Adventures in Signal Processing and Open Science

Category: Open access

My problem with ResearchGate and Academia.edu

TLDR; you can find my publications in Aalborg University’s repository or ORCID.

ResearchGate – wow, a social network for scientists and researchers you might think. But think again about the ‘wow’. At least I am not so impressed. Here’s why…

I once created a profile on ResearchGate out of curiosity. It initially seemed like a good idea, but I soon realised that this would just add to the list of profile pages I would have to update, sigh. But so far I have kept my profile for fear of missing out. What if others cannot find my publications if I am not on ResearchGate? And so on…

But updating my profile is just the tip of the iceberg. What I find far more problematic about the site is their keen attempts to create a walled garden community. Let me explain what I mean. Take this paper for example (this is not a critique of this paper – in fact I think this is an example of a very interesting paper): One-Bit Compressive Sensing of Dictionary-Sparse Signals by Rich Baraniuk, Simon Foucart, Deanna Needell, Yaniv Plan, and Mary Wootters:

  1. First of all, when you click the link to the paper above you cannot even see it without logging in on ResearchGate.
    “What’s the problem?”, you might think. “ResearchGate is free – just create an account and log in”. But I would argue that open access is not open access if you have to register and log in to read the paper – even if it is free.
  2. Once you log in and can finally see the paper, it turns out that you cannot read the actual paper. This appears to be because the author has not uploaded the full text and ResearchGate displays a button where you can “Request full-text” to ask the author to provide it.
    “Now what?!”, you are thinking. “This is a great service to both readers and authors, making it easy to connect authors to their readers and enabling them to easily give the readers what they are looking for” – wrong! This is a hoax set up up by ResearchGate to convince readers that they are a great benevolent provider of open access literature.

The problem is that the paper is already accessible here: on arXiv – where it should be. ResearchGate has just scraped the paper info from arXiv and are trying to persuade the author to upload it to ResearchGate as well to make it look like ResearchGate is the place to go to read this paper. They could have chosen to simply link to the paper on arXiv, making it easy for readers to find it straight away. But they will not do that, because they want readers to stay inside their walled garden, controlling the information flow to create a false impression that ResearchGate is the only solution.

As if this was not enough, there are yet other reasons to reconsider your membership. For example, they are contributing to journal impact factor abuse-like metric obsession with their ResearchGate score. The problem is that this score is not transparent and not reproducible contributing only to an obsession with numbers driving “shiny” research and encouraging gaming of metrics.

I don’t know about you, but I have had enough – I quit!

…The clever reader has checked and noticed that I have not deleted my ResearchGate profile. Why? Am I just another hypocrite? Look closer – you will notice that the only publication on my profile is a note explaining why I do not wish to use ResearchGate. I think it is better to actively inform about my choice and attack the problem from the inside rather than just staying silently away.

Update 6th of July 2016…

I have now had a closer look at Academia.edu as well and it turns out that they are doing more or less the same, so I have decided to quit this network as well. They do not let you read papers without logging in and they also seem to have papers obviously scraped from arXiv, waiting for the author to upload the full-text version and ignoring the fact that it is available on arXiv. Again, they want to gather everything in-house to make it appear as if they are the rightful gate-keepers of all research.

As I did on ResearchGate as well, I have left my profile on Academia.edu with just a single publication which is basically this blog post (and a publication which is a link to my publications on Aalborg University’s repository.

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Thoughts about Scholarly HTML

The company science.ai is working on a draft standard (or what I guess they hope will eventually become a standard) called Scholarly HTML. The purpose of this seems to be to standardise the way scholarly articles are structured as HTML in order to use that as a more semantic alternative to for example PDF which may look nice but does nothing to help understand the structure of the content, probably more the contrary.
They present their proposed standard in this document. They also seem to have formed a community group at the World Wide Web Consortium. It appears this is not a new initiative. There was already a previous project called Scholarly HTML, but science.ai seem to be trying to help take the idea further from there. Martin Fenner wrote a bit of background story behind the original Scholarly HTML.
I read science.ai’s proposal. It seems like a very promising initiative because it would allow scholarly articles across publishers to be understood better by, not least, algorithms for content mining, automated literature search, recommender systems etc. It would be particularly helpful if all publishers had a common standard for marking up articles and HTML seems a good choice since you only need a web browser to display it. This is also another nice feature about it. I tend to read a lot on my mobile phone and tablet and it really is a pain when the content does not fit the screen. This is often the case with PDF which does not reflow too well in the apps I use for viewing. Here HTML would be much better, not being physical page-focused like PDF.
I started looking at this proposal because it seemed like a natural direction to look further in from my crude preliminary experiments in Publishing Mathematics in e-books.
After reading the proposal, a few questions arose:

  1. The way the formatting of references is described, it seems to me as if references can be of type “schema:Book” or “schema:ScholarlyArticle”. Does this mean that they do not consider a need to cite anything but books or scholarly articles? I know that some people hold the IMO very conservative view that the reference list should only refer to peer-reviewed material, but this is too constrained and I certainly think it will be relevant to cite websites, data sets, source code etc. as well. It should all go into the reference list to make it easier to understand what the background material behind a paper is. This calls for a much richer selection of entry types. For example Biblatex’ entry types could serve as inspiration.
  2. The authors and affiliations section is described here. Author entries are described as having:

    property=”schema:author” or property=”schema:contributor” and a typeof=”sa:ContributorRole”

    I wonder if this way of specifying authors/contributors makes it possible to specify more granular roles or multiple roles for each author like for example Open Research Badges?

