EORI Bulletin

07/06/2021 5-minute update

EORI keeps an eye on changes in the fields of Open Science, FAIR data principles, and others, and directs any interested parties to important updates:

  • Worryingly, but somewhat predictably, nonreplicable publications are cited more than replicable ones (here). Worse, the difference in citation rates do not change after the publication of the failure to replicate. If you’re using R, then thankfully there’s a tool/ package which has been recently developed, Easyreporting, to help reproducibility in code, but if you’re not then we need to find other ways. It’s worrying that this knowledge which is ontologically false continues to be cited and spread, like science’s equivalent of fake news. This comes as others have made a suggestion to the culture around citation: the right to refuse citations. It’s discussed as a potential reaction to being citied by predatory journals or by papers with questionable ethics/ methods etc., and they make some interesting points. 
  • Following the news, mentioned in the last update, that Clarative Analytics had bought Proquest, there’s pushback and concern from the community (here). The drive towards a monopolistic control of these systems and data is spurring calls for regulation and oversight. Considering Times higher Education’s recent call for academics to become involved in the Open Access struggle, this could be a good place to start. It also comes as SAGE journals have announced that its offering Open Peer Review using Clarative’s Web of Science portal (here), which is simultaneously a great initiative to be implemented (of which EORI thoroughly approves) and also a monopoly-building action. Hopefully this will 
  • Here’s a nice explainer behind preprints, and there’s an interesting new course dedicated to them (here). 2/3 of preprints go on to be published in journals (here), which could be suggestive of the amount of knowledge which never sees publication, or possibly of the issues which arise in 1/3 of work. Either way, accessing this data can be of great use. 
EORI Bulletin

24/05/2021 5-minute update

EORI keeps an eye on changes in the fields of Open Science, FAIR data principles, and others, and directs any interested parties to important updates:

  • On a previous update, we’d mentioned Sci-hub, a website which gives access to research articles by cycling through IP addresses until it finds one which is permitted, and the FBI’s attempts to shut it down by accessing the founder’s data and Apple account. Thankfully, fans of the site are mobilising via Reddit to save the platform, by backing up its combined 77Tb of data – a rather large task. Even though Sci-hub’s website it still online, it’s been unable to add any more papers since this latest attack began, meaning that previous manuscripts can still be accessed with it – for now – but newer manuscripts cannot. Vice covers this here. Alexandra Elbakyan, the website’s founder, reasons that corporations are gatekeeping knowledge for profit, and that the public are the ‘real’ owners of that information. More developments will surely come! Also, if you want to get around the block that the UK’s internet suppliers have put on Sci-hub, there’s a guide here.
  • Clarative have bought ProQuest for the hefty sum of $5.3 billion (here), which adds to their portfolio of bought companies in library services which shows no sign of halting expansion. Reaction to this could be generously described as mixed. It comes as they’ve introduced their new research metric, the Journal Citation Indicator (JCI), which aims to normalise research fields to citation and publication rates to a single journal-level metric. However, following the rise of the Declaration on Research Assessment (DORA), which effectively states that assessing research with single level metrics is inappropriate and instead research should be judged on its own merits, the scientific community are moving away from simplistic reductions of research to arbitrary numbers. Other well-intentioned single-value metrics developed for this, such as the H-index, are also inappropriate. At best, the JCI can be described as well-intentioned, but considering it’s a black-boxed calculation which has the potential to cause many more problems than it solves, it’s a wonder why anyone spent time developing it. Unless, of course, it’s intention is to financially benefit the company but not the scientific community, but with the narrative framing of its introduction by Clarative (here) could that possibly be the case? I’ll leave you to decide.
  • After some long entries, here’s a short one: Dockstore is an open-source platform for publishing, sharing, and finding bioinformatics tools and workflows. More info here.
EORI Bulletin

10/05/2021 5-minute update

EORI keeps an eye on changes in the fields of Open Science, FAIR data principles, and others, and directs any interested parties to important updates:

