I started to write this post a long time ago in October; unfortunately before I finished I got hit with the start of teaching. I considered just ditching the post, as it is now so out-of-date and I am not usually a zombie poster. However, in this case, I shall post as a) it helps my mind to move back toward research after so long away and b) it will be my first of 2012, so I can check my makefiles work!

A couple of follow ups from my previous post.

Nicolas Le Novere commented via twitter on even the highest level assertion of that radioactivity is a dependent continuant.

@phillord fluorescence and radioactivity are occurrent not continuant. Freeze time to check.

@phillord hence the unit of radioactivity: per second (Becquerel)

— Nicolas Le Novere

In my original post, I suggested we needed Radiation, Radioactive or Radioactivity; in hind-sight, perhaps I should have used Radioactive rather than Radioactivity, which may have circumvented this issue. However, I think it is worth considering this a little further.

I would nearly agree with Nicolas that radioactivity is a process; actually, I would say that radioactive decay is a process, while radioactivity is a property of this process. However, in my last post, I was looking at a model which was “BFO-like” as OBI is based on BFO. For BFO, that radioactivity is a rate, is measured per second does not mean that it is an occurrent; any more than velocity which is also measure per second is an occurrent. Actually, in BFO land, radioactivity would be a quality of the atoms which are decaying and not a measurement of the process. This is because, as Pierre Grenon says, properties of processes do not exist.

In fact, if we look more at this more closely still, BFO would also claim that radioactive decay is not, as it might appear, a Process, because processes are continuous. This is not true for radioactive decay, even for a bulk of radioactive material. An atom decays, then there is a pause, then another decays. This makes radioactive decay a processual entity, which can contain discontinuities.

I am not arguing that BFOs treatment of processes is correct — in fact, I think it is nonsensical. However, it is this line of arguing that I was using in my previous post.

David Sutherland rather takes me to task about whether realism does what I suggest.

I agree completely, but what realist principle says you need to give something the most detailed classification you can come up with?

— David Sutherland

It’s a good question, but I would turn it around. I don’t think that realism requires you do this, although this quote from Barry Smith does rather distinguish between simplifications (i.e. not the most detailed classification you can come up with) and reality.

I am beginning to suspect that for you everything is a simplification (model) — for me, functions are part of reality; they are not simplifications; I am not interested in simplifications.

http://groups.google.com/group/bfo-discuss/msg/865e601864fbc2dc
— Barry Smith

The problem, though, is that realism elevates “reality” above all else. I think that this is wrong. Of course, in any scientific discipline, we should by aiming to model the experimental data that we have. But this is not all we need to do. As any statistician will tell you, models are compromises. It is very easy to build a model that perfectly represents the data that you have; you just build a model with as many variables as data points. The model will fit perfectly to the data, but ultimately the model is useless, since it lacks explanatory power. We need use cases, we need simplifications and sometimes we will need multiple representations of the same thing; there are examples galore in my paper (doi:10.1371/journal.pone.0012258) . In fact, Chris Mungall gives a good example when he talks about dispositions and their status as being real:

In fact, I have a particular problem with dispositions being “real” – BFO asks me to believe there are an infinite number of real but unrealized and perhaps wildly improbable dispositions floating around me every second

— Chris Mungall

And later he gives the solution.

taking a hard-headed pragmatic approach – e.g. avoid weirdo classes that don’t correspond to a term a normal scientist would use; introduce distinctions that give you the desired results to queries and inferences)

— Chris Mungall

In otherwords, reality is important. But we also need use cases, we need community norms, and we need applications. If ontologies do not fit with these, then can be as “real” as you like, but they are still wrong.

Bibliography

Well, I am pleased to say that we have now released the new version of kcite. It’s been a while in coming — I had the difficult bit of the code working about 5 months ago, but then got caught up in teaching. Kcite is our bibliography manager which enables citations such as this one (doi:10.1371/journal.pone.0012258) , using DOI or PubMed IDs.

Kcite now uses the marvellous citeproc.js to render the bibliography on the client. The main advantage of this for this release is that the biblography formatting is slightly more regular than before. We’ve also switched to name-author style as the default. There is also a disadvantage which is that the browser has to do lots of Javascript execution client-side; I’ve made efforts to ensure that this is not too onerous; on my desktop, I have been rendering 200-300 item bibliographies, which is much more than most people will use in practice.

In future versions, however, I feel the use of citeproc-js will really come into it’s own. We should be able to enable the user to select their own citation style (currently this is the choice of the authors which makes little sense). We can also add any semantics to the HTML that we choose — CiTO will come properly, for instance. I can also clean up the “unresolved” and “timed out” references. However, first thing on the list is to make the call back for the bibliographic data asychronous. Client-side this should be easy, as we are already using jquery. Server-side requires rewrite rules which I haven’t done before, but I think should not be too hard.

On a separate track, now that I have kcite on what I think is a stable technological footing, I can start to extend in other ways, the most obvious being additional forms of identifiers, critically including WordPress posts with kcite enabled. I’m also pleased that Cross-Ref have recently added the ability to drag metadata in citeproc format (JSON), which means I can skip an integration step.

However, before all of that, we need to restore kblog. We’ve taken the opportunity to move it to a better technological footing, and have started to prepare the new machine that it will be hosted on. This has taken a long time, due to a busy start to the (academic) year. Hopefully, getting hacked is not something we will repeat soon.

The current release of kcite is 1.4.1. This fixes two bugs, one reported by Carl Boettinger (so that now the Javascript only loads when necessary) and another I found which writing this post which made editors appears as authors.

Bibliography

It has been a long, long time since my last gig review. As this blog is mostly professional now, this is perhaps not such a bad thing. I did half write a review of Roy Harper and Joanna Newsome in Sept last year, but it never got posted. Don’t think I have been to gig since then. Still onwards.

I’ve been a fan of June Tabor for a long time, particularly her album with Martin Simpson even if it does have terrible cover art. Despite this, and the fact that she lives pretty close to my home town, I’ve never seen her live. Her music is dark and eclectic, her voice rich. Combined with the Oysterband’s tendency to do strange adaptations folk-style it was destined to be an interesting gig. The music is something like gothic folk if that is not a contradiction in terms. While singing, June Tabor comes as a foreboding presence on stage. Between songs though, she’s entertaining, witty and light, which was a bit of a relief.

The gig was fantastic. Her voice is as excellent live as on record, with adding prescence. She adds to the music by, erm, explaining what it is all about (this can be something of a problem otherwise). The evening was well managed, moving from gentle and quieter music to end-of-evening barnstormers. It was good to be listening to live music again.

But one thing I didn’t understand. Why does Ray Cooper stand on a box while playing bass? He’s already the tallest.

I once had cause to refer, somewhat mischievously, to “a kind of pasta from Tuscany, which is almost identical to spaghetti, but slightly different”; this was on a mailing list that was used by many Italians. It provoked the expected response; an offended Tuscan responded “I don’t know what you are talking about; but if you mean pici”, which I did, “it’s nothing like spaghetti”.

Recently, on the OBI mailing list, there has been much discussion about labels, markers or tracers. What ever you wish to call it, the basic idea is the same; a molecule which is easily detectable, is used to trace something else. This can involve adding a small amount of a radioactive isotope (P³²). This makes it possible to follow the molecule (which is otherwise hard) by tracing the radiation (which is generally easy).

So, how do we model this? As with many parts of ontology building, it turns out to be not straight-forward; during this discussion, an email from Philipee Rocca-Serra which left me asking the question, are we being too specific? I will work through an example to show what I mean. Feel free to skip to the punchline if you choose.

Consider, for example, the following models; these are not directly taken from OBI, as I want to reduce the complexity for this article; rather they are in the general spirit of the models which raised these questions.

A label, or something that has been labelled is clearly part of an experimental design. It is not intrinsic to this entity, rather it appears to be a role that the entity is playing in the experiment. So:

Class: Label
       SubClassOf:
          Role

There are, of course, labels of many sorts. The main types that I can think of are radioactive, fluorescent and what I call adherent. So, we might add the following, with a few subclasses of adherent as explanation.

Class: RadioactiveLabel
       SubClassOf:
          Label

Class: FluorescentLabel
       SubClassOf:
          Label

Class: AdherentLabel
       SubClassOf:
          Label

Class: BiotinilaytedLabel
       SubClassOf:
           AdherentLabel

Class: AntigenicLabel
       SubClassOf:
           AdherentLabel

So far so good. However, for a label to be useful, it needs to be manufactured (often in a bespoke fashion, depending on the experiment being performed) and it needs to be detectable. So, we might add classes like so:

Class: LabellingProcess
       SubClassOf:
           Process
           has_output some Label

Class: LabellingDetectionProcess
       SubClassOf:
           Process
           has_input some
                  Sample contains some Label

Now we have three classes for every label type. We can deal with this by generating a cross-product, either at development time, or at the time of use if we are using OWL. However, we need something to tie together these classes. We need a concept to know that we need a RadioLabellingProcess to produce a RadioLabel which we detect in a RadioLabellingDetectionProcess. In short, we need a concept of Radiation, Radioactive or Radioactivity.

Class: RadioactiveEntity
    SubClassOf:
        IndependentContinuant,
        bears some Radioactivity

Class: RadioactiveLabel
    SubClassOf:
        Role,
        RadioactiveEntity

Class: RadiationDetector
    SubClassOf:
       detects some Radioactivity

Class: RadioactiveLabelProductionProcess
    SubClassOf:
       has_input some RadioactiveEntity

This is where the situation gets difficult. What kind of thing is Radioactivity? Taking the realist approach, we need to consider this carefully, determining what this universal is. So, starting from the top, it is fairly obvious that we have a Continuant. Next question, do we have a Dependent or IndependentContinuant. Again, this is fairly clear: radioactivity cannot exist without something to be radioactive, hence Radioactivity is a DependentContinuant.

We have a set of DependentContinuant‘s that Radioactivity could be. The concept Role does not fill well; this is usually ascribed by socially or, in this case, experimentally determined behaviour. Perhaps, Disposition would be better. However, this does not really fit either, as a Disposition is realised “under specific circumstances”. Now this is not true of radioactivity. Either something is radioactive or it is not, and if it is, then it is, to the best of our knowledge, radioactive under all circumstances. It appears, then, that Radioactivity is a Quality, because “it is exhibited if it inheres in an entity at all”.

If we follow the same logic with our other label types, initially, we come to the same conclusions. However, Fluorescence is not exhibited under all circumstances. It only happens when the label is illuminated with the right kind of light. So, Fluorescence appears to be a Disposition. Following a similar logic, this is also true of Adherent. So the best we can say about the property of the substance that makes it usable in labelling is that it is a RealizableEntity.

Having Radioactivity stand out in this way is a little unsatisfying. Let’s consider the logic again. One classic experimental form is the pulse-decay experiment. I can, for example, feed a rat with, say, radioactive phosphorus briefly. After this, you can trace the course of phosphorus. Now during the course of this experiment, the rat becomes radioactive and then ceases to be radioactive again. But, it is notably, the same rat. So, perhaps, the statement that things are either radioactive or not is wrong. Perhaps, it is not a Quality at all. The flaw in the logic is the assumption that because an atom is either radioactive or is not, therefore anything made up from atoms must be so. But an entity can have its atoms totally replaced and still be the same entity. In this case, what is true of a rat, is also true of its DNA. We can replace the atoms in a sample of DNA with other ones and still, have the same DNA. So, maybe, Radioactivity is a Quality at an atomic level of granularity, but is, after all, a Disposition at others.

