Library Carpentry Bristol

Bristol Research Data Service recently hosted a Library Carpentry workshop in collaboration with colleagues at the University of the West of England and the University of Bath – read on to find out what it was about and what’s happening next.

What is Library Carpentry?

Library Carpentry is a set of software skills lessons created by librarians, for librarians, covering a variety of subjects including Git, SQL, Python, and using the Unix command line. The course materials are developed and maintained by volunteers, and are intended to be taught by one or more instructors (also volunteers). Each lesson is also suitable for self-study. All the course materials are freely available online under a permissive use licence (CC-BY) and can be reused and remixed if needed.

Library Carpentry is an offshoot of Software Carpentry and Data Carpentry (the latter are aimed at academic researchers) and follows the same basic lesson structure – short introductions to key concepts followed by examples to work through to solidify learning. The tools and software packages taught are typically open source to maximise opportunity of use.

Why Bristol?

Naked self-interest! Bristol Research Data Service staff were keen to learn more about data manipulation techniques, and an informal poll of the GW4 Alliance Data Services Working Group showed that there was interest in other local institutions as well. We ended up advertising the event to all GW4 and AULIC institutions.

Event specifics

We asked potential attendees which modules they would most be interested in, and on that basis selected the Introduction to data and OpenRefine lessons. Library Carpentry has a very active Gitter group, so after submitting a plea there and contacting the organisers of past workshops (thank you to Tabitha Witherick!) we had two instructors volunteer: Dave Rowe (introduction to data) and Owen Stephens (OpenRefine).

We also needed helpers: people to assist on the day with general troubleshooting (for example, network connection issues). We had volunteers from both library staff and IT Services across Bristol, Bath and UWE. It’s safe to say that the workshop would not have run anywhere near as effectively as it did without them, so thank you very much to all the helpers – and of course, our instructors!

Over seven hours we covered the two chosen modules, with time for questions, general discussion and working through examples using library-related data.

Outcomes and follow-up

Feedback from attendees has so far been excellent, with several people indicating that they’ll be using OpenRefine for specific tasks the near future, and even teaching colleagues how to use it. At Bristol we had several requests for a second workshop from people unable to attend the first one; whilst another formal workshop might not be possible, we’re looking into a ‘flipped classroom’ or collaborative learning approach of short 1-2 hour sessions to pass our learning on to other colleagues and keep our skills fresh.

All in all, it was a very useful day, and we’d highly recommend attending or hosting a Library Carpentry workshop if you have a chance.

Unlocking Open Access – Kopernio

Kopernio is an extension for your internet browser that quickly tells you if you have access to a version of the journal article that you are looking at. It detects when you are looking at an article’s page and, if you have access through either the library’s subscriptions or through an Open Access version, it will provide a link to the document.

The extension also keeps a record of articles you downloaded so you can find them again easily and can export a list of references to a .bib file for use with BibTeX.

The video gives a good indication of how the extension works. Why not try it out next time you’re looking for journal articles?

You can find Kopernio at https://kopernio.com/

The extension will work in Chrome or Firefox.

Edit: This extension was previously known as Canary Haz. We have updated the information here to reflect the new name and website.

Unlocking Open Access – Open Access DOIs

You’ve seen DOI numbers before. But did you know that you can use them to link to Open Access versions of articles?

DOI stands for Digital Object Identifier. They are unique identifying numbers for online publications, such as electronic journal articles. A DOI will look something like this: 10.1093/mind/fzr010

You can use a DOI to find a paper by pasting the DOI into the following format: https://doi.org/XXXXXXX.

Using the DOI from above, we’d get https://doi.org/10.1093/mind/fzr010

But, the above journal article is on a publisher’s website which hides the full text behind a paywall. You may have access thanks to the subscriptions provided by library services. But if not, you can try using Open Access DOIs to find an open access version.

The format for OADOIs is: https://oadoi.org/XXXXXXX

So with our example we would get: https://oadoi.org/10.1093/mind/fzr010

This looks for any Open Access versions and, if it finds any, it links you to one of them, rather than the publisher’s site.

