Scraped and typed into Arcturus

I have had thoughtful contributions from an academic and a publisher on my exploration of DRM. See http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=2434&cpage=1#comment-454356 for comments by Henry Rzepa, and in particular his concern about publishers’ roles, to which Ricahrd Kidd from the Royal Society of Chemistry has replied.

Richard has been an active collaborator with our group for over 5 years and has supported several summer students. Note also that the RSC has a responsible attitude as a closed-access publisher. They make closed material available (but not Open) after a time-lapse period and they do not force authors to hand over copyright on data, so we have extracted semantic information from their supplemental information.

I should make it clear that although I campaign gently for Open Access publishing (as opposed to frenetically for Open Data) I accept that there are closed-access publishers. My concern there is that they make it clear what they are providing, what rights they have extracted from the author, what restrictions they have placed on the reader (sorry, enduser-customer) and whether they provide reasonable value for money. For example, a closed-access publisher usually has an Open Access option where authors can pay – in some cases this is very good value (e.g. Acta Crystallographica) and in others (ACS) it’s very poor (the freely visible material is not open and festooned with restrictions).

So you should read Richard as somewhere in the mainstream of responsible closed-access publishing:

 Henry Rzepa says:

May 25, 2010 at 8:53 am  (Edit)

Yet another question, which perhaps the BL or a librarian might enlighten me on. Currently, our library spends a lot of money (£millions per year) on journal subscriptions. But interesting, a few quite new journals are not covered, and many journals have quite limited backnumbers. If I acquire e.g. a PDF article under this subscription, it (at least for now!) comes with no DRM. The article can be re-used in many ways. For example, it can be dropped into Mendeley, a software system that strives to add value to the document by extracting meta-data, indexing it, and much more. With some PDF documents, interactive 3D objects are included that can be manipulated.

Get the same document from the DL and it seems it comes with DRM that effectively limits it to a single print within 14 days. I doubt that the publishers are different, it is simply a different intermediary that is providing the document.

Since the above makes no sense, it would be tempting to conclude that in fact the BL is ahead on this, and that the DRM system will be eventually introduced to all academic library subscriptions as well. Please please can someone reassure me that it is not the plan?

 Richard says:

May 25, 2010 at 5:05 pm  (Edit)

I strongly doubt that’s the case Henry – my impression is that the DRM is just there for the historic/copyright/whatever issues around ILL. Publishers have no interest – as far as I’ve seen – in putting this stuff on published PDFs or asking subscribing libraries to do so.

There can be unintended consequences of good intentions though – a few years ago we were persuaded to lock our published PDFs (while still allowing printing, copy & paste), that it was something a reputable publisher should do to preserve the original published version. When we did it this actually caused much more difficulty to everyone – other online customers, students who needed to put the PDFs into their thesis, ourselves – so we quietly dropped it.

It’s clear that there is not only an ethical, but also utilitarian argument. If you mangle your product with DRM people either won’t use it, or hate you, or abuse it. If Richard is typical of most responsible closed-access publishers then DRM is NOT NECESSARY.

So why did the BL adopt it? I have the following hypotheses – not exclusive:

• A few publishers demanded it and the BL is too afraid to negotiate with them. So the BL applied DRM.
• It is more cost-effective to apply DRM to everything rather than try to work out what should be covered and what should not be DRM’ed,
• Librarians worship copyright and the BL has got an opportunity to show how smart and responsible it is by DRM’ing stuff.
• The marketing department of the BL is behavinf like marketers rather than scholars. They have invented a need and convinced themselves that adding DRM improves the product. They’ve said so.
• Non-academic content suppliers such as D*sn*y and its M*ck*y M**s* (I am too scared to actually type the full words as this is undoubtedly illegal and actionable somewhere) have terrified the BL. I am sure this is part of the case.
• It’s actually great fun to play with new toys. And librarians love worshipping copyright by fixing notices to photocopies. This is a new ritual in the cult of copyright.

But we’ll see from their FOI response.

BTW I am visiting the BL next month as a member of UKPMC advisory.

When I have got my FOI request off to the Russell group universities then I shall start slowing down until the responses come in.

Typed/scraped into Arcturus while waiting for Eclipse job to complete

I have been doodling round the DRM + BL theme and suddenly found Bethan’s information professional blog . From the About:

I’m a librarian, working for Library and Archival Services at Mimas (otherwise known as Copac and the Archives Hub). I started library work in 2006 as a Graduate Trainee at the John Rylands Library at the University of Manchester, and then went on to do an MA in Library and Information Management at MMU

[I’ve been invited to speak at at the John Rylands Library later this year…]

Anyway she has written a balanced and thoughtful piece

http://bethaninfoprof.wordpress.com/2010/05/11/why-cant-we-teach-peter-murray-rust-about-drm/

[The post doesn’t seem to carry a licence so I’ll assume she would like having it republished without permission (as I do for mine). Bethan, if this is the case, suggest you put CC-BY http://freedomdefined.org/Licenses/CC-BY-2.5 ) on it.] I quote it in full, and don’t need to comment. This is the sort of thing I had hoped for more of.