  • Many people will know of Scihub, a website which gives access to research articles by cycling through IP addresses until it finds one which is permitted. The founder, Alexandra Elbakyan, is being chased up by the FBI as the American legal system is trying to have it shut it down (here). Amusingly, Sci-Hub may be beneficial to research as Indian research which is available on Sci-Hub garners more citations than work which is not (here). Considering this, and the morality of Open Access (here), researchers should be in favour of the website, yet journals and publishers are not. As a website that gives access to (usually publicly funded) research, it seems to occupy a legal grey zone of being morally right but legally wrong. Worth keeping an eye on developments.
  • There’s an interesting question in the debate about predatory journals and conferences. Even if the journals/ conferences are predatory, the science held within the journals may still be perfectly sound, and the conferences may still yield genuine networking opportunities. Additionally, some publish in them as their articles may not be accepted elsewhere, meaning that without predatory journals/ conference that work & data may not be reported for some time, if at all. The question is, considering these (and cost aside), are predatory journals & conferences actually a bad thing? Influencing the answer, one group found that research in predatory journals are less statistically sound and data presentation worse (here). This finding runs against potential ‘benefits’ from predatory publishers. 
  • Nice and quickly, Dr Rhodri Leng presented to the Riot Science Club recently about citation biases (here). Well worth watching!
EORI Bulletin

27/04/2021

EORI keeps an eye on changes in the fields of Open Research, FAIR data principles, and others, and directs any interested parties to important updates:

  • This piece argues convincingly for Open Peer Review, where reviewer reports & interactions between the parties involved in the peer review process are published alongside the primary research output. It also misses some benefits of Open Peer Review such as providing a window for less experienced scientists to learn from and about the peer review process (important, as less-established scientists are among the best peer reviewers), and combat biases in reviewing (here and here). 
  • https://oa.works/ has some really straight forward Open access tools to use. Good to play with!
  • There are some interesting upcoming talks/ symposia on various aspects of Open Research, including Open Repositories,  Peer Review and Pre-printsOpen Scholarship week events, and critically analysing scientific reform etc. There are frequent talks on almost all areas of opens science, targeted at all levels ranging from the uninitiated to seasoned Open Research scholars. Additionally, many talks end up on Youtube, allowing anyone to access them any time (E.g. Edinburgh Reproducibility’s account). If you’re interested in any area of Open Science, just search it!
ReproducibiliTea Blog

A selfish guide to RSpace: Why and How?

In this session, Post-Doctoral Research Fellow Dr. Ralitsa Madsen covers why using an Electronic Lab Notebook (ELN) is a great idea. Dr. Madsen suggests that there are many rewards in using ELN for a reproducible workflow and they include:

  • Saving a lot of time while reading, searching the documents and so on.
  • If you are a postgraduate or graduate student, it will be more convenientwhile retrieving the details that you need for materials and methods section of your research.
  • ELN makes it easier to collaborate not only within but also outside of the group.
  • Lab members can pick up where you left off, therefore it ensures the continuity of the research.
  • It is much safer to rely on an ELN rather than your hard drive. Your documents will be accessible even if your computer gets damaged/stolen.
  • It is necessary to have an extensive documentation, version control and traceability of your work if you would like to make a patent application.
  • In addition, RSpace is well-integrated with many other services like Mendeley, Microsoft Office, Dropbox, Google Drive as well as data repositories like Git Hub.

After naming several great reasons, Dr. Madsen goes on to do a walk-through of the tool and gives useful tips to facilitate RSpace adoption within the lab: 

First, you should think FAIR: are your documents easily findable? Are they accessible to researchers inside or outside of the lab? Is it interpretable? Can others read through the lab book and reuse your protocol for their experiment?

But for this to work, says Dr. Madsen, you also need to create;

  • A lab book entry template which will ensure consistency and make it easier to collaborate,
    • Notebook based project organisation, 
    • Data storage rules that are motivating to use external repositories and
    • Consistent file naming rules

Do not forget to check Dr. Ralitsa Madsen’s RSpace demonstration on Edinburgh Reproducibility’s YouTube channel if you haven’t already!

This blog is written by Bengü Kalo

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EORI Bulletin

12/04/2021

EORI keeps an eye on changes in the fields of Open Science, FAIR data principles, and others, and directs any interested parties to important updates:

  • Wikipedia has launched a new project, Wikiexperiments. They want to collect & upload more videos of scientific experiments being conducted. For openness reasons this is a great idea, but there is also the potential for Wiki to extend this and act as a sort of Open repository for training videos etc. in the future. If this does end up happening, it could be a great thing for openness & reproducibility. Let’s keep an eye on it!
  •  The International Science Council has established their steering group for their next phase of their project addressing Scientific Publishing (here). They will work on enabling efficient dissemination and use of scientific work as part of Open Science, and it’ll be interesting to see what they come out with. Some previous work & recommendations of the group here.
  • Yet more work shows that publishing Open Access increases citations and altmetric numbers, this time in electrophysiology. Moreover, journals converting to Open Access increases citations & benefits the journals (here). These, combined with ethical reasons for scientists not to review for commercial journals (explored here), leave little justification for journals to not convert to Open Access publishing, though we may be biased on this conclusion…
EORI Bulletin

