academic publishing (11 out of 11)

I'm doing my thesis corrections.

As you may know, my whole thesis writing process has been public on Github throughout, in the interests of #OpenScience and #LinkedResearch. The feedback from my examiners during my viva is documented as issues with the 'viva' tag, and I also opened more issues from my own notes during the defense.

If there are bits of my thesis you've read on the past or are particularly interested in, now would be a great time to file any other issues you've spotted for things you'd like to see updated or fixed in the final hardbound copy of my thesis which will, I presume, live in the University of Edinburgh library, survive the impending technological apocalypse, and generally outlive all of us. I aim to print the thing by the 31st of October.

🏷 https://linkedresearch.org/ academic publishing linked research open science thesis phd phdchat academia

Sun 17th of September 2017 at 11:42am (+02:00)

Week in review: 17 - 23 July

• Spent the week in Southampton and one day in Oxford talking about decentralisation, scholarly communication, LinkedResearch, personal data stores and the like with cool people like emax, csarven, bblfish, TimBL, Wendy, Nigel, Ramine, Jun, DDR..
• Imagined eprints as a tiny LDN-powered JS app (ldprints).
• Net magazine issue 296 came out in print.. With an article about Linked Data Notifications!
• Missed a bunch of buses.
• Spent a couple of hours eating great food at the Southbank Center food market, just like summer 2014 weekends. Remembered why I love and hate London.
• Surprise visited my Mum. Now I can tweet again.

🏷 academia academic publishing decentralisation ldn linked research social machines sociam travel week in review workshop

Sun 23rd of July 2017 at 10:35am (+01:00)



Why are technology conference organisers scared to innovate?

Why are they scared of taking risks to advance and benefit the community? Where do they get their excuses from? They're all the same and all debunkable. Is there a centralised excuse provider? Do the publishers have dirt on all organisers?

🏷 https://linkedresearch.org/ academic publishing linked research

Thu 8th of June 2017 at 3:32pm (+02:00)

At the ICWE conference dinner last night, it was proudly announced that they have finally signed a long term contract with Springer for proceedings publication.

I. Am. Confused.

This seems like a backward step. Locking another generation of researchers into a broken system of academic elitism and inaccessibility of knowledge. This does not conjure an appropriate picture of the future for the Web engineering community. Why have we engineered ourselves into a paywalled corner of static PDFs? Aren't we supposed to be pioneering here? Why is it such an "achievement" to pay a huge pile of money to a for-profit company to keep all of our hard work in a dead end, which our libraries and institutions have to pay again to get it back out of?

Is everyone just cool with this?

🏷 https://linkedresearch.org/ academic publishing icwe2017 linked research springer

Thu 8th of June 2017 at 2:25pm (+02:00)

Elsevier keeps 'ghost profiles' for people who don't have Mendeley accounts. You can "claim" your ghost, and it's "yours".. but uh.. not really because it's centralised. And this is presented like a nice fun helpful thing. Ghost profiles is some facebook-level creepy surveillence profiling shit. Makes me sad :( But not surprised.

🏷 academic publishing https://rhiaro.co.uk/tags/eswc2017 social web surveillence

Sun 28th of May 2017 at 3:00pm (+02:00)

Review of "Utilising Semantic Web Ontologies to publish Experimental Workflows"

In reply to: https://openscience.adaptcentre.ie/publications/2017/eswc/

I can see how the ultimate goal described by the article - to publish semantic representations of experimental workflows - contributes towards the vision of decentralised scholarly communication. Unfortunately I'm missing how the work described in the article contributes towards this ultimate goal. The abstract says you want to see how semantic workflow creation can "be combined with traditional forms of documentation and publication" but I don't see a result pertaining to this.

To begin with, the purpose of the tool is quite narrow. How do you know for sure that "advancing knowledge about the use of vocabularies in facilitating sharing and repeatability of experiments and replication of results" ultimately contributes towards reproducability of results, which is the high level goal of this work? How does knowledge of OPMW tie in with the authoring or experimentation process, for example? Are researchers expected to document their workflows as they go along, or retrospectively after the fact (I imagine this depends on the task at hand). For which stage is your tool intended? Or is it simply a teaching tool rather than designed for actually documenting workflows? This isn't clear.

I thought I might understand better by running the tool, but it seems to be broken.

I'm skeptical about the open world assumption and the "nature of Linked Data" being used as a reason to not provide any instruction for using the tool... I would have thought that whether instruction is needed is a UI concern.

There is no results or analysis section, and the tense makes it sound like the described experiment hasn't actually been carried out. Are you asking for feedback about the design of the experiment? If so, you should state this clearly in the introduction and abstract. if not then I'd like to read this again when your findings are ready.

