petermr's blog

[This is roughly my presentation for the meeting, with conclusions. I may edit it during the day so early feed readers will have captured early versions]
The presentation concentrates on science, but applies to all scholarly journals. Addresses copyright and licenses; patents are completely separate issue.
Background Resources:

• Wikipedia Open Data
• SPARC Open Data Mailing list
• Budapest Open Access Initiative (para 3 “open access”)

petermr posts:

• Open Canada (a country at the forefront of Open)
  
• The importance of Open Data (clickable genome)
• The reality of closed access (access denied)
  
• The pit-bull and the pendulum (Closed publishers take action)

We must act:

• Need statement on Open Data (c.f. Open Access)
• Funders must insist on Open Data
• Institutions must insist that staff publish Open Data
• Authors should use Science Commons Author Addenda in all data
• Publishers should make all supporting information Open

In any case the scientific semantic web (2.0) will become so powerful it will ultimately sweep away twentieth century practices. Publishers, you have been warned.

Continuing the preparation of my WWW 2007 panel material blogwise (and with
apologies to those who have heard me before on this) the following epitomises the difference of interests in the Open/Closed Access/Data community. In 1994 Rudy Baum (C&EN: Editor’s Page – Socialized Science) wrote strongly against Opening chemical data:

	National Institutes of Health director Elias A. Zerhouni seems hell-bent on imposing an “open access” model of publishing on researchers receiving NIH grants. His action will inflict long-term damage on the communication of scientific results and on maintenance of the archive of scientific knowledge.More important, Zerhouni’s action is the opening salvo in the open-access movement’s unstated, but clearly evident, goal of placing responsibility for the entire scientific enterprise in the federal government’s hand. Open access, in fact, equates with socialized science.Late on Friday, Sept. 3, NIH posted its proposed new policy on its website, setting in motion a 60-day public comment period (C&EN, Sept. 13, page 7). Under the policy, once manuscripts describing research supported by NIH have been peer reviewed and accepted for publication, they would have to be submitted to PubMed Central, NIH’s free archive of biomedical research. The manuscripts would be posted on the site six months after journal publication. Many observers believe that, if the NIH policy takes effect, other funding agencies will quickly follow suit. In short order, all research supported by the federal government would be posted on government websites six months after publication. This is unlikely to satisfy open-access advocates, who will continue to push for immediate posting of the research. I find it incredible that a Republican Administration would institute a policy that will have the long-term effect of shifting responsibility for communicating scientific research and maintaining the archive of science, technology, and medical (STM) literature from the private sector to the federal government. It’s especially hard to understand because access to the STM literature is more open today than it ever has been: Anyone can do a search of the literature and obtain papers that interest them, so long as they are willing to pay a reasonable fee for access to the material. What is important to realize is that a subscription to an STM journal is no longer what people used to think of as a subscription; in fact, it is an access fee to a database maintained by the publisher. Sure, many libraries still receive weekly or monthly copies of journals printed on paper and bound as part of their subscription. Those paper copies of journals are becoming artifacts of a publishing world that is fast receding into the past. What matters is the database of articles in electronic form. As I’ve written on this page in the past, one important consequence of electronic publishing is to shift primary responsibility for maintaining the archive of STM literature from libraries to publishers. I know that publishers like the American Chemical Society are committed to maintaining the archive of material they publish. Maintaining an archive, however, costs money. It is not hard to imagine a scenario in which some publishers, their revenues squeezed at least in part by loss of subscriptions as a result of open-access policies, decide to cut costs by turning off access to their archives. The material, they would rationalize, is posted on government websites. Which is, I suspect, the outcome desired by open-access advocates. Their unspoken crusade is to socialize all aspects of science, putting the federal government in charge of funding science, communicating science, and maintaining the archive of scientific knowledge. If that sounds like a good idea to you, then NIH’s open-access policy should suit you just fine.