29/03/2021

EORI keeps an eye on changes in the fields of Open Science, FAIR data principles, and others, and directs any interested parties to important updates:

  • Lots of Open Science workshops are coming up, such as this one which will present 3 tools to improve transparency in 1 hour, this one discussing more open ways of researcher assessment, or this longer one covering many topics. There are also a huge number of videos now uploaded to Youtube – just search and you’ll be able to find explainers on most things!
  • Interestingly, it seems that simply advertising a manuscript as open access is enough to increase clicks through form social media (here). 
  • Another call to be mindful when reading pre-prints, as they’re not all wonderful. This study looked specifically at Covid pre-prints & noted that few of them made it to publication. This might, of course, be due to hastiness of the manuscript, or even opportunists trying to use it to further their careers, but either way – consider pre-prints accordingly.
ReproducibiliTea Blog

How (some) scientists talk about openness

Edinburgh ReproducibiliTea held another great session last Friday, with Dr. Rosalind Attenborough from University of Edinburgh – Science, Technology and Innovation Studies! Her research is focused on the researchers’ attitudes towards open science and here are the main points of her insightful talk for those who have missed;

For her PhD project, Dr. Attenborough interviewed 54 individuals from various career stages, genders and disciplines in biology. She mainly explored what does open science mean to them. Although the interviewees came up with various responses to her question, majority of them fell under three category: open access, open data and interpersonal openness.

In general, researchers tends to be positive while talking about open access and believes that it is a good idea. Yet, it does not go without mentioning the monetary and bureaucratic issues around it. 

Open data is a completely different story. While interviewing scientists and policymakers, Dr. Attenborough saw that people’s attitudes varied immensely. Some of the interviewees perceived it as a norm and embraced it with passion, while the others were cautious. What makes people refrain from sharing data seems to be stemming from the possibility of receiving destructive criticism and getting scooped.

The last category, interpersonal openness, refers to willingness and ability to talk about unpublished research ideas. Like data sharing, interpersonal openness also gets negatively affected by the competitive research culture as well as unsupportive mentorship.

Dr. Attenborough’s work is particularly insightful as it sheds a light on in which ways academia has to change so that the researchers , especially the ECR’s, can feel more comfortable embracing open science practices.

This blog is written by Bengü Kalo

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EORI Bulletin

15/03/2021

EORI keeps an eye on changes in the fields of Open Science, FAIR data principles, and others, and directs any interested parties to important updates:

  • This interesting PhD thesis has been published online about predatory journals and where research should be published. I’ve not finished reading all of it, but from the work so far & the titles of the rest of the document it looks interesting!
  • There’s green and gold open access publishing, and there’s also the lesser discussed – and best – diamond open access publishing. These are journals which are free to access & free to publish. Helpfully, this report delves into them in detail.
  • Are you considering pre-printing one of your upcoming papers? Maybe you’ve heard of it, but you’re unsure about the process. This blog is nice & short, discussing their experience and the benefits they found to pre-printing. Worth a read. 
EORI Bulletin

01/03/2021

EORI keeps an eye on changes in the fields of Open Science, FAIR data principles, and others, and directs any interested parties to important updates:

  1. Open Research Europe, the European Commission’s Open Research platform stemming from Horizon 2020 funding, is now accepting submissions. Thankfully, it’s not going to ask to be given an impact factor, and will be a peer reviewed platform for data & papers – all of which will be assigned a CC BY 4.0 license (which is good). Interestingly, they will publish before an open peer review process takes place, making it a hybrid of a pre-print and a repository platform for papers. Very interesting, and would be great to see the platform expanded for projects outwith Horizon 2020! For more European Open Science initiatives, the European Open Science Cloud looks interesting. 
  2. The University of Maastricht, Netherlands, is currently in their Open Science week! They’ve got a useful website here which contains a lot of very useful information, written in a way which is easy to engage with. I’m looking forward to Edinburgh’s first Open Science week!
  3. The calculation behind the impact factor is changing as early as June (more here) – sort of. Simply, it’ll change the publication date to the date of online (as opposed to print) publication. This has some obvious advantages, but one clear disadvantage is that Claritive doesn’t have publication data for half of the journals it indexes. This is also expected to cause uneven inflation of impact factor across journals (some up to a 250% increase in their impact factor!). We all know that impact factor is not a proxy for quality of an individual paper published within – maybe this switch will make that clearer for others to see.