This is a good trick for finding an Open Access version of an article you already know. It can also be a good way to link your readers to an open version of your work, ensuring they can read it.

Unlocking Open Access – Unpaywall

We talk a lot about uploading your articles to Pure so other researchers can benefit from Open Access. But we rarely talk about how you can use Open Access to benefit your own research. In this series of blog posts, we’ll show you some simple ways to find Open Access articles. First up: Unpaywall.

Unpaywall

The open padlock icon on the right hand side of the page shows that an open access version is available. Clicking the icon will take you to the article.

You’re searching for useful papers for your research. But the library can’t afford a subscription to all the journals you need. Papers hidden behind paywalls are a constant frustration. You could ask the library to get copies for you, but you’re on a tight schedule. You’d rather get that paper now.

Unpaywall is the solution. This browser extension adds an icon to your screen that lets you know if an Open Access version of the paper you’re trying to view is available. Click that and you’ll be reading the full text in seconds.

You can add the extension to Google Chrome or Firefox, even on university computers. Once you do, it’s always on and checking to see if it can provide a link to an Open Access version. If so, it’ll add an unobtrusive open padlock icon to the right of the screen, which will take you to the full text.

This is the easiest way we’ve seen to add Open Access to your research strategy. You can add Unpaywall to your browser here: http://unpaywall.org/

Twelve days of data

We’re all in the festive spirit here at the Research Data Service, and so Data Claus (pictured below) set us elves the challenge of finding data relating to the Twelve days of Christmas.

There were lively debates about what could be justified as the right data for each day, and lots of imaginative searching. Admittedly, some of the data is a little left-field (leaping Lords were an issue) but, we managed it.

If you want to know about the gold content in rings, would like to listen to songbirds or are interested in breastfeeding rates in the UK eight weeks post-partum, follow us on Twitter and enjoy our #12daysofdata.

christmas-1821425_1920

Thesis data in Russell Group universities

Guest blog post from the University of Bristol Research Data Service (data.bris.ac.uk), describing a recent investigation into retention of thesis data in Russell Group universities.

Thesis data at the University of Bristol

The University of Bristol research data repository, data.bris, has been running since 2014, and has been core funded since 2015. Use of the repository is becoming well-integrated into the research cycle, but whilst we accept deposits from postgraduate researchers (PGRs) as well as academics, the vast majority of these are data underpinning journal articles. Increasing the intake of data relating to other types of publications is an obvious next step.

Currently, Bristol PGRs may only deposit a hardbound copy of their thesis with the University Library; supporting data may be attached in physical storage media, but there is no requirement to make this available (in any format) as part of the final deposit process. Similarly, the University’s Research Data Management and Open Data Policy applies to PGRs and research staff, but doesn’t specifically address retention of thesis data. An investigation into how electronic final deposit of theses may be managed is underway, and we wanted to both support the wider investigation and increase use of the repository by extending the data.bris remit to data underpinning PhD theses.

The question

We wanted to understand how peer institutions across the UK handled thesis data, in order to see whether we could adopt an existing policy and/or infrastructure model. I was tasked with finding out whether relevant institutions had policies on thesis data retention, and if so, how this was managed and enforced. For brevity, I focussed my query on Russell Group universities.

Existing information

Some work had already been done in this area – the Unlocking Thesis Data (UTD) project [1] phase 1 survey included a question on depositing thesis data:
Q4. “If supplementary data files relating to the thesis are also deposited, where are these held?”
The survey results included responses from thirteen Russell Group universities [2], including Bristol, which have been summarised in the infographic [Figure 1]. Most respondents indicated that thesis data could be deposited alongside the thesis itself, with some institutions having multiple storage locations both linked and unlinked to the thesis record. At the time of the survey, no Bristol PGRs had attempted to deposit thesis data; we now have a number of PGR data deposits in the repository but as noted above, these are linked to journal articles rather than theses. Whilst UTD was a very useful starting point, it focussed largely on the thesis as an information object, rather that the data underpinning it. More information was needed.

