The power of preprints: an omicron case study

Much has been recently been written about the value of preprints which facilitate rapid and open dissemination of research findings to a global audience (if you’d like to read more about the rise of preprints in the life sciences I would recommend this editorial published in Nature Cancer). However, much of the discourse surrounding the benefits of preprints has been anecdotal. Of course sharing research findings early is a good thing, but what actual impact can a preprint have?

We present here a mini case study which highlights the initial effects of sharing a topical preprint during a pandemic. I plan to track the preprint over the next few months to see how this will translate into future publications.

Case Study: the EAVE II project

There were various headlines in the media on 22 and 23 December which reported the the discovery that the Omicron variant of COVID-19 appears to be much milder than Delta. This news was prompted by research from the EAVE II study carried out at the Usher Institute. The EAVE II team only finished their analysis on 22 December and were very keen to get their results out in a transparent manner as part of a media briefing they had agreed to do later that day.

Our Scholarly Communications Team helped the EAVE II project to post the results in the University of Edinburgh’s repository as a preprint. Subsequently, the University’s Press Office contacted us to say that this was initially beneficial when the world’s media contacted them to request the underlying data. The preprint is available here:

https://www.ed.ac.uk/usher/eave-ii/key-outputs/our-publications/severity-of-omicron-variant-of-concern-and-vaccine

The reaction was quick as the preprint was picked up and reported by the mainstream media like the BBC (this article in the BBC Science Focus Magazine is a good read), and also specialised services like the Science Media Centre:

expert reaction to preprint on the severity of the omicron variant and vaccine effectiveness against symptomatic infection in Scotland, from the EAVE II study

Various national advisory groups (e.g Australian Technical Advisory Group on Immunisation) were then quickly able to read the research and fold it into their evolving guidance on boosters.

https://www.health.gov.au/news/atagi-statement-on-the-omicron-variant-and-the-timing-of-covid-19-booster-vaccination

To date the preprint has 22,535 downloads, of which the majority were within the final week of December 2021. 21, 005 downloads in 10 days – that sure is RAPID communication!

If the EAVE II project team had sat on their results and waited for publication in a traditional journal article then all of this activity would have been not possible. I’m extremely interested to see what happens next to the publication.

Questions….

At the moment I mainly have many questions that I don’t have the answer for. Will this piece of research be submitted for publication in a journal? Publication in a journal and the peer review process will add validation of the results and subsequent kudos from basking in the reflected glow of an esteemed journal title and possibly good citation metrics. But how can the value of preprints be more widely recognised and rewarded? For me, this is a missing part of the process. Or, perhaps the benefit of rapid communication is good enough?

 

 

 

Unveiling the new Open Access policy at UoE

For Open Access Week 2021 we are pleased to announce a brand new Research Publications & Copyright Policy that will make it even easier for researchers from the University of Edinburgh to make their publications open access.

Earlier this month the University Executive approved the Research Publications & Copyright Policy (2021) which details our approach to the new open access requirements of major research funders from 1 January 2022.

The Research Publications & Copyright Policy (2021) can be read in full on the Information Services web pages, but the key details are outlined below:

  • The University of Edinburgh confirms staff members retain the copyright to scholarly works they produce (which is the opposite of UK employment law which states that employers own the copyright to works produced in work time).
  • To help comply with funders and other open access requirements, members of staff grant the right for the University of Edinburgh to make manuscripts of their scholarly articles publicly available under the terms of a Creative Commons Attribution (CC BY) licence upon publication.
  • This policy will begin on 1st January 2022, and will apply to journal articles and conference proceedings.

This new policy is in line with major organisations including UKRI and the Wellcome Trust and will allow all researchers to make their work open access immediately regardless of their funding situation. Support for implementation of the new policy is available through library research support staff. Any questions or comments regarding the policy can be directed to the Scholarly Communications Team at openaccess@ed.ac.uk.

 

Open Access Week 2021

Next week is the annual international Open Access Week where organisations celebrate and showcase open access developments and projects. It is a time for the wider community to coordinate in taking action to make openness the default for research.

This year’s theme of “It Matters How We Open Knowledge: Building Structural Equity” aligns with the recently released UNESCO Recommendation on Open Science, of which Open Access is a crucial component.

