Tag Archives: repository

In conversation with Wellcome Trust and CRUK

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On Friday 22 January Cambridge University invited our two main charity funders to discuss their views on data management and sharing with Cambridge researchers. David Carr from the Wellcome Trust and Jamie Enoch from Cancer Research UK came to the University to talk to our researchers.

The related blog ‘Charities’ perspective on research data management and sharing‘ summarises the presentations Jamie and David gave. After this event, a group of researchers from the School of Biological Sciences and from the School of Clinical Medicine at the University of Cambridge were invited to ask questions about the Wellcome Trust data management and sharing policy and CRUK data sharing and preservation policy directly of David and Jamie.

This blog is a summary of the discussion, with questions thematically grouped. These questions will be added to the list of Frequently Asked Questions on the University’s Research Data Management Website.

In summary:

  • It is not recommended that researchers simply share a link and release the data when requested. Research data should be available, accessible and discoverable.
  • The first responsibility is to protect the study participants. The funders provide guidance documents on sharing of patient data. Ethics committees also provide advice and guidance on what data can be shared. In principle, patient data should be safeguarded, but this should not preclude sharing. There are models for managed access to data that allow personal/sensitive data to be shared for legitimate purposes in a safe and secure manner.
  • The funders do not want to prevent new collaborations. When sharing data they recommend data generators provide a statement in the description of the data that they are willing to collaborate
  • It is recognised that it is often appropriate for researchers to have a defined period of exclusive access to the data they generate, but this should be determined by disciplinary norms. Any exemptions or delays have to be justified on a case by case basis, ideally at the outset of the project.
  • The funders expect research data that supports publications to be made accessible and publications should have a clear statement explaining how to access the underlying research data.
  • However researchers need to decide what is useful to be shared considering the effort of preparing the data for deposit and of sharing the data. If nobody is going to use the data, sharing is not a good use of researcher’s time.
  • Discipline-specific data repositories, where these exist, are recommended preferentially over general purpose or institutional repositories
  • Biosharing is an excellent resource with references to discipline-specific metadata schemas.
  • Staff members whose role is to manage data is an eligible cost on a grant
  • There are no funds for sharing data from old projects, although there are exceptions on a case by case basis
  • The funders are considering monitoring data management plans but their current primary goal is to encourage people to think about data management and sharing from the very start of the project

Access to research data

Q: Are funders benefiting from the expertise of organisations such as UK Data Service when providing advice on data access? UK Data Service has been managing controlled access to research data for a long time and it would be advantageous to benefit from their expertise.

A: Yes, we are in discussion with the UK Data Service. We are also working with the UK Data Service to consider whether it might be appropriate for hosting data from other disciplines beyond social science. We also believe there is significant scope to share lessons and best practices for data sharing between the social and biomedical sciences.

Q: Could we just share research data only when asked for it?

A: This is not a recommended solution: research data should be available, accessible and discoverable. Data access controls and criteria for what needs to happen for the access to be granted have to be made clear in metadata description.

Q: I have patient data which has to be stored in a secure space. I always say in my data management plan that I cannot share my data. I would like to get ethical guidance which will explain to me how to share these data. It is very easy to say that data cannot be shared. I would like to share my data, but I would like to do it properly. With patient data it is extremely difficult, especially with genomics data, where there is a risk that patients can be identified.

A: Sharing of clinical data is not easy. Both Wellcome Trust and Cancer Research UK are helping to drive a great deal of work which is considering access and governance models through which sensitive patient data can be made available for research in a safe, secure and trusted manner. They provide guidance documents on sharing of patient data. Safety of patients and patients’ data is important. Ethics committees also provide advice and guidance on what data can be shared.

Q: What about sharing of physical materials? I have received a request to share a culture derived from a patient material, but the Ethics Committee did not approve sharing of this material. What shall I do?

A (Peter Hedges, Head of Research Office): If your ethical approval says that you cannot share that material, you cannot share it. Your first responsibility is to protect your study participants.

