Posts Tagged ‘Electronic publishing’

Open Access journal publishing debates – the elephant in the room?

Sunday, November 4th, 2018

For perhaps ten years now, the future of scientific publishing has been hotly debated. The traditional models are often thought to be badly broken, although convergence to a consensus of what a better model should be is not apparently close. But to my mind, much of this debate seems to miss one important point, how to publish data.

Thus, at one extreme is COAlition S, a model which promotes the key principle that “after 1 January 2020 scientific publications on the results from research funded by public grants provided by national and European research councils and funding bodies, must be published in compliant Open Access Journals or on compliant Open Access Platforms.” This includes ten principles, one of which “The ‘hybrid’ model of publishing is not compliant with the above principles” has revealed some strong dissent, as seen at forbetterscience.com/2018/09/11/response-to-plan-s-from-academic-researchers-unethical-too-risky I should explain that hybrid journals are those where the business model includes both institutional closed-access to the journal via a subscription charge paid by the library, coupled with the option for individual authors to purchase an Open Access release of an article so that it sits outside the subscription. The dissenters argue that non-OA and hybrid journals include many traditional ones, which especially in chemistry are regarded as those with the best impact factors and very much as the journals to publish in to maximise both the readership, hence the impact of the research and thus researcher’s career prospects. Thus many (not all) of the American Chemical Society (ACS) and Royal Society of Chemistry (RSC) journals currently fall into this category, as well as commercial publishers of journals such as Nature, Nature Chemistry,Science, Angew. Chemie, etc. 

So the debate is whether funded top ranking research in chemistry should in future always appear in non-hybrid OA journals (where the cost of publication is borne by article processing charges, or APCs) or in traditional subscription journals where the costs are borne by those institutions that can afford the subscription charges, but of course also limit the access.  A measure of how important and topical the debate is that there is even now a movie devoted to the topic which makes the point of how profitable commercial scientific publishing now is and hence how much resource is being diverted into these profit margins at the expense of funding basic science.

None of these debates however really takes a close look at the nature of the modern research paper. In chemistry at least, the evolution of such articles in the last 20 years (~ corresponding to the online era) has meant that whilst the size of the average article has remained static at around 10 “pages” (in quotes because of course the “page” is one of those legacy concepts related to print), another much newer component known as “Supporting information” or SI♥ has ballooned to absurd sizes. It can reach 1000 pages[1] and there are rumours of even larger SIs. The content of SI is of course mostly data. The size is often because the data is present in visual form (think spectra). As visual information, it is not easily “inter-operable” or “accessible”. Nor is it “findable” until commercial abstracting agencies chose to index it. Searches of such indexed data are most certainly “closed” (again depending on institutional purchases of access) and not “open access”. You may recognise these attributes as those of FAIR (Findable, accessible, inter-operable and re-usable). So even if an article in chemistry is published in pure OA form, in order to get FAIR access to the data associated with the article, you will probably have to go to a non-OA resource run by a commercial organisation for profit. Thus a 10 page article might itself be OA, but the full potential of its 1000+ page data (an elephant if ever there was one) ends up being very much not OA.

You might argue that the 1000+ pages of data does not require the services of an abstracting agency to be useful. Surely a human can get all the information they want from inspecting a visual spectrum? Here I raise the future prospects of AI (artificial intelligence). The ~1000 page SI I noted above[1] includes e.g NMR spectra for around 70 compounds (I tried to count them all visually, but could not be certain I found them all). A machine, trained to identify spectra from associated metadata (a feature of FAIR), could extract vastly more information than a human could from FAIR raw data‡ (a spectrum is already processed data, with implied information/data loss) in a given time. And for many articles, not just one. Thus FAIR data is very much targeted not only at humans but at the AI-trained machines of the future.

So I again repeat my assertion that focussing on whether an article is OA or not and whether publishing in hybrid journals is to be allowed or not by funders is missing that 100-fold bigger elephant in the room. For me, a publishing model that is fit for the future should include as a top priority a declaration of whether the data associated with it is FAIR. Thus in the Plan-S ten principles, FAIR is not mentioned at all. Only when FAIR-enabled data becomes part of the debates can we truly say that the article and its data are on its way to being properly open access.

