The Golden Road and the Green Driver

Quote/commentary on the replies of Johannes Fournier [JF] to Richard Poynder in
The Open Access Interviews: Johannes Fournier, speaking for the Global Research Council.”

JF: “Personally, I see one definite advantage of the Golden Road: it brings with it clear regulations as regards re-use. Contrastingly, self-archiving will often not provide the legal basis that allows for specific forms of re-use like text-and data-mining.”

This is the classic example of “letting the ‘best’ become the enemy of the ‘better'”.

Free-access (“Gratis OA“) is within reach (via universal Green OA mandates), free-access-plus-re-use-rights (“Libre OA”) is not.

Re-use is use-less without access, and we are nowhere near having free-access to all, most, or much of the journal-article corpus.

Or, to put it another way, the first and foremost “use” is access. So losing more of the precious time (and use) that has already been lost by continuing to over-reach for re-use rights when users don’t even grasp the use that is already within reach, is, for want of a better word, a persistent head-shaker in the slow, sad saga of OA.

JF: “My views on self-archiving mandates are grounded in the philosophy of the organisation that employs me. The DFG is self-governed by researchers? And researchers don?t like to be forced to do things, they like to be supported and encouraged. For that reason, the DFG encourages open access by funding opportunities that facilitate providing research results in open access.”

If one thing has been learnt from the slow, sad saga of OA (now at least two decades old) it is that mandating OA works, but encouraging it doesn’t.

And neither the DFG nor DFG researchers are any different in this regard. The notion that mandating OA would be an illegal constraint on academic freedom in the DFG remains just as wrong-headed today as it has been since the first day it began to be endlessly parroted — as wrong-headed as the notion that mandating “publish or perish” (which is, of course, mandated in the DFG, just as it is everywhere else in the research world) would be an illegal constraint on academic freedom in the DFG.

JF: “a dichotomy between Green and Gold tends to obscure the question we really need to ask ourselves: what kind of mechanisms could be designed in order to shift money from acquisition budgets into publication funds? Because the transition to open access will only succeed if we find ways to reinvest those funds which are already used to pay for information provision.”

The goal of Open Access to research is Open Access to research. If we had universal OA to research, the “serials crisis” would instantly become a minor matter rather than the life/death issue it is now (Think about it.)

But, yes, universal, sustainable OA will indeed entail a “shift [of] money from acquisition budgets into publication funds.” The missing causal component in this irreproachable reasoning, however, is: “what will drive that shift?”.

And that missing causal component (again: think about it) is universal mandatory Green OA self-archiving. (I will not, yet again, spell out the causal contingencies. See here and here.)

JF: “the need to buy the subscription content remains. Yet although the transition requires additional money, it might not be necessary to really pay twice: one could operate more economically if the subscription prices for a local library or for a consortium were adjusted to the growth of publication fees. That?s how to avoid so-called double-dipping? I know this sounds very simple and might be rather complex in its implementation, especially because the implementation is likely to require that the funding streams are readjusted.”

The “implementation” might be rather complex indeed, without mandatory Green OA to drive down costs and force the shift. About as complex as alleviating world hunger, disease or poverty by likewise “readjusting funding streams”…

#openaccess; Let’s get rid of “Green” “Gold” and use precise language such as “CC-BY”. And be joyous.

Cameron Neylon has written a compelling article and why we should get rid of “Green” “Gold” “Open Access” as meaningful labels. Because they no longer mean anything. They are as useful as “healthy” in a burger advertisement. I’m not going to repeat Cameron’s arguments – just read them yourself and redistribute.

Most publishers now produce inconsistent quasi-legal rubbish on their web pages. The try to write terms and conditions that are meaningful and normally they aren’t. They are almost an insult to readers (most of whom are actually intelligent knowledgeable humans). There is a spectrum of rubbish, varying from specialist departments of “Universal Access” whose business is in producing platitudes and not answering questions, to others that think that “all-rights-reserved” means something.

I was alerted to an article in IOP (Don’t switch off – it’s about building Klingon-like cloaking devices)

New Journal of Physics
Volume 15 March 2013

J C Soric et al 2013 New J. Phys.
15 033037 doi:10.1088/1367-2630/15/3/033037

Demonstration of an ultralow profile cloak for scattering suppression of a finite-length rod in free space


And I could READ it! It proclaims:

Great – it’s CC-BY. I can download it and feed it to #ami2 – our semantic program for extracting science from PDFs. But can #ami2 use it? I’d better check…

I look for the terms that refer to an individual like me – and my #ami2. I don’t seem to have many rights (my emphasis):

You may access, download, store, search and print hard copy of text.  Copying must be limited to making a single printed copy or electronic copies of a reasonable number of individual articles or other similar items.  No text accessed via the Service may be made available to a third party, either for commercial reward or free of charge, except that for inter-library loan purposes a single paper copy of an electronic original may be made and sent non-digitally to a library in the same country as you under fair dealing/use exemptions.  In addition, for inter-library loan purposes, you may make a single paper copy of an electronic original available to a library in the same country by secure transmission using Ariel (or its equivalent) whereby that electronic file is deleted immediately after printing.  Such supply must be for the purpose of research or private study and not for commercial use or onward transmission or distribution.  In the USA, such copies may only be made in compliance with Section 108 of the Copyright Act of the USA and within CONTU guidelines.