Why can’t we teach Peter Murray-Rust about DRM?

May 11, 2010 in general ramblings | Tags: DRM, ILL, user ed

Yes, I know this is a deliberately provocative title, and I am not implying that Prof Murray-Rust needs teaching more than most, nor that he is particularly difficult to teach.

But, as his blog posts show (start here and read on), here is a prominent academic, who is well-known in the library world, who doesn’t understand why – or indeed how or when – the BL have DRM (digital rights management) on their electronic inter-library loans. (please note: I’m not going to discuss here whether they should have or not – merely that they do).

I understand why, although I couldn’t tell you when I learned. I’ve never worked ILL – is it some kind of librarianly osmosis? I’m sure you, as librarians and info profs, understand too (and if you don’t, go read Steph Taylor’s (@CriticalSteph) response on PMR’s blog).

So here is an issue which librarians understand, and which fundamentally affects the relationship of our users – arguably of our most sophisticated users – to the library. As PMR’s blog (and comments) show, it’s an issue which very negatively effects that relationship. It’s seen as a barrier to scholarship – PMR says ‘I believe that these represent a serious reduction in academic freedom‘.

If this is issue is so vital, why don’t they know why we are doing it? Prof Murray-Rust says ‘The BL’s responses are often masterly Sir Humphreydoms that say nothing‘, and he asks for professional advice from librarians about how to interpret the restrictions.

Why does he need this? I appreciate the need to have the legal disclaimers in place, but our primary role, as information professionals, is to get information to our users. We have obviously failed here. Why is there not a simple, accessible guide to DRM on ILL articles – in fact, to the role of copyright in ILLs as a whole?

The Cambridge University Library website inter-library loans page makes no mention of DRM – but that may be because it makes no mention of the fact that you can obtain journal articles electronically, through SED (secure electronic delivery). Surely Cambridge provides this service? Indeed, why else would PMR be questioning it? Yet no mention – that I could find. I’d be very happy to be proved wrong!

I’m not singling out Cambridge for condemnation here – it merely happens to be Prof Murray-Rust’s institution. Let’s look at some others, shall we? Manchester? No mention. Oxford and Sheffield? Some mention – they at least acknowledge the existence of SED. Edinburgh? Getting better – advice about the service, and a mention of why you can only print one copy. ‘Copyright restrictions’ is a pretty bare-bones explanation, but at least it’s a start.

So there is some information out there – but surely you’re not suggesting that this is providing an acceptable service to users? That to find information on a service you provide they have to find information on that service as provided by other libraries, and extrapolate from there?

(This is just a whirlwind tour of a few libraries that sprung to mind – if you know of a particularly good example of how libraries are communicating these restrictions, please let me know!)

So, on to the BL. After a bit of digging, I found the SED FAQ – it’s certainly not in a prominent or easily accessible place. And yes, it answers the technical questions. But nowhere is there a mention of the ‘why’. And without the ‘why’, it appears that we are restricting access to information for our own fun and amusement.

DRM on articles may or may not be deliberate barrier to scholarship, but not providing easy access to (in effect, withholding) all of the information users need to make the best choice about how to access those article, and how to make best use of them once they have obtained them, is. If we have to live with DRM, we have to learn how to make sure users get the most out of it – and that they understand why it is there. If we don’t, we’re failing in one of our fundamental trusts: to make the information our users need available to them – even if they don’t know they need it.

Scraped and typed into Arcturus

This is my FOI request to the British Library about their introduction of DRM. Note that I shall be sending out a similar request to a number of leading UK academic libraries so that it will be clear whether the apparent lack of public discussion over DRM on journal articles is due to a failure to solicit opinion, a failure to respond or both. I shall submit it later today so would appreciate any comments – they can be anonymous.

Dear British Library

I am writing under FOI to request documentary evidence for the motivation and governance processes for your introduction of Digital Rights Management (DRM) technology into the delivery of InterLibraryLoans (ILLs) for journals and journal articles in electronic form (e-ILL). The scope of the request is strictly limited to journal articles (“articles”) and not e-Books or other media (e.g. films). In all replies I request specific documentary evidence rather than general principles. Reference material is appended.

DRM raises major issues for libraries as evidenced by your own CEO, Lynne Brindley (Brindley2006) and the American Library Association [ALA2008]. They state:

providers can prevent the public from use that is non-infringing under copyright law as well as enforce restrictions that extend far beyond those specific rights enumerated in the Copyright Act (or other laws). Thus, DRM changes the fundamental relationship between the creators, publishers, and users, to the detriment of creators, users, and the institutions that serve them.

