Tag Archives: figshare

The purpose, practicalities, pitfalls and policies of managing and sharing data in the UK

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As part of the Office of Scholarly Communication Open Access Week celebrations, we are uploading a blog a day written by members of the team. Tuesday is a piece by Dr Danny Kingsley reflecting the talk she gave this morning to  the Royal Society of Chemistry, Chemical Information and Computer Applications Group conference – Measurement, Information and Innovation: Digital Disruption in the Chemical Sciences.

The data policy landscape

The policy position on data management in the UK is driven on many levels. Many institutions now have policies – an example is the Cambridge University Research Data Management Policy Framework. Increasingly publishers such as PLOS are requiring that research published in their journals is accompanied by the data underpinning the research. Some journals, such as Nature’s Scientific Data are specifically data-only journals

There has been a country-wide movement towards opening up data. Consultation on the Draft Concordat on Open Research Data released by the RCUK ended on 28 September. Cambridge coordinated a joint response to the Concordat with several other universities.

However the real driver for action this year has been funder policies – specifically, the Engineering and Physical Sciences Research Council (EPSRC) which announced it was going to (and has begun) checking compliance as of 1 May 2015.

The devil is in the detail

While the Research Councils UK have RCUK Common Principles on Data Policy stating “Publicly funded research data are a public good (…), which should be made openly available with as few restrictions as possible”, these common principles are idiosyncratic when looked at from the individual council perspective, as the graphic on the second page of this document demonstrates.

There are variations on whether a data management plan is required, where the data should be stored, the level of support offered and even whether this can be funded through the grant (in most cases it can, but not all).

Places to share data

Open (cross-disciplinary) repositories

These include commercial options such as figshare which is owned by Digital Science who also produce Symplectic Elements research management systems and are is an offshoot company to Macmillian/Springer.

Open source solutions such as Zenodo, an open dependable home for the long-tail of science, enabling researchers to share and preserve any research outputs in any size, any format and from any science, developed by CERN.

Disciplinary repositories

There are a significant number of disciplinary specific data repositories. In many ways these are the most natural place for data as disciplinary experts can curate the data. For example the Natural Environment Research Council (NERC) runs seven repositories.

The first repository ever created (in 1991) was arXiv, holding e-prints in Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics. The public functional genomics data repository is Gene Expression Omnibus . Social science data can be deposited in the UK Data Service. The Oxford Text Archive holds literary and linguistic texts for higher education.

Institutional options

Cambridge University is using its DSpace repository Apollo to store and share data. To date the largest dataset we have received is 28 GB – huge datasets need to sit externally to this repository. Not all institutions provide a data repository service. There are significant overheads associated with this activity both for the technology and the people to upload and curate the data.

Journals

Journals are increasingly requiring researchers to publish (or at least provide links to) their supporting data alongside their research articles. PLOS brought in their data sharing policy in December 2013.

There is also a growing selection of data only journals on the market, for example Nature’s Scientific Data. Others include Journal of Open Archaeology Data, Open Health Data, Journal of Open Psychology Data, Gigascience, Bodiversity Data Journal and Earth System Science Data.

Aggregating services

The Australian National Data Service has built Research Data Australia (RDA) which collates and displays information about datasets held all over the country, both open and closed. As of the 20 October, the RDA contains 115,823 datasets, of which 23,322 are open.

There appears to be little appetite yet for this sort of service in the UK, or at least for providing funds to create one.

What are we actually trying to achieve ?

Cambridge University has taken a proactive approach to the RCUK data sharing policies by inviting funders to come and discuss issues with the research community. We have written up and published these discussions as an ‘In conversation with..’ series on our Unlocking Research blog.

In addition to clarification on some aspects of the policies, one of the questions we are trying to answer is what is the actual goal of these policies? Ben Ryan the Senior Manager, Research Outcomes of the EPSRC clarified that researchers needed to share:

  • the data that underpins publications
  • the data that validates research findings
  • the data that is worth keeping

To summarise the philosophical goals of the EPSRC policy:

  • The default position is ‘data should be open’
  • Published research findings should be testable
  • Maximise the impact of publicly funded research
  • Maintain public trust in science and research
  • They are trying to create a new research culture

Researcher responses

While these might seem like lofty and even admirable goals, it does not mean that the academic response to being informed of their grant requirement for sharing data have been met with welcoming arms. Far from it in some cases.