[#ami2 asks me what an “Interlibrary loan” is. I tell her it’s a piece of paper. She crashes.]

So these TaC forbid me to (say) redistribute this article by posting it in a text-corpus – on Bitbucket – for mining. (That’s a really important activity, BTW).

We have a contradiction. And physics hates contradictions. I have always thought of the IoP as reasonably good guys (not all scientific societies fall into this classification). I think something needs fixing.

There is a spectrum of publisher attitudes to licences. At one end we have BMC, PLoS, eLife, peerJ Charlie, and Tim Gowers initiatives and Ubiquity Press and… They positively WANT people to re-use material. It’s honest. At the other end we have unnamed (because I will get sued) publishers who state they are “incredibly helpful” to people like me and somehow seem to make re-use impossible through fudge, inconsistency deliberately unhelpful licences, bad or non-existent labelling etc. Phrases on Open Access papers like “This journal is Copyright XYZ”. Yes, the *journal* is copyright but the paper is APC-paid Open Access and you haven’t the decency to tell the world. That’s weasel words and an insult to the authors and readers. Be honest and say

“This article is CC-BY”. Revere the authors. They want you to acknowledge them and use the article or bits of it for anything anywhere for any legal purpose and they rejoice in people making money out of it without their explicit permission because the more this happens the prouder they feel and the more others value them.

So maybe we need a joyous declaration on scholarly papers. After all Open Access is good and wonderful.

A; Open access means people can live and make a better planet. Not-A: Closed access means people die. A OR not-A ?

I agree there are technical difficulties in some of this. So why doesn’t OASPA produce a simple template for its OA publishers (the ones that actually believe in OA) making a clear positive statement that can be stuck on web pages. You are welcome to mine as a starting point.




Molecular Genetics & Genomic Medicine publishes first articles

MGGMWe are delighted to announce that Molecular Genetics & Genomic Medicine (MGGM) has now published its first articles.

The journal opened for submissions at the end of 2012 and accepts submissions across the fields of genetic medicine and human molecular genetics. MGGM is edited by Dr Max Muenke.

The first articles to be published online are:

purple_lock_open Clinical and mutation analysis of 51 probands with anophthalmia and/or severe microphthalmia from a single center by Christina Gerth-Kahlert, Kathleen Williamson, Morad Ansari, Jacqueline K. Rainger, Volker Hingst, Theodor Zimmermann, Stefani Tech, Rudolf F. Guthoff, Veronica van Heyningen & David R. FitzPatrick
Summary: Mutations in three genes, SOX2, OTX2 and STRA6, account for 75% of the cases of severe bilateral eye malformations in a consecutive series of cases from a single centre. The phenotypic spectrum associated with mutations in each of these genes is wider than previously thought. We also report the first observation of a heterozygous loss-of-function allele of SOX2 that is inherited from an affected parent.

purple_lock_open Biochemical phenotype of a common disease-causing mutation and a possible therapeutic approach for the phosphomannomutase 2-associated disorder of glycosylation by Giuseppina Andreotti, Emilia Pedone, Assunta Giordano & Maria Vittoria Cubellis
Summary: Phosphomannomutase 2 deficiency represents the most frequent type of congenital disorders of glycosylation. For this disease there is no cure at present. We identified molecules that activate a common phosphomannomutase2 mutant and improve its thermophilicity, thermostability and resistance to proteases.

All of these articles are open access: free to read, download and share!

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Is DOAJ inadvertently promoting publisher power over scholars?

The Directory of Open Access Journals has a new feature, to narrow a search by Creative Commons licenses. This can be very useful for the article level search, as searchers may be looking for re-usable content. I use this type of limitation when searching flickr for photos that I can re-use, for example.

However, when this is used to calculate the percentage of DOAJ journals using a particular CC license, as Peter Suber does in this post this inadvertently makes the assumption that choice of licensing is made (should be made?) by journals and publishers, not by scholars.

Merely framing a research question in this way can limit the way that we think of potential answers. For example, there appears to be no way in this categorization to consider an approach such as that of First Monday, which provides authors with a range of choices. This is the option that I recommend for journals, the one that is most compatible with author choice and Freedom for scholarship in the internet age. The last thing that scholars need in the transition to open access is to replace subscription-publisher overlords with open access-publisher overlords.