Thinking further, however, maybe it is not a Quality at all. A mass of P³² is always radioactive, but a single atom? Perhaps not, since it only displays this when it decays. So, perhaps, it is a Disposition after all. However, this makes no sense, because dispositions are displayed under “specific circumstances”. Now, to the best of our knowledge, radioactive decay is stochastic — it is so random, that radioactivity is often used to generate randomness. We cannot specify the circumstances under which it happens, it just does. More over, after it displays the radioactivity, what has happened to the atom? Using the same argument as before, we could say that, like the rat, the atom still exists, it’s just that (some of) the elementary particles that make it up have changed. But this way, surely, madness lies, as “being phosophorus” would become some sort of dependent continuant, which the atom displays during its decay, while it happens to have the right number of protons. So, probably it makes more sense to say that, the decay process represents the end of the existence of the phosophorus atom and the beginning of a new atom (and a radioactive particle). In which case, even our original decision that Radioactivity is DependentContinuant is wrong. It’s not a DependentContinuant at all, it’s only a process which over as soon as it begins.

So, what have we achieved? Well, I would argue, not a great deal, except for a lot of discussion. More over, we have ended discussing very detailed issues about the physical properties of matter, when we started discussing an ontology of biomedical investigations. This might be entertaining, or it might be very dull, depending on your point-of-view. But, what we have failed to produce is a specific conclusion.

The problem here is realism. A realist ontology represents portions of reality, that is classes of things that really have instances. We have to ask these questions to try and determine whether Radioactivity exists and what kind of thing that it is. We can set realism against pragmatism. Previously, Robert Stevens has described the problems that this causes by preventing the ontologist from modelling “unicorns“, such as Newtonian mechanics, or canonical anatomies. The unicorn principle says, if it is useful to model a concept in an ontology, then often we should. Here, I introduce what I call the “Pici principle” — if it is not useful to model a concept then we should not. As a British native, pasta is pasta; it all tastes much the same to me. Generally, I do not need the ability to be able to distinguish pici and spaghetti, unless I want to provoke a response from an over-excitable Tuscan. The sensible course is not to get involved in the discussion in the first place.

The same applies in this instance. There is a clear use case for the concept of Radioactivity; without it, we cannot say that a radio-label is radioactive, or that a fluorescence detector is not going to work detecting it. But to achieve this use case, we do not need to understand very deeply what Radioactivity is. Describing it as a DependentContinuant is enough, and it will fulfil the use cases. It will not enable us to ask questions about which kind of labels detect qualities and which detect dispositions. But in the absence of a use case, this is not an issue.

A chemist may care, and may want to classify radioactivity further. This is fine; as with pasta, we can safely leave these issues to someone else, in the knowledge that they are probably better qualified to give an answer anyway. So long as they decide that Radioactivity is a DependentContinuant, it does not matter to us what kind of DependentContinuant; we have said nothing incorrect. So, our ontology will integrate with theirs, without change to either. By being as vague as our use cases allow us, we have actually increased the ability of our ontology to integrate with others.

In short, the pici principle encapsulates the idea that deciding what we should not model in an ontology is as important as what we should model. And this decision comes from use cases, not reality.

While I am currently spending a significant amount of my time promoting the idea that blog technology can be, and should be used for serious scientific material, I thought I would make a post of a different and perhaps more traditional vein: that is, a light-weight idea, with no serious research behind it, but Years ago now, I created an Energy Wiki full of daft ideas for making energy. I last revisted this in 2009, with an idea for storing energy at sea. I’d actually forgotten that part of the reason for this was to try out Inkscape, which is part of the reason for this post. I wanted to try a bit of multi-media, that is, a blog post with an image in it. High tech.

So, the idea. One form of renewable is the Solar Updraft Tower, also known as a solar chimney. This works straightforwardly enough: you build a large greenhouse in a desert, with a very large chimney in the middle. The top of the chimney is in cold air, the bottom in hot, and an updraft results; stick a turbine in or at the base of the chimney, and you get energy out.

The problem is to work at all efficiently, you need a big temperature differential, so a tall chimney. This in turn means a wide chimney, both to support a substantial updraft, and for mechanical reasons. Tall means 500m or more. The bottom line of this is that a pretty significant capital expenditure is required, followed by a relatively long pay-back period, which in turn means that the biggest single expense of the project is likely to be interest charges, rather than anything else.

So, my idea, is to use an inflatable chimney instead. Initially, I thought about some kind of helium lifting scheme, but then I realised that this makes no sense; why not use hot air, which after all is what the whole system is designed to generate. Consider, for instance, the following organisation:

Essentially, it’s a traditional balloon with a hole in the middle. Obviously the whole system is stackable — a second balloon could be placed on top of the first and so on. The whole structure could be assembled or dissassembled as desired. Unfortunately, though this would probably take quite a bit of work.

My second thought came from the idea that, while most designs for solar chimneys have the chimney in the middle of the greenhouse, it doesn’t really need to be. A horizontal pipe to the middle would be enough. The chimney could be outside of the greenhouse. The advantage that this brings is that the tower could be raised or lowered in-situ, without the risk of it falling on, and damaging the greenhouse. So my second idea was to build the chimney as a two cylinders, with the gap between the serving as the inflatable, buoyant structure. By pleating the cylinders in opposite directions like so:

the whole structure should concertina up and down. By inflating from the top and deflating from the bottom, it should be possible to raise or lower the entire system by opening and shutting vents at the bottom or top of each section to the inside of the chimney.

One advantage with this system, is that as the chimney gets higher, the temperature differential between the inside and the outside gets greater, which should mean that the taller the tower, the more bouyant the sections get; this should help to keep the entire thing as upright as possible, as will the air travelling through the middle, like some gigantic party blower.

Another addition that cames to mind would be to add inflatable half-toroids around the chimney at regular intervals. With a curve on the top, and a flat bottom-side, the entire thing should operate like an aerofoil, lifting the tower up; so, the windier it gets, the greater the lift, which is just what is needed to keep it as upright as possible. This should mean that the chimney can operate in relatively high wind levels.

This kind of system could even work in concert with a fixed chimney — extending the height by 500m say, and increasing it’s efficiency. It could also act as a supplement — operating only on very hot days when the greenhouse has excess capacity. Or, finally, it could operate while the main chimney was being built, meaning that a plant can start generating income earlier, which should reduce the cost of interest payments.

Of course, this all comes with drawbacks: the ongoing running costs are likely to be a significant; wind will remain a significant factor regardless; and, finally, inflating the tower will using hot air, which will reduce the efficiency of the whole system. Are these flaws significant? Well, as I said, this post is light-weight with no serious research behind it. I have no idea, nor any really clear idea about how to work out these costs. Answers on a postcard please.

I have been pushing the idea of Kblogs — scientific publishing using commodity software — for a year or so know. Our main site, Knowledgeblog.org has got around 100 articles now, and has had about 50k page views (or about 4x the number of raw page hits) and has generated a certain presence on the internet. While this is generally good, the price of fame is that we have moved somewhat up the list of potential hack targets. Unfortunately, this has resulted in two compromises on the machine; they were probably not disconnected, although we have no evidence to link the two at the moment.

The first was through the timthumb zero day vulnerability. It involved a code injection into a WordPress installation using a thumb nail generator with a dodgy bit of PhP in it. We cleaned the system up as well as we are able and went from there. Sadly, a couple of days ago, we had a second break in. This was a more serious and directed attack (the timthumb was scripted, and we were one of several thousands of sites to be hit). In this case, the machine has been root compromised, and the web server used to gather username/passwords in a phishing expedition. We do have backups and all of the content. There were a number of things that we could have done to secure the machine further, at least one of which may have prevented the hack, but there are only so many hours in the day.

So, where does this leave us? Is the whole idea of knowledgeblog broken? Personally, I do not think so. While I have been critical of the cost associated with academic publishing, I am aware that it cannot happen for free. Running and maintaining a web server takes money; it is something that we have been doing on a shoe-string for a while, especially since our JISC money ran out. In the couple of years that we have run knowledgeblog, I think that we have learned and shown a lot. As well as page views and content, we have shown that scientific publishing can be easy for the author; that we can generate attractive articles this way; that we can start to embed computational accessible knowledge into these articles. We have shown that we can do peer-review, if we need. We have shown we can archive and preserve for the future. We have shown that knowledgeblog is good for grey literature. We have added DOIs. Multiple authors. Good looking maths. We even have some preliminary stats on how much publication costs from Word doc to website.

At the moment, though, we do not have a business model. It is clear that if we are to move this forward, it needs to be run as a service, managed, and looked after, something which is neither my expertise or desire. The analogy that I have made earlier with Wikipedia is, I think, a good one; it would be good to move this into a foundation status.

The path from here to there is a long one, however. For the moment, we will restore knowledgeblog, and it will re-emerge, although at this time of year, it will take a while. But we look to the future as well.

My first visit to Oslo was in 2006. That time, it was for work and we were some distance away from town. I remember the flight in gave a dramatic impression, and I remember sitting in the conference centre, looking over the hill side, breathing in the thick scent of pine watching the sun slowing crawl toward the horizon at about 11pm. I only got into town the once, on the last night, and saw little of it which I was disappointed about. My second visit to Norway was to Trondheim and I enjoyed that as well.

So I was looking forward to visiting Oslo again, for a few days, doing the tourist thing. But I am afraid that I have been disappointed again; this city has not really grabbed me. The architecture is impressive at points, but there is a random, thrown-together quality about the city overall; nothing to rival the magnificence that is Grainger Town in Newcastle. And some of the signature buildings are, again, just okay; the Opera House has a roof you can walk up, but that seems to be it. The night time is subdued to say the least, and the food is okay at best. The only stand out feature seems to be an extra-ordinary number of sculptures — mostly bronzes, and often not famous people. Lots of nudes in heroic poses; the number involving seals is also distinctly above the average.

Of the two best things I have seen are, first the Sculpture Park. Very classically laid out garden, but with some really very good sculpture, full of character and life. And seals. And second, the folk museum, which shows Norweigian life and buildings at different stages of history. I have to admit, though, that I was at a loss to see the difference, because over the last 4-500 years, this seems to basically have involved making robust, timber buildings on stilts. While the museum is good, I think, having less buildings, but better explained would improve it. When you get down to it, one wooden farmhouse looks very like another, especially when you can see it only from the outside.

Perhaps the biggest surprise though has been the accessibility for pushchairs. In Oslo, this is never an afterthought; they just have not thought about it at all. The tram doors slam on you if you take too long, which may happen if, say, you are struggling to get a heavy, unwieldy, pram-shaped object through a narrow door. My visit to the Opera House was limited to walking around the lobby, as walking up a sloping roof, with nothing but “slippery when wet” signs to break a clear run to the fjord is not my idea of fun. My visit to the National Gallery involved 20 steps to get in, to discover that the pushchairs are banned in the exhibition area; still, hey, you can visit the shop. Looking through the door of the National Museum (only 10 stairs up) and I could see a line of buggies next to the security guard. I didn’t even bother.