A small selection of the responses we have received in our meetings with over 1500 researchers this year at Cambridge include:

  • What’s the minimum we can get away with?
  • This is crap
  • ‘They’ are just doing this because ‘they’ can
  • But it will take a huge effort to get the data in a useable form
  • No-one will look at it
  • What a waste of time

This has prompted us to play a game we call ‘data excuse bingo’ at some of our Research Data Management Workshops – see slide 16.

We are trying to start at the end

The problem might be that everyone is fixated on sharing data at the end of the research process.  However this is one of the lesser data management activities if data management begins at the beginning.

The second of our “In conversation…” series was with Michael Ball the Strategy and Policy Manager at the Biotechnical and Biological Sciences Research Council (BBSRC). Amongst a long discussion about what exactly constitutes ‘data’ in the biological sciences, Michael emphasised that disciplines themselves must establish ways of dealing with data. This is the beginning of an ongoing process.

He noted that researchers need to consider how to deal with data from the beginning of a research project. Researchers can ask for money to manage data in the grant application (something which is currently quite rare).

The practice of sharing data requires the data to be: Accessible, Intelligible, Assessable and Reusable. So how do we achieve that?

Basics of Research Data Management

Good data management includes very basic practices such as:

  • Writing a research data management plan at the beginning of the research process – identifying all of these issues
  • Using a file naming protocol (including version control)
  • Backing up work in several places
  • Identifying any data that might be politically, personally or commercially sensitive
  • Determining who owns what data
  • Ensuring data that is being used for research across collaborations is shared in safe, secure and legal shared facilities, bearing in mind Export Control Legislation.
  • Having good metadata protocols
  • Using a reputable and reliable storage/sharing facility that offers persistent identifiers (DOIs)

Who owns the data?

This is an interesting question. EPSRC policies state that researchers should ensure that collaborators are aware of the sharing requirement before they embark on research. Then there are questions about who within the team might own the data – with again a suggestion to come to some sort of agreement before work starts.

Are all collaborators equal ‘owners’? Or does the Principal Investigator have a 50% stake, with the remaining split amongst the PhD students making up the remainder of the team? You might want to talk to your legal advisors and/or your research office about this issue.

There is also the related issue here of developing author-contribution transparency. Do you include author contribution statements in your articles?.

Staffing issues

If Michael Ball is correct and very few researchers are asking for funds associated with managing data, it is reasonable to assume that data is being managed in an ad hoc way – with reliance on the computer savvy postdoc the project hired …

Required skillsets for managing and curating data

There is a considerable range of skill sets associated with managing data, and these have been described by the Digital Curation Centre as data creator, data scientist, data librarian, data manager.

Alma Swan and Sheridan Brown’s 2008 report to Jisc on ‘The skills, role and career structure of data scientists and curators: an assessment of current practice and future needs’ described these as:

  • Data Creator: Researchers with domain expertise who produce data. These people may have a high level of expertise in handling, manipulating and using data
  • Data Scientist: People who work where the research is carried out – or, in the case of data centre personnel, in close collaboration with the creators of the data – and may be involved in creative enquiry and analysis, enabling others to work with digital data, and developments in data base technology
  • Data Manager: Computer scientists, information technologists or information scientists and who take responsibility for computing facilities, storage, continuing access and preservation of data
  • Data Librarian: People originating from the library community, trained and specialising in the curation, preservation and archiving of data

There is a simple graphic that clearly shows how these roles relate to one another.

Certainly an increasing number of data scientist jobs are being advertised. A search for ‘Data scientist’ + ‘London’ on the job site Indeed on 18 October produced 1,405 results. So where are all of these people coming from?

Training available

The Swan and Brown study in 2008 noted that ‘People in data science roles face a big, continuing challenge in remaining properly skilled up’ and this remain the situation today, although there are now many more opportunities for training – a few are listed here:

  • The Digital Curation Centre offers data management and curation education and training.
  • MANTRA is a free online course from the Data Library staff in Information Services, University of Edinburgh. It is designed for those who manage digital data as part of a research project. It was crafted for the use of post-graduate students, early career researchers, and also information professionals. It is freely available on the web for anyone to explore on their own.
  • Data Scientist training for Librarians is a collection of notes and discussions about data work done by librarians. They ran an experimental course in August to teach “the latest tools for extracting, wrangling, storing, analysing, and visualising data”.

In addition, the professionalisation of these skills is beginning. For example, Data Science London is a community of data scientists that meets regularly to discuss data science ideas, concepts, and tools, methods and technologies used by many startups to analyse large scale data (big data), extract predictive insight, and exploit business opportunities from data products. Their website offers a list of free data science courses.