The background work sections appear to be fairly comprehensive, but this is not my area of expertise, so if there is related work or other background information missing I am unable to point it out. It's not entirely clear how all of the related work describe relates to the problem at hand though so I'd like to see this be made explicit.

The discussion about nuances of licensing is interesting, for example licensing different parts of a workflow separately, and conveying this to people who want to replicate experiments and use the data produced. I think maybe the licensing topic deserves an article and experiment all of its own. Colour coding or different levels of alerts for different licensing to help people understand is an interesting UI challenge. I think ongoing work on Data Terms of Use might be interesting to you (this is about personal data rather than experimental data).

In summary, the stated goals make this worth further discussion, but it's not clear how the work you've done so far meets these goals. I'd like to know what are your next steps forward for this work, and technically how this could integrate with other projects related to exposing more semantically enriched academic research to the world.

🏷 academic publishing edsc2017 linked research reviews semantic web

Sat 27th of May 2017 at 6:35pm (+02:00)

Review of "Decentralized creation of academic documents using a Network Attached Storage (NAS) server"

In reply to: https://www.fiduswriter.org/2017/05/24/decentralized-creation-of-academic-documents-using-a-network-attached-storage-nas-server/

This article addresses quite a specific problem: collaborative document editing without third-party servers. The reasons for not wanting to rely on Web servers, even if they're under the control of the document author, is fairly well explained and motivated.

Addressing authoring solutions to MS Word users is diving in the deep end, but a worthy goal as this reaches a lot of researchers. However, I question that the idea of installing software is too complicated for most people.. do you not think it's possible to get the installation process for FW to be as simple as for MSWord?

I realise that this article is not about FidusWriter, but rather collaborative document editing via a NAS, but it would be helpful to explain more about what FidusWriter does and how it is normally run, ie. not on a NAS, and some comparison.

The authors seem to feel strongly about data ownership, mentioning privacy potentially being violated by corporations and governments. It's not clear however that FidusWriter provides a publishing solution, only an authoring solution. That is, once an article is finished it seems that a PDF is exported and turned over to third parties anyway? Relatedly, I would love to know more about how the authors envision this fitting in with the rest of the scholarly communication process, as mentioned in the abstract, particularly peer-review. Could a similar setup be purposed to permit reviewers to control their review contents as well? I assume FidusWriter takes care of access control, citations, formulas and figures, though the article does not state that.

The article mentions that there are other web services for academic authoring, but doesn't name any. I'd be interested to know which ones the authors analysed. Is it only the ones in the footnote? In which case only Authorea and Overleaf are problematic in the ways mentioned for running on third-party servers. I don't really see evidence that the authors have performed a comprehensive search for alternatives in this space. There are certainly clientside document authoring applications which run on personal data stores, such as Laverna which can talk to RemoteStorage servers, and dokieli (which I'm pretty sure the authors have heard of) which can talk to LDP servers, not to mention 'decentralised Google Docs' type things like NextCloud and CosyCloud. It would be worth finding out how easily any of these could be extended to add collaborative editing if they don't have it already, since they have the decentralisation part covered.

Thus, perhaps it's worth comparing running FidusWriter on a NAS to running various generic personal datastores. It seems to me that FidusWriter rather ties the editing application with the storage, which prevents the user from easily switching applications. It's not clear if FW follows a standard protocol for data exchange with the server either. These aren't really the problems of the authors in this context, but it is a downside of a non-standard system even if it's open source and installed on the user's machine. Useful future work might be taking the idea of a NAS forward with other storage/server and client/application options.

That said, I would love to see a docker image prepared to easily set up FidusWriter on any server, if that doesn't already exist!

Limitations are appropriately mentioned as cost and power of NAS devices, though no specifics are given.

Finally, the authors assume a status-quo vision of academic authoring (eg. the "need" for blind peer review) and proceed from there with a decentralisation angle. More interesting would be a paragraph or two about how an approach like this is setting the stage for future advancement in the space. I like the idea of meeting in the middle; addressing immediate problems authors have with their current tooling, whilst laying some foundations for progressing in the direction opened up to us by Web technologies.

Minor comment: what is meant by "Linux boxes" (in quotes)? Are you getting at things like Raspberry Pis?