DRM also appears to break accessibility law and guidelines [RNIB2010].

e-ILLs are generally requested by academics through their University Library and provided by the BL. They are governed by “part 4 of The Copyright (Librarians and Archivists) (Copying of Copyright Material) Regulations 1989 – http://www.opsi.gov.uk/si/si1989/Uksi_19891212_en_1.htm and schedule 2 – http://www.opsi.gov.uk/si/si1989/Uksi_19891212_en_3.htm ” (Copyright1989). The academic has to sign a contract that they will adhere to these conditions. It is my contention that this act, together with the professional standards of academics and the easy identifiability of anyone breaking it, is sufficient to control the unlawful copying of copyright material. It is the introduction of DRM in addition to this process that is the essence of this request (i.e. e-ILL vs e-ILL-DRM). Please do not conflate the benefits of electronic delivery with the introduction of DRM as you do in your press-release (“The British Library Improves Electronic Access with New DRM Platform” BL2009)

The introduction of e-ILL- DRM by the BL started about 5 years ago and was specifically introduced by them (i.e. not simply passing through a content provider’s own DRM). The technology was Adobe Digital Editions (ADE). I can find no public record of discussion or governance of this process. I formally request the following information which must be supported by documents such as minutes, internal memos or public pronouncements:

1. Did the BL consult (a) its advisory board (b) Universities (c) the public before introducing e-ILL-DRM? Please provide documentation. [I shall also be making this FOI request to Universities].
   
2. Has the BL formally considered the negative effects of DRM on e-ILLs as shown by the ALA’s concerns (“first use”, “pay-per-use”, “time limits” and “fair use”). Please document which of these were considered? [I shall also be making this FOI request to Universities].
3. What feedback (please document) did the BL obtain from which stakeholders (Universities, academics) before introducing e-ILL-DRM?
4. Did the BL take legal advice as to whether the law required it to introduce DRM for e-ILLs? Please document.
5. Has the BL formally considered whether Adobe Digital Editions conforms to the BL’s Accessibility policy or to legal requirements? Please document.
6. Has the BL canvassed opinion about e-ILL-DRM from stakeholders such as the RNIB? Please document.
7. BL2009 speaks of “The decision to add FileOpen [another DRM] … was driven by customer demand”. Please document who are these customers and in what form they demanded DRM. [I shall also be making thisFOI request to Universities].
8. At what level of governance was the decision taken (please provide documentation)?
9. After e-ILL-DRM was introduced what feedback was received from (a) Universities and their libraries (b) academics. Please document. [I shall also be making thisFOI request to Universities].
10. What role have content providers (“publishers”) had in encouraging the BL to introduce DRM? Please document all non-confidential information.
11. What role does the requirement for the BL to recover costs play in introducing DRM?

I look forward to your reply.

References

[ALA 2008] http://www.ala.org/ala/issuesadvocacy/copyright/digitalrights/index.cfm

DRM: A Brief Introduction

The purpose of DRM technology is to control access to, track and limit uses of digital works. These controls are normally imbedded in the work and accompany it when it is distributed to the consumer. DRM systems are intended to operate after a user has obtained access to the work. It is in this “downstream” control over consumer use of legitimately acquired works that DRM presents serious issues for libraries and users.

DRM technology is new and evolving. Different schemes are being proposed, developed in the laboratory, and experimented with in the marketplace. In general, these technologies are intended to be flexible and to provide a wide range of options to the content provider, but not the user or licensee. Importantly, DRM technology can have profound effects on a wide range of policy issues, including intellectual property, privacy, access to government information, and security. As a consequence, it will be very important for Congress to carefully consider the impacts on many different constituencies, including libraries.

Key concerns for libraries

The principal policy issues for libraries and schools are not derived from DRM technology, itself, but from the business models the content industry chooses to enforce. DRM has uses far beyond simply enforcing traditional and long-standing protections extant in current law. By embedding controls within the product, providers can prevent the public from use that is non-infringing under copyright law as well as enforce restrictions that extend far beyond those specific rights enumerated in the Copyright Act (or other laws). Thus, DRM changes the fundamental relationship between the creators, publishers, and users, to the detriment of creators, users, and the institutions that serve them. DRM, if not carefully balanced, limits the ability of libraries and schools to serve the information needs of their users and their communities in several ways by:

Eliminating the “First sale” doctrine by limiting the secondary transfer of works to others. First sale has been for centuries a bedrock principle governing the balance of rights between consumers and sellers of information products. It is first sale that allows people to share a favorite book or CD with a friend and that creates secondary markets for works. It is first sale that allows libraries to loan lawfully acquired works to the public.

Enforcing a “Pay-per-use” model of information dissemination that, if it becomes the dominant or even sole mode of access, will be contrary to the public purposes of copyright law. It should not be the business of government to favor or enforce any particular business model in the information marketplace, particularly one that raises major issues of equity and potentially severe economic consequences for public institutions.