Q: If I share my data via a repository and people can simply download my data, I can no longer collaborate with them to work on the data and I have lost the possibility of getting credit for my data.

A: Nobody wants to prevent new collaborations from happening. A solution might be to add a statement that you are willing to collaborate in the description of your data. Your data requestor might be interested in collaborating, simply because you know your data the best. Funders also expect that the data re-used by others is appropriately acknowledged/cited, and they want to ensure that due credit results from the secondary use of data.

Quality control of research data

Q: If researchers start sharing unpublished research data via data repositories there is a risk that these data will not be of good quality as they will not be peer-reviewed.

A: Authors of unpublished data can simply state in the data description that the item was not peer-reviewed. If applicable, funders also encourage reciprocal links between publications and supporting research data.

What data needs to be shared and when?

Q: If researchers start to share everything there will be a lot of useless data available in data repositories. How to prevent a flood of useless data on the internet?

A: We would like researchers to decide what data is useful to be shared. If nobody is likely to use the data, sharing is not a good use of researcher’s time. Repositories also need to make decisions over what is worth keeping over time.

Comment (Peter Hedges, Head of Research Office): The Research Council UK focuses on research data supporting publications and this is what we recommend to researchers: share research data which underpins publications.

Q: Are we expected to share large datasets resulting from bigger projects (databases, long-term datasets) or data supporting individual publications?

A: We expect research data that supports individual publications to be made available with a hyperlink to the data. We also want researchers to consider and plan more broadly how they can make data assets of value resulting from our funded research available to others in a timely and appropriate manner.

Q: What about images? Is it useful to share them? It involves a lot of time to organise images. Besides, a single confocal picture with multiple layers is 1GB. In theory it is possible to share all raw data and all raw images, but who would want to look at them? 10 figures of 10 images is already 100 GB of data. Where would I store all these images, who is going to use these data and how am I going to pay for this?

A: The effort of preparing the data for deposit and of sharing the data should be proportionate to the potential benefits of data sharing. Researchers need to decide what is useful to be shared, following disciplinary best practices and norms (recognising that disciplines are in very different places in terms of defining these).

Q: Is there a set amount of time for exclusive use of research data?

A: Researchers should adhere to disciplinary norms. For example, in genomics research data is frequently shared before publication (sometimes under a publication moratorium which protects the data generator’s right to first publication). Any exemptions or delays have to be justified on a case by case basis.

Comment (Peter Hedges, Head of Research Office): Research is competitive. Sometimes it might be useful for researchers to know who wants to get the access to data and what do they need them for.

Cost of data sharing

Q: Can I ask in my grant for a staff member to help me with data management?

A: Yes, this is an eligible cost on grant applications: you can request a salary to support a research data manager for your research project, as long as it is justified.

Q: According to CRUK policy, costs for data sharing can be budgeted in grant applications only from August 2015. What about research data from older projects, when these costs were not eligible in grant applications? Is there any transition fund available to pay for this?

A: Unfortunately, there are no additional funds to pay for these costs. Researchers who have older datasets that might be of significant value to the community should contact CRUK – all requests for support will be considered on a case by case basis.

Q: Wellcome Trust encourages data sharing and data re-use, but does not allow for costs of long-term data preservation to be budgeted in grant applications. This does not make sense to me.

A: We are still reviewing our policy on costs of data management and sharing and we might be revisiting this issue – however, it is problematic for us to consider estimated costs for preservation that extend before the life-time of the grant. Our understanding is that costs of long-term data preservation are often less significant than costs of initial data ingestion by the repository (and we will cover ingestion costs).

Q: Who is then going to pay for the long-term data storage?

A: Wellcome Trust funds some discipline-specific repositories, but this is done jointly with other funders. We support bigger undertakings and we are also working with partners to develop platforms for data sharing and discoverability in some priority areas (notably clinical trials). Cancer Research UK pays for some long-term storage options, if these are justified for particular needs of the project. These decisions are made on a case by case basis, depending on how the costs are justified and whether these are directly related to the scientific value of the project.