And I can't help but ask: did you collaboratively author this article using FidusWriter on a NAS? Some screenshots of doing so would add a whole new layer of credibility to your analysis :)

🏷 academic publishing authoring decentralisation fidus writer linked research reviews https://linkedresearch.org/

Sat 27th of May 2017 at 5:05pm (+02:00)

A response to "Scholarly Social Machines"

In reply to: http://www.oerc.ox.ac.uk/sites/default/files/users/user384/scholarly-social-machines.html

This article looks at the scholarly communication ecosystem through the lens of social machines; something I have thought about a lot but only partially articulated through my contributions to Linked Research. In particular, the hypothesis that we are struggling to improve the state of scholarly communication despite advancements in technology because we are trapped in a machine we have ceased to see is interesting. I've had many conversations with people over the last couple of years who balk at any suggestion of a radical upheaval of scholarly communication, hiding behind notions of futility of incentivising researchers to do anything other than pubish or persih, the immovability of the for-profit publishing industry. They complain about the state of things, yet are transfixed by the status quo. I think that framing this problem as a 'trap' will perhaps nudge folks into looking for a way out, and social machines is a useful concept to work with, something very demonstrably real in other domains, and this might help with finding a perspective on scholarly communication.

The article mentions the 'ecosystem' and lists some of the stages. I think it's worth noting that in Linked Research: An Approach for Scholarly Communication we characterised the different stages, roles and actors in scholarly communication in detail (there's even a diagram!). It's important because this is a hard problem, too big a space, to talk about all at once, and breaking it down into smaller chunks that nonetheless interlink (and the interlinking is critical) can help.

Dave writes that we see the same articles about how to improve being published over and over again, and this is true. I assembled a collection of some of them here. People lament that it's too hard to change, and us Linked Research-y types release software and publish our work in a Webby decentralised way (just like Dave has done, for the version of his article that I'm reading) and shove it under peoples' noses and cry that here is the proof that it's not too hard, and if only a few more people would bother we could iron out the wrinkles and make it easier and easier for everyone to participate. It's catching on, but agonisingly slowly. Most people still smile sadly, with a look of concern about the non-future of our academic careers. Dave writes of the "Catch-22" of using traditional publishing to try to solve some of the problems; and it's true. Even csarven is pushing 'papers' to academic conferences about Linked Research and related tooling in the hopes that academics will pay attention (and so he can get his PhD within this broken system). We console ourselves that at least the PDFs were generated from HTML and CSS, and a link to an open access Web version remains in the abstract even from behind Springer's paywall. Yet somehow the dual effort of publishing 'properly' and demonstrating alternatives is still not ticking the right boxes! What's up with that? So we need a new tactic, and the questions raised in this article are pragmatic and challenging, and a step in the right direction.

Question 8 is important because I often find that when we provocatively push "extreme decentralisation" via Linked Research, people push back against that as too difficult, too flakey, underdeveloped. We're arguing from this end of the spectrum because we're fighting against the very other end right now. But it is a spectrum, and better - more robust, more powerful - would be something in between. One example: the response that an individual can't possibly be counted on to keep their research online for eternity ignores the roles libraries and institutions (and indeed traditional publishers) can play in archiving and indexing work over time.

Another note to reinforce the importance of stepping outside to look in at scholarly communication: people, mostly software engineers, with whom I work on decentralised Social Web technologies look on at academia with confoundment. People claiming to be Web Scientists are putting PDFs behind paywalls? Life-saving medical research is accessible to what percentage of human beings? It seems obvious to the outside that we're really screwing things up here. Dave implies that we need to push people towards revolution over evolution, but we need to open a few more eyes before this can happen.

So how do we get people to step outside and look back in? This article doesn't address this. Arguably the people who will show up to Dave's presentation of this are already eyes-open, so perhaps together we can scheme to break the spell that the status quo holds over others.

Framing this (improving the scholarly comms ecosystem) as an interdisciplinary research problem could be emphasised more. Certainly we could solve all of the technical problems, but the social and political ones remain. I hope that we can take some inspiration from SOCIAM in tackling this in the years to come.

🏷 academic publishing edsc2017 linked research reviews social machines https://linkedresearch.org/

Sat 27th of May 2017 at 3:47pm (+02:00)

Review of Instrumenting Continuous Knowledge Extraction, Sharing, and Benchmarking

In reply to: https://marco-brambilla.com/2017/05/11/instrumenting-continuous-knowledge-extraction-sharing-and-benchmarking/

I like how this article seeks to accommodate a broad view of viable data sources for research, and particularly encourages data sharing and reuse between researchers.

The authors provide three examples of existing tools which could do (or be adapted to do) parts of the suggested pipeline. I hope that publishing this encourages others who are developing tools along these lines to come forward and let the authors and others know so that the community can start a comprehensive directory, as I'm sure there are plenty more.

It would be helpful to also have a characterisation of what is definitely missing as far as the authors know, and what the authors think are good directions to priortise for near term research and development.

Obviously I agree with the authors' call to open source such tooling for community benefit. I'd be particularly interested to hear your thoughts on the "agreed-upon integration platform" and what you think the best forum for discussing such a platform would be. Hopefully we can come up with ideas for that during the EDSC workshop discussion sessions!