Infographic summarising thesis data retention in Russell Group universities, 2015-2016 — Figure 1: Thesis data in Russell Group universities, 2015-2016

New information

Twenty of twenty-three other Russell Group (RG) universities responded to an informal email enquiry on their thesis data deposit policies. Their responses are summarised in the infographic [Figure 1] and are discussed below. Anonymised aggregated results are shown in [Figure 2].

Table containing 2016 responses to enquiry on retention of thesis data in Russell Group universities — Figure 2: Thesis data retention in Russell Group universities – 2016 responses

Of the eleven universities with an explicit or implicit policy on thesis data, five had optional deposit of thesis data, and six mandated deposit (thesis data ‘should’, ‘must’ or ‘is expected to’ be retained in a suitable repository for a minimum time). However, the majority of universities with a mandatory retention policy reported that the policies were unenforced and compliance was very low, and/or that there was no infrastructure for retention in an institutional repository. Seven universities had policies on management of thesis data, either as an explicit part of their general RDM policy, their good research practice policy, or a separate thesis submission policy. Four universities indicated that their general research data policies were intended to cover thesis data although this was not explicitly mentioned in the policy text. Nine had no policy on thesis data.

Conclusion

There is little uniformity across RG institutions in their approach to thesis data retention. In particular, there is a discordance between policy and the infrastructure required to support it. When both exist, only a minority of institutions report that the policy is enforced, meaning that in this instance there isn’t a great deal of sector knowledge to draw upon! However, many institutions reported that they were, like Bristol, actively considering the topic, so it seems likely that this situation will change over the next year or two.

Next steps

As noted previously, we are currently investigating ways to facilitate electronic deposit of theses at Bristol. Alongside this, we’re also looking to pilot a process for depositing thesis data and are planning to assess requirements for this based on the input of departments participating in the trial. Both projects are in their infancy at the moment, but I hope to provide further updates as they progress.

Acknowledgements

With thanks to colleagues at responding institutions and the Unlocking Thesis Data project for supporting information.

References

[1] Grace, Stephen and Whitton, Michael and Gould, Sara and Kotarski, Rachael: Unlocking Thesis Data phase one. DOI: 10.15123/PROJECT.15

[2] Cardiff University, Durham University, King’s College London, London School of Economics and Political Science, University of Birmingham, University of Bristol, University of Cambridge, University of Edinburgh, University of Liverpool, Newcastle University, University of Oxford, University of Southampton, University of Glasgow

Victor Frankenstein’s Data Management Plan – a Halloween special

Guest blog post from the University of Bristol Research Data Service (data.bris.ac.uk), featuring extracts from Mary Shelley’s Frankenstein.

What may be the first ever Data Management Plan has been discovered by archivists at the University of Ingolstadt.

The fascinating document describes the applicant’s intention to make exciting advances in the fields of biochemistry and human physiology. Archivist Lizzie Lavenza told us: “We don’t know whether or not Victor successfully completed his project but we’re grateful that he’s left us with such a unique and invaluable historical document.”

Click for larger image

Behind the scenes in the Open Access Team

Today’s blog post comes from Tim Riley, Open Access Senior Supervisor at the University of Bristol

open-access-team-infographic

Like many institutions up and down the UK, Bristol has an Open Access Team. We’re a small team of staff based within Library Services, but you’re unlikely to see us out and about in the campus libraries: we work ‘behind the scenes’, supporting authors to make their research outputs (journal articles, conference papers, books chapters, and more) open access.

Our work not only helps authors to make their research available to a much wider global audience but also enables them to meet HEFCE and other funder requirements on open access.

We support two main processes:

‘Green’ open access – where authors archive a version of their paper in Pure, our institutional repository.
‘Gold’ open access – where articles are made open access in journals themselves, usually on payment of a fee to the publisher, known as an article processing charge (APC).

See the infographic for some key facts and figures about the team and our work in these two areas.

Validation, validation, validation – supporting green open access

A large part of the work we do consists of validating records for research outputs that authors have uploaded to Pure. Validation is essentially a checking process where we make sure that the information in the records is accurate and, just as importantly, that the documents we’re making available to the public via the repository are the correct version and do not infringe any copyright restrictions. Most publishers place restrictions on the version of a research output that can be made available via a repository, and they usually specify an embargo period during which we’re not allowed to make the deposited document public too.

