Monday, 28 January 2013

The definite article?

I recently attended the IDCC (International Digital Curation Centre) conference in Amsterdam where my colleague, Neil Jefferies and I were giving a talk on development of Oxford’s DataFinder, the catalogue for Oxford research datasets. The theme of the conference was "Infrastructure, Intelligence, Innovation: driving the Data Science agenda." One of the keynote speakers was the formidable Herbert van de Sompel, team leader of the Prototyping Team at the Research Library of the Los Alamos National Laboratory, a place well known on the digital repository map. In repository circles he is also revered for his work on what are now standard metadata protocols – so altogether a well-respected and influential individual.

He gave a wonderful potted history of interoperability between digital systems i.e. how different services interact with each other, and then proceeded to describe how scholarly outputs change over time, resulting in difficulties of access to different time specific snapshots. This idea is increasingly important as scholars begin to use the Internet not as a place to mount a frozen account of research at a specific point in time – a fixed PDF that tells a brief story of that research on a particular day – but as a dynamic tool that enables research to transform and develop collaboratively in time as the topic is discussed and built upon. The research article in its traditional sense is not always a suitable vehicle as a rich description of the complexities of research over time as it develops, incorporating all the detail that other researchers need in order to reproduce, and therefore ratify that research.

I’ve heard comments on this matter before – the research article as an endorsed and quality controlled summary of the research, that could become a vehicle purely for assessment, as a snapshot in time. In this scenario, a research article in the traditional sense is a long way from the actual research process. I should add two huge caveats here – firstly, the context of this presentation was that of scientific research, and secondly that I am not a researcher and so my commentary comes from a digital librarian’s perspective (views and comments from researchers are welcome).

Van de Sompel went on to describe some of his current work which is developing a tool called ‘Memento’ which enables people to see the state and context of a given work at any point in its development. This is useful when tracking down citations in an article. Over a period of time, sometimes quite a short period, links to cited references die and it becomes increasingly difficult to track them down and understand the environment in which the research took place. Memento enables a reader to reconstruct the environment of the research at the moment of publication, by easily tracking down sources wherever they might have been relocated. It can do this by using web archives and because the items in question, because they were open, were archived. As time passes and further changes and links are made, future researchers can access links to related works at any point along the research timeline.

The reason for wanting to do this is because increasingly since original publication, researchers are commenting on and annotating articles, using other dynamic online formats, and adopting new models of peer review, resulting in research developing visibly in the public arena. In this respect, the emerging output, commonly called the research article, is no longer guaranteed to be THE version of record, but is transforming into A version of the scholarly record.

From my experience, this is a new concept to many, but certainly not all researchers. Some are already working in this dynamic and digitally collaborative environment. It will not suit all disciplines, nor all researchers. I will be watching for moves towards dynamic versions (definitely plural) of scholarly record.

Monday, 7 January 2013

Open Access Oxford

The latter half of 2012 was a busy period in terms of open access (OA) to research publications. The Finch report (‘Accessibility, sustainability, excellence: how to expand access to research publications’) was quickly followed by a government response. Hot on its heels came a revised policy from RCUK (Research Councils UK). However, these changes have not just been in terms of recommendations and policies – money has been forthcoming.

As part of the government response, the University of Oxford has been granted funds via BIS/RCUK ‘to pump prime open access in universities and help with establishing open access policies and funds that will support academics.’ This is excellent. However, the catch is that the time period for spending this tranche of money is very short. There are in fact two funding streams i) a lump sum to pump prime open access, awarded in November 2012, to be spent by mid 2013 and ii) an annual block grant (first instalment in April 2013) to pay for author processing charges (APCs) to pay publishers for publication of open access articles (sometimes referred to as the ‘gold route’ to open access).

The University is certainly not letting the grass grow under its feet, and a major programme, OA Oxford, to address open access at Oxford has been initiated in response to the RCUK funding allocation. The programme comprises 10 projects under four main themes.

The programme focuses on the ‘green route’ to open access ie using ORA (Oxford University Research  Archive) as the most cost effective method of making the considerable number of Oxford authored publications open access. In tandem, Oxford will set up procedures for managing authors’ payment of article processing charges (APCs) for open access articles published within journals (‘gold route’ to open access).  The University is committed to the widest possible free dissemination of its research, and sees this funding as an opportunity to make rapid progress in this area. The ‘OA Oxford’programme will support improvements to existing services and infrastructure, and new initiatives towards this goal. The programme runs late 2012 until July 2013 and will focus on actions that enable members of the University to comply with the RCUK policy on open access.

The Bodleian Libraries are actively involved in this programme. Working in collaboration with colleagues in Research Services, IT Services, academic divisions and across Oxford libraries, projects include areas central to Bodleian services:

  • Support and information services for researchers via a single point of access website and subject librarians
  • Progress with uniquely identifying Oxford authors within ORA
  • As many as possible OA copies of research publications not already OA available via ORA (‘Green route’):
  • A full and re-usable record of publications by Oxford academics and researchers freely available in ORA
  • Enhancements to the ORA online service
  • Extend the existing work taking place in the JISC-funded Damaro project for linking publications with underlying research data
  • Better integration of technical systems used to manage OA at Oxford
  • A managed APC fund for Oxford authors, and recommendations for future provision of such a fund to support ‘gold route’ publishing, managed by the Bodleian Libraries. 