Cambridge University is one of the five founding university partners of the about to be launched Alan Turing Institute, which is intended to be the UK’s national institute for data science. The Institute will be addressing some of the issues with the data management skill gap.

Issues with sharing data

For all of the ‘feel good’ ideals about sharing data, and the processes being put in place to support this, there are some serious issues raised by researchers about the requirement to share data.

To start, there is a very real concern that the UK will become unattractive for collaborations. Why would a commercial collaborator choose a UK partner when a partner from elsewhere is not under obligation to share their data?

There have been some discussions at information sessions about the possible need to change the type of research being done to reduce the amount of data being produced because of the cost of long term storage of this data.

Indeed, there is discussion in some circles about whether applying for EPSRC funding is worth the hassle. It is a fair bet that none of these were intended outcomes of the RCUK policies.

Consequences of not sharing data

However, this does need to be a balanced strategy. There is a considerable argument that openness is related to academic integrity as it allows work to be verified and validated.

Here are examples in three disciplines where sharing data had a dramatic effect:

  • Medicine – having the data publicly available in two trials of deworming pills demonstrated that a population wide deworming program did not improve school performance.
  • Economics – A study widely cited to justify budget cutting in the US had a mistake in the calculations which was only revealed when the Excel file was released
  • Physics – It took 12.5 years to withdraw Jan Hendrik Schon’s work on ‘organic semiconductors’ because the reviewers were unable to replicate the results without access to the original data or lab books.

Conclusion

Sharing data offers great challenges to the research community, not least because it is less than clear what ‘data’ means in different disciplines. It will take some time for the research community to change its philosophy and practice. But the positives outweigh the negatives and with hope we will look back at this time as a short transition period.

Note the slides from the talk are available in Slideshare.

Published 20 October 2015
Written by Dr Danny Kingsley
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Libraries of the future – insights from a talk by Lorcan Dempsey

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There is no argument even from traditionalists that the library role is changing. But there is a great deal of confusion and sometimes fear about what that means, and what the future might look like.

On 3 June, Lorcan Demsey*  came to speak to staff at Cambridge University Library about how the role and purpose of libraries are changing. The slides from his talk are available on Slideshare.

The one sentence headline from the talk was that research libraries are moving from licensing published content to managing workflow and research outputs – which means the print collection needs to be managed down to free up resources for the new roles. The subhead is – if we don’t do this, the publishers are waiting in the wings to take over.

Modern libraries in research environments

The Library role is distilling from owned materials to facilitating access to many things. Changing focus to ‘discovery’ in the collection means there must be a loss of some of the items.

Lorcan noted that his sense is that there is still a low uptake of this concept. As someone who has been working in scholarly communications for over a decade. I agree.

The collection as a means to an end rather than an end it itself – in some ways this is obvious but in others it is a huge psychological shift. 

  • In a print world, researchers and learners organised their workflow around the library. The library had a limited interaction with the full process.
  • In a digital world the Library needs to organise itself around the workflows of research and learners. Workflows generate and consume information resources.

In libraries there is a separation of the discovery and the collection – library users are on the global level. The library will make some available and own some of those.

Change of focus

The research endeavour has moved from a focus on outcomes to begin to think about a range of activities around the process and the aftermath.

The traditional role of a library – outside of special collections and manuscripts – deals with outcomes like the books and journals. In this model students and researchers interact with the books and journals and then turn it into classically published works that come back into the library.

But we live now in an online world and the Library is interacting with the content in many different ways. There is interest in the process of research –methods, evidence and research data. There is also interest in the discussion around research through pre-prints, working papers and a variety of prepublication activity. This involves revision, derivative works and reuse. Copyright is important in these cases to let people know how things will be used.

This means that ‘collections’ from a library perspective now include the process, methods, discussions and outputs as well as books and journals.

From curation to creation

Mediated access to licensed material is becoming more streamlined, and other items becoming more available. Libraries are supporting creation, not just consumption.

Libraries need to be seen as a source for collaboration. There needs to be a partnership between the Library and the Faculty. The library is a partner in terms of the creation activity. The mediating role will continue.

Managing this transition is often done opportunistically – when people retire they are replaced with new skill sets.

The repository was seen by the Libraries initially as something in relation to artefacts but now it is seen as part of the workflow of the research lifecycle. There is less attention on what is coming in and more focus on sharing material back out.

Show me the money

There is a question around how much of this activity will be supported by the institution? And how is the resource shifting occurring in the libraries?