The validation process can be complex and time-consuming but always needs to be done accurately. Having a team of specialist staff to do this removes some of the headache for authors and makes it easier for the University to stay the right side of the copyright lawyers!

As well as navigating the copyright requirements stipulated by publishers, we also help authors to meet the requirements of major funders such as HEFCE, RCUK and the COAF partner medical charities. By timely checking of the versions of documents which authors upload, and making sure documents remain embargoed for only as long as is absolutely necessary, we can help ensure that authors are meeting their REF and funder requirements within the restrictions set by their publishers.

Going for gold – payments for gold open access

The second main activity our team supports is ‘gold’ open access. Some major research funders, namely RCUK and the medical charities in COAF, have awarded the university funds in the form of block grants which can be spent on open access publication charges in eligible journals. At its simplest, eligible authors request funding via our team, and we pay the publisher on the author’s behalf using the appropriate block grant money. This sounds straightforward enough, but in practice this process can become rather Byzantine as there may be many additional layers of complexity.

Before any payment can be made, we check and advise authors whether their papers are actually eligible for funding. We also have to check that the journals which authors wish to publish in meet the open access criteria for their funders. We report back to our funders on a regular basis and we need to show that we’re spending their money appropriately on papers which meet all their conditions.

When it comes to payment, we have entered into deals with a number of publishers which give APC discounts – but only to certain authors, with certain funders and in certain journals. Members of our team will run through the various permutations and select the most cost-effective payment method permissible for each paper. And although the vast majority of payments are straightforward, we spend a fair bit of time unravelling things when the payment and publication process hasn’t gone quite as smoothly as was planned for one reason or another.

Even after payment has been made, our work is not over. In a significant number of cases, articles are published under incorrect reuse licences or without the correct funder acknowledgements. There can also be issues around the mandatory deposit of papers with medical funding in the medical subject database Europe PubMed Central. We check every article which we have paid for once it has been published, and chase errant publishers where we spot any of these publication problems. This is another key part of keeping our funders happy and showing them that they’re getting value for money for the block grants they award to Bristol.

Request a copy – connecting authors and external researchers

We also mediate a ‘request a copy’ service for papers which are held in our repository but are not yet publicly available. This service enables us to put external requesters who are interested in these papers in contact with the Bristol authors. These requesters have included people working for government agencies, policy makers, charities and NGOs – people who don’t have subscription access to the original published articles but who still need access to Bristol research for their own work and research.

Collaboration with colleagues in the institution and beyond

As might be expected, the UK open access community is very open and collaborative. As a team, we not only work closely with other teams in the University, such as the Research Enterprise Development (RED) team, but we also engage with colleagues at other institutions in our region and more broadly across the country via discussion lists, social media and various meetings, events and conferences. In such a fast-changing field, it really pays to keep up to speed with the latest developments and tap into the collective wisdom of colleagues across the country for the vexing and thorny issues of the day.

Working together, we have negotiated improvements for future upgrades to our repository system, put pressure on recalcitrant publishers and shared solutions to all manner of shared problems. Plus, it’s always nice to have a day away from the office to meet like-minded people, even if you are discussing technical repository requirements for REF compliance!

Further information

You can find further information about open access at the University of Bristol via our webpages: http://www.bristol.ac.uk/library/research-support/open-access/

You can also contact the team directly: open-access@bristol.ac.uk

Tim Riley
Open Access Senior Supervisor, University of Bristol

Open Access: an administrator’s perspective.

Today’s post describes open access from an administrator’s perspective. Claire Evans is Senior Executive Assistant in the School of Biological Sciences at the University of Bristol.

I’ve been working as a Senior Executive Assistant at UOB for several years – most recently in the School of Biological Sciences; previously in Social and Community Medicine (the largest School in the University) where I worked closely with the Head of School and School Manager.

As well as Open Access, I am responsible for managing the admin team, providing project support, staff recruitment and financial management and I am PA to the Head of School. Open Access has become a central part of my remit since the arrival of a government mandate to make all publicly funded research accessible to everyone.