Although in some disciplines, it is relatively uncontentious, the rise of open access publishing has produced a lot of comment in others. In one of my two disciplines, computing science, this form of publication is still the minority, and still raises comment. For instance, Michel Beaudouin-Lafon has commented suggesting this scientists are highly naive about the costs of publishing. He argues that scientific publishing is intrinsically expensive, and that open access will have negative implication for science as a whole.

Over the years, commercial STM publishing has become a cutthroat business with cutthroat practices and we, the scientific and academic community, are the naive lambs, blinded by the ideals of science for the public good-or simply in need of more publications to advance our careers.

— Michel Beaudouin-Lafon

Personally, I think that “naive” is the wrong word; scientists are often not good at operating in a co-ordinated way. Although, we work together in small groups, and sometimes in large groups, in general, we are still very much a cottage industry; at any one time the number of scientists working in a distinct discipline is not that large, even on a world-wide basis. Of course, this works pretty well for scientific advance; we are not a production industry, but researcher. No one knows the best way forward, and we need to experiment to find out. But it does mean that we often play second fiddle to those capable of more co-ordinated action; compare for example, scientists to the medical community with its tightly controlled professional bodies. Or, of course, the STM publishing industry, particularly as it has become focused in fewer and fewer competing publishers.

For example, ACM spends several million dollars every year to support the reliable data center serving the Digital Library

— Michel Beaudouin-Lafon

Clearly, it is true that the cost of data centres and storage are not trivial. But the cost of servicing data has plummeted over recent years. Scientific papers largely consist of storing words and figures; these do not take up much space. The laptop I am working on has a copy of my email directory; it’s not complete but it carries most of my outgoing email since 1994 and a lot of the incoming; this is a lot of words! But the total size is now less than 5G, which will fit on a 3 pound pen drive, or my phone. Now if ACM were storing research data, then it would be a totally different issue; the costs here are significant, problematic and rising. But they do not.

The ACM might spend several million dollars a year, but the bottom line here is that this does not account for the cost of publishing. The Wikimedia foundation which supports Wikipedia spends around 10 million dollars a year, in total, on one of the top ten websites in the World. This is about the daily cost of the whole scientific publishing industry.

The quality of a journal is typically measured by its impact factor

— Michel Beaudouin-Lafon

And a very bad measurement of journal quality it is too. As someone who works in two disciplines at once, I constantly get hit by this: my best computing publications have laughable impact factors when compared to my bio publications; when judged against computer scientists, however, my bio publications have such high impact factors, that they have to be ignored as outliers.

At $5,000 per publication, my lab is broke.

— Michel Beaudouin-Lafon

It is not clear where the $5,000 figure comes from, as most open access is less than this. But, anyway, this argument makes no sense. Our labs are already paying a vast amount of money for publications; usually this is squirrelled away in overheads, taken from our budgets before we see the money. And, although it doesn’t happen so much in computing, many journals levy significant page charges.

They are the big pharmaceutical labs and the tech firms who publish very little but rely on the publication of scientific results for their businesses. With author-pay, research will pay so that industry can get their results for free. Is this moral?

— Michel Beaudouin-Lafon

Open access on its own is not enough. we also need public disclosure about the process. Perhaps the examples of the pharmaceutical funding journals directly are unusual. It is not so easy to tell at the moment. In this context, it could be argued that the last thing we need is the pharmaceutical industry paying for the results of science. Of course, conversely, the pharmaceutical industry could argue that they already do pay for the (publically funded) research by way of taxation.

While they are interesting, all of these arguments really miss the point: the pharmaceutical industry already get their results for free, as their subscription fees do NOT pay for the research just its publication. The publishing industry also get the results that they depend on for free or with page-charges by charging the authors. And for every paper that researchers publish for free, they pay more to read someone elses.

So, we are already in the situation that we are told is not moral.

It is important to understand that the scientific community is largely at fault

— Michel Beaudouin-Lafon

There is some truth in the idea that scientific community has let itself walk into the situation, but ultimately I feel, that this is like blaming the financial crises on those recieving subprime mortgages. It is true that it is scientists who submit their best work to expensive closed publishers; but, especially in early and mid “career”, we do this to safe-guard our futures.

The problem with the subscription model is not the model but the fees.

— Michel Beaudouin-Lafon

Quite the opposite. Ultimately, I don’t pay the fees, so how much do I really care? But the subscription model prevents re-purposing, it limits access, it prevents competition. I work at a university as a scientist because I value the ability to be able to swap and discuss my work. I want the general public to be able to access my research. Dissemination of knowledge should be part of my job; I think it is reasonable that I, or my employers, should pay for it.

Which is not to say that the level of fees are fine; they are not. They are far to expensive under any model.

The added value provided by publishers is twofold: reputation (the value of the imprimatur), and archiving (the guarantee that the work will be available forever).

— Michel Beaudouin-Lafon

And this is it? Is this all that we are getting, given the costs? Especially the the reputation comes from the work, not the journal, and the archiving should be a rapidly decreasing cost.

Actually, in practice, I think the current publishing industry brings more value; selection of reviewers, sometimes copy-editing and, critically, advertising of the content. But, again, times have changed, and publishing practice in these areas has not.

The only other area in publishing where authors pay to get published is called the vanity press. Do we really want to enter that model?

— Michel Beaudouin-Lafon

This is a low blow, nor is it true. Many people pay for their own publishing costs. The government pays to publish election results; health service pay to publish public health information; companies pay to publish product safety recalls. All circumstances where the value to the author of public awareness of their content far exceeds the income they would recieve from charging. And the biggest example of this is the advertising industry.

Nor is the implication that this will necessarily result in low quality true. Consider the blogosphere; of course, there is much junk, the standard of science journalism is very high; frankly, when ever respecting sources like the BBC start talking about pixie dust, it’s probably at least as high-standard the as mainstream media.

All this aside, what do I, as a scientist, actually care about? Some of these leap to mind:

• Stable location and content.
• archiving
• peer review
• discovery and selection

Open access was built on the basis of replicating the existing publication. PLoS for example did this precisely so that it did not challenge both the business model and the publication procedure at the same time. How much of the costs stem from this? I think that we, as authors and readers, should know. How much of the millions the ACM spends on it’s data centre is involved in managing access controls, for example? How much on advertising? How much at booths at meetings?

Open access has opened the door, but now we need to challenge and change the process. Hosting data is not free nor is archiving. And, yet, I can find own my website from 2002 and enjoy it’s gaudy colour scheme all again. If this blog post is so exciting to the world, that the load brings the server down, you will be able to read it on coral cache. The peer review is expensive and time-consuming; I know because I’ve organised enough of it for BioOntologies. But then I did not get paid for this and how many of the real costs of peer-review do publishers bear? And discovery and selection? Well, we have google, and I follow my peers on twitter.

Author fees are not a solution. […] Finally, nonprofit publishers should take advantage of their unique position to experiment with sustainable evolutions of their publishing models.

— Michel Beaudouin-Lafon

And on this, I could not agree more. Our experiment with Knowledgeblog suggests that we can get 90% (or 80% or 70% depending on who you ask) with commodity software. It’s only a small start, but then I was on the mailing list that saw the first email about the creation of wikipedia, and that wasn’t long ago.

This is a paper we wrote for STLR2011 also published directly on Knowledgeblog

Abstract

Authors

Phillip Lord Newcastle University Newcastle-upon-Tyne, UK

Simon Cockell Newcastle University Newcastle-upon-Tyne, UK

Daniel C. Swan Newcastle University Newcastle-upon-Tyne, UK

Robert Stevens University of Manchester Manchester, UK

Introduction

The Web was invented around 1990 as a light-weight mechanism for publication of documents, enabling scientists to share their knowledge, in the form of hypertext documents. Although scientists and later most academics, like the rest of society, have made heavy use of the web, it has not had a significant impact on the academic publication process. While most journals now have websites, the publication process is still based around paper documents or electronic representations of paper documents in the form of a PDF. Most conferences still handle submissions in the same way¹. Books on the web, for example, are often limited to a table of contents.

For the authors (certainly from our personal experience), the process is dissatisfying; book writing is time-consuming, tiring and takes a number of years to come to fruition. If the book has one or a few authors, it tends to reflect only a narrow slice of opinion. Multi-author collected works tend to be even harder work for the editor than writing a book solo. Books do not change frequently; they are therefore out-of-date as soon as they are available. Authors feel a greater pressure for correctness, as they will have to live with the consequences of mistakes for the many years it takes to produce a second edition; most scientists welcome feedback, but being asked to justify something you wish you had not said becomes tiresome, especially if you are waiting to update it.

For the consumer of the material (either a human reader, or a computer), the experience is likewise limited. Books on paper are not searchable, not easy to carry around, are often not cheap to buy and more commonly very expensive to buy. For the computer, the material is hard to understand, or to parse. Even distinguishing basic structure (where do chapters start, who is the author, where is the legend for a given figure) is challenging.

All of this points to a need to exploit the Web for scientists to publish in a different way than simply replicating the old publishing process. Here, we describe our experiment with a new (to academia!) form of publishing: we have used widely-available and heavily used commodity software (WordPress [7]), running on low-end hardware, to develop a multi-author resource describing the use of ontologies in the life sciences (our main field of expertise). From this experience, we have built on and enhanced the basic platform to improve the author experience of publishing in this manner. We are now extending the platform further to enable the addition of light-weight semantics by authors to their own papers, without requiring authors to directly use semantic web technologies, and within their own tool environment. In short, we believe that this platform provides a ‘cheap and cheerful’ framework for semantic publishing.

The requirements

The initial motivation for this work came from our experience within the bio-ontology community3. Biomedicine is one of the largest domains for use of ontology technology, producing large and complex ontologies such as the Gene Ontology [28] or SNOMED [27].

As an ontologist, one of the most common questions that one has is: ‘where is there a book or a tutorial that I can read which describes how to build an ontology?’. Currently, there is some tutorial information on the web, there are some books; but there is not a clear answer to the question. Many of the books are collections of research-level papers, or are technologically biased. Currently many ontologists have learned their craft through years reading mailing lists, gathering information from the web and by word of mouth. We wished to develop a resource with short and succinct articles, published in a timely manner and freely available.

We wished, also, however to retain the core of academic publishing. This was for reasons both pragmatic, principled and political. Consider, for example, Wikipedia, that could otherwise serve as a model. Our own experience suggests that referencing Wikipedia can be dangerous: it can and does change over time meaning critical or supportive comments in other articles can be ‘orphaned’. Wikipedia maintains a ‘neutral point-of-view’ which, many are of the opinion, makes it less suitable for areas where knowledge is uncertain and disagreement frequent. Finally, Wikipedia is relatively anonymous in terms of authorship: whether this affects the quality of articles has been a topic of debate [17], but was not our primary concern; pragmatically, the promotion and career structure² for most academics requires a form of professional narcissism; they cannot afford to contribute to a resource for which they cannot claim credit. Of course, our experiences may not be reflective of the body academic overall; there has, for example, been substantial discussion of the issues of expertise on Wikipedia itself [8]. Although the reasons may not be clear, it is clear that academics largely do not contribute to Wikipedia, and that Wikimedia sees this as an issue [16].

