generated by CAS,
and all but a fraction of one percent is reinvested back into our publishing
activities-journals and CAS products and services--or into Society programs
and member services. A serious reduction in revenues from CAS will have
immediate and severe consequences for the viability of our publishing
operations and thus for our ability to continue many of our member services
· We question the premise that the federal government should be the
funder, publisher, and repository of all scientific information. That's what
is happening now with NIH and the National Library of Medicine. Yes, Rudy
Baum has called this "The Socialization of Science." Concerned citizens
should be alarmed.
Chemical information is the cornerstone of the ACS mission and its Federal
Charter. There is no other organization more devoted to the mission of
ensuring accurate and timely chemical information and its stewardship. ACS
journals and CAS products such as SciFinder and SciFinder Scholar are
mainstays in universities, corporations, and government labs around the
globe. The business model for CAS products makes them available to the
academic world at discounts of up to 90 percent and still provides enough of
a return to fund remarkable innovation. Later this year, CAS will
introduce CAS Mobile, which allows users to conduct complex searches from
BlackBerrys and other hand held devices-a first for scientific information
retrieval. Also, in July, CAS will be introducing a new data mining tool
that will help scientists glean even more information from the
ever-increasing reams of information. New and important features in
SciFinder are being introduced early next year. This is the kind of
innovation we have come to depend upon and we cannot afford to take for
By contrast, creating and publishing chemical databases is not the primary
mission of the NIH. Their $30 billion budget dwarfs the ACS budget, as does
the size of their workforce. NIH's mission is to fund medical research and
find cures for diseases, for which we are all grateful beneficiaries. In a
time of flat budgets, when we would all like to see more research money
across the board, is duplicating a highly respected database a good-or
proper-use of government resources and our collective tax dollars? The rate
of success for research grants has been declining, despite a growing NIH
budget. I hope you agree with me that NIH should use its money to support
research grants to advance its mission.
In addition, as someone who talks to thousands of our industrial members
each year, I am alarmed when I hear an NIH official tell me, as he did in a
meeting with ACS in March, that "the CAS business model is outdated and
outmoded." Our free enterprise society in the U.S. operates on the premise
that the government will not unduly compete with its citizens. The U.S. also
operates on the premise that the users of information, not taxpayers, are
the appropriate people to pay for these services. ACS information services
cost substantially less than information services provided by the private
sector. Our journal prices and costs per article are among the lowest among
Our hope has been to reach an agreement with NIH whereby they would focus
PubChem on its stated mission. We believe that both of our organizations
can have an optimal role in promoting and facilitating scientific research
without jeopardizing the value either of us brings to the community. NIH has
turned down our approach for a working group that could resolve the
controversy. Indeed, one NIH director has stated that "NIH will not back
We are still trying to work with NIH to resolve this issue for the
advancement of science. In the meantime, it is clear that there are
individuals who want to cast ACS in the worst possible light.
When I have talked to our members and explained in detail what it is we are
asking of NIH, they do understand why what NIH is doing is unfair
competition. They do not like the idea of their tax dollars going to
duplicate a service that is used in thousands of organizations around the
world. If NIH would stop putting out misleading and erroneous
information-including taking statements out of context in letters that ACS
has sent in good faith-and come to the table to work out this situation in
good faith, instead of waging a media campaign, this entire controversy
would be resolved.
On several other points, I would add the following: The lawsuit against
Google is about the use of a name we have had in the marketplace for many
years: SciFinder Scholar. It is strictly about unfair competition, not
about its product per se.
ACS remains firmly committed to its charter. I sleep with a copy of it by my
bedside. It is perhaps the most important 100 words in the ACS Constitution
and Bylaws. I believe firmly that we are carrying out that mission in good
Executive Director and Chief Executive Officer
American Chemical Society
1155 16th Street NW
Washington, D.C. 20036
Phone: (202) 872-6310
Fax: (202) 872-6055
Wednesday, June 01, 2005
Dear Dr. Namaroff:
I regret that I am going to have to pull out of the ACS-CSIR conference in India next January. For some time now I have been deeply troubled by the actions of the ACS and this has finally reached breaking point with the violent opposition to the PubChem initiative at NCBI. I find myself no longer able to support anything that carries the imprimatur of the ACS.
I was greatly troubled when ACS so vehemently opposed the Open Access initiative. This led me to resign my membership in the society after more than 20 years as a member. The recent legal actions against Google have also disturbed me very much, but the current opposition to PubChem is reprehensible and without any redeeming merit. As an advisor to PubChem I am aware of what they are trying to do and it is in no way a threat to anything that ACS is doing. Rather it complements those activities very nicely and provides for the biological community an important resource that is not provided by CAS. Furthermore, PubChem is keen to provide links to CAS and thereby enhance the usefulness of both resources.
My only interpretation of the recent actions by the ACS Board and management is that it is no longer trying to be a scientific society striving towards the goals of its Congressional charter, which is to represent the best interests of the scientists who form its membership. Rather it seems to be a commercial enterprise whose principle objective is to accumulate money. The ACS management team might be well-advised to poll its members to discover if they are happy about the recent actions taken in their names.