‡The FAIR concept did not originally differentiate between processed data (i.e. spectra) and the underlying primary or raw data on which the processed data is based. Our own implementation of FAIR data includes both types of data; raw for machine reprocessing if required, and processed data for human interpretation. Along with a rich set of metadata, itself often created using carefully designed workflows conducted by machines.

♥The proportion of articles relating to chemistry which do not include some form of SI is probably low. These would include articles which simply provide a new model or interpretation of previously published data, reporting no new data of their own. A famous historical example is Michael Dewar’s re-interpretation of the structure of stipitatic acid[2] which founded the new area of non-benzenoid aromaticity.

References

  1. J.M. Lopchuk, K. Fjelbye, Y. Kawamata, L.R. Malins, C. Pan, R. Gianatassio, J. Wang, L. Prieto, J. Bradow, T.A. Brandt, M.R. Collins, J. Elleraas, J. Ewanicki, W. Farrell, O.O. Fadeyi, G.M. Gallego, J.J. Mousseau, R. Oliver, N.W. Sach, J.K. Smith, J.E. Spangler, H. Zhu, J. Zhu, and P.S. Baran, "Strain-Release Heteroatom Functionalization: Development, Scope, and Stereospecificity", Journal of the American Chemical Society, vol. 139, pp. 3209-3226, 2017. https://doi.org/10.1021/jacs.6b13229
  2. M.J.S. DEWAR, "Structure of Stipitatic Acid", Nature, vol. 155, pp. 50-51, 1945. https://doi.org/10.1038/155050b0

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Two stories about Open Peer Review (OPR), the next stage in Open Access (OA).

Thursday, October 5th, 2017

We have heard a lot about OA or Open Access (of journal articles) in the last five years, often in association with the APC (Article Processing Charge) model of funding such OA availability. Rather less discussed is how the model of the peer review of these articles might also evolve into an Open environment. Here I muse about two experiences I had recently.

Organising the peer review of journal articles is often now seen as the single most important activity a journal publisher can undertake on behalf of the scientific community; the very reputation of the journal depends on this process being conducted responsibly, thoroughly and with integrity by the selected reviewers. Reviewers conduct this process voluntarily, mostly anonymously, without remuneration or recognition and often with short deadlines for completion. After one such process, I recently received an interesting follow-up email from the journal, suggesting I register my activity with Publons.com, a site set up to register and give non-anonymous credit for reviewing activities. I should say that Publons is a commercial company, set up in 2012 to to “address the static state of peer-reviewing practices in scholarly communication, with a view to encourage collaboration and speed up scientific development”. Worthy aims, but like many a .com company nowadays, one might ask what the back-story might be. Thus many of the Internet giants, Google, Facebook, Twitter etc, do have back-stories, which often underpin their business models, but which may only emerge years after their founding. With only a hazy idea of what Publons’ back-story might be, I went ahead and registered my reviewing activity.

After doing so, I then accessed my entry. You only learn that I have reviewed for a particular journal, but nothing about the actual process itself. I did not really think that this experiment had done much to encourage collaboration and speed up scientific development. It might be useful for early career researchers to get their name exposed however.

I can almost understand why the review itself might not be publicly displayed, but as a result you learn nothing about the factual basis of the review and whether it might have been conducted responsibly, thoroughly and with integrity. Instead, I now suspect that the presence of my name on this site might merely encourage other publishers to deluge me with requests for further (freely donated) refereeing.

Discussing this at lunch, a colleague (thanks Ed!) reminded me of a veritable journal called Organic Syntheses. Here, authors submit a synthetic procedure and open identified “checkers” are invited to repeat the procedure and comment on it. The two roles are kept separate (i.e. the checkers do not become co-authors), but they could get credit for their activity. Thus if you view a typical recent entry[1] you will see a full biography and affiliation of the checkers given at the end, with footnotes often describing their own observations if they differ from those of the authors. 