Metadata standards

Q: At the moment there are many general purpose and institutional repositories, which are not well structured. To support efficient re-use of data it is important to use structured data repositories and adhere to metadata standards. What are funders’ opinions about this?

A: Wherever possible, discipline-specific data repositories should be used preferentially over general purpose or institutional repositories. Adherence to discipline-specific metadata standards is also encouraged. It has to be acknowledged that development of well-structured data repositories is very resource-intensive and not all disciplines have good quality repositories to support them. For example, it took over 30 years to adapt unified metadata standards at Cambridge Crystallographic Data Centre. The time need to properly solve problems should never be underestimated.

Q: Are funders planning to provide researchers with a list of recommended schemas for metadata?

A: Biosharing is an excellent resource with references to discipline-specific metadata schemas. It is a useful suggestion to include a reference to Biosharing on our website.

Policy implementation

Q: Are you planning to monitor researchers’ adherence to data management plans? For example, the BBSRC does not have the manpower to check all data management plans manually, but they are planning to create a system to check if data has been uploaded automatically.

A: We are considering this. At the moment we require data management plans with the primary goal to encourage people to think about data management and sharing from the very start of the project.

Published 5 February 2016
Written by Dr Marta Teperek, verified by David Carr and Jamie Enoch
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Could the HEFCE policy be a Trojan Horse for gold OA?

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The HEFCE Policy for open access in the post-2014 Research Excellence Framework kicks in 9 weeks from now.

The policy states that, to be eligible for submission to the post-2014 REF, authors’ final peer-reviewed manuscripts of journal articles and conference proceedings with an ISSN must have been deposited in an institutional or subject repository on acceptance for publication. Deposited material should be discoverable, and free to read and download, for anyone with an internet connection.

The goal of the policy is to ensure that publicly funded (by HEFCE) research is publicly available. The means HEFCE have chosen to favour is the green route – by putting the AAM into a repository. This does not involve any payment to the publishers. The timing of the policy – at acceptance – is to give us the best chance of obtaining the author’s accepted manuscript (AAM) before it is deleted, forgotten or lost by the author.

Universities across the UK have been preparing. Cambridge has had the ‘Accepted for publication? Send us your manuscript‘ campaign running since May 2014 with a very simple and well liked interface allowing researchers to submit their work. The Open Access team then deposits the item, checks for funding and the publisher policies and then organises payment for open access publication if required.

To give an idea of the numbers we are dealing with at Cambridge, during 2015 the Open Access team deposited 2553 articles into our repository Apollo.

Compliance levels

We have been reporting to Wellcome Trust and the RCUK over the past few years to indicate compliance levels with their policies. However the ‘compliance level’ for the HEFCE policy is a slippery concept. For a start, the policy has not yet come into force. Another complicating factor is the long term nature of the ‘reporting’. We will not truly know how compliant we have been until the time comes to submit to REF – whenever that will be (currently it seems 2021).

At Cambridge have been working on the assumption that because we do not know which outputs will be the ones that we will claim we should collect all eligible articles. However, the number of deposited articles Open Access team received over the past year represents approximately 30% of the full eligible output of the University. This might seem concerning in some ways, but it must be remembered that each researcher in the University will only be reporting four research outputs for the REF.

There are some articles that are obvious contenders for REF. By concentrating on researchers who are publishing in very high impact journals we have been trying to catch those articles we are extremely likely to claim.

During the course of 2015 we discovered 93 papers published in Nature, Science, Cell, The Lancet and PNAS. 33% of these papers were already HEFCE compliant. Of the remaining non-compliant papers we contacted 47 authors, made them aware of the HEFCE open access policy, and invited them to submit their accepted manuscript to the Open Access Service. Less than 40% of those authors who were contacted responded with their accepted manuscript. Therefore, even after direct intervention only 49% papers were HEFCE compliant, which means that still more than half of all eligible papers published in Nature, Science, Cell, The Lancet and PNAS during this period would not have been HEFCE compliant had the policy been in place.