Aside from the listed recipients of this letter, I am prepared to make to make it publicly available if requested. Frankly, the recent actions of the ACS are a disgrace to its image in the USA and around the world. They engender such bad feelings as to raise in question the motivations of its leadership. I cannot in good faith support any of the activities of a body that has gone so seriously wrong.
Richard J. Roberts
1993 Nobel Laureate in Physiology or Medicine
Dr. Richard J. Roberts
New England Biolabs
32 Tozer Road
Beverly, MA 01984
Tel: (978) 927-3382
Fax: (978) 921-1527
Tuesday, May 31, 2005
From Peter Murray-Rust-naturally occurring substances in living organisms;
As major users of PubChem, Henry Rzepa and I have
written an Open statement of its value. You are free
to copy, quote from, redistribute or re-use this
AN OPEN STATEMENT IN SUPPORT OF NIH/NCBI's PubChem
We write as scientists committed to the sharing of
chemical information on the public Internet. For 12
years we have developed and promoted the technology
and culture of a global, open, approach and have freely
contributed specifications, software and data. We are
frequently invited to present these at International
conferences, including many in the US.
We have done this in the belief that this creates a
better infrastructure for scientific research of benefit
We believe that bioscience and healthcare have benefited
greatly from the aggregation of and free access to
research data such as genomes, protein structures and
sequences. Scientists and lay people alike can search
the international databases for disease information,
and drill down to find the most recent information about
the molecular basis.
We wish to emphasize in the strongest terms the current
and future value of the NCBI/NIH's PubChem to the
scientific and medical community.
(SPARC's recent statement
the concerns that PubChem may be closed down or severely
restricted). We have been using the molecules in PubChem
and promoting their value in research.
The substances in PubChem are those critical for research
in bioscience and healthcare. They include:
-synthetic substances with known biological action,
including drugs and toxic materials
-reagents for performing standard biological and chemical
assays such as in drug discovery
Each PubChem entry is curated and includes:-the precise chemical formula for the substance
-one or more common names for the compound
-properties by which the compound can be identified and on
which its physical and biological activities depend
-the new InChI identifier from the International Union of
Pure and Applied Chemistry. Through this PubChem has become
a unique resource for reference and discovery, especially
on the Internet.
Until PubChem, virtually no chemical information was freely
available (i.e. without a library or a subscription to an
information supplier). It is generally not possible to look
up freely the chemical formulae of common drugs, food
additives, or materials in the environment. Yet much of
this information was first published many decades or centuries
ago. PubChem provides a reliable, instant, resource for anyone.
As an example of its value, the UK had a recent concern about
a red dye in chili powder. From home we were able to use
PubChem to find out what the chemical formula of this material
is and what its reported toxicity and biological properties are.
We know of no other freely available resource that we could
have used with confidence.
In our laboratories we are using PubChem for systematic research
and are enhancing its value by publishing the results to the
world. We have systematically computed the properties of over
200,000 molecules and published our peer-reviewed results freely.
These properties are typical of those used in computer-aided drug
discovery or the prediction of the safety of compounds. We have
automated the process so that eventually all molecules in PubChem
will have this information. Using InChI we have recently created
a web site so that anyone can use search engines (e.g. Google(TM)
or MSN(TM)) on this database without prior chemical knowledge.
This is typical of the way in which information-driven science
builds on, and enhances, existing knowledge.
Even now it is very difficult for many bioscientists to read
papers which include chemical names. We have therefore recently
urged  that scientific publishers should link their electronic
publications to PubChem to help the reader understand the chemistry.
Since PubChem also provides important biological background to many
entries it enhances the scientific process, speeding it up and
reducing the chance of error. We see PubChem as a universal tool
for authors, helping them to reduce the chance of mistakes.
Finally we re-emphasize the global nature of scientific information.
By sharing resources freely we detect and correct errors, and
encourage innovation in the way we access information. Many
developments in bioscience and healthcare come not from the wet
laboratory, but through computational knowledge-driven methods.
PubChem represents the start of such a process in chemical bioscience.
No one site holds the totally of the world's knowledge and through
the Web we create distributed resources from which all of us benefit.
Peter Murray-Rust, Reader in Molecular Informatics, University of
Henry Rzepa, Professor of Chemistry, Imperial College, UK
This statement may be copied and redistributed under Creative Commons
(Attribution-NonCommercial-NoDerivs 2.0). We urge others to circulate
it freely and use it to promote the continued use of PubChem.
 Preprints for BMC Bioinformatics in our Institutional Repository:
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069 Fax: +44 1223 763076
Friday, May 20, 2005
A short invited presentation to JISC2005 - the UK's information infrastructure organisation, in which he emphasizes that machines read publications as well as humans.
An invited overview for BioMedCentral Bioinformatics on Open chemical data in biosciences and how it can be accelerated by forward looking publishers and funders
An accompanying technical article for BioMedCentral Bioinformatics on the extraction of such data in XML
Thursday, May 19, 2005
"It is remarkable that the same society that accepted millions of dollars in grants from the NSF for establishing the chemical registry system, now objects to the government's use of the data."
He puts his finger right on the sore spot.
Tuesday, May 17, 2005
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