Enforcing time limits or other limitations of use that prevent preservation and archiving. Many market models of DRM distribution systems envision content that essentially disappears after a specific period of time or number of uses. DRM technologies can also prevent copying content into new formats. Such controls will prevent libraries, historical archives, museums, research institutions, and other cultural institutions from preserving and providing long-term access to the knowledge products of our society. From the days of the Great Library of Alexandria, society has turned to such institutions to preserve its cultural heritage and provide access to it. There is no evidence that alternative organizations currently exist or will form to play that role in the digital pay-per-use
world.

Eliminating “fair use” and other exceptions in Copyright Law that underpin education, criticism, and scholarship. DRM technology can prevent normal uses of works protected by copyright law, such as printing or excising portions for quotation. For libraries and schools to serve their educational, research, and information roles, the public must be able to use works in the full range of ways envisioned by the Copyright Act in its limitations and exceptions.

[Bl2009] http://www.bl.uk/news/2009/pressrelease20091126.html

Responding to customer demand, the British Library, supplying over 1.6m articles every year to researchers all over the world, has added FileOpen to its choice of delivery options via its Document Supply Service. FileOpen’s DRM technology will improve accessibility and extend the reach of the British Library’s vast resources.

The British Library’s Document Supply services have been at the heart of the national and international research community for 50 years, enabling users to exploit a wealth of information for the benefit of research. In the digital age increasing customer demand for electronic delivery, both remotely and immediately, has seen the number of Document Supply users requesting content delivered electronically raise to over 70%.

In an effort to provide customers with greater flexibility when receiving electronic documents, the British Library has teamed up with FileOpen Systems, a leading provider of a Digital Rights Management platform to the information industries. The FileOpen option offers users an alternative to the Library’s existing Adobe Digital Editions platform, enabling them to access copyrighted material in their Adobe PDF Readers without the need to download a new viewing application.

“The decision to add FileOpen to our Document Supply delivery options was driven by customer demand, they wanted a choice of electronic delivery options,” says Barry Smith, Head of Sales and Marketing at the British Library. “Customer feedback from the testing phase was very positive, and we are pleased to announce that we are now recommending FileOpen as our preferred electronic delivery option to all customers.”

“We’re delighted to be working with an organisation with such worldwide prestige as the British Library, and to be providing their customers with a robust, user-friendly solution for secure document access,” said Elizabeth Murphy, Vice President of Sales and Marketing at FileOpen Systems. “FileOpen Systems is the leading provider of DRM for Scientific, Technical, and Medical (STM) information, and continues to innovate to meet the high standards of that market.”

The FileOpen secure delivery option is now available to all Document Supply customers but is currently unavailable via British Library Direct or British Library Direct Plus.

[Brindley2006]

Quoted in http://www.pcpro.co.uk/news/94639/british-library-shouts-out-against-unfair-drm:

“As one of the world’s great research libraries we are equally mindful of the threat that an overly restrictive, or insufficiently clear, IP framework would pose to future creativity and innovation”

And http://www.pcpro.co.uk/news/88316/uks-top-librarian-calls-for-digital-protection

“Lynne Brindley, chief executive of the British Library, warned that DRM is already having an impact on the traditional exceptions to copyright law that have existed for libraries”.

Read more: British Library shouts out against unfair DRM | News | PC Pro
http://www.pcpro.co.uk/news/94639/british-library-shouts-out-against-unfair-drm#ixzz0ok64SAex

[RNIB2010]: http://www.rnib.org.uk/livingwithsightloss/readingwriting/ebooks/Pages/ebook_formats.aspx

“Adobe’s DRM requires you to download your ebook to ebook reading software called Adobe Digital Editions. Adobe Digital Editions (version 1.7.1) currently has no real keyboard access and does not work with access technology. So if you purchase books that are secured with Adobe DRM, you may not be able to read them using Adobe Digital Editions,” [Note: PM-R: Adobe Digital Editions is the DRM employed by the BL from 2005 onwards

Typed in support of a community that cares passionately into Arcturus

Here’s an excellent example of a community that is racing towards mandating data deposition as part of publication. And to give credit where it’s due it’s reported by an ACS journal (J. Proteome Research) http://pubs.acs.org/doi/full/10.1021/pr900912g which is also slowly picking up the momentum.

Don’t switch off at “Proteome”. The discipline is about finding what proteins are produced in living organisms and often how they affect disease or act as signals for it. The subject is data-rich as it involves injecting samples into a mass spectrometer; from the peaks in the spectrum (see image, stay with me) it’s possible to identify the proteins. So the data really matter.