The lack of engagement by members of the academic community with this process is a serious concern – and potentially due to four reasons:

  • Lack of awareness of the policy
  • Putting it off until the policy is in place
  • Deliberately choosing not to submit a work because it is not considered important enough or they do not consider their contribution to be significant enough
  • Some form of conscientious objection to the policy

We should note that the third reason is a matter of some concern to the University as it is not the researcher who decides which articles are put forward for REF. In addition, the University is interested in having a high overall level of compliance for REF as it considers making the research output of the institution available to be important.

Temporary reprieve

Cambridge is no island when it comes to facing significant challenges in capturing all outputs in preparation for HEFCE’s policy. While the highly devolved nature of the institution and the sheer volume of publications may be a problem unique to Cambridge and Oxford, other institutions are still developing the technology they intend to use or are facing staffing issues.

In a concession to serious concern across the sector about the ability to meet the deadline, on 24 July 2015 HEFCE announced that there was a temporary modification to the policy. They now allow research outputs to be made open access up to three months after publication until at least April 2017 (and until such time that the systems to support deposit at acceptance are in place).

This means for the first year of the policy we have a small window after publication to locate articles, determine if they are in our repositories, and if not chase the authors for the Author’s Accepted Manuscript.

The trick is knowing that an article has been published. At Cambridge our ‘best bet’ is to use Symplectic which scrapes various aggregating sources such as Scopus. However Symplectic is hindered by the efficiency of its sources. There is no guarantee that a given article will appear in Symplectic within three months of publication. And even if it is, we have already discussed the low engagement by the research community to approaches from the Open Access team for AAMs.

Subject based repositories

So far this blog has been talking about using institutional repositories for compliance. But the policy specifically states: “The output must have been deposited in an institutional repository, a repository service shared between multiple institutions, or a subject repository“.

The oldest, most established subject repository is arXiv.org and it makes sense for us to consider using arXiv as part of Cambridge’s compliance strategy. After all, some areas of high energy physics, most of computer science and much of mathematics use arXiv as a means to share their research papers. In 2014, the number of articles that were deposited into arXiv.org and subsequently picked up in Symplectic and approved by researchers were 582 – approximately 6.5% of Cambridge’s total eligible articles.

If we are able to claim these articles for HEFCE compliance without any behaviour change requirement from our academic staff then this is an ideal situation. But how do we actually do this? There is a footnote to the HEFCE statement above which says that: “Individuals depositing their outputs in a subject repository are advised to ensure that their chosen repository meets the requirements set out in this policy.” And this is the crunch point. arXiv does not currently identify which version of the work has been deposited, nor does it record the acceptance date of the work. Because of this we are currently not able to simply use the work being uploaded to arXiv.

There is work underway to look at this possibility and what would be required to allow us to use the subject based repositories as a means for compliance. HEFCE themselves have identified under ‘Further areas of work‘ that  “measures to support compliance in subject repositories” is an area of uncertainty and they will work with the community to address this.

Alternative approach?

It is possibly a good moment to take a step back from the minutiae of the means and the timing of the HEFCE policy and focus on the goal that publicly funded research is publicly available. We are in a complex policy environment. HEFCE affects all researchers but many researchers are also funded through COAF or the RCUK with their respective (gold leaning) Open Access policies.

Of the HEFCE eligible articles submitted to to Open Access team in 2015, after working through all the different funder requirements, there was a split of 44% gold Open Access and 56% green Open Access. Of the gold payments the split is approximately 74% for hybrid journals and 26% for fully open access journals.  That said, the three journals with which we have published the most – PLOS ONE, Nature Communications and Scientific Reports – are fully Open Access journals with APCs of $1495, $5200 and $1495 respectively.

A highly relevant question is – outside of the efforts by our Open Access compliance teams, how much Cambridge research is being made open access anyway?

Open access articles

The Web of Science (WoS) allows a filter on ‘Open Access’. It does not appear to list articles that are made open access on a hybrid basis, only picking up fully open access journals. While these are not definitive numbers, it does give us some idea of the scale we are looking at. In 2014 WoS gives us a figure of 981 articles published as open access by a University of Cambridge author in a fully open access journal.