“put the [] government in charge of funding science, communicating science, and maintaining the archive of scientific knowledge. If that sounds like a good idea to you, then [] open-access policy should suit you just fine.
Well, I can’t see much wrong with that – it’s certainly a major theme of funding in the UK. It’s not the government alone, of course, there’s the splendid work being done by the Wellcome Trust and other funding bodies. There is the problem of cost, of course, and publishing and archiving costs money. But if a funding body funds research it has a right (and a duty IMO) to make sure that work is as widely available as possible for the longets possible time.
Of course not all publishers use words like “socialized science” – which sounds slightly strange in other countries. But, lest you think that this was a storm in a teacup 3 years ago we have (news @ nature.com – PR’s ‘pit bull’ takes on open access – Journal )

Nature Published online: 24 January 2007; Corrected online: 25 January 2007 | doi:10.1038/445347a PR’s ‘pit bull’ takes on open access Journal publishers lock horns with free-information movement.Jim Giles The author of Nail ‘Em! Confronting High-Profile Attacks on Celebrities and Businesses is not the kind of figure normally associated with the relatively sedate world of scientific publishing. Besides writing the odd novel, Eric Dezenhall has made a name for himself helping companies and celebrities protect their reputations, working for example with Jeffrey Skilling, the former Enron chief now serving a 24-year jail term for fraud. Although Dezenhall declines to comment on Skilling and his other clients, his firm, Dezenhall Resources, was also reported by Business Week to have used money from oil giant ExxonMobil to criticize the environmental group Greenpeace. “He’s the pit bull of public relations,” says Kevin McCauley, an editor at the magazine O’Dwyer’s PR Report. Now, Nature has learned, a group of big scientific publishers has hired the pit bull to take on the free-information movement, which campaigns for scientific results to be made freely available. Some traditional journals, which depend on subscription charges, say that open-access journals and public databases of scientific papers such as the National Institutes of Health’s (NIH’s) PubMed Central, threaten their livelihoods. Media messaging is not the same as intellectual debate. From e-mails passed to Nature, it seems Dezenhall spoke to employees from Elsevier, Wiley and the American Chemical Society at a meeting arranged last July by the Association of American Publishers (AAP). A follow-up message in which Dezenhall suggests a strategy for the publishers provides some insight into the approach they are considering taking. The consultant advised them to focus on simple messages, such as “Public access equals government censorship”. He hinted that the publishers should attempt to equate traditional publishing models with peer review, and “paint a picture of what the world would look like without peer-reviewed articles”. Dezenhall also recommended joining forces with groups that may be ideologically opposed to government-mandated projects such as PubMed Central, including organizations that have angered scientists. One suggestion was the Competitive Enterprise Institute, a conservative think-tank based in Washington DC, which has used oil-industry money to promote sceptical views on climate change. Dezenhall estimated his fee for the campaign at $300,000–500,000. In an enthusiastic e-mail sent to colleagues after the meeting, Susan Spilka, Wiley’s director of corporate communications, said Dezenhall explained that publishers had acted too defensively on the free-information issue and worried too much about making precise statements. Dezenhall noted that if the other side is on the defensive, it doesn’t matter if they can discredit your statements, she added: “Media messaging is not the same as intellectual debate”. Officials at the AAP would not comment to Nature on the details of their work with Dezenhall, or the money involved, but acknowledged that they had met him and subsequently contracted his firm to work on the issue. “We’re like any firm under siege,” says Barbara Meredith, a vice-president at the organization. “It’s common to hire a PR firm when you’re under siege.” She says the AAP needs to counter messages from groups such as the Public Library of Science (PLoS), an open-access publisher and prominent advocate of free access to information. PLoS’s publicity budget stretches to television advertisements produced by North Woods Advertising of Minneapolis, a firm best known for its role in the unexpected election of former professional wrestler Jesse Ventura to the governorship of Minnesota. The publishers’ link with Dezenhall reflects how seriously they are taking recent developments on access to information. Minutes of a 2006 AAP meeting sent to Nature show that particular attention is being paid to PubMed Central. Since 2005, the NIH has asked all researchers that it funds to send copies of accepted papers to the archive, but only a small percentage actually do. Congress is expected to consider a bill later this year that would make submission compulsory. Brian Crawford, a senior vice-president at the American Chemical Society and a member of the AAP executive chair, says that Dezenhall’s suggestions have been refined and that the publishers have not to his knowledge sought to work with the Competitive Enterprise Institute. On the censorship message, he adds: “When any government or funding agency houses and disseminates for public consumption only the work it itself funds, that constitutes a form of selection and self-promotion of that entity’s interests.”

So the pit-bull is loose – which way will the pendulum swing?

Here’s a typical example of getting information from the literature. Assume I don’t belong to a rich University
and I need to find out about cystic fibrosis. I can go to the splendid Pubmed (MEDLINE)

PubMed is a service of the U.S. National Library of Medicine that includes over 17 million citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. PubMed includes links to full text articles and other related resources.