• Is the experiment valid? A less-than-careful scientist could get impurities in the sample (or other artefacts) and come to the wrong conclusion. The data are a major step in allowing the referees and later readers to decide whether the experiment might be flawed.
• There is huge potential for re-using the data. This could be between species, cell types, diseases, etc. It’s still at an early stage because the data are complex but I am certain it will happen.

I quote selected chunks from the article (pleading fair use, especially as the article is Freely (if not Openly) published) . Here’s a spectrum – a piece of FACTUAL data (not a creative work) lifted without permission or shame or foreboding from the ACS. The peaks in the spectrum are chopped up proteins (peptides) from which the proteins can be identified. I make a few comments at the end

ely (if not Openly) published).lished). (pleading fair use, especially as the o-auth eases, etc. It’ong conclusion. The data a

MCP ups the ante by mandating raw-data deposition

J. Proteome Res., 2009, 8 (11), pp 4887–4888 DOI: 10.1021/pr900912g Copyright © 2009 American Chemical Society

Yet again, the editors of Molecular & Cellular Proteomics (MCP) are leading the way toward stricter publishing requirements for the proteomics field. At the First International Forum of Proteomics on September 26, 2009, and then two days later at the HUPO Eighth Annual World Congress (both held in Toronto), MCP Co-Editor Ralph A. Bradshaw announced that the journal will require its authors to deposit supporting raw MS data into a public repository at the time of publication. The new mandate will likely take effect in January 2010.

[…]

The ultimate goal of the mandate for raw-data deposition is to provide further proof that proteomics is a valid pursuit. “There’s an important sense that we need this in order to make proteomics more legitimate than it presently is,” says Bradshaw. “We think we need to raise the bar even further in terms of getting the proteomics literature validated and getting rid of the errors.”

[…] An increase in raw-data submissions would be a boon for bioinformaticians, who are always hungry for more data sets for tool development and testing. Philip Andrews of the University of Michigan adds that some valid identifications might be salvaged if researchers could reevaluate data from published experiments with other algorithms. In addition, some useful information, such as data about the instrument’s parameters, is lost when data are processed.

[…]Daniel Figeys of the Ottawa Institute of Systems Biology says that, in theory, raw-data deposition shouldn’t be a big deal for proteomics researchers. After all, researchers in the gene-expression field have been required to deposit all of their data into public databases for years. Also, the infrastructure for handling this type of proteomics data has been evolving and improving, says Andrews, who is the principal investigator of the Tranche Project. (Tranche is a repository for the long-term storage of data of any format.)

… The Amsterdam Principles, […] encourage open access to proteomic data. (Disclosure: K. Cottingham is a o-author of this manuscript.) …. “The community is going from asking questions such as, ‘Should there be data-release policies for proteomics?’ to asking, ‘What are the policies, and how and when will they finally be implemented?’” he explains.

… researchers have uploaded 10.8 terabytes of proteomics data into Tranche. Researchers also are using the data. “Since February, 8 terabytes of data have been downloaded by investigators, and that’s a lot of data to be downloaded from a repository like this,” he explains.

Although Bradshaw says that MCP will not specify that researchers must upload the raw data to Tranche, he admits that it is “probably the only place where this would work” currently; other proteomics repositories and databases accept only processed data. Because Tranche is part of the ProteomExchange consortium, however, other resources, such as PRIDE and Peptidome, have access to its data and routinely download new data sets.

“I think the biggest concern about Tranche is that it’s supported with soft money, and it doesn’t have

Bradshaw hopes that researchers won’t view the requirement as a hardship and says, “The last thing in the world we want to do is create burdens and obstacles for authors.” Andrews explains that researchers uploading data to Tranche for the first time may experience a learning curve, but “once they realize how easy it is, I don’t think they’re going to be too concerned.”

• Top of Page
  
• Why make this move?
  
• Data in, data out
  
• Will other journals at the table follow suit?
  
• MCP’s hand: on the table for public comment
  

…Proteomics and Proteomics: Clinical Applications strongly encourage the submission of processed data, but change is coming. Michael Dunn, who is at University College Dublin and is editor-in-chief of these journals, says, “We now propose that we will make a change in our next release of the Instructions to Authors, for January 2010, to state that we strongly encourage deposition of raw and processed data…

JPR‘s editor-in-chief, William Hancock … “My position was that we would strongly encourage authors and reviewers to support this initiative.”

• Top of Page
  
• Why make this move?
  
• Data in, data out
  
• Will other journals at the table follow suit?
  
• MCP’s hand: on the table for public comment
  

Right now, all of the proposed changes exist in draft form and will be posted soon on the MCP website for public comment. Bradshaw explains, “Some of this could change, but I feel very confident in saying that the mandatory [raw-data] requirement is not going to change.”

We know Ralph very well and I have close relations with a scientist who reviews for MCP. When we visited Ralph earlier this year I told him about the Panton Principles (http://pantonprinciples.org/ ) and he enthusiastically communicated them to Tranche.