  3. Under article structure, they list the following types of sections:

    Sections are expected to be typed using the typeof attribute. The following typeof values are currently understood:

    sa:Funding (which has its specific structure)
    sa:Abstract
    sa:MaterialsAndMethods
    sa:Results
    sa:Conclusion
    sa:Acknowledgements
    sa:ReferenceList

    I think there is a need for more types of sections. I for example also see articles containing Introduction, Analysis, and Discussion sections and I am sure there must be more that I have not thought of.

Comments on “On the marginal cost of scholarly communication”

A new science publisher seems to have appeared recently, or publisher is probably not the right word… science.ai is apparently neither a journal nor a publisher per se. Rather, they seem to be focusing on developing a new publishing platform that provides a modern science publishing solution, built web-native from the bottom up.

The idea feels right and in my opinion, Standard Analytics (the company behind science.ai) could very likely become an important player in a future where I think journals will to a large extent be replaced by recommender systems and where papers can be narrowly categorised by topic rather than by where they were published. Go check out their introduction to their platform afterwards…

A few days ago, I became aware that they had published an article or blog post about “the marginal cost of scholarly communication” in which they examine what it costs as a publisher to publish scientific papers in a web-based format. This is a welcome contribution to the ongoing discussion of what is actually a “fair cost” of open access publishing, considering the very pricey APCs that some publishers charge (see for example Nature Publishing Group). In estimating this marginal cost they define

the minimum requirements for scholarly communication as: 1) submission, 2) management of editorial workflow and peer review, 3) typesetting, 4) DOI registration, and 5) long-term preservation.

They collect data on what these services cost using available vendors of such services and alternatively consider what they would cost if you assume the publisher has software available for performing the typesetting etc. (perhaps they have developed it themselves or have it available as free, open-source software). For the case where the all services are bought from vendors, they find that the marginal cost of publishing a paper is between $69 and $318. For the case where the publisher is assumed to have all necessary software available and basically only needs to pay for server hosting and registration of DOIs, the price is found to be dramatically lower – between $1.36 and $1.61 per paper.

Marginal Cost

This all sounds very interesting, but I found this marginal cost a bit unclear. They define the marginal cost of publishing a paper as follows:

The marginal cost only takes into account the cost of producing one additional scholarly article, therefore excluding fixed costs related to normal business operations.

OK, but here I get in doubt what they categorise as normal business operations. One example apparently is the membership cost to CrossRef for issuing DOIs:

As our focus is on marginal cost, we excluded the membership fee from our calculations.

However, in a box at the end of the article they mention eLife as a specific example:

Based on their 2014 annual report (eLife Sciences, 2014), eLife spent approximately $774,500 on vendor costs (equivalent to 15% of their total expenses). Given that eLife published 800 articles in 2014, their marginal cost of scholarly communication was $968 per article.

I was not able to find the specific amount of $774,500 myself in eLife’s annual report but, assuming it is correct, how do we know whether for example CrossRef membership costs are included in eLife’s vendor costs? If they are, this estimate of eLife’s marginal cost of publication is not comparable to marginal costs calculated in Standard Analytics’ paper as mentioned above.

We could also discuss how relevant the marginal cost is, at least if you are in fact

an agent looking to start an independent, peer-reviewed scholarly journal

I mean, in that situation you are actually looking to start from scratch and have to take all those “fixed costs related to normal business operations” into account…

I should also mention that I have highlighted the quotes above from the paper via hypothes.is here.

Typesetting Solutions

Standard Analytics seem to assume that typesetting will have to include conversion from Microsoft Word, LaTeX etc. and suggest Pandoc as a solution and ast the same time point out that there is a lack of such freely available solutions for those wishing to base their journal on their own software platform. If a prospective journal were to restrict submissions to be in LaTeX format, there are also solutions such as LateXML and ShareLaTeX‘s open source code could be used for this purpose as well. Other interesting solutions are also being developed and I think it is worth keeping an eye on initiatives like PeerJ’s paper-now. Finally, it could also be an idea to simply ask existing free, open-access journals how they handle these things (which I assume they do in a very low-cost way). One example I can think of is the Journal of Machine Learning Research.