Questions remain as to how the future will pan out, both in terms of how the external landscape continues to evolve, and how precisely University services develop to help academics meet these changing requirements. For example, the RCUK block grants are to fund APCs only (ie not for further development of ‘green route’ services such as ORA) and will only cover 80% of each APC meaning the university has to find the remaining 20% - a not inconsiderable sum.


Thursday, 12 January 2012

An invitation from Bodley's Librarian to Oxford D.Phil. authors

Response to the Bodleian Libraries’ call for DPhil theses to be digitized has been extremely good (and if you have already proposed your thesis for digitization, there is no need to contact us again). We are pleased to let you know that there is still an opportunity to take up this offer and add your digitized thesis to the Bodleian’s digital collections at no charge.

Theses in digital format are rapidly becoming ubiquitous, as scholars want to make their research widely available and easily find the work of others. Thanks to the generosity and vision of Dr Leonard Polonsky, the Bodleian Libraries are able to offer to digitize a number of Oxford D.Phil. theses. This opportunity enables us to add to the growing Oxford digital thesis collection, and should result in new citations to your work. Digital copies will be made available online in ORA (Oxford University Research Archive).

ORA is the university's principal online collection of research outputs produced by Oxford scholars. It offers high visibility for Oxford research. Wherever possible, the full text of research is made freely available for easy online access. You can find out more about Oxford digital theses on the ORA Help & Information website.


If you would like us to digitize your DPhil thesis and make it available in ORA, please send details to 
as soon as possible, having provided the information below:

* Your name (as it appears on your thesis):

* The title of your thesis:

* The year of your thesis:

* If possible, the Bodleian shelfmark of your thesis on SOLO [eg MS.D.Phil. d.2804] (You may be able to find this on SOLO):

* An email (or postal) address where we can contact you: 
You will be informed if your thesis is included in this digitisation and the URL will be sent to this address.

Also, please indicate your responses to the following questions:
* Do you grant the Bodleian Libraries permission to digitize the print copy of your thesis and make the digital copy available online in ORA? YES/NO

* I agree to be bound by the terms of the ORA Grant of Non-exclusive Licence and I warrant that to the best of my knowledge, making my thesis available on the internet will not infringe copyright or any other rights of any other person or party, nor contain defamatory material. I AGREE / I DISAGREE

If you already have a digital copy of your thesis which you would like to deposit in ORA, please contact 

I very much hope you will take advantage of this exciting opportunity.

Please send details for the digitization of your thesis to 

Wednesday, 4 January 2012

Non-publication of negative results: Today on 'Today'

This morning the 'Today' programme on Radio 4 featured a problem that is highlighted in the current issue of the BMJ. In its editorial, 'Missing clinical trial data' the BMJ goes as far as to use a subtitle 'A threat to the integrity of evidence based medicine.' This is not a new problem and I am no medical scientist, but the main points seem to be:
  1. selected results of clinical trials are published. Inconclusive, un-interpretable, negative or (in the words of Prof Colin Blakemore on the Today programme) 'boring' results are not favoured by traditional journals and therefore remain unpublished
  2. results of trials can be scattered around various locations and difficult (even impossible) to locate
  3. although the Government and Research Councils are doing sterling work to ensure that the publications and data of publicly funded research are made freely available (see previous blog 'Government research strategy for innovation and growth'), this is not necessarily the case for research funded by private organizations nor for all publicly funded research (possibly because of 1). 
This can result in:
  • an incomplete picture of the results of trials
  • erroneous conclusions about the efficacy of treatments - both positive and negative
  • possible harm to patients
The BMJ states that 'what is clear from the linked studies is that past failures to ensure proper regulation and registration of clinical trials, and a current culture of haphazard publication and incomplete data disclosure, make the proper analysis of the harms and benefits of common interventions almost impossible for systematic reviewers.'

The logical conclusion would appear to be that results of trials need to be:
  • easily available
  • in a timely fashion
  • and complete (ie include all information provided that allows for the most accurate conclusions to be drawn)
Prof Blakemore agreed with Evan Davies on the Today programme, that making information freely available online is easy and 'everything should be out there' so that scientists can scrutinze, use and datamine the data produced by their fellow researchers. The editor-in-chief of the BMJ, Fiona Godlee, agreed: 'technology can improve the access to data.'

This is where services such as ORA (Oxford University Research Archive) provided by the Bodleian Libraries can step in. An online archive like ORA provides a means for researchers to disseminate research outputs where the papers (or reports or other documents whether published or not) can be safely stored for the long-term (including after an academic has left the university), easily discovered and read by other researchers. Such services do not offer peer review, however the current problem seems mainly in disseminating this information so that other researchers can have an opportunity to evaluate the findings. In doing this, other researchers check, review and comment on these 'boring' results, which will then add to the body of knowledge and could lead to a different direction in treatments and other outcomes. 