This post is part of the Creative Commons and Open Access Critique series.

March Madness: PLOS ONE News and Blog Round-Up

1660014877_10c78dd1a9For the month of March, a variety of papers caught the media’s attention, from distracting cell phone conversations, to the devastating decline in forest elephants.  Here are some of the media highlights for this month:

Have you ever wondered where your hound originated from? In a paper featured this March, researchers have identified the fossil remains of the oldest domestic canine ancestor. In this study, researchers analyzed the DNA of a 33,000 year old tooth belonging to a Pleistocene dog from central Asia. In their evaluation of the fossil, they assessed its relationship to modern dogs and wolves’, concluding the tooth was more closely related to the domestic canine.

In another study, researchers at the Cleveland Clinic have found that football players might sustain long-term brain injuries without ever having a concussion. 67 players who had never suffered a concussion underwent testing over the course of a season.  The testing, which included blood sampling, brain scans, cognitive and functional assessments, screened for potential brain damage among the participants. The researchers searched for S100B in the blood, an antibody linked to brain damage. This antibody was found in many of the participants, with the highest levels belonging to the players with the most hits.

Have you ever found yourself distracted when a co-worker is on a phone call? In an eye-catching paper published this month, PLOS ONE authors examined the effects on attention and memory when listening to cell phone conversations, versus two-sided conversations. The participants were assigned a task while two conversations were in progress, one on a cell phone, and another between two individuals.  After the task was completed, the participants were assigned a recognition memory task and questionnaire measuring the distracting nature of the conversation. The participants who overhead the cell phone conversation measured it as much more distracting compared to the two-sided conversation.

And in a fourth study capturing the attention of many, researchers have examined the decline of forest elephants in Central Africa. The study concludes that forest elephants are being poached at increasing rates. Poaching, in addition to the human population rise and the absence of anti-poaching law enforcement, is contributing to the elephant’s population decline. The analysis revealed that 62 percent of the African forest elephants have been eliminated in the last decade due to poaching.

These four papers are just a taste of the variety of papers published this month. For more research headlines, visit our site here.



Druzhkova AS, Thalmann O, Trifonov VA, Leonard JA, Vorobieva NV, et al. (2013) Ancient DNA Analysis Affirms the Canid from Altai as a Primitive Dog. PLoS ONE 8(3): e57754. doi:10.1371/journal.pone.0057754

Marchi N, Bazarian JJ, Puvenna V, Janigro M, Ghosh C, et al. (2013) Consequences of Repeated Blood-Brain Barrier Disruption in Football Players. PLoS ONE 8(3): e56805. doi:10.1371/journal.pone.0056805

Galván VV, Vessal RS, Golley MT (2013) The Effects of Cell Phone Conversations on the Attention and Memory of Bystanders. PLoS ONE 8(3): e58579. doi:10.1371/journal.pone.0058579

Maisels F, Strindberg S, Blake S, Wittemyer G, Hart J, et al. (2013) Devastating Decline of Forest Elephants in Central Africa. PLoS ONE 8(3): e59469. doi:10.1371/journal.pone.0059469

Image: by digitalART2 on Flickr

Food Science & Nutrition – Issue 1:2 now live!

Food Science & Nutrition CoverYou can read Issue 1:2 of Food Science & Nutrition online now!

The journal publishes articles relating to all aspects of human food and nutrition, as well as interdisciplinary research that spans these two fields.  Food Science & Nutrition is an open access, fully peer-reviewed journal providing rapid dissemination of research in all areas of food science and nutrition. 

Read all our open access articles online here>

Below are some top articles which Editor-in-Chief Dr. Y. Martin Lo has highlighted from the second issue.

purple_lock_openNoni juice reduces lipid peroxidation–derived DNA adducts in heavy smokers
Mian-Ying Wang, Lin Peng, Claude J. Jensen, Shixin Deng and Brett J. West

Summary: A double-blind, placebo-controlled clinical trial revealed that noni juice may reduce lipid peroxidation–derived DNA adducts in the lymphocytes of heavy smokers. This effect is associated with antioxidant activity of noni juice and the presence of iridoids, the major phytochemical constituents of noni fruit.


Summary: Intact starch granules are an interesting stabilizer candidate for food grade Pickering emulsions. The stabilizing capacity of seven different intact starch granules for making oil-in-water emulsions has been the topic of this screening study. Among all types of starch studied quinoa had the predominantly best emulsifying properties and surprising long term stability over 2 years of storage.

Submit your paper here>    Sign up for eToC Alerts here>

#openaccess Can I use Wiley’s “Open Access” for teaching? NO

Wiley has an “Open Access” offering. I couldn’t find papers any so I tweeted and got:

“gold padlocks” and “purple padlocks”. “free” and “open”. Words and images that can mean anything. No idea whether it’s usable for teaching. Another tweet:

So off I go to the URL, find a paper on chemistry (there aren’t many, of course):

Is it actually Open? I find

So NO. I can’t use it for teaching (which is a commercial activity). I look for permissions:

And I get back

Which is useless.