We also had an explicit set of non-functional requirements. We needed the resource to be easy to administer and low-cost, as this mirrored our resource availability; authors should be offered an easy-to-use publishing environment with minimal ‘setup’ costs, or they would be unlikely to contribute; readers should see a simple, but reasonably attractive and navigable website, or they would be unlikely to read.

The Ontogenesis experience

Our previous experience with the use of blog software within academia was limited to ‘traditional’ blogging: short pieces about either: the process of science (reports about conferences, or papers for example); journalistic articles about other peoples research; or, personal blogging, that is articles by people who just happen to be academics. Although we wished to develop different, more formal content, this experience suggests that many academics find blogging software convenient, straight-forward enough and useful.

To test this, we decided to hold a small workshop of 17 domain experts over a two day period, and task them with generating content, conduct peer-review of this content and publish it as articles on a blog.

Terminology and the Process

Like many communities, the blogosphere has developed its own and sometimes confusing terminology. To describe the process we adopted we first describe some of this terminology. A blog is a collection of web pages, usually with a common theme. These web pages can be divided into: posts that are published (or posted) on an explicit date and then unchanged; and pages that are not dated and can change. Posts and pages have permalinks: although they may be accessible via several URLs, they have one permalink that is stable and never changes. Posts and pages can be categorised – grouped under a predefined hierarchy – or tagged – grouped using ad hoc words or phrases defined at the point of use. A blog is usually hosted with a blog engine, such as WordPress that stores content in a database, combines it with style instructions in themes to generate the pages and posts. Most blog engines support extensions to their core functionality with plugins. Most blogs also support comments or short pieces of content added to a post or page by people other than the original authors. Most blog engines also support trackbacks which are bidirectional links: normally, a snippet from a linking post will appear as a comment in the linked to post. Trackbacks work both within a single blog and between different distributed blogs. Many blogs support remote posting: as well as using a web form for adding new content, users can also post from third party applications, through a programmatic interface using a protocol such as XML-RPC or even by email. Posts and pages are ultimately written in headless HTML (that part of HTML which appears inside the body element), although the different editing environments can hide this fact from the user.

Our initial process was designed to replicate the normal peer-review process, with a single adjustment, that peer-review was open and not blind: papers would be world-visible once submitted; the identities of reviewers would be known to authors; all reviews would be public. We adopted this approach for pragmatic reasons. WordPress has little support for authenticated viewing and none for anonymisation. The full process was as follows:

• Authors write their content and publish using which ever tooling they find appropriate.

• The author posts their content, categorising it as under review.

• An editor assigns two reviewers.

• Reviewers publish reviews as posts or comments. Reviews link to articles, resulting in a trackback from article to review.

• The author modifies the post to address reviews.

• Once done to the editors satisfaction, the post is recategorised as reviewed.

Our expectation was that following this process, articles would not be changed or updated; this is in stark contrast to common usage for wiki-based websites. New articles could, however, be written updating, extending or refuting old ones.

Reflections on the Ontogenesis K-Blog

Our initial meeting functioned to ‘bootstrap’ the Ontogenesis K-Blog. This was useful to acquire a critical mass of content, but also, on this first outing, to explore the K-Blogprocess and technology. The setup for the day was the vannilla WordPressinstallation. The day started with a short presentation on the K-Blogmanifesto [22] and an overview of the process, including authoring and reviewing. The guidelines to authors were to write short articles on an ontology subject (a list of suggestions was offered and authors also made their own choices) and to produce the article in whatever manner they felt appropriate. There was a certain level of uncertainty among authors as to the K-Blogprocess (partly because one of the objectives of the meeting was to ‘force out’ the process) and this, naturally, pointed to the need to document the K-Blogprocess so that authors could have the typical ‘instructions to authors’.

This first meeting produced a set of 20 completed and partially completed articles. Some even had reviews. Even on the day itself there was some external interest seen from Twitter. The first external blog post (outside of those produced by attendees) happened during the meeting [19] with a second shortly after [18].

We also held a second content provision meeting and together these generated a collection of articles that felt like an academic book in terms of content, but generated with considerably less effort. This experience was also sufficient to gather requirements on how to improve the K-Blogidea. A useful K-Blogon the K-Blogprocess itself was produced by Sean Bechhofer [13]. There is also a K-Bloglooking back on the first year of the Ontogenesis K-Blog [23].

Several requirements emerged with respect to authorship. The principle of the short, more or less self-contained article was attractive (though the audience were somewhat self-selecting). Authoring directly in the editor provided by WordPress was felt to be poor by those that tried it. Authoring in a favourite editing tool and then publishing via WordPress worked reasonably well for most authors. There were, however, a variety of issues with the mechanism of this style of publishing; referring to articles that will be, but have not yet, been written. To some extent this was an artefact of the day (many articles being written simultaneously), but authors needed to refer to glossaries and articles in progress.

One stylistic issue was the habit of putting full affiliations at the top of an article. The ontogenesis theme presents the first few lines when displaying many articles, but in many cases this was simply showing the title and author affiliation; where it would be more useful to have the first sentence or so of the article itself.

For the whole K-Blog, a table of contents was felt to be important. This would give an overview of contents and a simple place for navigation about the K-Blog. This raised the issue of attribution; the table of contents needed to expose the authors, including multiple, ordered authors. This is not an unsurprising need, as the authors’ scientific reputation is involved. In this vein, making K-Blogarticles citable by issuing of Digital Object Identifiers (DOI) was requested.

For scientific credibility, the ability to handle citations easily was an obvious requirement. Natively, WordPresshas little or no support for styling citations and references. The ability to cite via DOI and, in this field, PubMed identifiers to automatically make links and produce a reference list was felt to be important. Also, having the Ontogenesis K-Blogarticles in PubMed would also be attractive to authors.

The last authorship issue was the mutability of articles. One aim of K-Blogis to enable articles to change in the light of experience and scientific development, as well as a procedural requirement for updates following review. There was felt to be a conflicting need for articles not to change, so that comments and links from other documents work in the longer term.

The last significant issue was the reviewing of articles. The aim was to have this managed by authors choosing reviewers (with editorial oversight). On the Ontogenesis K-Blogday this could work with authors calling across the room for a review. This is, however, not a sustainable approach. WordPress, however, lacks tracking facilities to manage the reviewing process, whether this is done by an author or an editor. The realisation that such management support is needed is not the greatest insight ever gained, but the requirement is there even in a light weight publishing mechanism.

Improvements to the technology

Our initial experiment with the ontogenesis K-Blogsuggested a significant number of issues with the use of WordPressfor scientific publication. In this section, we describe the extensions that we have made or used to the publication process, documentation or to WordPressitself. Following our initial experience with Ontogenesis, we have started to trial these improvements, including through another workshop which resulted in a new K-Blog [12], describing the scientific workflow engine Taverna [24]; work is also in progress on the use of a K-Blogfor bioinformatics [1], and another for public healthcare [3].

Currently, we have 11 plugins extending the basic WordPressenvironment. For completeness, all of these are shown in Table 1. Our theme is also extended in some places to support the plugins. In general, the plugins are orthogonal and will work independently of each other. One advantage of using WordPressis that many of these plugins are freely available, written and maintained by other authors; while other academic publication environments, such as the Open Journal System [5] exist and are relatively widely-used, but WordPress is used to host perhaps 10% of the web, making the plugin ecosystem extremely fertile.

Reviewing: The initial process was self-managed and required two reviews per article; this was found to be cumbersome. We have addressed this in two ways; first, we have defined a number of different peer-review levels (public review, author review, editorial review [15]), including a light-weight process now being used for Ontogenesis; authors now select their own reviewers, and decide for themselves when articles are complete. Second, we have added software support. Initially, we attempted to use RequestTracker – an open source ticket system, but found the user interface too complex for this purpose. We are now using the EditFlow plugin to WordPress that was designed for managing a review process—albeit a hierarchical rather than peer-review process.

Authoring Environment: The standard WordPresseditor was found impractical by most authors, even for short articles. WordPressdoes provide ‘paste from word’ functionality, but this removes all formatting which defeats the point. While the lack of a good editing environment could have been a significant problem, our subsequent experimentation has shown that it is possible to post directly from a wide variety of tools, including ‘office’ tools such as Word, Google Docs, LiveWriter and OpenOffice. This is in addition to a variety of blog-specific tools and text formats (such as asciidoc), which are suitable for some users. We have added documentation to a kblog (http://process.knowledgeblog.org) to address these. In practice, only L^aT_eX proved problematic having no specific support. To address this, we have produced a tool called latextowordpress; this is an adaptation of the plasT_eX tool, a python based T_eX processor, to produce simplified HTML appropriate for WordPresspublishing. Our experience with using the tools is that while none are perfect, sometimes requiring ‘tweaking’ of HTML in WordPress, most reduce publishing time to seconds.

Citations: We have addressed the lack of support for citations within WordPresswith a plugin called kcite. This allows authors to add citations into documents as shortcodes with either a DOI or Pubmed ID (other identifiers can and are being added to kcite). Shortcodes are a commonly used form of markup of the form: [tag att=”att”]text[/tag]; they are often found where a simplified HTML-like markup is desired. A bibliography is then generated automatically on the web server. Requiring authors to add markup to otherwise WYSIWYG tools is damaging to the user experience. We believe that this is soluable, however, by extending bibliographic tools, by developing a ‘kcite’ style-file or template; we have a prototype of this (using CSL [10]) for Zotero and Mendeley, and another for asciidoc with bibtex. It is also possible to just use native tool support in Word or L^aT_eX, and convert bibliographies to HTML; the disadvantage with this approach is discussed later.

Archiving and Searching: Archiving is primarly a social, rather than technological, problem. A blog engine is fully capable of storing content in the long-term, but authors and readers have to believe that it will do so. As a novel form of academic publishing, K-Blogis not automatically archived by as a scientific journal. However, we have taken advantage of its web publication; the main K-Blogsite is now explicitly archived by the UK Web Archive, as well as implicitly by other web archives. We have enhanced the website with an ‘easy crawl’ plugin–that is a single web page pointing to add articles classified as reviewed. We now support the (technical) requirements for LOCKSS and Pubmed. Simultaneously, this also enhances the searchability of K-Blog, fulfilling the requirements for Google scholar.

Non-repudiability: The K-Blogprocess does not allow authors to make semantically meaningful changes after an article has been reviewed. Unfortunately, it is hard to define ‘semantically meaningful’ computationally, so we have made no attempt to address this by locking articles; rather, all versions of articles are now accessible to the reader (WordPressprovides this facility to the authors by default). This enables community enforcement of a no-change policy.

Multiple Authors: We believe that authoring is best done outside WordPress. This also means that we do not support multiple-authorship; we have made no attempt to add collaborative features to WordPress. However, we did need articles to carry a byline attributing the articles to multiple authors; although not critical to the functioning of a K-Blog, it is socially critical to appease the professional narcissism (see Section ) of scientists. Fortunately, this is a common requirement, and a suitable WordPressplugin existed.