We will be publishing a series of blog posts to showcase the best of Open Access at the University of Edinburgh. To give you a sneak peak here is the publishing schedule:

  • Monday: Unveiling the new UOE Research Publications & Copyright policy
  • Tuesday: Transformative Agreements: a new way to ‘Read & Publish’
  • Wednesday: Edinburgh Diamond: a new OA platform for UOE
  • Thursday: Repository Downloads: a year of Open Access
  • Friday: Meet the Team: the experts providing help and support at UOE

 

Open Library of Humanities Bronze Supporter

The University of Edinburgh has opted to support the Open Library of Humanities for another year- this time as a Bronze level supporter. This additional support will enable the OLH to continue its growth mission to convert subscription journals to a solid, ongoing, open-access model, with no author-facing charges.

Open Library of Humanities Bronze supporter badge

Theo Andrew, Scholarly Communications Manager at the University of Edinburgh, said: “The OLH is such good value for money. Library budgets are always tight, but we feel that we should be doing more to support academic-led publishing. OLH puts a lot back into the academic community and we are pleased to help with its ongoing sustainability.”

Introduction to Leadership

This is a not one of my usual posts about Open Research, but rather a short essay written about and submitted for a Leadership course that I recently completed.

I have been in my current role as Scholarly Communications Manager since 2017. When I first began the role was very hands on, but over time the line management responsibilities have significantly increased. Initially I was the line manager for two staff, however over the last couple of years the team has grown to a total of six. I’ve never had any formal training on how to manage staff or provide leadership, and have up to now just got on with the basic mechanics of the job – performing annual development reviews, reporting sickness absences and annual leave requests. Unfortunately, this has meant that I’ve not had much time dedicated to improving the team work environment or developing the members of my team.

It was recently pointed out to me that many jobs (especially teaching, clinical medicine or emergency services) require significant training and qualifications before you can start, but with management roles you are quite often thrown in at the deep end and told to just get on with it. The University has started delivering training for leadership and management roles and I was keen to enrol on one of the many courses to learn new skills and hopefully see how management should be done.

So, at the start of the year, as part of a cohort of 14 managers and academics all from different departments and units spread out across the University, I started out on an ‘Introduction to Leadership’ course.  The course itself started in February and consisted of several monthly one day workshops spread over six months. We were able to have the first two sessions in person, however due to the COVID-19 pandemic the course had to quickly reorganise and switch to online delivery. Lots of credit is due to the trainers Agnes and Lesley who were able to act quickly and resume the course.

At the end of the course it was an expectation that attendees would deliver a Leadership Journey presentation in a format they were comfortable with – some chose a video recording, others a written document. I have chosen a public blog post to document my leadership journey over the last few months pre-and-post lockdown, focussing on some of the things I learnt during the course and how I have built them into my working practices.

Motivation Values

The Introduction to Leadership course introduced to me the idea of motivational values which I had not encountered before. Each of the participants took a Strength Deployment Inventory (SDI) test which consisted of a series of behavioural questions which asked what people do when things are going well and also when they face conflict. Depending on how you answered a profile was built up which describes your own personal motivational values focussing on three end points: People (empathy), Processes (logic) and Performance (results).

Strength Deployment Inventory plot showing motivational values

I found out that my answers placed me at the intersection of People and Processes, and that under stress I would verge towards Process based behaviour. This made sense to me as in my job I try to deliver a quality service focussed primarily on people and making sure they are happy with the outcome, rather than focussing singly on results. To run the service we have to develop new processes and protocols under rapidly changing scenarios. The guidelines and criteria we develop make sure the service we run is equitable and is understandable to our staff despite arising from an extremely complex set of policies and rules imposed on us by research funders and journal publishers who are often at odds with each other.

The technique of looking at peoples motivational values has helped me better understand my team members by understanding a little of the motives that drive their behaviours. For example, someone who is Green and values analytical approaches will feel more comfortable with clear instructions within a framework, whereas someone with Blue tendencies will prefer an empathic approach. In the last few months, I have tried to tailor my team management approach by considering the personalities involved and although it is difficult to monitor and assess I personally think that the team has been functioning better despite the difficult general circumstances we have found ourselves in. I cannot take credit for individual’s performances, but it is definitely easy to manage a team full of diligent and talented people so I can at least take some credit for hiring them!