So Wiley would like to hear from me, it says.

OK Wiley – I don’t think you are really trying hard enough. Open Access is about helping people get material, not making a trail of difficulties through purple and gold and open and half open and …

You’re actually telling us we don’t matter.

Just do the honourable thing like BMC PLoS and eLife and PeerJ and make it


That’s simple. It’s BLACK but it reads the same in any colour

Tuberculosis: Raising Awareness Through Research

One of the world’s deadliest infectious diseases has been with us since the time of the ancient Greeks and Romans. It has been found in thousand-year-old Egyptian mummies and is still present in millions of homes today. What is this ancient disease you may ask? Tuberculosis.

Pulmonary tuberculosis (TB) is a contagious bacterial infection in the lungs, which can spread to other organs. According to the CDC, TB is one of the most common infectious diseases in the world. And although significant progress has been made to eliminate this illness, 9 million new cases of tuberculosis were reported in 2011.

Tuberculosis is spread when an individual is exposed to a sneeze or cough of a person suffering from the disease. TB can also be contracted if someone has poor nutrition or living conditions.  In some cases, the infection can lie dormant in the body for years, and in others, it may become active and cause major complications. The primary stage of tuberculosis has no symptoms, but as the disease progresses, patients can suffer from bloody coughs, fatigue, fever and weight loss.

Ancient Roman physicians recommended treatments including bathing in human urine, eating wolf livers and drinking elephant blood. Today, though, modern medicine has found that Tuberculosis is preventable and treatable by more modern methods,  with early treatment being essential to stopping its progression.

In honor of World TB Day, observed yesterday on March 24th, here are some recently published papers from PLOS ONE on the subject:

Diabetes is a risk factor for TB, and it can also affect the severity of the infection and success of treatment. In a recent study, authors have researched the connection between diabetes, smoking and tuberculosis.  The cohort study featured patients suffering from their first episode of tuberculosis. Out of the 657 participants analyzed, diabetes was present in 25 percent, which increased the risk of death in the first 12 months after enrollment. Tobacco smoking also increased the risk of TB and caused further complications among diabetic patients.

In another recently published paper, researchers have investigated the outcome of aggressive treatments for multidrug-resistant tuberculosis. The patients analyzed were treated in a national outpatient program in Peru from 1999 to 2002. Participants received individualized regimens for laboratory-confirmed tuberculosis.  In this cohort examination, authors found that TB was cured in 66 percent of the patients, showing that aggressive regimens for multidrug-resistant tuberculosis can be extremely successful.

Lastly, the link between poverty and TB has been well established, but the mechanisms behind this link have not.  In a third PLOS ONE paper, authors investigated why the poor are at a greater risk for tuberculosis in India.  With data from the 2006 Demographic Health Survey, researchers analyzed incidences of TB and household economic status. They found low body mass index and air pollution may be partly responsible for the link between poverty and tuberculosis.

Further initiatives are needed to assist in the global eradication of tuberculosis. To expand your own awareness of this infectious disease, please explore additional PLOS ONE research here.



Reed GW, Choi H, Lee SY, Lee M, Kim Y, et al. (2013) Impact of Diabetes and Smoking on Mortality in Tuberculosis. PLoS ONE 8(2): e58044. doi:10.1371/journal.pone.0058044

Mitnick CD, Franke MF, Rich ML, Alcantara Viru FA, Appleton SC, et al. (2013) Aggressive Regimens for Multidrug-Resistant Tuberculosis Decrease All-Cause Mortality. PLoS ONE 8(3): e58664. doi:10.1371/journal.pone.0058664

Oxlade O, Murray M (2012) Tuberculosis and Poverty: Why Are the Poor at Greater Risk in India? PLoS ONE 7(11): e47533. doi:10.1371/journal.pone.0047533

Image: By isafmedia on Flickr

#scholrev: Strategy and decentralisation

I have already suggested our #scholrev should be decentralized (,,

) – now I’ll say why and suggest how we proceed.

Those of us in #scholrev are disillusioned enough that we want to do something different. Perhaps the most well promoted was “an alternative to Google Scholar” ( ) by Stian Håklev .

We need an open alternative to Google Scholar (like OSM [OpenStreetMap] is to GMaps). Imagine OJS/EPrints/DSpace pinging a central server with bibliographic metadata whenever a new article is published (like blogs pinging pingomatic), letting users contribute their own bibliographies. Every article would have a unique ID, enabling easy citation in any setting (a simple API would give citations in any format given the identifier, would also let you look a PDF file based on its hash, like MusicBrainz, or search). The database would be available for bulk download and data mining. Strongly integrated into all OA tools/citation managers, etc.