Lorcan said that while libraries talk about a growing interest in special collections and archives, there is no evidence from a budget perspective that this is being supported.

Publishers are trying to muscle in

Managing online identities

There is considerable interest amongst researchers in having a carefully tended online presence. This is time consuming, and would appear to be important to the researchers. This process is becoming intimately tied to publication – it is where people are announcing their publication.

Lorcan mentioned a study in Nature which was a survey of 3,000 scientists and engineers. They found 6% used Google Scholar, but more than half were using ResearchGate more regularly than LinkedIn. Not surprisingly this behaviour can be broken down by discipline. The social sciences tend to use Google Scholar, and academic.edu has low use by engineering and sciences. There are many solutions to the workflow to help researchers. Many of these will go away, but some are quite heavily used.

Thinking historically, a catalogue covers the material a library owns. The library has a discovery layer and a license. However this activity will have to shift to support creation. We have repositories, Google Scholar, ResearchGate etc. The incentive to use the repository is very low compared with these services.

A gap in the market?

Workflow is the new content – managing identity is where a lot of the focus is. Publishers are trying to position themselves as the service provider in this space.

Many libraries do not see their role as managing evolving scholarly records – the research and learning material. The curation of identity for researcher profiles is a big interest. This is often currently managed by research offices.

However this is a space into which publishers are moving. Several big publishers are now trying to be part of the full cycle for researchers.

For example Elsevier has two products – Pure is a content management system for research reporting and Mendeley is an academic social network. It is no coincidence that the word ‘solution’ is in the url thread. Similarly, Macmillian (publishers of Nature) recently bought Digital Science the company that created the equivalent products Symplectic and figshare. Digital Science was not included in the Macmillan Springer merger, possibly because they still need substantial investment. Lorcan noted that people see them as ‘plucky start-ups’ but they are owned by big publishers. There has been a big take-up of these services.

Lorcan showed a quote from Annette Thomas, CEO of Macmillian Publishers about ‘A publisher’s new job description’.

Her view is that publishers are here to make the scientific research process more effective by helping them keep up to date, find colleagues, plan experiments, and then share their results. After they have published, the process continues with gaining a reputation, obtaining funds, finding collaborators, and even finding a new job. What can we as publishers do to address some of the scientists’ pain points? 

As Lorcan observed – you can take out the word ‘publisher’ and replace with the word ‘library’.

Managing down collections

Libraries are increasingly wanting to organise their space around the student experience not around collections. Lorcan used a grid to illustrate the changing focus. The two distinctions were:

  • Whether items are in many collections or are rare or unique.
  • Whether items require stewardship. Items that are high stewardship items are looked after and resources are spent on them. Items that are low stewardship don’t get looked after in Libraries.

At one extreme is licensed materials which are high stewardship/many collections. The opposite corner is research materials which are only available in a few collections and are low stewardship.

Lorcan said he thinks in the future there will be a focus on distinctive collections. There needs to be a lot more money to do this. So licensed purchased material will be more streamlined. Management attention 15 years ago was on highly managed, licensed items, but now the focus has shifted to items of low stewardship.

Inside out library

Market materials: licensed/purchased stuff. Library as broker and telling users that these things are available in a special way.

Distinctive collections: Library is provider and want to maximise discoverability. Want other people to know about faculty expertise, and research data. Putting into own discovery layer doesn’t help there. Think about metadata and which aggregators are important. Been slow to realise that discoverability is vital.

These have very different dynamics. We want to share material held within the library with the rest of the world. The licensed stuff is external and libraries bring it in to share internally. This is inside out.

Traditionally libraries deal with published, purchased material (including special collections). However there is a shift away from acquisitions to demand. This means that libraries need to redirect their resources towards research support. One way of doing this is to manage down the print collection.

There was an explosion of publishing after the Second World War. In the same way that baby boomers are all retiring at the same time, we are now faced with the challenge of managing these collections down.

Challenges for identity

The managing down of print collections coincides with the push to repurpose space in libraries. There are many discussions with architects – managing down print means there must be refurbishment.

One of the issues emerging for libraries is: Without the books, does the campus see this as the Library? Is the space needed for the Library – could they be replaced by learning commons or the student union?

We can see the identity discussion about libraries emerging now. If we are managing down collections, what is the space for? What are the new services we offer? Lorcan mentioned media stories where librarians are being attacked by historians who see this as managerial, technocratic activity.

Lorcan described some of the shared collection activities happening in the USA.