Situational Leadership

Building upon the last point the next main concept that the Leadership Course introduced and I have found really interesting/useful is the idea of Situational Leadership. The basic premise is that a leader further tailors their approach depending on the people and task in hand.

Naturally, I found that I was changing my approach when working with colleagues – for example with new team members I was being very hands-on and with experienced team members I was able to rely on them to get on with things. However, having a framework to fit my behaviour in has given me an understanding on how to improve both my own management and my co-workers skills.

I now recognise that I have been poor at delegating tasks despite people offering to help.  My resistance is not really a fear of losing power, or believing that I can do it better, but rather I have been put off somewhat by the time involved in explaining the task, and a general unwillingness to accept risk for certain high-priority’ tasks. Acknowledging this has been useful as I can now move forwards and change from an ‘Instructing’ style through ‘Mentoring’ and ‘Coaching’ to ‘Delegating’. By developing and trusting my colleague’s skills I have been able pass work on to them and carry out other tasks.

As shown in the graph below, since working from home starting in March 2020 we have seen the volume of team calls double when compared to previous years. It seems many of our academic colleagues (those without children anyway!) are using the time away from the workplace to write up papers, or carry our peer review to get through the backlog of submitted papers. More journal articles being accepted for publication means more work for my team as they deal with open access enquiries from academics.

Number of calls per month received by the Scholarly Communications Team has significantly increased during COVID-19 lockdown

During lockdown I have been working reduced hours to look after and teach my school-age children. With the increased workload I found myself working late into the evening to keep on top of things, but I soon realised that I could not keep up my old hands-on working behaviour in the long term. I would not have survived the last few months if I had not been able to fully delegate work tasks to my colleagues and I am extremely grateful that I have been supported by a wonderful team that has stepped up and responded to the challenges of working from home.

The leadership course has given me a set of tools and a framework with waypoints that I can use to inform my decision making. More importantly it has provided a support network of fellow managers who were part of this cohort.

New: DOI minting for PhD theses

We are pleased to announce that from January 2020 all new PhD theses submitted to the Edinburgh Research Archive (ERA) will be assigned a Digital Object Identifier (DOI). The Library will be using the DataCite DOI registration agency to provide this service.

What is a DOI?

A DOI is a character string (a ‘digital identifier’) used to uniquely identify and provide a permanent link to a digital object, such as a journal paper or other scholarly work.

Benefits of having a DOI

Assigning DOIs to PhD means that researchers are able to confidently cite theses alongside traditional journal articles knowing that a link will be persistent. The benefits for authors include gaining due academic credit for their efforts to produce these valuable research outputs and the ability to track and measure online attention via alternative metrics like Plum X or Altmetric.

Which PhD theses will get DOIs?

In the first instance the Library will give all new PhD theses a DOI once the final version has been submitted to Pure and graduation has occurred. Before a DOI is registered the PhD thesis must be archived fully in ERA. Some PhD theses submitted for Winter 2019 graduation which have not yet appeared online in ERA will be assigned a DOI.

We aim to roll out and assign DOIs for all of the PhDs in the existing online collection, but since the collection is large (>20,000) we will have to approach this in stages.

 

Beginning of a new ERA

We are pleased to announce that the Edinburgh Research Archive (ERA) has recently had a lot of work done to improve it’s looks, add new functionality and clean up some of our collections data.

For those of you who are not familiar with ERA it is is a digital repository of original research produced at The University of Edinburgh. The repository contains documents written by, or affiliated with, academic authors, or units, based at Edinburgh that have sufficient quality to be collected and preserved by the Library, but which are not controlled by commercial publishers. Holdings include around 27,000 full-text digital doctoral theses, 1,500 masters dissertations, and numerous other project reports, briefing papers and out-of-print materials. In October 2019 we recorded 223,000 visitors to ERA who downloaded 51,984 items.

Details of some of the improvements are listed below:

Software upgrade The DSpace platform was upgraded from version 4.2 to 6.3
Face lift Visual redesign and styling ERA to make it more appealing
DOI allocation New functionality to assign DOIs to deposited items

New domain

New URL => era.ed.ac.uk
Fix subject terms Change scanning metadata information to be stored in dc.relation.ispartof and not dc.subject.

Log-in expiry time Set login expiry time to an hour.

Date-format Go from yyyy-mm-dd to dd-mm-yyyy

UX improvements
Move Edit Item button up, to the top of the bar, customise drop down list to have most used elements at the top.