This set me thinking whether an open peer review process might also contain such an element of checking, as well as informed comment, nay opinion, about the article itself and the conclusions it makes. The opportunity arose when I was contacted by an author who was about to submit a computational article to a journal. This journal allowed open peer review. If I agreed to review, my name would be attached to the article if accepted for publication. I undertook this on the basis that I would use this review to conduct some limited checking of the computations and other assumptions underpinning the conclusions in the submitted article. I also wanted this open process to include the data on which my review was based. Most importantly if anyone wished to replicate my replication, the barriers to doing so should be as low as is possible. Shortly thereafter, I received a formal invitation from the journal and I set about my task. Crucially, all my own calculations supporting the review were archived in a data repository, albeit under embargo. In my cover letter I included the DOI for my data and the embargo access code, so that the authors (and the editor of the journal if they so wished) could inspect the data against which I wrote my review.

Then followed standard procedures, whereby the authors took my comments into consideration, revised the article and the final version was indeed accepted and published.[2] You will find the two referees/checkers listed, although unlike Organic Syntheses,  there is no bibliographic information about them or their affiliation. I did ask the journal if they could at least link my ORCID identifier to my name, but that request was refused. If my name had been a common one, then disambiguating it into a unique identity could be a challenge. There was also no mechanism to associate my identity on the journal with any data on which I had based my review. Really, the only open aspect of this process was just my (potentially ambiguous) name, nothing else. No follow-up was received from the journal to add the review to Publons. 

The next stage was to contact the author who had originally set the process under way to ask them if they would mind my releasing the data on which my review had been based. They agreed, as also they did to my telling this story. The overall outcome is thus a published article with the reviewers (if not their reviews or any supporting evidence for their review) openly named. In this specific case, there is also an open dataset with a formal link back to the article in the form of a DOI (10.14469/hpc/2640, although I suspect this aspect is unique, even precedent setting), but one driven by the reviewer and not the journal. It would be nice to have bidirectional links between both article and the review data, but I do not know any publishers currently operating such a mechanism (if anyone knows such, please tell).

Now to the broader questions about the process described above. I think that the aspiration to encourage collaboration and speed up scientific development may indeed have been promoted by this association between article and the data assembled by the reviewer. Whether the final article was improved as a result of the processes described here I will leave the authors to comment if they wish. As with the checkers employed by Organic Syntheses, such a review process takes not just time, but resources. Resources that currently have to be freely donated by the reviewers and their host institution and which clearly cannot become expensive, time-consuming or onerous. That was not the case as it happens here; my contributions were facilitated by my having sufficient expertise to perform the tasks I undertook really quite quickly.

I will raise one more issue; that of whether to add my review to the dataset which is now openly available. In fact it is not included, in part because it related to the initially submitted version of the MS. The final MS version has been revised and so many of the comments in my review may only make sense if you have the first version to hand. It would be perhaps unreasonable to make the first drafts of manuscripts routinely available (although historians of science would probably love that!) alongside the reviews of that first draft. But I could also see a case for doing so if the community agreed to it. One to discuss for the future I think. There is also the associated issue of what should happen to any dataset associated with a review in the event that the final article is rejected and not accepted. Should the data remain permanently under embargo and the reviewer’s identity permanently anonymous? Perhaps opening up even such datasets might nevertheless  encourage collaboration and speed up scientific development, but I fancy some would consider that a step too far!

References

  1. J. Zhu, "Preparation of N-Trifluoromethylthiosaccharin: A Shelf-Stable Electrophilic Reagent for Trifluoromethylthiolation", Organic Syntheses, vol. 94, pp. 217-233, 2017. https://doi.org/10.15227/orgsyn.094.0217
  2. L. Li, M. Lei, Y. Xie, H.F. Schaefer, B. Chen, and R. Hoffmann, "Stabilizing a different cyclooctatetraene stereoisomer", Proceedings of the National Academy of Sciences, vol. 114, pp. 9803-9808, 2017. https://doi.org/10.1073/pnas.1709586114

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Conference report: an example of collaborative open science (reaction IRCs).

Thursday, May 25th, 2017

It is a sign of the times that one travels to a conference well-connected. By which I mean email is on a constant drip-feed, with venue organisers ensuring each delegate receives their WiFi password even before their room key. So whilst I was at a conference espousing the benefits of open science, a nice example of open collaboration was initiated as a result of a received email.‡

Steven Kirk  contacted me with the following query: Do you know of any open-access database of calculated IRCs with coverage of as broad a range of classes of chemical reactions as possible? I recollected that about six years ago, I was exploring the use of iTunesU as a system for delivering course content in a rich-media format. I produced animations for about 115 reactions (many of which as it happens were taken from this blog, but quite a number were also unique to that project) and placed them into iTunesU, and now sending the URL https://itunes.apple.com/gb/course/id562191342 to Steven.

