Research Data Network – University of York – June 2017

If Jisc’s 4th Research Data Network earlier this week felt a bit rushed at times, it only reflects the sheer number of exciting projects happening across the sector.

There’s still a long way to go but it felt like the dots are really starting to join up and there was lots of energy in both real and virtual space – see Storify of tweets on the #JiscRDM tag during the event.

Delegates busy networking on Tuesday evening at RDN York (thanks to Paul Stokes for the photo, used with permission)
Delegates busy networking on Tuesday evening at RDN York (thanks to Paul Stokes for the photo, used with permission)

Two packed days in York were bookended by an inspiring opening keynote from Mark Humphries asking “Who will use the Open Data?” and by a panel session the following afternoon on the principles and practice of open research, informed by the open research pilot project at the University of Cambridge.

Mark emphasised that there is a clearer rationale in some academic contexts than others. Clinical trials, for example, are time consuming and expensive and need to be safe and effective which provides a clear motivation to share data and check conclusions.

Mark singled out his own discipline of neuroscience however as lagging behind, with no discipline specific open data repositories, and inclined to “data worship”. New data is hard to get and requires considerable skill (to implant electrodes in a rat’s cortex for instance) and will underpin high-impact papers, that universal currency of academia. It’s not for sharing!

Mark reassured us, nevertheless, that open data is the future. Inevitably. If only due to the sheer scale of data being generated which simply has to be shared if it is to be analysed effectively, citing an instance whereby a single dataset generated 9 high quality papers from several labs. RDM isn’t trivial though, one of the main reasons that funding bodies are mandating data sharing.

Some 28 hours later, we were back in the same lecture theatre for the final session chaired by Marta Teperek. Our four panelists fielding questions from the floor were David Carr (Wellcome Trust), Tim Fulton, Lauren Cadwallader (both University of Cambridge) and Jennifer Harris (Birkbeck University).

There was a great deal of emphasis on the cost of open research and sustainability – by way of answer to the question above, Lauren Cadwallader referred to her recent blog post Open Resources: Who Should Pay? and shared her reservations about the ‘gold’ model of open access that is sustained by expensive Article Processing Charges to commercial publishers.

There are similarities and synergies between OA and open data initiatives, including increasing interest from publishers. There are also significant differences and it was pointed out from the floor that long term preservation is a cost that needs to be borne by someone.

Betwixt these bookends were far too many sessions to discuss in detail, covering everything from the European Open Science Cloud (EOSC) to an update on the work HESA is doing in relation to research data in the context of REF2021, Archivematica for preservation and some fantastic resources for business case development and costing for RDM (including a number of useful case studies). Then there’s the Research Data Alliance which *anyone* is able to join and which offers a window onto many different communities.

It was particularly interesting to learn about ongoing developments with Jisc’s shared service which is working with 13 pilot institutions on repository and preservation solutions and comprises a range of tools to capture, preserve, disseminate and allow reporting. The pilot offer also includes training, support and gathering of best practice. Pilot users will be testing these systems throughout the summer and providing feedback with a view to rolling out production between April and July 2018.

The UK research data discovery service (beta), part of the Jisc Research at Risk challenge to develop RDM infrastructure, enables the discovery of data from UK HEI’s and national data centres.

Leeds contributed to the event by sharing lessons learned when setting up our RDM service and with a lightning talk.

All in all a valuable couple of days with lots of information still to synthesise and file away. Indeed to preserve in one’s cortex…now where’s that neuroscientist?

Slides from all sessions and extensive notes are available from https://research-data-network.readme.io/v2.01/docs/4th-research-data-network-york-university

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A pioneer of kidney dialysis: the Frank Parsons Archive

It’s been just over 60 years since Frank Maudsley Parsons performed the first kidney dialysis at the Leeds General Infirmary on 30th September 1956. The Artificial Kidney Unit at the Infirmary was the first of its kind in the UK.

Special Collections holds Frank Parsons’ archive, and we’re pleased to announce a new catalogue is now available online.

Explore the Frank Maudsley Parsons Archive

Frank Parsons Archive catalogue screenshot
Special Collections website: Catalogue of the Frank Maudsley Parsons Archive

Parsons’ pioneering work in the use of dialysis for treating kidney failure was significant in the development of renal medicine. Born in 1918, he was an alumnus of the School of Medicine at the University of Leeds, graduating in 1941. After this, he worked as a surgical trainee at the Leeds General Infirmary (LGI) under the urologist Leslie Norman Pyrah (1899-1995). 

He went on to become the Director of the Renal Research Unit at the Infirmary in 1967. Parsons also held a research post at the university in the 1950’s, and by 1974 was Senior Clinical Lecturer in Renal Medicine. He retired in 1983.