Default language boxes Give “en” as default to language boxes.

Of all the new improvements I am most excited about the new functionality to assign Digital Object Identifiers (DOIs) to items deposited in ERA. All new items will be automatically assigned a DOI, and we will investigate how to do this for the rest of the nearly 35,000 items already online.

Open Access Scotland Group meeting

Photo by @hblanchett : https://twitter.com/hblanchett/status/1110843583320473600

On 27th March the Scholarly Communications Team at the University of Edinburgh were delighted to host the 6th regular meeting of the Open Access Scotland Group at the impressive Paterson’s Land building (pictured above).

The Group aims to provide a voice for open access in Scotland, allow the sharing of best practice, facilitate opportunities for networking between stakeholders, and lobby on behalf of Scottish organisations. It is an open group and comprises members from Scottish HE institutions and other allied organisations, like academic publishers, software vendors, local and national government agencies and research funders. The group also has honorary members from Iceland and Northern Ireland.

The event on 27th March was attended by 40 people representing over 20 organisations.

Photo by @hblanchett

The first speaker was Pauline Ward who gave a well received talk on Open Science Approaches – including the fantastic Research Data Service at the University of Edinburgh.

During the main session we had a facilitated discussion around issues such as the use of research notebooks, how to do open access for Practise-led Research, and updates on Plan S, UK-SCL and Jisc Support.

The draft notes from the event are available online here:

https://docs.google.com/document/d/19OZEX6QajIl-LNgUrGsY-Fdk7LSGUUhvfp0GM2Jubg4

If you are interested in Open Access and are based in Scotland then I would heartily recommend joining up to the Open Access Scotland Group. The next meeting is pencilled in for September and will probably be hosted by the University of the Highlands and Islands in Inverness. Hope to see you there!

 

 

 

 

PubMed LinkOut for Pure users

Instructions for Pure users on how to find data to join PubMed LinkOut

PubMed LinkOut is a service where you can send data to NCBI which will allow them to link PubMed records directly to your institutional repository:

PubMed LinkOut

Whilst the benefits for repository owners are obvious – e.g. massively increasing the visibility of your open access content – not many repositories are actually doing this. At the time of writing, in the UK there are only 4 other repositories in the LinkOut programme: University of Strathclyde, Imperial College London, the White Rose consortium & the London School of Hygiene & Tropical Medicine. Currently there are no other institutions that use Pure so I thought I would investigate and create some instructions.

This blog post will help Pure administrators find URLs to full‐text open access items that have a PMID, but not a PMCID which can be used to send to NCBI.

Step 1: find Pure records that have a PMID, and also have open access full-text.

Note: Pure only holds PMIDs for records that have been imported from PubMed. Unfortunately, PMC IDs are not stored like other identifiers like ISBNs or DOIs. Set up a new report with the following filters:

  • Organisation Unit – include all underlying subunits
  • Source: select value is PubMed
  • Electronic version(s) of this work: Accepted author manuscript/Submitted manuscript

Recommended values for data table:

  • Electronic versions(s) of this work > DOI
  • System info > Source-ID
  • System info > UUID
  • System info > ID
  • Add access version of this item > Open Access embargo date

This report will pull all records from Pure that have been imported from PubMed, and will show the Pure ID/DOI/PMID/UUID and OA embargo date. The UUID will be used to generate a stable URL to the item page in the portal. Export the report as an Excel spreadsheet.

Step 2: Find out which Pure records with PMIDs also have PMCIDs

If a paper has a PMC ID then it will have an open access version in PubMed Central and the LinkOut won’t be interested in including that record. You can use the online PMCID – PMID – Manuscript ID – DOI Converter to find out if the items in the Pure report have PMC IDs:

https://www.ncbi.nlm.nih.gov/pmc/pmctopmid/

Cut/paste PMIDs into the box, select CSV result format and convert 100 records at a time. Any more will likely to produce an error.

Ignoring the results with PMCIDs, cut/paste the remaining PMIDs (Identifier not found in PMC) into a new column in the Pure report spreadsheet.

Step 3: Identify the Pure records which can be included in PubMed LinkOut.