Such archives are not going to solve all the problems, and as An-Wen Chan describes in the article 'Out of sight but not out of mind: how to search for unpublished clinical trial evidence' (BMJ 2012;344:d8013), there are plenty of existing places that researchers can track down evidence information. Most HEIs now provide some form of managed online repository for research outputs that can contribute to rectifying this unacceptable situation. In addition, here at the Bodleian Libraries in Oxford, we're working on creating a data repository and Oxford data catalogue to do much the same thing for research data.

Fortunately the articles published in the BMJ about this matter are open access, so anyone who is interested can easily get hold of them and read about this topic for themselves. The editorial and item by An-Wen Chan aren't.

Tuesday, 3 January 2012

Government report on Innovation & Research Strategy for Growth

In Dec 2011 the UK Government published its paper 'Innovation and Research Strategy for Growth.' This paper is of great interest to anyone working within the area of research dissemination be they author or other actor in the dissemination process, because the government states its view of the economic benefits to the country of open access to research publications and data.

In the section 'Expanded Access to Research Publications and Data' (paragraphs 6.6 - 6.10) the Government states that it is 'committed to ensuring that publicly-funded research should be accessible free of charge.' Harvard University is cited as an example of a university where academics often make their research publications freely available via the University's DASH service. The report is more than a statement of the status quo: it sets out concrete actions, some of which are already underway. An independent working group has been set up under Janet Finch to consider how access to research publications can be improved. Other actions include those for investigating how research data might be made more accessible, and for making government data more accessible. The government has also asked the Research Councils to ensure that researchers comply with Council policies on access to publications. It's great to see positive actions such as these actually getting off the ground. Let's wait to see if these concrete actions deliver concrete results.

The main tenet of this report is one of economic advantage to UK PLC by supporting innovation, leading to economic growth, and it acknowledges that change will not happen quickly. It is hardly surprising that the Department for Business, Innovation and Skills would do anything other than focus on the economic benefits of open access, particularly in the current challenging economic times. However, one should not be completely swept up by the economic argument: there is one section that reads 'free and open access to taxpayer-funded research offers significant social ... benefits by spreading knowledge.' This not only points out that the hard-pressed taxpayer has a right to access what he/she has ultimately paid for, but also raises the prospect of enabling easy access to knowledge which offers other significant benefits to society. 

Thursday, 13 October 2011

Open Access Week

I expect many academic authors are not aware that open access week exists. But here we are on the brink of the 5th annual OA week which takes place 24 - 30 October 2011. International OA week is organised and promoted by SPARC (Scholarly Publishing and Academic Resources Coalition) and is described as "A global event...promoting open access as a new norm in scholarship and research."

In a nutshell, open access (OA) means free and unrestricted online access to research publications. The idea being that publications can be accessed by anyone, online without the need for payment or any other form of barrier to access. This model for access is promoted by many major research funders who require funded authors to provide free and open access to publications produced as a result of their funding. You can check major funders' policies in this matter on the Sherpa/Juliet website.

There are two ways to achieve open access to publications:

  • The GOLD route: publishing in an open access journal, or selecting the open access option in a journal that offers it
  • The GREEN route: depositing a copy of the work in an online open access repository such as ORA (Oxford University Research Archive)

The Bodleian Libraries offer guidance and information for Oxford authors in matters concerning open access. The Libraries provide the ORA service, Oxford's OA archive, as a green route to OA for University authors*. To mark Open Access week, the Bodleian Libraries are running a lunchtime event:

There will be two short presentations:

  • The OA movement in Law: Ruth Bird, Bodleian Law Library
  • Access to digital theses: Sally Rumsey, ORA, The Bodleian Libraries
Date:      Wednesday 26th October 2011
Time:     13.15 - 14.00
Venue:   RSL Lounge, Radcliffe Science Library

Members of the University are welcome to attend. Light refreshments will be available

* NEWS FLASH: Watch this space for news about easy deposit in ORA using Symplectic.

Friday, 2 September 2011

Research data workshop, Oxford, 14 - 16 September

The UK Digital Curation Centre is running a series of inter-linked regional workshops as part of the DCC Roadshow, aimed at supporting institutional research data management planning and training.

The fourth DCC Roadshow is being organised in conjunction with the Oxford eReseach Centre, Oxford University Computing Services and the Bodleian Libraries, and will take place from 14 - 16 September 2011.

Running over 3 days, different workshops will provide advice and guidance tailored to a range of staff, including PVCs Research, University Librarians, Directors of IT/Computing Services, Repository Managers, Research Support Services and practising researchers. We encourage you to select the workshop/s which addresses your own particular data management requirements.

Click here to find out more about the workshops 
Registration for the workshops is free. 

Sent on behalf of Dr Liz Lyon, Director, UKOLN and Associate Director Digital Curation Centre, Anne Trefethen, Director of the Oxford eResearch Centre, Professor Paul Jeffreys, Director of IT at the University of Oxford and Sally Rumsey, Bodleian Libraries.