Identifiers: WordPress already supports permalinks; although we believe that URLs are entirely fit for purpose technologically while DOIs do little other than introduce complexity [11], K-Blogrequired DOIs for professional narcissism. We considered becoming an DOI authority, but this proved impractical. Instead, we have used DataCite [2]. This has required a small extension to WordPress to extract appropriate metadata and to store the DOIs once minted.

Metadata: K-Blognow uncovers various parts of its metadata in a number of ways; unfortunately, there appear to be a large number of (non-)standards in use, each with its own application. K-Blogcurrently provides: COiNS, enabling integration with Zotero and Mendeley; meta tags for Google Scholar; and Dublin Core tags for no specific reason than completeness. We are in the process of providing bibtex export (for bibtex!), and a JSON representation to support citeproc-js [14] in the second generation of kcite.

Mathematics and Presentation: We have also provided several pieces of technology that did not stem from concrete requirements arising from the initial Ontogenesis meeting. We have improved parts of the presentation system by adding, for example, syntax highlighting to code blocks. Additionally, we have created the mathjax-latex plugin enabling the use of T_eX(or MathML) markup in posts that are then rendered in the browser using scalable fonts. WordPresshas native math-mode T_eX support, but using image fonts which do not scale and have an ugly pixelated display.

Discussion

We have been motivated by a lack of enthusiasm for traditional book publishing to devise another mechanism by which we can achieve the same ends. We wished to avoid the downsides of an ‘all or nothing’ approach to creating a ‘static’ paper document that is read by relatively few people due to price. The K-Blogapproach allows authors to publish in a piecemeal fashion; writing only that which they are motivated to write using a mechanism that avoids a third party making arbitrary decisions on formatting with peculiar time-scales.

To avoid all this, the K-Blogis a light-weight publishing process based on commodity blogging software. We have taken an approach of writing short articles around a theme of ‘ontology in biology’; the Ontogenesis K-Blog. At the time of writing we have 26 articles and page viewing numbers that are pleasing (see Figure 1). These statistics are generated by WordPressdirectly, and represent (an approximation of) ‘real’ page reads, with robot and self-viewing removed. This is confirmed by the ten most read articles (Table 2) that reflect our expectations – ‘What is an ontology’ being first. In this sense, we consider the K-Blogprocess to be a success, especially when considered against the circulation of an equivalent book.

Figure 1: Month page view statistics for the Ontogenesis K-Blog.

The social processes with K-Blogare largely similar to traditional publishing, with one exception – reviewing is public. While we may have been interested in experimenting with this for principled reasons, in practice we adopted it because we did not know how to support blind anonymous review with WordPress. Open review is not a new idea: Request For Comments are common in standards processes; both Nupedia [4] (the fore-runner of Wikipedia) and H2G2 [6] (which predates Nupedia) use public peer-review. It is still, however, unusual in academia. In our experience from Ontogenesis, it raised no worries from among our contributors, except that reviewers often wanted to be more involved in the proofing, a role normally played by authors low down the author list; open review processes blurs these lines somewhat.

One open area for the discussion is the extent to which authors can, should be and wish to change articles after publication. While the ability to update is inherent in the web, the desire for non-repudiability was considered to be important; the contradiction here appears fundamental, and we do not feel we have reached a good compromise yet. In one sense, our use of the post-revision display plugin solves this problem; even if the article changes, it is still possible to refer to a specific version. However, like all automated versioning tools, many versions get recorded often with very fine-grained changes, which makes selection of the ‘right’ version hard to impossible. We could replace this with an explicit versioning tool, similar to a source code versioning system; but these systems are hard-to-use for those unused to them, as well as being difficult to implement well. An environment like K-Blog, however, does allow rapid publication of and bi-directional linking with articles; combined with typed linking with CiTO, the ability to publish erratum, addendum and second editions may be a better solution.

Our experiences with K-Blog, we think, are useful in understanding how semantic web technology can and will impact on the publication and library process. Both from our initial work with Ontogenesis, and subsequent work with http://taverna.knowledgeblog.org, it has become obvious that good tool support is critical. ‘Good’ in this sense can be straight-forwardly interpreted as ‘familiar’ that in general can be interpreted as MS Word. Our choice of a blogging engine here was (unexpectedly) well-advised, as this form of publication is already supported by many tools. It is also clear that there are many other tools that could be added; while Ontogenesis has the content, for example, that might be found in an academic book, it does not currently have the presentation of the book. Articles are already available as ePUB, and more recent work has used our Table of Contents plugin to provide a single site-wide ePUB of all articles [25]. Pre-existing tools such as Anthologize [9] may also be useful for adding organised collections of articles gathered from the whole.

This has a direct implication on the addition of further semantics to content. On the positive side, the use of WordPress makes semantic additions plausible in a way that many conventional publishing processes do not. For example, the publication of our (PWL, RS) recent paper [20] required conversion from the LaTeX source to PDF (by latex), to another PDF, to a MS Word file (by hand), to XML before arriving at the final HTML form. This process took many weeks, required multiple interactions between the authors and publisher. It still failed to preserve the semantic use (to humans) of Courier font highlighting in-text ontology terms and requiring post-publication correction. The equivalent blog post [21] gave us nearly instantaneous feedback on the final form, allowing us to check that the semantics was present and correct.

The requirements for semantics have, however, to be light. We have concentrated throughout K-Blog on the ease of delivery of content; even with this focus, it is hard. In most cases, asking for more work, for more semantics than authors are used to giving in papers is problematic. For example, I (PWL) attempted to add microformat-based markup to Ontogenesis, again, identifying ontology terms. So far, all article authors have ignored this markup (including, embarrasingly, myself).

One solution to this issue is to ensure that authors themselves benefit directly from extra semantics. For example, the Mathjax-Latex plugin allows WordPressto present mathematics in T_eX or MathML markup in the final document, which is more semantically meaningful than the default WordPress behaviour of rendering an image. From the authors perspective, it also enables the use of T_eX markup in Word, and the end product scales and looks less ugly on the web page.

With Kcite, we allow the user to embed DOIs or Pubmed IDs; this can be achieved at no cost to the user, if they already use a bibliography tool, as it can transparently produce citations for them using Kcite shortcodes. Development versions of Kcite already allow easy switching of bibliographic style that we hope will become at the option of the author (rather than the website or publisher as is currently the case), and/or the reader. With this additional information, we can also embed more semantics into the end document at no additional cost to the author, using for example the least specific CiTO cites term. However, further use of CiTO that will require the author to decide which term to use, with relatively little gain to themselves, and may require extension to bibliographic tools if we are to maintain transparency of Kcite shortcodes; even if the tools are present, it is unclear whether authors will use them. We note that semantics useful to domain authors is likely to be domain-specific; mathematicians are more likely to care about maths presentation, but less likely to care about Pubmed IDs. We need to be able to extend the publishing model and environment for different journals to cope.

From a technological perspective, we have found the use of shortcodes to be a good mechanism for readers to add semantics. They are simple and relatively easy to understand. In some cases they can be hidden from the user entirely; forcing users to add markup to otherwise WYSIWYG environments such as MS Word is best avoided. Although the direct use of a more standard XML markup would seem more sensible, in practice it requires tool support, as XML markup will be escaped by helpful remote posting tools. Extension of remote posting tools is hard (for tools like MS Word) or impossible (for cloud tools such as Google Docs or LiveWriter). A blogging engine such as WordPress makes it trivial to replace shortcodes both with a presentation format and machine interpretable microformat; for example, the development version of Kcite transforms DOI short codes ([cite]10.232/43243[/cite]) into in-text citations (Smith et al, (2002)) embedded in a span tag (<span kcite-id="10.232/43243">Smith et al, (2002)</span>) that are subsequently transformed into final presentation form within the browser using Javascript. The presentation form can also support additional semantic markup such as CiTO [26].

Although we believe that additional semantics are a good thing, we will not enforce a requirement for additional semantics on authors. If authors choose not to use kcite, then this is their choice. We need to show that they are useful. Our experience with many (non)standards such as CoINS, DOIs, OAI-ORE, LOCKSS is that they are not simple, speaking primarily to publishers or librarians. For a semantic web approach to work, it must focus on authors and readers, as they produce and consume the content. Extracting even light-weight semantics even from authors who are ontology experts is hard. For other domains, the situation may be worse.

Current publishing practices make use of semantic web technology impractical; semantics added by authors are unlikely to be represented correctly if the end product is a PDF typeset by hand. More over, we can see little point adding semantics to individual articles if this is done in a bespoke way. With K-Blog, we have focused on providing both content, and a full process, with review, using existing tools and workflows, adding semantics secondarily or incidentally where we can. As a result, the level of semantics that we have achieved is light-weight. However, we believe that K-Blog and WordPress combined with associated tooling provides all the basic requirements for a publishing process, and that it provides an attractive framework on which to build a semantic web.

Acknowledgements

We would like to acknowledge the contribution of the authors of articles for both the Ontogenesis and Taverna K-Blog, whose feedback was essential for this process. K-Blogis currently funded by JISC.

Josh Brown from JISC has given his permission for me to reproduce the feedback from the peer-reivew of my last JISC grant which bounced. A shame, as it would have provided us with an opportunity to test out knowledgeblog on papers from the wild, while also producing an great demonstrator of the advantages of using the web to distribute papers with web technology rather than just dumping a link to a PDF.

With luck, we can rejuvenate this work in another way.

“One bid (Bid no 8: Newcastle University) was flagged by one of the markers as being out of scope, despite receiving good marks and positive comments from the other two markers.

The original terms of the call specifically state that projects must add value to existing peer reviewed journals. Projects seeking solely to create new publications are specifically excluded. (Please review the sections Expected Outputs and Requirements of the call for more detail on these conditions.)

Bid no 8 states:

“we will identify authors within Newcastle, take their open-access publications and recast them into a form suitable for WordPress”

The bid is clearly designed to aggregate content that has been published elsewhere, largely based on content held within Newcastle’s institutional repository. No existing, peer-reviewed scholarly journal is involved in this project.

While the creation of a web-native publishing tool clearly has merit, as identified by the two markers who praised this bid, the funding call is, as stated, intended to add value to existing publications. In the absence of an existing peer-reviewed publication as a partner in this project, the bid is out of scope”

The panel agreed with this analysis, which meant that, despite the fact that the project was viewed unanimously as very strong proposal on its own merits, we were obliged to decline to fund this project. The requirement for direct partnership with an existing peer-reviewed scholarly journal for all projects in this strand was imposed after lengthy discussion, and for a range of reasons, including sustainability, tight time-frames and so on, and it was felt that this should be upheld.

— Josh Brown

So, to start with a rant.

I have reached a key and pivotal point in my life. I have decided that I never, ever, ever want to see permalinks with any semantics in them, ever again. And before any one gets clever, yes, I know that this post has semantics in its permalink.