Conclusion

We used to think of the Library as a collection. Now we need to think of the Library in terms of the user and their workflows.

We must move to more facilitated access to items, also move to the management and disclosure of curated materials. The print and digital scholarly record needs curation and co-ordination at a conscious national level.

The job is about restructuring the means but we need to make decisions about moving resources or bets on the future. Libraries must shift from an organisation where the end was known to one where we must take some risk.

Published 6 June 2015
Written by Dr Danny Kingsley
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* Lorcan coordinates strategic planning and oversees Research, Membership and Community Relations at OCLC. He has worked for library and educational organizations in Ireland, the UK and the US. His influence on national policy and library directions is widely recognized. He is on Twitter – @LorcanID

 

Data management – one size does not fit all

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As the Research Data Facilitator at the University of Cambridge, I am part of the team establishing a Research Data Management (RDM) Facility at the University. This blog is a note of my impressions from the Digital Curation Centre (DCC) meeting held in London on the 28th April 2015: Preparing Data for Deposit.

As always, the DCC meeting was extremely useful for networking. I met with people at similar roles at other institutions. And again, the breakout sessions were invaluable – they allowed us to exchange precious experience, feedback gained and lessons learnt while developing RDM services.

What could have been done better though is more appreciation for differences between universities.

Unrealistic staffing

The talk from the keynote speaker, Louise Corti, the Associate Director at the UK Data Service, was very inspirational. I loved the uplifting expression that RDM supporters are like artists evangelising researchers. It was great to hear about RDM solutions available at the UK Data Service, and the professional approach to research data, with every aspect of data curation addressed by the excellent team of 70 dedicated people, with precise workflows for data processing.

However, how realistic it is for a university to develop similar solutions locally? Which University would be able to dedicate similar amount of resources for the development of an RDM facility?

At the University of Cambridge, I am the only full-time employee dedicated to work on establishment and provision of RDM services to our researchers. There is a team of people supporting the facility but these staff are shared with other projects. I would have very much appreciated what would be the scalable solution that the UK Data Service could recommend universities to develop, knowing that resources available are nowhere near what a 70 people team could offer.

Scalability

On the other hand, we had a presentation from the University of Loughborough. The University, represented by Gary Brewerton, teamed up with Figshare and Arkivum (Mark Hahnel and Matthew Addis, respectively). The three of them explained to us the infrastructure developed to support RDM management at the University of Loughborough. The University data repository, DSpace, has been equipped with archival storage provided by Arkivum, which guarantees 100% data integrity. Additionally, researchers at the University of Loughborough can benefit from the use of Figshare, which provides them with a user-friendly research data sharing platform.

These systems seemed to offer excellent solutions to researchers, but somehow I could not help having the impression of listening to sales pitches. Are there any disadvantages of these solutions? Are there any alternatives?

Figshare charges for the file transfer (downloading of openly accessible data is actually not free for institutions). How substantial would be these charges for bigger institutions, producing huge amounts of valuable research data, frequently sought after and downloaded by others? Would institutions be able to sustain the cost of data access to their most valuable research datasets?

Risk management

The Loughborough solutions do not appear to take into account risks associated with implementation of services from third party providers at bigger, research-intense universities. At the University of Cambridge we have almost 300 EPSRC-funded research grants. In April this year alone our data repository received 40GB of research data deposits coming from EPSRC-funded projects. Producing valuable research outputs is business-critical for universities.

What would be the costs associated with the data transfer of supposedly open-access datasets if these were available via Figshare? Is there any upper limit on possible transfer charges?

What is the long-term risk of handing over university’s research data holdings to a third party service provider? Note that some UK research funders expect data to be stored long-term, and in some cases in perpetuity (10 years from the last access). What will be the conditions for research data storage offered by these external providers in 10, 20, 30 years time? How will the cost change? Will it be easy/possible to transfer all research data somewhere else?

Figshare has recently entered into a legal partnership with Macmillan (you can read more about it in a blog post from Dr Peter Murray-Rust) – how will this partnership evolve in the future?

Suggestion

It would be extremely valuable if RDM solutions proposed at DCC meetings could be discussed taking into account the size of the institution, the amount of research conducted at the University, and the size of the RDM team locally available to work on the implementation of the solution.

One size does not and will not fit all, and a better recognition of differences between organisations would greatly help developing optimal solutions for each individual institution. Additionally, it seems to me of key importance to openly talk about drawbacks of each solution for universities to efficiently mitigate future risks.

Published 14 May 2015
Written by Dr Marta Teperek
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