🏷 academia academic publishing edsc2017 linked research review semantic web https://linkedresearch.org/

Fri 19th of May 2017 at 1:01pm (+02:00)

It's about keeping our jobs and keeping publishers in business. It's not about advancing the state of the Web. Boring.

Keeping your job is more important than your research having an impact. Okay fine, you can have that opinion. But get out of my way.

I struggle to relate to pushback against Linked Research ideas because of money/job/norms problems. I get that these are important issues for some people, but I'm so TIRED of people using this to blockade even discussing it. It's like they don't want the status quo to change; it's comfortable. They know one way to keep their job or get funding, and won't contemplate developing others. Use the goverment funding assignment as an excuse. Easy out, no point in bothering, the government will never change. Reinforce this for the next cohort of student. Keep perpetuating the problems for the next generation. This isn't what I want from academia, and I won't play.

🏷 academic publishing linked research #WOW2017 WWW2017 https://linkedresearch.org/

Tue 4th of April 2017 at 5:00pm (+08:00)

Pioneering the Linked Open Research cloud

This year, the Linked Data on the Web workshop at WWW2017 held an open discussion session about academic publishing. In particular, about what is getting in the way of us getting more research outputs into the LOD Cloud. The discussion was led by Sarven Capadisli, the loudest voice behind the Linked Research initiative, who did his best to remain a neutral facilitator, and let others in the room argue about the things he is normally arguing about.

There was a general consensus that we should have research from the Linked Data on the Web community in the form of Linked Data, and on the Web. Sounds like kind of a no-brainer, but you'd be surprised. Or maybe you wouldn't. The group, around 30 people, discussed the reasons why we, as a community, are lagging.

One of the reasons is tooling. Nobody wants to hand-author HTML, especially not with RDFa in. Nobody really wants to turn their research articles into datasets in any other syntax either. There are (apparently) still a large portion of researchers even in CS who use MSWord to generate their final PDFs so they need something that works at least as well as that to generate Web-friendly submissions.

There is also a matter of incentives, on several different fronts. Most researchers are a-researchin' and publishing their work to advance their career, and to get funding so they can do new cool stuff. So how are individual researchers incentivised to put in the extra effort it takes to generate HTML? On another level, how do we incentivise researchers to improve the state of tooling and resources? The first can be tackled along multiple fronts, one of which is petitioning publishers to demand HTML (just like today they demand LaTeX). What are the incentives for publishers to do this? There were a few ideas thrown around, including how they can improve their SEO, access, discoverability, and creating more pleasurable reading experiences than PDFs can deliver.

But there's a large faction ill-at-ease with depending so much on publishers to drive this change, even if it didn't look like it would be an agonisingly slow process. Some of us, myself included, would like to shift the whole scholarly communications process to be more self-sufficient and less dependant on centralised third parties. We do not want to do this at the expense of quality of work of course! (Which some people immediately assume is the case). Beyond publishing, we want to open up the review process, so it's both more transparent, and so researchers get the credit they deserve for this work. Conversations can continue well beyond the submission process if the reviews are open and public. But again, we need to work on the tooling and incentives to enable this.

Whilst I agree that we are woefully underdeveloped on the tooling front, I object to the weight this was given in the context of getting just Linked Data researchers to adapt to the Web. Personally I think if Linked Data researchers are going to cry about being required to submit their contributions as Linked Data, I will have trouble taking them seriously. Writing HTML is not a high bar. If you're comfortable with LaTeX, you can switch off a few neurons and write HTML instead. Or you can use Pandoc. As Jens Lehmann succinctly put it, the LDOW workshop is about advancing the state of Linked Data on the Web. If this community is not prepared to drive the state of this forward, even (especially?) if it includes working outside of the current system and taking some risks, who is going to?

So overall there was a vague feeling of consensus that we need to do something to take better advantage of Web technologies, and that LDOW as an established and respected venue is a good grounds for an experiment. I don't know if LDOW will manage to require HTML submissions next year, but the organising committee seem like they'll be inclined to strongly incentivise it. Stay tuned (watch the public-lod@w3.org mailing list. And speak up, if you care. Notes from the session are here.

We'll be continuing this discussion in the Web Observatories workshop this afternoon, around 4pm.

PS. the Enabling Decentralised Scholarly Communication workshop at ESWC this year requires Web-based submissions and is all about building and connecting the tooling to advance the state of academic publishing on the Web. Deadline is 17th of April. See you there.

🏷 academia academic publishing csarven ldow2017 linked data linked research Open Access WWW2017

Tue 4th of April 2017 at 9:51am (+08:00)