Recently I was looking through Knowledge Blog and realised that I have made a mistake with the permalink structure. When we created Ontogenesis I used semantic links — that is permalinks with the title of the article in them, because I thought that they would be more popular with authors and easier to remember. However, I didn’t want name clashes, land grabs or disambiguation of the sort that you get on Wikipedia(website). So I added in a date as well as a uniquish identifier. I realised quickly that I had manage to combine the worst of both worlds; people wished to change the titles of their articles, and the permalinks no longer fitted. And the links were still hard to remember. So I moved ontogenesis onto the simple number-based permalink structure that it has today. As a concession to usability, I didn’t use the basic ?=192 that is the default, but instead the rewritten 192 which is easier. As far as I can tell, WordPress remembers old permalinks — they do not just go away when the overall structure is changed and links are preserved. They really are as permanent as these things go.

But I had fixed the other knowledgeblogs subdomains consistently. My update to Process which defines and documents the process of knowledgeblog itself was still set up with the older style identifiers. So I changed it; for example, http://process.knowledgeblog.org/archives/19 became plain http://process.knowledgeblog.org/19. I don’t understand why, as WordPress seemed to maintain the links last time, but apparently this broke an email Dan Swan had sent out advertising out Bioinformatics Write-a-thon.

While I have generally purged semantics from links, WordPress still maintains the “title as link” approach for pages, as opposed to posts. I guess this makes sense, as you generally don’t have that many pages, but in this case it has shot me in the foot. I started to re-create a “Who are we” page for the www main domain of knowledgeblog. This ended up with a URL of http://www.knowledgeblog.org/who-are-we; but then I got distracted and left the job half-done. More I wanted to use my normal editing environment. So I trashed the page. Today, I created another page with the same name. But this got a URL of http://www.knowledgeblog.org/who-are-we-2. Ugly. WordPress would not let me rename this permalink, so I tried resurrecting the trashed post and changing it’s content. For reasons that I don’t understand, this didn’t work either and I ended up with http://www.knowledgeblog.org/who-are-we-3. I tried changing this to http://www.knowledgeblog.org/who which works, but redirects to http://www.knowledgeblog.org/who-are-we-3.

So, WordPress is doing (mostly) the right thing, but it still all worked against me. I don’t understand however, why, WordPress doesn’t allow you to set default permalinks for Pages as well as posts. It should do, but as far as I can tell, it does not.

The irony of this is that this is not a new issue. I even wrote a post about Manchester syntax and OBO which largely revolves around this issue. I know about the importance of semantics-free identifiers, and I should have known better then to make a mess of things this way, but on knowledgeblog and indeed on this blog. It just goes to show that handling change is hard and living with a nasty legacy is often the result. I guess that it is a nice example of the advantages and disadvantages of semantics and the compromises that have to be made in any engineering situation.

I haven’t decided yet, but I think I will change the permalink structure of this blog in a few days time. I am hopefully that existing links will be maintained, but that all future ones will exist only in numeric form. Fingers crossed, it will all work.

In a typically thoughtful post, Peter Sefton discusses the advantages and disadvantages of WordPress as an authoring environment. I though I would clarify my feelings on this a little.

Previously, from our experience on Knowledge Blog suggests to us that the WordPress environment is very poor for editing, something we have expressed in our process documentation.

I should be clear that this is in the context of knowledgeblog. Academics have their own way of working, and normally are used to this. They use tools which fit with their lifes. For example, Google docs is a good tool but, basically, useless if you do most of your paper writing on an plane. The same will be true for tools such as Annotum if it ever appears. It is hard to beat Word and email (or frequently dropbox nowadays).

Of course, there are other ways; for example WordPress offers “A complete revision history of the document is maintained with the ability to roll-back to earlier versions”. But, then, so does Word with dropbox. And the WordPress facilities are in no way comparable to the versioning that you get with latex, or asciidoc and Subversion or Git. Although, in practice, I rarely use versioning when authoring, and dropbox’s poor-mans roll-back is enough.

The only clear advantage of using WordPress tools is that you don’t need a two stage publication process. But, the general idea behind blogs, is that publication does not happen often; it happens once, and then the post remains. This is in contrast to a Wiki, where using external editing tools is impractical at best. And the situation is very similar to current publication where PDF is the common medium.

My conclusion — there are lots of people, lots of use cases, and lots of requirements. I don’t say that authoring must be independent from the publication environment; I do say that publication environment must not require a single authoring tool. Fortunately, for the tools that we have created for kblog, we can afford to be agnostic. They will work integrated with WordPress editing also. Still, I just spent 10 minutes longer making this post than I need to, to stop the shortcodes in Peter’s quote below from being kcite’d (check the source for the trick!), which was harder because I use asciidoc. There are going to be problems. Supporting a heterogenous environment is painful. I wish there were a perfect solution, but there there are just a set of messy compromises.

Peter also makes a second point about our plugins (and others): that is, that they are non-standard.

There are similar issues/risks with stuff like WordPress shortcodes such as KCite from KnowledgeBlogs. It’s a great tool for authors, allowing them to cite things in a rational way:

DOI Example – [cite source=’doi’]10.1021/jf904082b[/cite]

PMID example – [cite source=’pubmed’]17237047[/cite]

But it’s proprietary to a particular processing environment.

There is a risk of creating a new form of the proprietary lock-in we had up until recently (and arguably we still have) with document formats like Microsoft’s .doc.

— Peter Sefton

It’s a fair point, and one which I agree with. The last thing that we need is hundreds of independent shortcode or other syntaxes; I mean, imagine what a nightmare it would be if every single Wiki engine and text conversion tool used their own, almost identical, but slightly different and incompatible syntax. Hmmm.

We chose to use shortcodes for two highly pragmatic reasons. First, WordPress has nice support for them. Building a shortcode handler is nice and simple and does not require us to build regexps (the first version did it by hand for one reason or another, and the regexps were painful). The second reason stems from our desire for a decoupled authoring environment. Shortcodes pass through the HTML publishing step without escaping; to use XML or HTML compliant mechanisms would require us to change, for example, the HTML export mechanism of Word. Not somewhere we wished to go.

In practice, however, I don’t think that this is a major problem, if the code is written carefully. With Mathjax-latex, the shortcodes are transfered into Mathjax syntax, then mathjax does the rest. The development version of kcite works this way — the shortcodes are translated into a span-tag based microformat, then the bibliography tools operate on the client to format the bibliography. So long as the code is crafted reasonable, it should not be dependant on WordPress.

This is just a short introduction to Michael Bell, my PhD student. He’s now in the second year of his PhD, and has been looking at annotation in biological databases. More specifically, we are trying to define quality measures for textual annotation, based around the bulk properties of these databases. It’s related to, but distinct from my early work on semantic similarity. The question is whether we can judge the quality of sentences, words or records based on how they have been used previously, and how far they have spread.

Michael has now started to blog his work, following on from my own knowledgeblog work, and our general commitment to open science. As part of his work, he is starting to build web delivered tools, as it is a useful way of navigating the complex knowledge space of biological data. So, his website is also part of his work.

A good example of this recent blog post discusses the creation of word clouds for all historical versions of Swiss-Prot and TrEMBL and, because everyone loves a word cloud, it is well worth a look.

This is latest grant that we have submitted to JISC, in this case for a new application of the knowledgeblog platform. As usual, it is a direct post from word, so there may be a few presentational issues in it.

The grant is currently under review; I will post the outcome and any feedback (if possible) once I have a result.

Outline Project Description

In this project, we will generate a large body of web content, demonstrating the applicability of commodity blogging technology as supplement to the Universities existing eprints archive. Through a use of technology pioneered by the JISC funded Knowledgeblog project, we will publish 100+ scientific articles, from a variety of different word-processing environments, in a structured-web capable form rather than as PDF. This content will then be augmented to demonstrate the advantages of leverage from a commodity platform, enabling novel mechanisms of publication.

1. Introduction

¹The modern publishing industry has been massively affected by the development of the web. However the impact has been highly varied across different domains. Publications that address news events or encyclopedic knowledge have been very heavily affected; other areas have changed little. The web initially developed from the desires of scientists to share knowledge; in some areas, such as biology, the uptake of web technologies has been little short of extraordinary. It is ironic, therefore, that the publishing of formal academic papers has been affected relatively little by the web. Although, content page listings may have been largely replaced by RSS or email, and papers may be available as HTML, they are still largely constrained by the print requirements, packaged as PDFs, poorly linked, with static figures.

²An alternative publication mechanism has already been funded by JISC as part of the “Managing Research Data” programme. As part of the Knowledgeblog project, we have investigated using a publication tool, which integrates well with scientists’ existing work-practices, based around a commodity blogging engine, namely WordPress. There are a number of tools such as Open Journal Systems, or organizations like Scielo which allow the web publication of academic articles. While these have large user bases (OJS — 6000 journals, Scielo — 600), currently, WordPress is used to drive around 10% of the world‘s websites; a user base orders of magnitude larger. WordPress, therefore, performs the basic tasks of publishing articles extremely well, scaling to millions of page hits, enjoys tool support from many word processing environments and benefits from many augmentations for specialist audiences. We have extended this tool with a few specialised extensions of our own and, as a result, made it more suitable for academic publishing. We have then used this tool as the basis for two journals, in this case, aimed at producing educational resources describing ontology technology (http://ontogenesis.knowledgeblog.org), and the JISC-funded Taverna workflow system (http://taverna.knowledgeblog.org).

³These two resources are, in effect, “gold open-access” — although not requiring author payment. They present content which has not been presented elsewhere, but was written for the purpose; articles have been (or are progressing through) a formal review process. While this has provided a useful resource, generating over 15k page views, these resources are designed to be coherent in scope; although this is generally a positive virtue, by definition it allows us to investigate the suitability of the tooling for only a small number of articles and a limited domain.

⁴Newcastle University has a strong history in supporting gold open access publication: it was the site for the first open access law journal in the UK (http://webjcli.ncl.ac.uk/). In addition, it also has a large and successful eprints repository (http://eprints.ncl.ac.uk) archive, currently hosting 50k articles or bibliographic records; in this project, we will exploit the eprints archive to provide content, building a substantial knowledge resource; this will both demonstrate the suitability of the Knowledgeblog tool-chain as the basis for green open access publication, the value of this novel form of publication, and provide the vital testing against content “from the wild”, allowing us to extend the suitability of this tool-chain to as many areas of academic discourse as possible.

2. Fit to call

⁵The project call notes that JISC is or has funded many projects relating to scholarly communication. These include: infrastructural support in the form of institutional repositories; support for open-access; and support for novel mechanisms of publication such as overlay journals. Specifically, theme D – campus-based publishing – is aimed at increasing the capacity of the sector to publish and disseminate research outputs directly. The call also highlights attempts such as the “Beyond the PDF” workshop to move toward more structured forms of knowledge; while, in theory, PDF is capable of supporting relatively rich structuring, in practice, most of the tools which generate files in this format produce a relatively opaque, binary artefact from which it is difficult to extract information, or to repurpose or recast that in any way.

⁶While open-access publishing has made significant strides in the last 10 years, becoming an accepted part of the academic landscape, Gold open-access – the publication of original content – still accounts for the minority of academic publications. Green open-access – author publication of content often published elsewhere – now accounts for up-to 25% of the literature in some fields.