We were faced with the challenge of developing standard procedures for everyone to follow – based on the HEFCE workflow process. It is basically a simple 3-step process: when a paper is accepted for publication the author needs to create a record in our research repository, Pure, with the basic details (authors, title, journal, etc) and add their accepted manuscript to the record, then forward their acceptance email with the Pure ID to the library open access team who will do the rest.

Despite this simplicity, there has been a tremendous amount of resistance, particularly amongst some academics who felt it was ‘time-consuming’ and ‘complicated’ – whereas the admin staff just get on with it! I think there’s also a certain amount of fear – “it’s a big scary thing” – like it was worse than it actually was. People didn’t understand just how simple it was.

We’ve tried all sorts of ways of getting the word out to researchers that Open Access is not that difficult! There is plenty of support available – from us, from the Library and from the repository team – and training sessions have been provided in a number of locations at different times.

At the beginning of 2016, because busy academics were increasingly relying on their friendly local administrative staff to help them with the Open Access tasks, we decided to commission a training course especially for support staff in the School. Many were already adding publications to Pure on behalf of academics – or whole research groups – while others were destined to do so in the near future! It was a new task to add to our already complex workload and at first seemed quite daunting.

The course was run by staff from the library and repository team and was designed to give us a good grounding in the principles of gold and green OA, and specifically in the procedures required to make the School’s publications compliant with the HEFCE policy. That way we could provide practical support and advice to busy researchers.

Some administrators felt a bit apprehensive about the responsibility this implied – would they do something to jeopardise the School’s chances in the next REF by inadvertently making a publication non-eligible for submission? They felt it needed to be clearly stated that the responsibility should lie firmly with the academics – both for notifying the relevant person that their article had been accepted for publication, and ensuring that the manuscript was added to Pure within the 3-month timeframe. We encouraged academics to keep an eye on the process – and their publications – to make sure they were happy with the details.

This has been endorsed by the senior management in the School, particularly the Head of School and Faculty and School Research Directors. It is in the interests of individuals to make sure their publications are up-to-date and accurate in Pure, and that they’ve followed the correct procedures. If not, their REF submission – and ultimately the School’s performance and funding are all at stake – not to mention the potential impact on their individual careers!

When Bristol published its Institutional Mandate for Open Access (based on the HEFCE policy) the library started to record each School’s compliance with open access on a monthly basis by checking a list of published articles against the publications in Pure – to see how well we were doing. It was early days, and it’s a very big school, but we were dismayed to find that our compliance rate was only 19% – worryingly low!

The Faculty Research Director is phenomenally busy but took it all in her stride and managed to galvanise and motivate people to ‘act on acceptance’. The last compliance report showed a distinct improvement – up to nearly 70%. There are about 18 ‘repeat offenders’ who are receiving regular reminders.

The more junior researchers – sometimes more IT-savvy and used to learning new things – have been able to help others to get to grips with the systems and start integrating open access into their workflows. Those academics ‘in the middle’ of their careers were in the worst situation – not so ‘clued-up’ with the systems – and without secretarial or admin support to take on the tasks on their behalf.

One of the best bits of Open Access has been the support and help we’ve received from the library team – and their liaison and communication has been all-important in spreading awareness and emphasising the importance of the HEFCE policy.

We’ve been working hard to publicise the Open Access mandate through a wide variety of routes – the staff intranet – linking to the library Open Access and Pure web pages, items in regular newsletters, emails to the all-School email group, posters and fliers on people’s desks and in their pigeonholes, short presentations at school meetings, research forums and training events.

It’s true that staff have a myriad of things to do, not least a full teaching schedule throughout the academic year and the increasingly complex requirements of research funders – ResearchFish, Impact Case Studies, Data Management to name just some of them.

Admin staff play a key role in supporting these activities, and the work we do in relation to Open Access publishing – advising on the policies and procedures, chasing up authors for their acceptance emails and manuscripts, uploading the correct version to Pure on their behalf and sending reminders to the non-compliant ones – even training staff in the simple 3-step process – are all vital.