Why hasn’t this happened already? Because libraries would rather buy things than build them. That gets us locked into an increasing cycle of deprivation – the more we buy the less capacity we have for building. And every year it gets worse. We already see that institutional repositories look 10 years out of date – they aren’t full, no-one wants to put things in, they can’t be searched etc. Compare that with Stackoverflow, Github and Bitbucket, OpenStreetMap, etc. and you can escape the sense of frustration.

We want to do our own thing.

So for me, #scholrev has the following drivers:

  • Innovation
  • Social justice
  • Cost-effectiveness
  • Democracy

How to proceed? We have a lot of ground to catch up. But if OSM could change the world in 5 years so can we. We face two main problems:

  • The indifference and possibly hostility of universities
  • Lawyers and vested interests

The first problem just requires courage and determination (Wikipedia was trashed by Universities until they couldn’t ignore it). The second is a real problem and we have to minimise it. But both suggest that we should have some or all of our work outside the current academic infrastructure. If we are to reach out to the #scholarlypoor (the global South, SMEs everywhere, patients, etc.) we cannot do this through centralised mechanisms. Wikipedia and OSM had single clear goals initially (an open encyclopedia of everything, and an open map of the world). Our task is more varied. The grand visions for reforming scholarship include (and you will think of more) :

  • Machine semantic Indexing/access to some/all of the literature (“some” if the lawyers stop us doing “all”)
  • Democratising scholarship
  • Creative approaches to combining scholarship and authoring
  • Intelligent machines for reading and interpreting the literature
  • Alternatives to monographs

(these are all impossible at present).

These visions are too large and varied to plan top-down and must be bottom-up. They are also too large to coordinate at a detailed level. However #scholrev has shown there are lots of groups starting to do-their-own-thing. The history of the web shows that some of these will flourish and others won’t. This is an absolute judgment, it’s more that the time is right for some and not for others (it’s taken us 20 years to get semantic Chemistry moving). So we shouldn’t judge new developments too quickly but give them time to flourish.

What about duplication and waste? Wouldn’t (say) 20 independent authoring systems be worse than none at all? Shouldn’t we coordinate this centrally and have just one? In fact both are problematic. In the Blue Obelisk (v.i.) we’ve effectively solved this by constantly keeping in touch and watching what others do. For example I once spent a lot of time on developing a graphical display for chemistry. It wasn’t very good. And then I saw Jmol ( and realised that *I* didn’t need to do it all myself.

I junked my code. A year’s worth. And rejoiced. From there we went on to the Blue Obelisk and now we have this great ecosystem. A few partial duplicates – but that’s useful for checking correctness, different platforms. And because we have legitimised the idea of components that interoperate the world has come to understand and respect what we have done.

That’s the key step. We don’t have to boil the ocean by ourselves. Or even in our groups. We build components. It’s the right way to build.

Can you publish components in high-impact closed journals?

Probably not. But that is not why we are building them. By building components we can reach out well beyond academia. An open scholarly indexer does not have to be built solely or even by academics. Let’s get software engineers and journalists and graphic designers involved. And patients.

We couldn’t have done this 5 years ago. We can now. What’s happened?

  • Wikipedia, OSM have shown that grand visions can be accomplished
  • GalaxyZoo has shown that meaningful subtasks can be created and that huge numbers of citizens can take part. Bringing their own innovation and enhancing the process.
  • StackOverflow has shown that social tools can be compelling and exciting
  • Github and Bitbucket have shown how to create repositories that people want to put things in because these repos do something useful
  • New lightweight tools such as NoSQL , d3.js, and HTML5
  • (and in Open Knowledge Foundation) we see the world outside academia adopting new ideas by the week.

So we can’t tell where and how the new things will happen. Something that looked impossible 2 years ago may now be very tractable. Glueing distributed systems together is far easier than it used to be.

So a distributed system is now a positive asset, not a problem to be solved by aggregation and central control. In the same way the communities can be glued by modern approaches and culture. That’s why I’m suggesting we should be distributed but communicating.

There are only a few basic rules:

  • Respect others
  • Try to work with people rather than compete
  • Keep everything completely open. An open API is problematic if the data can’t be dumped. Code relying on a closed component will crash when that component disappears.
  • Creating and giving are critically important. Some jobs are boring, tedious and necessary. We must find social ways of making them worthwhile.

So we can have more than one discussion list. More than one wikipage. Let’s first see what we can offer rather than what we want to accomplish. (Doesn’t have to be gold-plated.) And make these creations and their creators easy to find.

To start the process here’s some of what I and my collaborators can Openly offer:

  • A PDF2XHTML converter for scholarly articles and converters
  • Pubcrawler to discover and collect bibliographic metadata
  • Semantic scientific units of measurement
  • Semantic tools for physical science (especially chemistry) (useful for indexing and transforming)

So let’s see what we want to bring to and get from our marketplace of tools and ideas.