⁷Institutional repositories such as that run by Newcastle (http://eprints.ncl.ac.uk) or author archiving on their website (e.g. http://homepages.cs.ncl.ac.uk/phillip.lord/publications.html) are the most common route for green open-access publication. While increasing access to academic materials is a very positive step, this form of publication is largely limited to providing access to a PDF. From neither the authors, nor the readers point of view, is there significant added value to the publication. For example, our experience is that authors are often equivocal or disinterested in publication in institutional repositories as it is “just-one-more-thing” to do, while maintaining a website requires significant technical expertise.

⁸For this grant, academics at Newcastle supported by the infrastructure provided by the local librarians will provide an alternative; we will identify authors within Newcastle, take their open-access publications and recast them into a form suitable for WordPress. We will do this with their active permission and engagement, using the tooling we have developed or documented as as part of the previously-funded JISC “knowledgeblog” project. Where authors wish to, we will support them in performing this work for themselves; where they do not want “just-one-more-thing”, we will leverage off the existing eprints process, and perform this work for them. In general, this can be performed directly using MS Word, latex or other word-processing software, whichever is the authors’ preferred editing environment. In addition, we will use this process to increase the usability of the tooling, increasing the ability to and likelihood that authors will directly publish their work in fashion. As this proposal is built on existing work from the University eprints archive, library-support is implicit within FEC and not specifically or additionally costed.

⁹Once publications are available in this framework, authors and readers will be able to take advantage of the additional features which come either from WordPress directly, or from augmentations provided or assessed by the WebPrints team. For example, authors will be able to see rich content-access statistics, including page-views, referrer and incoming link information. Published articles will be bi-directional linkable using trackbacks. Authors will be able to add tags, zoomable equations or automatically generated reference lists depending on their level of technical competence. For viewers, category and tag based RSS feeds will be available, searching, bi-directional linking (again!) will be possible. As a result of the work from the previous knowledgeblog grant, all posts will be tagged with metadata, in various forms, and will be available for formal archiving outside of the University.

¹⁰The publication framework is based around WordPress which is freely available, scalable, stable and hardened by its multiple user base. The system is continually updated, but has a good reputation for maintaining backward compatibility. The authoring framework is based around commodity tools such as Word or latex. Most of the workflow process within Newcastle is pre-existing as part of the eprints service. This project therefore provides a sustainable and novel enhancement to the existing process.

3. Workplan

3.1 WP1 Management, Systems Administration and Set up.

¹¹This work package will fulfil the basic management and administrative tasks required for the project. This will include setup of the repository, styling and theming appropriately for the project; definition of a basic workflow for management of documents and metadata; fulfilment of standard JISC reporting requirements.

¹²We request additional funding of 1k as part of this work-package for virtual server upgrades (additional disk space), dropbox space to enable document management, and wordpress anti-comment spam support.

3.2 WP2 User documentation.

¹³Most of the operational, “how-to” documentation is already available: either at http://process.knowledgeblog.org (developed by the JISC funded knowledgeblog project); or, as the repository is based on commodity technology, from many publicly available websites.

¹⁴However, there will be information specific to the Webprints archive; about copyright, about document management, and about the relationship to the university. For this, we will need to generate some specific documentation.

¹⁵As the project progresses, we will improve and enhance this documentation, based on our experiences, including for example, statistics on how long author self-deposition takes.

3.3 WP3 Author advertising and Material identification

¹⁶We will seek active engagement with our user community, by linking into the current eprints system. Combined with the Newcastle-specific, internal “myimpact” database (which was designed to capture research outputs for the next REF), this will enable us to identify new publications as they come out. In the first instance, we will select material that has been published in open access journals (or where embargo periods, or other conditions allow). We will contact authors individually, inform them of our project, and advising them about the methods for recasting of their paper (see WP4).

¹⁷We will not preselect on the basis of academic quality, only technical and legal (copyright) grounds. Although the eprints service displays full text as PDF only, the myimpact database in many cases also stores MS Word (or equivalent) formatted data. We will, therefore, prefer papers where this data is available. We will prefer papers which are recent over those which are older. Finally, we will prefer papers which give us a wide spread of authorship and discipline.

¹⁸Although the focus of this proposal is on the provision of a service for publication of green open access material in a fully web-capable format, we will be happy to receive grey literature, on an author-publication basis.

3.4 WP4 Paper recasting

¹⁹This work package will take papers selected as part of WP3 and publish them to the webprints archive. In most cases, this work will be performed using tooling developed or documented by the previously funded JISC knowledgeblog project.

²⁰We will publish articles in three ways:

Webprints team published. All work will be performed by members of the Webprints team. For each paper, we will write a short report, describing any issues with the publication process, and any errors seen (which we will hand-correct). We will gather statistics on the time taken to publish. Papers will be published on an “as-is” basis; that is we will not seek to enhance the content at this point. We will add metadata in a structured way, which will be accessible from the web presented version.

Author published, webprints supported. We will work directly with authors to publish papers and help them. Where possible, we will augment and add new features (latex maths support, citation). These papers will be marked as featured, and augmented. Again, we will gather statistics on the time taken to publish, broken down for additional functionality.

Author published. Authors will publish directly into Webprints, using either their pre-existing experience, or our own user documentation. We will request, but not require statistical feedback. Publication will be as the author wishes — as-is, or augmented with additional functionality.

²¹All papers will be annotated with standard metadata in a structured form; our previous work means that this metadata will be available from the web presentation of the paper.

3.5 WP5 Repository and process enhancement

²²For this package, we will focus on two key aspects: tooling for publishing papers and their presentation once there.

²³For the presentational issues, in the first instance we will focus on enhancements which do not require support from the article material. For example, as we will add metadata to articles, which will allow us to generate metadata headers (CoINS, standard meta tags etc) without further analysis of the article material itself. Likewise, our experience with the knowledgeblog project means that we can support “out-of-the-box”: multiple export formats (including HTML, PDF and ePUB); site wide indexes (by year, author, subject etc); comments; trackbacks and page feeds (including from subsections). Through use of third-party software, we will also be able to add: related papers through textual analysis; tag clouds; twitter backs; automated multi-lingual presentation and social networking support.

²⁴We will also investigate enhancements which require modification of the original content (and therefore increased interaction with authors). From the knowledgeblog project these will include: scalable equation presentation; and client-side generated bibliographies. We will also add “custom posts” for supplementary material (spreadsheets for instance). And, finally, through the use of third-party material, enhancements such as syntax highlighting, zoomable maps, slideshows and so forth. This part of the proposal is designed to be open-ended and exploratory; which forms of enhancements, we pursue will depend on the types papers selected and interactions with the authors. There are currently over 13,000 plugins available for wordpress, which provides us with a considerable resource to build from.

3.6. Timetable

4. Deliverables

²⁵A repository of open-access articles in a fully web-capable format. This will act as a supplement to the existing eprints archive at Newcastle. We expect to generate around 100 articles in this form, although this is likely to be an underestimate. We are currently estimating throughput from our experiences with Knowledgeblog, which involved relatively few articles. The process should benefit from high-throughput experience. Further documentation, published on http://process.knowledgeblog.org, describing the process that we have used to set up this repository. Enhancements to tooling, enabling others to publish more easily in this manner. Additional experience and software enhancing the presentation of data held in this form.

5. Project management arrangements

²⁶The project will be managed by Dr Lord, who will be responsible for:

• Developing Project Management Plans;
• Ensuring that the Project work package objectives are met;
• Prioritising and reconciling conflicting opportunities;
• Reporting and collaborating with JISC programme manager
• Dissemination of research results.

²⁷Project progress will be evaluated through scheduled, short, “stand-up” meetings on a weekly basis, conducted face-to-face, via Skype or phone as appropriate. Primary unscheduled communication will be via public mailing list, ensuring maximum visibility and openness. We will use other readily available tooling to manage the document process pipeline – Google spreadsheets, dropbox, and likewise for software development (Google code). All staff are associated with other projects or service provision (research, teaching, training); they will be individually responsible for managing these workloads, and are highly experienced at doing so.

5.1 Risk Management

²⁸Staff risks – the basic organisation of the project has been designed to mitigate against staffing issues. All staff are in post and are highly experienced, with long-track records at Newcastle. Costs have been split three ways, therefore even if in the unlikely event that one member of the team leaves during the project, it will not cause significant distruption.

²⁹Software risks – we are using commodity technology, which is very well proven and supported. None of the software is critical (even our basic blogging engine, wordpress, is replaceable). Therefore, while changes in third-party software might degrade or slow progress, it will not halt.

³⁰Engagement Risks – the project requires a level of engagement from Newcastle researchers, which may not materialize. We have minimized this risk by minimizing the effort the engagement takes on behalf of the researchers. The project members are well known to many in the university (DS and SC comprise the “Bioinformatics Support Unit” and have worked for many PIs personally). We have active engagement from the library, in particular from Moira Bent (Science Faculty Liaison Librarian), and Paula Fitzpatrick (Digital Libraries).

5.2 IPR position

³¹The bulk of the content handled by this work will come from authors within the University. The current restrictive copyright requirements of many publishers place uncertain limits on what can or cannot be done with this content. For this reason, we will use articles that have been published with or have become available under creative commons or other open access license.

³²Project members will release written work (documentation etc) under a Creative Commons Attribution ShareAlike 3.0 Unported License (CC BY-SA), which allows re-use and modification for non-commercial purposes with attribution. This is in line with the JISC Model Licence. Software linked to WordPress will be released under GPL, as required by the WordPress license. Software which is separable will be released under LGPL. Software linked to other third-party libraries may use other license if required; this will be limited to Free/Open source licences.

5.3 Sustainability

³³This project is largely based around innovative, novel and leading use of existing software. As such the sustainability of the majority of the technology base is not dependent on project members but large companies with established and proven business models.

³⁴The WebPrints archive will be run from the same server as knowledgeblog.org; this is being developed and maintained and will be for the foreseeable future, and the additional of the WebPrints archive will not be a substantial additional cost. However, should this cease to happen, the content of the WebPrints archive will be creative commons or an equivalent permissive license. This will make it possible for the JISC funded UK Web Archive to store the website for the future.

³⁵Although, we will not be able to sustain publication by the WebPrints team past the lifetime of this proposal without further funding, author publication will be possible; our experience with existing tooling is that this is possible for many, although requires some level of technical skill, depending on the word-processor package, and level of complexity of the paper.

5.4 Staff Recruitment

³⁶All staff are already in post. Recruitment during the project will therefore be unnecessary.

5.5 Key Beneficiairies

³⁷Our immediate beneficiaries Newcastle University staff, who will have their work published using a new and novel publication technique. Critically, we will demonstrate the value of this form of publication technique to both researchers and librarians within the University who will in future be better placed to use or support this technology to publish their own or others work in future.

³⁸Although presented here as a discrete project, the work fits within the background of the wider blogging community. So, our own knowledgeblog project and website will be able to take advantage of software improvements that will happen as a result of this work. Additionally, the general academic blogging community will gain a new resource. Increasingly, this community is a critical path for public engagement in the academic process.