In addition, senior management have clarified to staff aspects of the policy and the consequences of non-compliance – ie that key publications will not be eligible for REF submission, thus losing vital income for the School. Ultimately the lead University of Bristol author on the paper is responsible even if the lead or corresponding author is abroad. The original, accepted manuscript must be in Pure within 3 months of firm acceptance from the publisher.

Through our contacts with administrators in other Schools, we’ve found that the knowledge and expertise developed over the past 18 months has really helped speed up the progress of engagement with Open Access and also keep track of the Schools publications and ensure their compliance.

Experiences of OpenCon

Today’s post is by Jon Chappell, a former PhD student in the History department at University of Bristol and now a Teaching Fellow at New York University.

I attended OpenCon, the Right to Research Coalition and the Scholarly Publishing and Academic Resources Coalition’s annual conference promoting Open Access Publishing, Open Data and Open Educational Resources, from 14-16 November 2015 in Brussels, Belgium. I found the conference both extremely interesting and useful. In the course of the three days I attended conference sessions covering all three areas. Through meeting librarians and academics from all disciplines I developed my understanding of the importance of open access, data and education.

In the field of open access, I attended a keynote speech by Bjorn Brembs, a Professor of Neurogenetics at the University of Regensburg who highlighted research suggesting that scientific papers in top flight journals such as Science and Nature are less academically rigorous than less prestigious journals. He pointed out that the number of papers retracted after publication by these journals is far higher than is the case for other journals in the field. This suggests that scientists may be exaggerating or skewing their findings specifically to secure publication in these journals. He noted that this trend was on the increase, suggesting that the current system of basing articles’ quality on the impact factor of the journal in which they are published is encouraging manipulation of data and thus disrupting scientific research. An open access model of publishing with articles being given an impact factor rather than journals would put a stop to this growing trend.

A number of conference speakers, including Salvatore Mele, the Head of open access at CERN, raised the importance of Open Data in science. This was discussed not just in terms of the need for scientists to publish their data openly in order to advance scientific research but also in terms of the processes by which this is done. Speakers stressed that data should be stored in sustainable centralised repositories and should be delivered in machine readable formats. This will allow other scientists to build on the data or use it in a different way, promoting faster scientific advance.

Finally, I attended a keynote speech by Martin Eve, a Senior Lecturer at Birkbeck College, University of London, introducing the Open Library of the Humanities (OLH). The OLH is a Birkbeck-led international consortium of libraries which has launched an online publishing model for humanities scholarship. In the last year 11 journals have flipped to publishing open access through the OLH. The OLH does not require Advanced Publishing Charges and instead is paid for through library subscriptions to the consortium. The journals published through OLH include revolutionary functions such as publishing a tool allowing online readers to contribute by translating articles into different languages, further widening the scope of the material the OLH publishes.

OpenCon changed my perspective on the possibilities of research. Even in the humanities the twentieth century model of sharing research only through conference papers and then to two peer reviewers before an article is published is no longer sufficient. Humanities scholars increasingly recognise that the potential benefits of sharing research widely before publication are great. Since attending OpenCon I have tried to share my research at all stages as widely as possible. Attending OpenCon also made me very conscious of submitting my research only to open access journals. Not only is this a requirement of UK funders but it ensures that my research is open to the widest possible audience of scholars. In my own field, Chinese history, this is essential because I want to be able to communicate with scholars not just in Europe and America but also in China where it is by no means a given that universities will have paid subscriptions to English language journals.

Finally, attending OpenCon encouraged me to be particularly aware of the ways I can share my research without violating the copyright restrictions necessitated by some open access models, such as green open access. Even using this model, it is still possible to share a final peer reviewed, but not type-set, word document version of an article on your own websites or blog, thus encouraging as wide a readership as possible. I believe open publishing will help to break down some of the barriers created by the subscription model. As academics, writing is not enough. We must also be read. Since OpenCon I have graduated from my PhD at Bristol and taken up a teaching fellowship at New York University’s campus in Shanghai. While I have left Bristol behind, the lessons of OpenCon 2015 have stayed with me.

Jon Chappell
Global Perspectives on Society Teaching Fellow
New York University, Shanghai