#scholrev: #BTPDF2, FORCE11, Current position and ways forward

I’m blogging some of my ideas about the Scholarly Revolution (#scholrev) and how it should proceed. I’ve already said I think it should be decentralised and I’ll explain what that means and why. I’m going to concentrate on the underlying social and political aspects – the technologies will follow. But first I am recapping where it started.

To recap, we gathered for an ad hoc meeting at Beyond the PDF 2 at lunchtime on Wednesday (2013-03-20) and we’ve been blogging and tweeting since then. #scholrev would not have happened without the wider meeting which Maryanne Martone has described at .

I think that I share with many the recollection that BtPDF1 was a unique and transformative event. It was the first venue where many different groups with clearly a lot of pent up frustration with the current state of scholarly communication and a lot of tools and ideas for moving us beyond the pdf (including new types of pdf’s) came together.  Unlike most conferences where there were a few polite questions, the discussion was lively and uninhibited.  I’d been to conferences where hash tags were posted, but few people used them beyond a few graduate students.  Here the twitter stream regularly exploded and discussion lists were used well before and after the conference..   Many of the audience were clearly masters of new modes of feedback and communication and weren’t afraid to use them.  Indeed, it was the level of enthusiasm and the quality of the discussion that led to formation of FORCE11, because we wanted a vehicle for capturing and focusing the energies on display.  FORCE11 and its Manifesto was produced by the follow up workshop at Dagstuhl later that year.   But I consider the first BtPDF conference the beginning of the movement, if we can call it one. 

PMR: Agreed. I was at BTPDF1 and felt it was transformative and exciting. I wasn’t at Dagstuhl so I can’t comment on the atmosphere. But yes, I hoped that something would come from BTPDF1 and looked for it in BTPDF2.

Looking over the program from the first BtPDF, we are clearly continue to struggle with some of the same issues:  semantic mark-up, authoring tools, data, nano-publications.  But a lot of work has been done and a lot of progress made.  … Open Access is being openly debated and supported by funding agencies, institutional repositories and researchers. 

PMR: I was particularly concerned about authors at BTPDF1 and the way they are treated in the current system. They have no effective voice and are largely pawns in any debate of #openaccess (and there is little constructive debate). The authors should be a major part of new communications, as should the readers and both groups have been marginalised. Personally I feel no excitement for the current approaches (“Green” and “Gold”) which both allow injustice, vested interests and massive waste to continue.

So are we done yet?  I would say no.  By and large, I would say, we still have failed to deliver tools and convincing use cases to the larger scholarly community, who are still locked in old modes of publishing and evaluation.  All one has to do to have one’s enthusiasm on the state of scholarly publication dampened is to sit on a promotion committee or a meeting of an editorial board. 

And that’s the problem. Put simply, while rich (Northern) academics debate evaluation, publications are still locked by piublishers.

And lack of publications mean people die. I’ve said that before and Eve Gray said it very clearly at the meeting. The first three presentations at BTPDF2 addressed the inequities, but the meeting slipped into cosy introspection during the rest. The meeting should have been angry at injustice. It wasn’t.

Data:  where to put it, what to do with it, when to do it, and who will do it, still looms over everything. 

YES. And unless we do something different we’ll end up with the same mistakes – data publication controlled by vested interests. (Some weeks ago a librarian came to me and said: “Isn’t it wonderful, we can now buy a data citation index”. I screamed).

The scholarly corpus in biomedical science is still fractionated, with no global access to the entire biomedical literature by automated agents.  The inefficiences of spending large amounts of time and money to turn complex research objects into digestible narratives and then an equally large amount of money trying to extract and recover the research objects from the narrative still need to be overcome.  And, as will be explored in the business case, we still haven’t figured out the model that will pay for it all. 

Biomedical science would be automated if it was legally allowed by the publishers (I sit on EuropePMC and we could index the whole literature technically.) Get angry, for goodness sake!

But I am confident that change is a comin’ and I look forward to BtPDF2 as an incubator and catalyst for that change. 

I looked for fundamental changes at BTPDF2 and I didn’t see them. A great deal of incremental stuff about how we could tinker with the current system. Very little about its fundamental sickness. About how we could revise the scholarly monograph (i.e. books) – we had a good lead on that but no follow-up. Well the world is reinventing the book and academics don’t seem to realise that books are for reading, not primarily for generating an ivory tower reputation.