The Springer Compact to which many institutions (including Cambridge) have signed up means that now all articles published by that research community will be made open access. In 2014, the Open Access Service had paid for 21 articles to be made open access. In the same period across the institution we had published 695 articles with Springer. (Note that in 2015 we paid 51 Springer  APCs). This means that for the cost of the Springer subscription and our APC payments for the previous year we will have a good proportion of Cambridge articles published as open access articles.

These two sets of numbers only allow for articles published either in fully open access journals or with Springer. It does not account for the articles where the University (or a Department or individual) pays an APC to make an article available in a hybrid (non Springer) journal. The upshot is – a significant proportion of Cambridge research is published open access.

Skip the AAM on acceptance part?

So what does this published open access research mean for compliance with the HEFCE policy? The updated HEFCE policy has addressed this:

“… we have decided to introduce an exception to the deposit requirements for outputs published via the gold route. This may be used in cases where depositing the output on acceptance is not felt to deliver significant additional benefit. We would strongly encourage these outputs to be deposited as soon as possible after publication, ideally via automated arrangements, but this will not be a requirement of the policy.”

This makes sense from an administrative perspective if the article appears in a journal where there is an embargo period on making the AAM available, forcing the University to pay an APC to make the work Open Access to meet RCUK requirements. It would avoid the palaver of:

  • obtaining the AAM from the author
  • depositing it into the repository
  • having to check to see when the article has been published
  • updating the details and
  • either set the embargo on the AAM or change the attachment in the record to the Open Access final published version

However journals where there is an embargo period on making the AAM available forcing an APC payment is in fact almost a definition of hybrid journals. We know there are issues with hybrid – of the extra expense, of double dipping, of the higher APC charges for hybrid over fully Open Access journals. Putting these aside, what this HEFCE policy change means is that publishers have effectively shifted the HEFCE policy away from a green open access policy to a gold one for a significant proportion of UK research. This is a deliberate tactic, along with the unsubstantiated campaign that green Open Access poses a major threat to scholarly publishing and therefore embargoes should be even longer.

We are already facing the problem that hybrid journals are forcing the move towards green open access being ‘code’ for a 12 month delay. This is the beginning of a very slippery slope. We have been outplayed. It really is time for the RCUK and Wellcome Trust to stop paying for hybrid Open Access.

But I digress.

The cons

The message is confusing enough – three sets of policies and three different requirements in terms of the timing and the means to make work compliant and available. We are trying to make it as simple as possible for researchers – with limited success.

The move to widespread Open Access in the UK is a huge shift for the research community and those that support them. It would be very difficult to debate the ‘against’ argument for the statement that publicly funded research should be publicly available but the devil is very much in the detail.

It would be an incredible shame if the HEFCE policy is hijacked into a partial gold OA policy, but as administrators we are drowning in compliance. There needs to be a broad discussion across the funders to try and address the conflicting compliance requirements and the potentially negative effect these policies are having on the future of open scholarly publishing. 

We welcome the opportunity to discuss these issues with HEFCE, Wellcome Trust and the RCUK. There’s plenty to talk about.

Published 25 January 2016
Written by Dr Danny Kingsley
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Research Support Ambassadors – a progress update

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On Thursday 19th November the participants of the Research Support Ambassadors programme presented their work to date. This blog from Yvonne Creba, a member of the Research Data Facility team in the Office of Scholarly Communication, summarises these presentations of their progress so far.

A good start

Attending the Research Support Ambassadors programme presentation I can only say how impressed I was with the amount of time and effort contributed by the participants of each group. This is even more notable considering that the following was achieved outside of their normal working hours. Each of the groups produced an informative and interesting session on each of the topics.

What is the Ambassadors programme? It’s an opportunity for interested library staff to receive specialised training, to allow them to become the local ‘go to’ person on some scholarly communication issues. The programme is intended to develop a team of Ambassadors who feel confident and able to assist researchers with queries about publishing processes, data management, open access/open data policies and research sharing options, to name but a few.