So far we have a list of records in Pure that have a PMID (which may or may not have PMCIDs), and a list of PMIDs that have been checked to make sure they don’t have PMC IDs. What we need to do now is merge the data. There are a number of different ways to do this in Excel, but I chose to use the conditional formatting function to highlight duplicate PMIDs in Pure that are on the ‘not in PMC list’ we created. Filtering by colour will then give you a list of records which can be included in the PubMed LinkOut programme. I chose to remove the items which are currently under an embargo which can be identified from the Open Access embargo date, and removed using a filter.

All that is remaining to do is to tidy up the records and add the stable URL. This can be done by taking the UUID-4 value from the Pure report and concatenating with the handle server ID for Pure, for example:

Handle + UUID-4 = URL , e.g:

http://hdl.handle.net/20.500.11820/e22c7edc-9533-4ad3-ae44-3f706dd7682c

Now you have a list of URLs of items in Pure that have PMIDs – but crucially not PMCIDs – which you can submit to the LinkOut Programme. You can download a printable PDF version of these instructions here:

Pure PubMed LinkOut instructions

 

 

Open Access update

The University of Edinburgh is a strong supporter of open access (OA), and in 2018, researchers at Edinburgh published over 7,000 peer reviewed research outputs, of which over 5,181 (74%) are openly available from the University’s research portal (www.research.ed.ac.uk). As a large and diverse organisation there is naturally a large variation in the way in which we make our research openly available. From our total of 5,181 open access research outputs we find that 2,959 outputs (or 57%) are published as Gold OA – where the publisher makes the version-of-record open sometimes for a fee – and 2,222 (or 43%) are available as Green OA – where the author makes their accepted manuscript open from our Institutional or Subject Repositories for free.

Over the last 5 years the University has spent in the region of £5 million with publishers to make around 2,800 papers Gold OA.  The majority of these papers were published as ‘hybrid OA’ in subscription journals where the publisher charges subscription fees to access the closed content, and also charges an open access fee to make individual papers open access. This practice of charging twice is called ‘double-dipping’ as large research intensive institutions have not seen their subscription costs lowered in proportion to their open access expenditure.

Over the last 5 years we have seen a period of significant consolidation of the open access publishing market with just three companies responsible for publishing 51% of Edinburgh’s journal articles, whilst receiving 57% of the money available for open access. The bulk of the University of Edinburgh’s RCUK block grants have been spent on ‘Hybrid OA’ journals as shown in the diagram below. Only 3 out of the 10 most popular publishers are purely Gold OA and don’t charge subscriptions :

Block chart showing the top 10 publishers

Block chart showing the top 10 publishers who received funds from the RCUK open access block grant during 2013-2018. The number in the top left of each box is the total number of Gold OA papers published, the number in the middle of the box is the total expenditure and the name of the publisher is in the bottom left of the box.

Research funders like UKRI and the Wellcome Trust previously supported this ‘hybrid-OA’ model, but they no longer believe that it supports a transition to full OA which is their aim. To precipitate a change in the publisher’s behaviour and to increase the adoption of open access, a number of important European research funders, co-ordinated by Science Europe, developed Plan S.

Plan S update

Plan S requires that, from 2020, scientific publications that result from research funded by public money must be published in compliant Open Access journals, and specifically states that ‘hybrid OA’ journals won’t be supported. As it currently stands, Plan S will be hugely disruptive as researchers will potentially not be able to publish in their journal of choice.

In order to understand the impact of how Plan S will affect our research staff, departments and the broader academic community, Library & University Collections carried out a wide ranging consultation exercise. The Scholarly Communications Team held a series of eight open meetings, during the period 23rd – 30th January 2019, which were attended by over 260 staff. As far as we are aware this was the largest consultation held by a HE institution.

Based on feedback gathered at these meetings, the University has submitted a balance response to that is supportive of Plan S and the time frames set down, but also reflects the concerns raised about risks to international collaboration – specifically co-publishing work with collaborators in non-Plan S regions of the world. The response, and more general information about Plan S, can be read in full on our web pages:

https://www.ed.ac.uk/information-services/research-support/publish-research/open-access/plan-s

UKRI will decide how to apply the principles of Plan S once it has concluded an ongoing review of its own open-access policies, which is not likely to be completed until next autumn. The current Open Access policy is firmly in place until 31st March 2020 and it would be improbable for UKRI to change terms and conditions of grant awards midway through the year. We can therefore expect UKRI to adopt Plan S from 1 April 2020.