Other Opinions

I just became aware that Cameron Neylon also wrote a post: The Marginal Costs of Article Publishing – Critiquing the Standard Analytics Study about Standard Analytics’ paper which I will go and read now…

Open Access Journals: What’s Missing?

I just came across this blog post by Nick Brown: Open Access journals: what’s not to like? This, maybe… That post was also what inspired the title of my post. His post really got me into writing mode, mostly because I don’t quite agree with him. I left this as a comment on ihs blog, but I felt it was worth repeating here.

Read the rest of this entry »

Episciences.org progress

Lately, I have been following the Episciences project as you may have noticed in my previous post. It seems there has been some more progress recently: I have just noticed that another “epi-committee” has been added to the site (I understand these epi-committees as a sort of editorial boards responsible for a given subject area). In addition to the existing math committee, the new committee is Episciences IAM (Informatics and Applied Mathematics). This sounds a bit closer to my area. I wonder if they consider signal processing to be in their area?
The page so far says that the committee is being formed and as such does not list any members yet. It will be interesting to see what this turns into.

Episciences.org update

I mentioned the Episciences project the other day in Scientific journals as an overlay. In the meantime I have tried to contact the people behind this project and The Open Journal, apparently without any luck.

I went and checked the Episciences website yesterday and it actually seems that they are moving forward. They changed the page design completely and there is now a button in the upper right corner to create an account and log in. I took the liberty of doing so to have a look around. I was able to create an account, but is just about it so far. The site still seems quite “beta” – I was not able to save changes to my profile and I cannot yet find anywhere to submit papers. It is nice to see some progress on the platform and I will be keeping an eager eye on it to find out when they will go operational.

Scientific journals as an overlay

There is an update on this post in Episciences.org update

In many of my posts since I started this blog, I have been writing about open peer review. Another topic related to open science that interests me is open access (to scientific papers). Part of open access in practice is about authors posting their papers, perhaps submitted to traditional journals, to preprint servers such as arXiv. This is used a lot, particularly in physics and mathematics.
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The Winnower officially launches today

I have written about The Winnower here before. I have been involved in testing the platform during the past couple of months and must say that it looks very promising.
Today they officially launch! Now it is just up to us to participate and make a change towards transparent publishing with open review.

Rock Your Paper

I noticed a new web site some time ago: rockyourpaper.org. It is first and foremost a search engine for open access research papers. You can search for open access papers from lots of different publishers and they aim to be the place to go for open access research.

Their initial motivation is to provide easy access to research to students and researchers from countries that typically cannot afford access to the expensive subscription journals. I talked to Rock Your Paper co-founder Neeraj Mehta about their platform to find out a bit more about it.

Rock Your Paper (RYP) started on October 18th, 2013. It is not the only place to search for open access papers. Other possibilities of course include the publishers’ sites themselves, but this is hard work considering the many different publishers you would have to visit. Another centralised place to search for papers is the Directory of Open Access Journals (DOAJ) where you can search among, at the time of writing, 1,573,847 open access papers. When I spoke to Neeraj in January, RYP was hoping to index 20 million research papers by January 31st. In addition, they provide another layer of service to its users. You can create an account with RYP and save both searches and individual papers so that you can keep track of “what was it I searched for the other day when I found that paper…”

Rock Your Paper is a for-profit startup company that of course hopes to earn money from their services, but they promise that their basic search and access features will remain free for users. This seems very much in line with their initial purpose. They may extend their services along the way with additional features such as formatting, editing and translation which users will need to pay for.

Initially, they are aiming to establish themselves first and foremost as an open access search engine. Later on, they may also extend the platform to let users publish research. They have also approached publishers of subscription-based journals about the possibility of providing discounted access to these, but unfortunately they have not had any luck with this yet.

I think Rock Your Paper sounds like one of many interesting new players in the open access / open science area that will be exciting to follow.

A look at the process of submitting articles to OA journals | Open Science

A look at the process of submitting articles to OA journals | Open Science.

If you are thinking of publishing your article in an open access model, there are usually two paths to choose from. One – you can publish in Green OA, which means adding the paper to a specially prepared repository (self-archiving). Two – you can choose the Gold OA model and submit your article to an OA journal, where it will be corrected, peer-reviewed then published. At this point I would like to briefly describe the process of submitting articles to OA journals for those who are considering just that option. It is a general description, and various steps may differ depending on the publisher and the journal.

Forest Vista

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Academic Karma

Re-engineering Peer Review

Pandelis Perakakis, PhD

Academic Website

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PEER REVIEW WATCH

Peer-review is the gold standard of science. But an increasing number of retractions has made academics and journalists alike start questioning the peer-review process. This blog gets underneath the skin of peer-review and takes a look at the issues the process is facing today.

Short, Fat Matrices

a research blog by Dustin G. Mixon

www.rockyourpaper.org

Discover and manage research articles...

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