Find out more about Frank Parsons (1918-1989).

The archive contains files of papers, letters and publications by Parsons, spanning the course of his career. Many of the files contain notes and papers for a range of lectures he delivered, at conferences and events across the UK and around the world.

Cataloguing this archive has been fascinating, with the records providing an insight into Parsons’ research and how the technology used for dialysis developed. Interestingly, one of the files includes documents relating to a BBC series Your Life in Their Hands, as one of the programmes covered a visit to the LGI and the Artificial Kidney Unit in 1958 (see LUA FMP/1/2).

The new catalogue has been prepared as part of our Medical Collections Project, funded by the Wellcome Trust.

Research data: enabling peer review

We are starting to get requests to make data available for peer review prior to the journal paper being accepted. Some authors are happy for the data to go live in the repository with a note explaining the data is under review and may be subject to change. However, not all authors are happy with putting their pre-review data into the public domain and a better model would be restricted access. There are additional challenges associated with single and double blind peer review and any model based on the (institutional) repository will necessarily reveal the affiliation of an author due to the institutional URL.

Images from datasets in the Research Data Leeds Repository
Images from datasets in the Research Data Leeds Repository

Increasingly journals manage this themselves via a partnership with Data Dryad* or Figshare but not all have a suitable mechanism set up for access to data in addition to the draft of the paper. Moreover, such a journal-centric model will disadvantage institutionally based data repositories, potentially even render them obsolete (see pros and cons of journals handling data below).

* http://datadryad.org/pages/submissionIntegration

Might there be a role for Jisc here to build suitable mechanism into their shared service which, from a blind-review perspective would have the advantage of obscuring author affiliation?

Potential solutions

1. Make the data available in the repository. Don’t mint a DOI. Send the URL to the reviewers. Include a prominent note on the eprint record ‘This data is associated with a paper which has been submitted for publication. The data may be subject to change [date]. Full details of the associated publication and the final dataset will be made available in due course.’

2. Make the data available in the repository with access control. Repository account enables access to the dataset only from specific user account(s). Problem: this is not available yet (for EPrints)?

3. Share the data via OneDrive. This may not be suitable for double blind peer review. However, if the journal can act as a liaison point i.e. the editor is given access to the data on OneDrive, the journal could then provide access details to the peer reviewers. This could be a good solution if the journal is willing.

4. Share the data in another repository – Figshare, Zenodo – which supports restricted access prior to publication of a dataset. This is a good way to share data with a restricted group, but may not be suitable for single or double blind peer review – unless the journal publisher can act as the access gateway as in the OneDrive model outlined in 3. One downside – why bother to deposit in RDL if the data is already in Figshare or similar?

5. Ask the journal if they can help – there may be a mechanism for providing access to the data. This may not be in place. There is a risk data will become supplementary information or be deposited in another repository (if we see this as a problem) so reduces the role for RDL.

Hide Creator Hide reviewer Hidden to world
1 Data available in repository N N N
access through publisher N Y N
2 Data available in repository with access control N N Y
access through publisher N Y N
3 Share data via OneDrive N N Y
access through publisher N Y Y
4 Share data in another repository Y N Y
access through publisher Y Y Y
5 Ask journal if they can help Y Y Y
Jisc Shared Services? ? ? ?

RDN Lightning talk – Open Research Leeds (@OpenResLeeds): networks, metrics and #openresearch

These are slides for a lightning talk next week at the Research Data Network in York:

N.B. Altmetric data (slide 9) – I ran all DOIs available from IRUSdata-UK against the Altmetric.com API on 22/06/2017, available in this Google sheet.*

Note that not all repositories appear to expose DOIs in a manner that is currently available to IRUSdata. In addition, several repositories do not differentiate types of DOI (i.e. DataCite DOIs assigned to a dataset vs publisher DOIs pointing at an associated journal article.)

* Instructions how to do this available at http://ukcorr.org/2015/06/12/ranking-altmetrics-diy/

Spatulas, bulldog clips and digitisation!

Our Digitisation Assistant, Rosie Dyson, talks about some of the more unusual tools the Digital Content Team uses in its work.  The team is lucky to work with some high tech photographic equipment but without a number of more rudimentary tools we would be unable to capture our Special Collections to such a high standard.

The Digitisation Assistants are trained in handling delicate material as a large percentage of our collections are fragile. Regardless of condition, all items must be treated with utmost care and attention. When capturing tightly bound items the humble plastic spatula is exceptionally helpful to hold pages back.

Recently we have been digitising our impressive collection of medieval manuscripts. It is usually possible to work on a manuscript alone but as these are particularly fragile and valuable, we have often worked in pairs to ensure the best possible capture. Sometimes the nature of the binding requires one person to support the book and hold it in place and another to photograph the item. The image at the top of this post shows a bulldog clip and spatula doing the work of one Digitisation Assistant!