Typed in support of a community that cares passionately into Arcturus

I recently blogged about how a community wanted access to raw experimental data:

http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=2424

They begged the authors, database, publishers, etc. to ensure that data was published as soon as the publication appeared.

Here’s the reply from the database. http://proteincrystallography.org/ccp4bb/message15287.html It gives a balanced account of how it requires continual effort to achieve routine deposition of effort. They outline the key forces: the community, the journal/editors, the funders. The good news is that in favourable cases the process has speeded up considerably – we can measure in years not decades. And we all agree that it’s not trivial to do this. Communities are resistant. But the process is autocatalytic – the more frequently we see a community adopting Open Data, the more rapidly the other communities will be encouraged and learn from this. And we believe it’s possible to create useful general guidelines – there is nothing special about protein data.

Read it carefully and replace ${cryoEM} by your own discipline. Try “proteomics”. If you don’t know about this, read the next blog.

Subject: Re: electron microscopy: where open access fails
From: Cathy Lawson cathy {- dot -} lawson {- at -} RUTGERS {- dot -} EDU
Date: 2010-05-21

Dear Filip, CCP4BB, 3DEM, and PDB-L list members,

Thank you for your enthusiastic showing of community support for mandatory deposition of cryoEM maps to EMDB and for their timely release.

The two year hold is available to EMDB depositors for just one practical reason: it encourages deposition of maps that we would probably otherwise not be getting at all (and those experiments would thus never be falsifiable). Until journals and major funding agencies make deposition and immediate release mandatory, we have to compromise. A large number of petition signatures ( http://www.petitiononline.com/cryoEM/petition.html ) will certainly help us to solidify our case.

It is easy to forget that it was not until 1989 (17 years after the PDB began collecting X-ray structures) that community-set guidelines were published for X-ray crystallography coordinate deposition, and several more years before the journals required deposition as a prerequisite for publication. Structure factor deposition only became mandatory in 2008. These policies emerged from cooperative action by the community of experimentalists and interestingly included a petition that was led by Fred Richards. The same process will be effective for the EM community.

Sincerely,

The EMDataBank.org team
http://emdatabank.org

Scraped into Arcturus in an attempt to energize the community

I reproduce in full a recent helpful comment on this blog and then comment.

1. Stuart Bentley says:
   

   May 21, 2010 at 11:45 am
   

   Whilst I don’t disagree with the spirit of what you’re saying, I think there are a few faulty premises in your post.
   

   The reason academic librarians are paralyzed by copyright is that it’s the law, and the librarian is often responsible for managing the institution’s licence for copying (you can read standard licences for education at http://www.cla.co.uk/) because it sits nicely administratively with the place where all the materials are kept. You can find the Act of Parliament at http://www.opsi.gov.uk/acts/acts1988/Ukpga_19880048_en_1.htm and if you read the sections on fair dealing and what librarians and education are allowed to do – including regarding inter library loan -, you will see that the restrictions aren’t imposed by librarians but by Government. Failure to comply can result in the rescinding of licences and large fines against the institution and the person named as the institution’s copyright officer is likely to be fired. Which does not help anyone’s agenda.
   

   Similarly, my understanding is that the BL’s hands are similarly tied by the licences granted them by the publishers, who are the people who make the money in the scenario and so have the vested interest in keeping things under a tight leash. However, they will be better placed to respond on that.
   

   The law is outdated by any means and the digital economy bill is going to take things in a worse direction. What is required is academics to come together with librarians and lobby for change, rather than demonising them.
   

I am now familiar with the Copyright Act (having been made aware of it by a non-librarian reader of this blog). I fully agree that it is incredibly constraining. However it does NOT mandate DRM (as it came from a pre-digital era).

You argue that I demonize librarians. I do not. I have some limited sympathy for the constraints on them. But UK librarians have done absolutely nothing in public to show that they care about DRM. From casual conversations over the last 2-3 weeks with librarians I believe that they do not know about or do not care about DRM applied by the BL. Where they know about it they accept it as inevitable without even publicizing the problem.

You say “What is required is academics to come together with librarians and lobby for change”. But this requires action. I am an academic. I am trying to find a single UK librarian who cares publicly about DRM. If they existed they would have come forward over the last month. For me what is required is for librarians actually to do something. I and others will meet them more than halfway.

The US librarians have raised concerns about DRM. The UK librarians have done absolutely nothing. The DRM on InterLibraryLoans (ILL) has been going on for 5 years and not a single public paper debating the issue. I don’t find this acceptable. I believe that any professional body should identify issues of general public concern and initiate debate. Librarians in academia are paid for, in part, by the revenue brought in by research grants, such as I apply for and often get. I and my colleagues are a constituency they would do well to involve.