I should at this point explain something of the structure of such an iTunesU course.

  1. An essential feature is the course icon, seen below on the left. Since the course is hosted by Imperial College, it had to be an officially approved icon. I am sure you can believe me if I tell you that this took a month or so to obtain, with a fair bit of persistence required!
  2. I also had to get approval to place the iTunes app on all the teaching computers so that students could open the course. Believe me again when I tell you that I had to persuade the Apple lawyers in Cupertino to release a special license for this app to persuade our administrators here to install it on the Windows teaching clusters. Another few months had passed by.
  3. When creating an entry (using e.g. https://itunesu.itunes.apple.com/coursemanager/ ) one has to specify values for various descriptors, also often called metadata. Thus any one entry has fields for name and description, with the popularity added by Apple. Only a few words are visible in the description field, which can be expanded in iTunes using the i button.
  4. Steven meanwhile had replied asking if the original data that was used to generate the IRC might be available. Specifically his second question was “So the DOIs are only stamped into the animation’s bitmaps, or are they also somewhere in the metadata?“. That little i button is not easy to spot, and there is no indication, in the event, of what information it might actually contain.
  5. Here it is expanded. The contents are unstructured text, into which I have placed the required DOI.
  6. The lesson here is that I had fortunately had the foresight to include a link to the IRC data in anticipation of just such a question from someone in the future. But black mark to Apple here; the text cannot be selected and copied into a clipboard! It is fairly unFAIR data, since it can only be inter-operated (the I of FAIR) by a human re-typing it by hand. And the human has also to recognise the pattern of a DOI; a machine could not obtain this information easily. Moreover Steven is a Linux user; he does not readily have access to the iTunes app on this operating system!
  7. Also, there were 115 such entries, and now the prospect was rearing that each would have to be hand processed. Moreover, because the text was unstructured, there was no guarantee that I would have adopted the same pattern for all 115 entries.
  8. Fortunately Steven was on the ball. I quote again: it turns out iTunes isn’t needed at all. A service I found on the web http://picklemonkey.net/feedflipper-home/ takes an ITunes URL and converts it to an RSS feed. Opening this feed in Firefox and RSSOwl respectively let me save the feed as XML and HTML (both attached).
  9. This is currently where we stand (Steven’s first email was two days ago), but it’s not finished yet. Depending on how assiduous I was five years ago, some DOIs to the data may be acquired from the list. Sometimes I simply wrote e.g. See http://www.ch.imperial.ac.uk/rzepa/blog/?p=6816 knowing that the links to the data were there instead. I can already see that some descriptions have neither a DOI nor a link to the blog. More detective work will be needed, unfortunately.

How might the situation described above been avoided? Well, Apple in iTunesU only provided in effect one metadata field, and this was an unstructured one. Anything went in that field. Had they provided (or had the course creator been able to configure it themselves) there might have been another field entitled say “data source“. This could moreover been made a mandatory field and a structured one. Thus it might have only accepted known types of persistent identifier, such as a DOI. Further, the system could have checked that the DOI was actually resolvable. Before you ask, I did log a “bug” with Apple asking this be done, but nothing ever was. With such a tool to hand, I might have achieved data sources for all the 115 entries. The resulting XML (as generated above) could have been used to automate the retrieval of all 115 datasets describing this course. 

At this stage then, Steven can follow-up his interest in building a reaction IRC library and analysing it. I will do all I can to encourage Steven not to make the mistakes I did and to ensure that any further data that is required to augment the library does not suffer the problems above. On the other hand, I console myself that in two days, much of the data for the course I created five years ago was salvageable; I wonder how many other iTunesU courses there are for which that can be said!

I will let (with some blushing) the final word be Steven’s: You are one of the few chemists who has both pioneered and built the principles of ‘open chemistry’ into their actual scientific work. I visit your blog occasionally knowing that there is a very high probability I could download and tinker with the results of real calculations.

‡Might I assure all the speakers that I concentrated totally on their talks rather than incoming emails!

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