Which is why we so rapidly gathered a group under the banner of “Scholarly Revolution”. I don’t know whether BTPDF2 will generate revolution, but it’s got to start doing it soon or not at all. It needs to tap into the twenty-first century and here are some ideas:

  • Make change, don’t just talk about it. I’m now so used to hackathons that I find 2 days sitting and listening to people talking makes my fingers twitchy. I and others said that next time there must be a hackathon where we create something new.
  • Bring in the outside world and listen to them. Academia is behind the times, not in front of it. At our hackdays we get journalists, medics, banks, creatives, central and local government and much more. They’re not hung-up about impact factors – they want to see information developed into communal knowledge. Tools that promote democracy. New ways of working.
  • Trust the young. The new world is a young world, not a continuation of the existing one. I was pleased to see special representation of young people and I hope they are brave enough to say what they want.
  • Fight injustice. The current system is seriously unjust – to the world.

I’m grateful to #BTPDF2 organizers for the meeting. Maryanne has rightly asked that we link to and they have highlighted #scholrev. . I’m very happy for FORCE11 to provide resources for #scholrev. But they will only keep connected if they each tap into the other’s social and political dynamics.

#scholrev: Decentralized Open infrastructure: an example from The Blue Obelisk

I have suggested that the Scholarly Revolution should be decentralized and communicating and this post gives an example of why and how. “Decentralized” means that no one person or subgroup is critical to its operation and more importantly its continued operation. It also means that we do not have to agree on everything (and we certainly shan’t – the mess in “Open Access” should be a clear warning). We should not have to rely on key components – for example building the roads before the houses and then finding people don’t want to live where the roads are but where they can cross the river.

The good news is that information infrastructure can be very cheap and – certainly at an early stage – can be radical altered (refactored) if the community wants. The key thing is COMMUNICATION. As long as we know what other people are doing and saying many of the difficulties are solved.

So here’s an example of a bottom-up community that works. It costs me 20 pounds a year to run – that’s less than a dinner. It’s growing and it’s changing the world of chemical science. It would continue to run and flourish if I weren’t able to be involved. Everyone has their own homestead ( ) but there is also a commons. It’s a bazaar ( – if you don’t know this, read it – it’s Open). There are other similar metaphors – “cooperative”, “tietotalkoot” ( ), “marketplace”, etc.

I’ve written it as part of a chapter we’ve offered for the because it’s more important to spread new ideas than gain impact factor.

Bottom-up Open Chemistry – the Blue Obelisk


Chemical software and data is a major activity, almost certainly exceeding 1Billion USD per year. But almost all of it is Closed, represented mainly by domain-specific software companies and traditional STM publishers. This is often aggressively protected; when the NIH set up an Open[*] database of chemicals and compounds the American Chemical Society (ACS) lobbied to politically to have this curtailed and threatened Wikipedia with legal action for publishing the widely used CAS identifiers for chemicals. A major software producer will take legal action against licensees who publish program output, including bugs.

A number of independent, often unfunded, chemical hacker activities grew up during the 1990′s and by 2000 a handful of codes were available but there was little continuity or coordination. We used to meet occasionally at ACS meetings and in 2006 we met in a bar near the large Blue Obelisk in Horton Plaza , San Diego. We felt that we had a consensus of philosophy, that the world undervalued our software and that we had the potential to change the future. We then agreed to loosely coordinate (not pool) our efforts. I suggested the name “Blue Obelisk” and our mantra ODOSOS – “Open data, Open Standards, Open Source “. To support this we created a Wiki, a mailing list and agreed to meet for dinner whenever we had a critical mass. There is no budget, no membership, no formal mechanisms – the mantra is our collective and very powerful DNA.

This has proved extremely successful and might work in other disciplines. We have about twenty projects which are happy to be counted as Blue Obelisk ( ) and which fit into our criteria of ODOSOS. Our dinners are open to all – and closed source providers have attended and been relaxed. In 2007 we published a paper outlining our components. Recently we reviewed this in a 2011 paper with about 20 groups as authors.

When someone or organization does something meritorious (normally an identifiable software product or data resource) I award a quartz Blue Obelisk (remarkably these are common and inexpensive). These loose traditions work. We now have software components in most of the chemical infrastructure for pharmaceuticals and increasingly in materials. The biggest problem is data – chemists do not publish machine computable data (though they should) , instead embedding a subset in formal (Closed Access) publications. We have machine extraction software but risk being prosecuted for extracting data.

Governance is minimal and we have been blessedly spared form either factionalism or imperialism. Each project is self-contained but uses other B/O libraries where possible or more recently runs them as web services. The main language is Java, followed by Python and C(++) – with some historical FORTRAN. There is generally a leader to each project and while the Benevolent Dictator for Life (BDFL) occurs the commonest is “Doctor Who”, where the Doctor hands on to a successor at irregular intervals.

Originally dismissed as cranks, we are now taken seriously. Companies (e.g. Kitware, NY, and CCG) contribute significant amounts of code (and as importantly) the critical mass of internal and external confidence. National labs (e.g. PNNL in US) have been awarded Blue Obelisk for collaborating on Open Source. We know that or code is widely used in pharma companies but we have few metrics (a common problem of Open Source in secretive industries).