Because if they don’t, the role of the academic librarian will be taken over by direct sale of material from mega-publisher (SpringWilesevier) to researcher, perhaps mediated through the British Library (which to my eyes appears to be acting excessively on the side of the publisher rather than the scholar).

But this will be revealed when I finally send my FOIs to the BL and academic librarians. If either have taken the case of the researcher over the last 5 years in this matter then I am sure they will be delighted to change my perceptions.

If not our new MP for Cambridge understands all about scholarly publication and I shall be WritingToHim.com

Typed in support of a community that cares passionately into Arcturus

I’ve spent two days this week at a useful meeting run by JISC (Simon Hodson) on Managing Research Data. As readers of this blog know I am a passionately supporter of the “Data wants to be free” (I know there is some data which cannot be free… but most of it does). If you don’t believe this, here is a grassroots cry which no-one could ignore: from (http://www.petitiononline.com/cryoEM/petition.html ).

This is a typical example of multidisciplinary science. CryoEM is often complementary to XRay crystallography (these are both techniques for finding out what protein molecules look like – think of microscopes which magnify 10^8 times. ).

In essence:

• WE need YOUR data to help us understand OUR data.
• PLEASE can we have it.

There is the implication that it works the other way round. So collaboration rather than isolation is the most productive approach.

To:  CryoEM community, EMDB, Journals

CryoEM is an important tool to describe the structures of large macromolecules that currently escape standard X-ray crystallography and NMR techniques. Integrating cryoEM data with existing biochemical data and high-resolution structures of individual components is invaluable in the generation of high-resolution models of the intact complexes.

For the sake of progress of science, and for the sake of being able to test the validity of published articles on cryoEM structures, we request that all authors of new manuscripts describing cryoEM particle reconstruction deposit their maps in the Electron Microscopy Data Bank (EMDB) and have these maps released without restriction upon the date of publication.

In addition, we also request:

1. That all journals considering manuscripts describing cryoEM structures adopt the strictly enforced policy of not publishing the manuscript prior to deposition AND guaranteed public release of the cryoEM maps on the date of publication.

2. That the EMDB streamlines this process with the journals and does not allow for loopholes that can keep maps on hold even after publication.

3. That the authors of previously published cryoEM structures, for which the corresponding maps are currently not available in any database, deposit their maps for immediate release in the EMDB.

4. That potential reviewers of a manuscript describing a cryoEM structure make a strong point to the editors that the manuscript will not be reviewed unless it can be guaranteed that the corresponding maps would be released in the case of positive reviews.

Scraped with appreciation from OKF blog into Arcturus

I am delighted to record the first 1.0 release of CKAN, the Comprehensive Knowledge Archive from the Open Knowledge Foundation. This is, of course, a communal work but much of the credit goes to the indefatigable Rufus Pollock who conceived it, built it despite doubters such as me, and persuaded people (in the unique Pollock manner – i.e. you can’t refuse) to contribute.

CKAN is based on Open Knowledge – i.e. you can use anything in the catalog without worrying about lawyers and infringing rights. We’re delighted that of the 900-odd entries, nearly 30 are from chemistry and this represents a major input from the Blue Obelisk and elsewhere. Our own Nick day’s Crystaleye is in there.

Enjoy!

CKAN v1.0 Released

May 18th, 2010

We are pleased to announce the availability of version 1.0 of the CKAN software, our open source registry system for datasets (and other resources). After 3 years of development, twelve point releases and a several successful production deployments around the world CKAN has come of age!

As well as being used to power http://ckan.net and http://data.gov.uk CKAN is now helping run 7 data catalogues around the world including ones in Canada (http://datadotgc.ca / http://ca.ckan.net), Germany (http://de.ckan.net/) and Norway (http://no.ckan.net).

CKAN.net has also continued to grow steadily and now has over 940 registered packages:

Typed into Arcturus

I am giving a talk in the Biochemistry Department (at Cambridge) this morning (1015) and here is a brief outline of some of the topics I might cover. As always I don’t know what I shall say in detail until I meet the audience. In this case I am hoping that I get useful feedback and discussion.

I think that within the next 5 years technology will allow scientists to have machines that manage their immediate information environment – reading the literature, recording many of their actions, remembering their preferences, helping them write papers, theses and grants, etc. These “amanuenses” will be built from standard technology and will have natural interfaces – speech, gestures, etc. They will be built on communally agreed semantics and ontologies – technologies where bioscience is leading the world. It should, for example, be possible to ask a machine (using speech)

“What papers published last week do I need to know about? Summarise the most important points.”

“Consult our lab thesis-bank and find the most commonly used buffers – has our use changed over 5 years?”