The focal depth of our lenses is impressive but extension rings allow us to push the lenses to their limits. As a rule, we try to use the full area of the exposure and leave as little blank space around the item as possible. Sometimes due to the size of object and constraints of the lenses and setups we are unable to get the lens close enough. Extension rings give an additional zoom and can be affixed to our lenses. The images below show items with and without the rings – what a difference!

Medieval manuscript
BC MS 18 ‘Horae Beatae Mariae Virginis’ in the process of being photographed

We have been continuing to digitise the ever popular Godfrey Bingley collection. This is made up of thousands of glass plate and cellulose nitrate slides taken by the Victorian industrialist and serves as a comprehensive social and geological history of the UK and further afield. We are currently digitising the more fragile section of the collection prior to freezing for preservation purposes.

During digitisation gloves must be worn and good ventilation is essential as the slides are capable of off-gassing. Many of the slides are not flat so a plate of glass with feet (made by our conservator) is placed over the slide on the flatbed scanner to gently flatten it without applying pressure. Without this it would be difficult for the scanner to focus on the image and produce a legible image.

Reflection is a major issue for digitisation. Because our studio has a white ceiling, sometimes the lights bounces back off this and presents a problem for our shots. In the left hand image of the medieval manuscript BC MS 23 ‘Legenda aurea sanctorum’ below, you can see the shadow of the camera reflected in the binding. To counter this, we had to think creatively. We cut a lens shaped hole in a piece of black card and held it around the lens to block out the camera reflection.

Cover of medieval book
BC MS 23 Legenda aurea sanctorum cover being digitised

As you can see from the middle image, the first attempt wasn’t big enough and light was still able to reflect off the ceiling. We tried again with a larger area of card and were pleased with the resulting image.

All Change!

The month of May saw many changes in the Treasures of the Brotherton Gallery.

Travelling Library
Travelling Library, 1617

Some of our items had been on display since 1 February 2016 so they have now been retired to the cool, dark conditions of our stacks in order to give their pages, spines and print time to recuperate.  Thanks to the vastness and variety of the diverse collections within Special Collections, picking alternative items was akin to being children in a sweet shop for our curators!

Several objects have been replaced with material by the same author, for example, we have a new Branwell Brontë letter and a French notebook by Charlotte, however, with other items, we have opted for something completely different.

We welcome material by Tolkien, William Hey, Persian poet Sa’di and artist Fred Lawson, not to mention an adorable World War One mascot, a spectacular Ovid and the literal, literary treasure chest that is the Schatzbehalter. We also have two new Artists’ Books colourfully displayed alongside a leaf from the Gutenberg Bible.

Arguably the change that has made the biggest impact is the departure of Shakespeare’s First Folio. After 15 months on show in the huge case that greets visitors as soon as they enter the Treasures Gallery, it’s time for the Bard to take a break. We needed an item that was equally jaw-dropping so we’ve brought out our glorious Jacobean Travelling Library, one of only four of its kind in the world. See our video to discover how and why Shakespeare’s Folio was replaced.

New accessions – May 2017

We have received a collection of print and archive material from the University’s Centre for Disability Studies. A strength of the Centre for Disability Studies’ Collection is the great variety of campaigning literature produced by, and for, disabled people it contains. Much of the material was generated by regional bodies such as the Greater Manchester Coalition of Disabled People, Disability West Midlands, Leeds Disability Information Network, the West of England Coalition of Disabled People, and the Greater London Association of Disabled People.
The collection includes papers from other organizations focusing on particular conditions, such as spinal injuries, neuromuscular impairments, learning difficulties, polio and blindness. Yet others speak for disabled women or LGBT people. All of these bodies work to develop solidarity among disabled people, to raise awareness of the difficulties they face, and to campaign for improvements in their treatment by officialdom and society in general.
J. H. Taylor’s “Against the Tide” is a study of war-resisters in the South London borough of Southwark in the First World War, based on local newspapers and other primary sources. Opposition to conscription came from organizations such as the No Conscription Fellowship, the Independent Labour Party and the Quakers, as well as from individual objectors and campaigners.
Those directly affected were all men, but women played a vigorous part in campaigning. Taylor gives a detailed study of the proceedings of the Military Service Tribunals which examined individual cases. There are some vivid accounts of the brutality and torture suffered by conscientious objectors in prisons and barracks.
We have received a further accrual to our Sadler Collection.  This consists of a box of notes and scripts of papers and speeches by Sadler, and articles about him.  The material was collected by Professor J. H. Higginson, who previously donated large amounts of Sadler material to the Library.