As with all volunteer Open Source projects we do not have clear timelines, but progress over the last 5 years has been very good. It’s possible to find high-quality components in most subdomains, including unit and regression testing.

The main problems we face are that chemistry (surprisingly) often does not engineer its own solutions but prefers to buy them. This puts a value on shrink-wrapping and hand-held maintenance which gratis Open Source cannot easily provide. Academics producing new code often get little credit and it’s worse when they reengineer existing solutions, even when the result is markedly superior. It’s also difficult to get funding (“it’s a solved problem”). The fragmented nature of the commercial domain makes semantic interoperability very difficult –companies protect legacy walled garden approaches. The internal messes created by unvalidated variants of legacy files in the pharma industry (e.g. when the result of a merger requires data reconciliation) has probably cost well over 100 million dollars in human effort, while the B/O could have provided common semantics.

However I think we are approaching a breakthrough. Chemical software has made few objective advances in the last 10-15 years so that we now have implemented most of the major algorithms. For an organization which takes a responsible view of costs and values innovation, the Blue Obelisk can be an attractive part of a solution.





? ^ Guha, R; Howard, MT; Hutchison, GR; Murray-Rust, P; Rzepa, H; Steinbeck, C; Wegner, J; Willighagen, EL (2006). “The Blue Obelisk-interoperability in chemical informatics”. Journal of chemical information and modeling
46 (3): 991–8. doi:10.1021/ci050400b. PMID 16711717. [for bean counters: cited 281]

? ^ O’Boyle, N; Guha, R; Willighagen, EL; Adams, SE; Alvarsson, J; Bradley, JC; Filippov, IV; Hanson, RM et al. (2011). “Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on”. Journal of Cheminformatics
3. doi:10.1186/1758-2946-3-37. PMC 3205042. PMID 21999342.



URGENT: Blogs could be banned in UK

The Open Rights Group has unearthed an appalling proposed restriction on bloggers like me. In essence regulation of the press will be extended to bloggers. Unless I get a licence I will be closed down. (I know some people would like this). We have till Monday to act. In :

Cameron, stop the Dangerous Blogs Bill

The Leveson regulations are being applied to UK websites – in ways that could catch more or less anyone who publishes a blog. Ordinary bloggers could be threatened with exemplary damages and costs. If this happens, small website publishers will face terrible risks, or burdensome regulation – and many may simply stop publishing.

Lord Leveson’s regulations are being applied to UK websites – in ways that could catch more or less anyone who publishes a blog. Ordinary bloggers could be threatened with exemplary damages and costs. If this happens, small website publishers will face terrible risks, or burdensome regulation – and many may simply stop publishing.

We have until Monday to stop this happening.

Lord Leveson said he wanted to regulate print media. He proposed that judges  be allowed to award exemplary damages and full costs against unregulated publishers. These are stringent and controversial measures, but he only envisaged them applying to large and powerful publishers. Not websites, unless they belonged to print publishers.

Last weekend, the proposals were agreed in a rush, without public consultation, and with no attention to the detail.

Outrageously, they have given the Lords until Monday to fix their mistakes.

The result is that they apply to any size of web publisher – if there’s more than one author, the content is edited and there’s a business involved, then you must join a self regulator.

Most blogs like this aren’t powerful publishing houses. Even ORGZine would need to be regulated, or face punitive measures if it ended up in court.

The threat of websites being regulated like this was never the purpose of Lord Leveson’s recommendations. Websites weren’t involved in phone hacking. There is no evidence that they need to be forced into self-regulation like this.

We need you to email Nick Clegg, Harriet Harman, and David Cameron to ask them to back off and leave the Internet out of Leveson.

A copy will go to your MP so they know how you feel as well.

Physiological Reports, new open access journal, is open for submissions

Physiological ReportsPhysiological Reports is now open for submissions, the first 100 articles accepted for publication will be published free of charge.  Susan Wray, Editor-in-Chief and Thomas Kleyman, Deputy Editor-in-Chief  lead the Editorial Board for the new online only, open access journal.  The journal will publish peer-reviewed research across all areas of basic, translational and clinical physiology and allied disciplines. Physiological Reports is a collaboration between The Physiological Society and the American Physiological Society, and is therefore in a unique position to serve the international physiology community through quick time to publication while upholding a quality standard of sound research that constitutes a useful contribution to the field.

The journal offers:

  • High standard, rigorous peer review
  • Rapid time from submission to decision
  • Rapid time from decision to publication
  •  ”Article by article publication” – no delay in waiting for the issue to close
  • Open Access – published articles are licensed under Creative Commons Attribution (CC BY), and authors are the copyright holders
  • Compliant with open access mandates
  • Wide dissemination
  • Promotion of, and publicity for quality research

Submit a manuscript >