“find me all the selective inhibitors of CYP2D6 and compute the energy of docking them into my mutant PMR123”

This is possible in bioscience because the community has been committed for over 3 decades to publishing Open information in semantic form and building ontologies (e.g. Go, CheBI). There are agreed universal identifiers for information. As a result it is possible to build Tim Berners-Lee’s vision of a semantic web of Linked Open Data which then links to all the other Open data on the web – geonames, bibliography, institutions, etc. This distributed knowledge base is at the core of scientific machine intelligence.

But this vision is threatened by major information and media interests. We are starting to see new restrictions on our use of scientific information, e.g. through Digital Rights Management in the library system and the power of the publishers to restrict and control innovation to their advantage. As a result it is critical that the bioscience community continues to challenge for Open Science (Data, Source, Access, Standards).

The talk will give demos of scientific speech recognition, machine understanding of theses and the semantic web.

Typed and scraped with a heavy heart into Arcturus

I’m still putting together my FOI request to the British Library. My concern is that DRM is deeply damaging, and that when done by a National library it is almost catastrophic. It could mean the effective destruction of the academic research library, by replacing it with commercial publishers suppying DRM’ed materials directly to “end users”.

This may sound like scaremongering, but I am taking my lead from the American Librarians Association, a sober professional organisation. They have raised 4 very serious concerns about DRM which they say strike at the very heart of academic library freedom. It’s a pity that no-one in the UK was able to help me find this document – I had to find it for myself. The concerns are put better than I would have done, and I have no evidence that the BL took them into account (I have no evidence they didn’t until I get my FOI back).

I am still convinced that no one in the UK library world really cares about DRM. I’ll retract my view if they can point me to a similar document written in the UK warning of the appalling results of DRM. I’ll add that I think there should be a fifth concern, that of accessibility – the current technology has clearly no concern about unsighted “end users”. After all the end user is no longer a person, but a purchaser.

The document speaks for itself. I have published it in full, without asking permission as “fair use” to help save our academic freedom.

http://www.ala.org/ala/issuesadvocacy/copyright/digitalrights/index.cfm

Digital Rights Management (DRM) & Libraries

DRM: A Brief Introduction

The purpose of DRM technology is to control access to, track and limit uses of digital works. These controls are normally imbedded in the work and accompany it when it is distributed to the consumer. DRM systems are intended to operate after a user has obtained access to the work. It is in this “downstream” control over consumer use of legitimately acquired works that DRM presents serious issues for libraries and users.

DRM technology is new and evolving. Different schemes are being proposed, developed in the laboratory, and experimented with in the marketplace. In general, these technologies are intended to be flexible and to provide a wide range of options to the content provider, but not the user or licensee. Importantly, DRM technology can have profound effects on a wide range of policy issues, including intellectual property, privacy, access to government information, and security. As a consequence, it will be very important for Congress to carefully consider the impacts on many different constituencies, including libraries.

Key concerns for libraries

The principal policy issues for libraries and schools are not derived from DRM technology, itself, but from the business models the content industry chooses to enforce. DRM has uses far beyond simply enforcing traditional and long-standing protections extant in current law. By embedding controls within the product, providers can prevent the public from use that is non-infringing under copyright law as well as enforce restrictions that extend far beyond those specific rights enumerated in the Copyright Act (or other laws). Thus, DRM changes the fundamental relationship between the creators, publishers, and users, to the detriment of creators, users, and the institutions that serve them. DRM, if not carefully balanced, limits the ability of libraries and schools to serve the information needs of their users and their communities in several ways by:

Eliminating the “First sale” doctrine by limiting the secondary transfer of works to others. First sale has been for centuries a bedrock principle governing the balance of rights between consumers and sellers of information products. It is first sale that allows people to share a favorite book or CD with a friend and that creates secondary markets for works. It is first sale that allows libraries to loan lawfully acquired works to the public.

Enforcing a “Pay-per-use” model of information dissemination that, if it becomes the dominant or even sole mode of access, will be contrary to the public purposes of copyright law. It should not be the business of government to favor or enforce any particular business model in the information marketplace, particularly one that raises major issues of equity and potentially severe economic consequences for public institutions.

Enforcing time limits or other limitations of use that prevent preservation and archiving. Many market models of DRM distribution systems envision content that essentially disappears after a specific period of time or number of uses. DRM technologies can also prevent copying content into new formats. Such controls will prevent libraries, historical archives, museums, research institutions, and other cultural institutions from preserving and providing long-term access to the knowledge products of our society. From the days of the Great Library of Alexandria, society has turned to such institutions to preserve its cultural heritage and provide access to it. There is no evidence that alternative organizations currently exist or will form to play that role in the digital pay-per-use
world.

Eliminating “fair use” and other exceptions in Copyright Law that underpin education, criticism, and scholarship. DRM technology can prevent normal uses of works protected by copyright law, such as printing or excising portions for quotation. For libraries and schools to serve their educational, research, and information roles, the public must be able to use works in the full range of ways envisioned by the Copyright Act in its limitations and exceptions.