Monthly Archives: March 2019

Open Access Scotland Group meeting

Posted on by
Reply

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!

 

 

 

 

Open Science Conference 2019

Posted on by
Reply

This week, I attended the International Open Science Conference in Berlin.  I attended this event last year, and found it so inspiring, I was keen to attend again this year.  Open Science, or Open Research, as we tend to refer to it here in Edinburgh is an important development which will fundamentally change the way researchers and those who support them will work over the coming years.

We are in the process of adopting the LERU Roadmap on Open Science and are working with colleagues across the University with the aim of implementing as many of its 41 recommendations as possible.

The programme was comprehensive and there were far too many good ideas to summarise here, so instead I’d like to focus on a number of key take-home messages I came away with in no particular order:

  1. I need to get to grips with the European Open Science Cloud. It’s such a major intiative and I need to get to grips with what it is, how it works, and how it applies in the Edinburgh context (in an increasingly likely post-Brexit world).
  2. I’m very keen to work more closely with our Research Support Office to see what more we can do to ‘hack’ research proposals before they are submitted to make them more open right from the opurset. Thanks to Ivo Grigorov’s FOSTER Open Science CLINIQUE for the inspiration!
  3. Peter Kraker’s powerful presentation highlighted the risks we leave ourselves open to by allowing commercial monopolies to form within the research lifecycle. I’m increasingly worried that we are sleepwalking from a monopolistic market for library subscriptions to an even more dangerous situation with just one or two for-profit companies owning all the tools that are essential to the research endeavour.   We need to do more to make open infrastructure sustainable.  #dontleaveittogoogle

So, from my reams and reams of notes, those are my three key action points to take forward within the University of Edinburgh.

It was really great to hear Eva Mendez re-stress the importance of seeing the transition to open science as a process of manged, complex, cultural change.  I think that is something I and my colleagues already understand very well, but it’s good to have this re-affirmed!  It was also useful to think about how we need a complete picture of vision, skills, incentives, resources and action plans to avoid confusion, anxiety, resistance, frustration and false starts.

I’d highly recommend this conference and would encourage anyone with an interest in Open Research to attend again next year.  #OSC2019

Dominic Tate

PubMed LinkOut for Pure users

Posted on by
Reply

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

Posted on by
Reply

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.