The Ambassadors programme aims to provide ‘what the researchers want, where & when they want it’.  To start, the Ambassadors have embarked on development of training and information materials on the following four topics: Research Lifecycle, Research Support Services, Managing your Online Presence and Open Access to theses. Below are some of the highlights from their presentations.

Open Access to theses

The Ambassadors team assigned to this project – Matthais Ammon, Phillipa Grimstone, Charlotte Hoare, and Stephanie Palek – aimed to develop guidance materials on how to make PhD theses Open Access.

There is a need for a one-stop webpage for PhD students to answer basic questions about making their theses Open Access and the need for thesis submission to the institutional repository (now called Apollo) to be clarified in terms of Open Access.

The team  have already developed an impressive amount of resources and collated information about Open Access to theses and the advantages for PhD students, challenges with Open Access to theses and (traditional) publishing, copyright concerns and patenting & sensitive data. They referred to some of the material they have found in their research such as ‘Benefits of making theses available online’.

The team is now trying to answer how theses fit into the Open Access research landscape, the potential impact of making theses available online, fulfilment of funder requirements.

Managing your Online Presence

This team, consisting of Andrew Alexander, Céline Carty, Kasia Drabek, Agnieszka Drabek-Prime, Agnieszka Kurzeja and Brendan King, initially discussed and brainstormed this subject, as it is a large area and they wanted to define the scope of support to be offered.  The team’s strategy was focused on creating a potential outline for a session that the Ambassadors could run.

The group presented a demonstration on the creation of an ORCiD ID. ORCiD stands for “Open Researcher & Contributor ID” and it is a free, unique, individual, global, permanent identifier ideal for researchers and scholars to help them keep track of their research outputs. The group proposed some ideas on how to attractively present ORCiD to researchers.

The group thought that those who attend the session will be asked to bring along their laptops, so that after a short demonstration on how to create an ORCiD each participant will actually create their own. This will provide a tangible output of the session.

Research Support Services across the University

The idea for this topic was to provide clear signposts to the range of help on offer, rather than reinventing the wheel by creating something new. The group working on this topic are Colin Clarkson, Lindsay Jones, Mary Kattuman and Claire Sewell. There is a great deal of support available for researchers, both within the University and outside but there’s no one place where everything is listed in an accessible format.

The research doughnut available on the Office of Scholarly Communications (OSC) website has a nice, intuitive graphical display, hence the idea to use this format to present the services of the research lifecycle. The group hopes to make keywords within the cycle into clickable links, which will thus allow users to find related information and resources.

One of the sources that were highlighted in the directory was the LibrarySearch. Rather than just including a link to the static LibrarySearch interface, the group thought it would be a good idea to create a predefined search on various stages of the research process. That way the researcher can just click on a link and go straight to the required search results.

The group suggested promotional activities including a pop-up presentation of a maximum of ten minutes which could be included at the start or finish of other taught sessions. Something that will briefly introduce the concept of the site and showcase what it contains. This could be delivered by any Research Ambassador and would be a ‘presentation-in-a-box’ that people could just pick up and deliver.

One of the first things the group intends to do is to improve the general look and feel of the site and they intend to do some user testing with researchers to see how they use the site and get their feedback about the content.

Research Lifecycle

This is intended to be a web resource using the Research Lifecycle with links out to information about each of the points in the cycle – presented by Clemens Gresser, Jo Milton, Veronica Phillips, Meg Westbury.

This team reviewed the Research Lifecycle from the perspective of a researcher. They have looked at existing websites to see what information is already available and reviewed the graphical displays used by different universities – to look for content which is accessible in a user-friendly manner.

Ideas provided by the group on reaching the required audience were to plug into orientation sessions, advertisements by faculty librarians and plugging into sessions on managing an online presence.

The group also suggested that having a glossary of various terms related to the Research Lifecycle would be useful. The group is still reviewing what type of information to put up for the cycle and which format would be the most fit for purpose to best suit researchers in Cambridge.

Published 14 December 2015
Written by Yvonne Creba and Dr Danny Kingsley
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