I type in “cystic fibrosis” and find 27497 articles! Here’s #7:

7:	Dellon EP, Leigh MW, Yankaskas JR, Noah TL.	Related Articles, Links
	Effects of lung transplantation on inpatient end of life care in cystic fibrosis. J Cyst Fibros. 2007 May 2; [Epub ahead of print] PMID: 17481967 [PubMed – as supplied by publisher]

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[title and authors omitted]

BACKGROUND: The impact of lung transplantation on end of life care in cystic fibrosis (CF) has not been widely investigated. METHODS: Information about end of life care was collected from records of all patients who died in our hospital from complications of CF between 1995 and 2005. Transplant and non-transplant patients were compared. RESULTS: Of 38 patients who died, 20 (53%) had received or were awaiting lung transplantation (“transplant” group), and 18 (47%) were not referred, declined transplant, or were removed from the waiting list (“non-transplant”). Transplant patients were more likely than non-transplant patients to die in the intensive care unit (17 (85%) versus 9 (50%); P=0.04). 16 (80%) transplant patients remained intubated at or shortly before death, versus 7 (39%) non-transplant patients (P=0.02). Do-not-resuscitate orders were written later for transplant patients; 12 (60%) on the day of death versus 5 (28%) in non-transplant patients (P=0.02). Transplant patients were less likely to participate in this decision. Alternatives to hospital death were rarely discussed. CONCLUSIONS: Receiving or awaiting lung transplantation affords more aggressive inpatient end of life care. Despite the chronic nature of CF and knowledge of a shortened life span, discussions about terminal care are often delayed until patients themselves are unable to participate.

But I want to know more… maybe the data need re-interpreting … so let’s read the whole article …

Effects of lung transplantation on inpatient end of life care in cystic fibrosis Journal of Cystic Fibrosis, In Press, Corrected Proof, Available online 3 May 2007, Elisabeth P. Dellon, Margaret W. Leigh, James R. Yankaskas and Terry L. Noah View Abstract

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… and it will cost you 30 USD…
So that – I hope – is an accurate depiction of the difference between Open (PubMed) and Closed (Journal of Cystic Fibrosis)

(Note for true effect, go to the real live pages mentioned here).
Here is a page from the Canadian National Committee for CODATA (sent by Alison Ball). I’m going to choose just one of many data sources:

About This Database This database is devoted to the collection of mutations in the CFTR gene and is currently maintained by Julian Zielenski, Anluan O’Brien and Lap-Chee Tsui as a resource for the international cystic fibrosis genetics research community. It was initiated by the Cystic Fibrosis Genetic Analysis Consortium in 1989 to increase and facilitate communications among CF researchers. The specific aim of the database is to provide CF researchers and other related professionals with up to date information about individual mutations in the CFTR gene and phenotypic data associated with CFTR genotypes. While we will continue to ensure the quality of the data, we urge the international community to give us feedback and suggestions. Since the purpose of this database is to facilitate research, we ask our colleagues to use the information with great discretion in clinical settings. Similarly, we ask those who are looking for genotype-phenotype correlation to exercise extreme care in interpreting the recorded data. For information related to this mutation database, please send an email to cftr.admin. For general information on cystic fibrosis, please use our linked sites. Previous website can be found here.

Comments or questions? Please email to cftr.admin The Database was last updated at Mar 02, 2007

If you have never seen a bioinformatics database, try following: mRNA(cDNA) and Polypeptide Sequence
and you might get something like:

Click in the following graph to get the CFTR mRNA(cDNA) sequence of 600nts <!– –> Enter the start and end Nucleotide of the CFTR mRNA(cDNA) sequence From: To: 100 Enter the start and end Amino Acid of the CFTR polypeptide sequence From: To: Move: 100nt 500nt 1000nt 2000nt 5000nt Move Left Move right Don’t Move Zoom: 200nt 400nt Zoom In Zoom Out Don’t Zoom mRNA(cDNA) and polypeptide sequence: Get a sequence only copy: DNA sequence Three-letter symbol polypeptide sequence One-letter symbol polypeptide sequence

The point here is that the data is of great interest to many people – by no means just scientists. It allows you to query mutations in every part of the genome. Imagine if this data were locked up behind a commercial firewall…