5.6 Community Engagement

³⁹Community engagement will take place initially by direct contact; we will email authors to ask for their engagement in the publishing process. This should have the secondary effect of advertising the presence of our project. We have active engagement from the library staff, who are well known within the University. In terms of engagement with the resource outside of Newcastle, we will make active use of various web and social networking facilities. Our experience has shown that this can generate significant amounts of engagement in a relatively short period of time. Finally, we will advertise the work through standard academic channels of conference and journal publication; although effective, this tends to be slow. This is problematic for a short project, hence we consider this to be a secondary means of communication.

6. Budget

Removed for privacy reasons.

7. Project Team

⁴⁰Dr. Phillip Lord is a Lecturer of Computing Science at Newcastle University. He has a PhD in yeast genetics from University of Edinburgh, after which he moved into bioinformatics. He is well known for his work on ontologies in biology, as well as his contributions to eScience beginning with his role as a RA on the myGrid project. Since his move to Newcastle, he has been an investigator on there more eScience projects; CARMEN, ONDEX and InstantSOAP, as well as maintaining an active engagement in standards development (OBI, MIGS, MIBBI), and publishing on the fundamentals of ontology design. He is a active participant in the Scientific Blogging community, developed the initial idea for knowledgeblogs. As well as managing the knowledgeblog project, he is the developer of tools such as “Latextowordpress”, as well as WordPress plugins such as “Mathjax-latex” and “Kcite” all of which improve the usefulness of wordpress for academic communication.

⁴¹Dr. Daniel Swan has a PhD in developmental biology and continued to work in developmental biology as a post-doctoral researcher before moving into bioinformatics in 2001. Subsequent positions included working for Bart’s and the London Genome Centre and the Centre for Hydrology and Ecology in informatics driven roles dealing with large, distributed biological datasets generated by large user communities. Currently the manager of the Newcastle University Bioinformatics Support Unit, he leads a small team aiding biological researchers generate, capture, store and analyse their digital data. His interdisciplinary background means he has grounding in both computer and biological sciences and is comfortable working on CS focused projects (CARMEN, InstantSOAP, Bio- Linux) as well as acting in a research capacity analysing high-throughput data. He is currently active within the knowledgeblog project, having been responsible for adding software support for a review process, gravatars, syntax highlighting, PDF and ePUB exports.

⁴²Dr. Simon Cockell has a PhD in Genetics from Leicester University, and refocussed into Bioinformatics with a Masters degree from Leeds in 2005. From there he moved to Newcastle, and the Bioinformatics Support Unit. Since coming to Newcastle, Simon has worked on a range of projects involving large scale analyses (AptaMEMS-ID), data integration (Ondex) and health informatics (MRC Mitochondrial Disease Cohort). He is currently active within the knowledgeblog project, having been responsible for metadata support (including Coins), navigational support (for both humans and robots) and is a co-author of kcite and mathjax-latex.

⁴³Allyson Lister worked for 6 years at the EBI in Cambridge, developing and producing the UniProt/TrEMBL protein database. She is currently focusing on the use of ontologies for the semantic integration of systems biology data with her current job at CISBAN in Newcastle University. Both at the EBI and at Newcastle University, she developed structured data formats including UniProt/TrEMBL and SBML. She has also been an early adopter of blog technology as a mechanism for communication of both her own and others primary research. Since 2006, she has co-authored a number of posts with other bloggers in the community and has been invited to be a guest author at both the ISCB news and the BioSharing blog. She has published papers highlighting the importance of social networking and live blogging to bioinformatics.

Paola Marchionni of JISC has give her permission to reproduce the feedback from the peer-review of my last JISC grant which sadly failed. I want to publish it here, as part of my desire for open science rather that as an opportunity to reply which, perhaps unfortunately, the JISC process does not otherwise allow.

I am a little surprised by some of the comments, to be honest. The main criticism was more expected though, which essentially says “it’s not crowd-sourcing if you pay people to develop content”. You have to try these things, but I did think that actually paying for content might be considered to be a little revolutionary. Ah, well, better luck next time.

Markers felt the form of this proposal was “robust”, however there wasn’t enough clarity on the deliverables and especially on how the value of what was being produced would be assessed down stream. They felt there was also some lack of information on how the currently JISC funded K-Blog project, due for completion in July 2011, related to this project and what the impact on its team would be, which seems to be the same team as the one proposed for this project.

The main concerns, however, were around whether this could really qualify as a crowdsourcing or community project – it was felt it was more about disclosing data than community engagement – also considering that the authors of the articles would be paid. There were some doubts about the sustainability of the project beyond the 7 months duration of the funding, as lack of funding would prevent more articles being created and metadata added by the team. One marker also felt that a risk analysis should have taken into account the risk of disparate communities not being aware of the content and using and engaging with it. A more clear identification of the various communities the project aimed to reach and a more targeted strategy for engaging with such communities would have been useful.

Finally, another issue that was raised was that there wasn’t sufficient information on how the partnership with Manchester University would work, either formally or informally, and the dissemination plans could have been stronger, as they relied mainly on the role of K-Blog.

— Paola Marchionni

About

This is the full text of a grant called “Knowledge in Biology” that we submitted to JISC, as a follow-up to our knowledgeblog grant. Unfortunately, this grant was not accepted. This blog post is the direct output result of Word; apologies if the conversion is imperfect.

Outline Project Description:

Many disciplines within the sciences are knowledge-rich; of these, biology is an extreme example. In order to make advances, biologists need to be able to access knowledge from both their own and related communities in an easily digestible form. However, the publishing of this knowledge does not fit well with existing scientific communities, as it is often not regarded as “research based” – rather it is a stored body of grey literature, often not publically available. In the Knowledge in Biology project, we will engage with disparate communities in disciplines that engage with biologists as well as the community of biologists themselves. We will generate substantial content describing how “Knowledge in Biology” is both produced and consumed in the pursuit of new discoveries, by commissioning the authorship of this content directly from the funding for this project.

We will leverage the output of the JISC-funded Knowledge Blog platform, as a tool for coordination, publication and dissemination of this content. The result will be a publically accessible, high-impact resource of short, readable and accessible articles describing how to gather, manipulate and synthesise knowledge in biology. This will be of significant value in supporting the multidisciplinary research that is necessary for advance in modern biomedicine.

1. Introduction

¹This document describes a proposal for a project within the JISC “e-Content” programme call.

²Modern biology is a rich, complex, multi-disciplinary field. In particular, practitioners need knowledge about how to access, organise and structure knowledge itself. As a result, members of the community often need to cross the boundaries of traditional societal structures within research. By definition, this is not well supported by the more formal structures that scientists use for the publication and dissemination of knowledge. So while the information exists, it is not accessible; hidden from the community on the desks and hard-drives of individuals.

³One of the difficulties with migrating this community-based knowledge away from grey literature to a more openly-accessible archived and referenceable form is the lack of a formal reward structure. Although scientists may engage in this form of activity from a sense of public duty, this form of documentation is not critical for their career advancement, or for gaining academic creditability, and so it is rarely made a priority. While technological advances have made publication of this material straightforward, the social structure of science has not supported it. As a result, there is a large body of knowledge about how biologists conduct their work that is simply lost to the community, meaning considerable lost time and effort recreating this knowledge, only for it to be lost again.

⁴We plan to circumvent this societal barrier using a novel approach – we will directly commission the authoring and reviewing of articles embodying this content. As the knowledge will often be readily available to individual members of the community, and we are aiming for articles which are neither of the size nor complexity of formal research publications, it will be possible to generate a substantial body of content, at relatively low-cost.

⁵An ideal mechanism for publication of this knowledge has already been funded by JISC as a part of the “Managing Research Data” programme. This is the Knowledge Blog project: a light-weight publication tool, that integrates well with scientists’ existing work-practices, based around a commodity blogging engine. This ‘Knowledge in Biology’ project (KiB) will utilize the work from Knowledge Blog, to the benefit of both: this project will gain a technological underpinning at little cost – Knowledge Blog already exists and will require a small increase in resources to manage the additional content and traffic; Knowledge Blog will gain substantial content and enormously increased visibility.

⁶The KiB project will provide a small amount of funding for the management and commissioning of articles, but the majority of the funds will be spent by using individually small amounts of money, crowd-sourcing the development of a novel digital content resource, engaging the community of biomedical researchers, both as authors and reviewers. The content will address key issues relating to knowledge in biology such as, data standards, linked data, knowledge in synthetic biology and statistical approaches to knowledge, as well as “softer” issues such as the use of Web 2.0, the social web, and the blogosphere as tools for the biomedical researcher.

2.1 WP1 – Knowledge Blog (k-blog) maintenance and support

⁷The primary purpose of this proposal is to generate significant quantities of digital, community-developed content. The k-blog platform already exists, supported by a previous JISC call. We are not, therefore, proposing to make significant enhancements to either the process or the software in the course of this project. However, the additional load placed on the platform will require a small amount of administrative work in terms of maintenance.

⁸In addition, we will need to provide support to the users of the platform; while k-blog is relatively easy-to-use, issues do arise with authoring, with formatting or with exceptional requests (for example, multi-media documents).

⁹For articles to be properly citable and maintainable, manual intervention is required to supplement the text with computationally accessible metadata, including DOI assignment. This enables improved archiving and discovery, which increases the value of the resource. As part of WP1, we will annotate documents with this metadata to ensure consistency and to avoid placing the burden on the main authors.

¹⁰We will install and refine a licensing plugin for the k-blog platform, which clearly displays license information for each article, based on the author’s selection.

2.2 WP2 – Management of publication process

¹¹Articles in KiB will be produced by crowd-sourcing and by the in-house team (WP4). Our aim is to bootstrap the KiB k-blog so that it reaches a critical mass of articles that will attract both readers and more authors. We will commission articles from specified, expert authors with the attractor of a small payment. The payment will require the contributor to both submit an article and a review for another article.

¹²In preparation for this work, we have compiled a list of topics for KiB and put names against these topics. We have clustered the topics around themes in KiB: The role of semantics In biology; the representation of knowledge in ontologies, terminologies and vocabularies; data integration to create knowledge resources; data and knowledge standards; knowledge technologies such as RDF, Linked data, OWL, etc.; text mining; case studies and applications of knowledge in biology. These clusters, and more, will become the categories in the KiB k-blog. The letters of support indicate the significant number of authors that have promised to author an article on one of these topics. We will seek as wide a selection of authors as possible, guided by our advisory committee (see Section 2.8), to help give the KiB k-blog a balanced view on knowledge in biology. A significant part of this WP will be the commissioning of these articles and discussions with authors on this new digital content sourced from the community.

¹³This process will need managing: requests for particular articles (WP2.1); negotiation on topic and scope (WP2.2); managing of the author-guided review process (WP2.3); and, enabling payments to be made. This activity will help ensure that the core of the KiB k-blog will be of sufficient quality to attract readers to comment and contribute articles, as well as to simply read and learn.

2.3 WP3 – Outreach and Community Engagement

¹⁴Outreach and community engagement are intrinsic to this project. The presence of a high-quality, organised resource, freely available on the web will attract readers; likewise, a widely-read resource will be attractive as a publication centre for authors, particularly when supported by funding as part of WP2. The use of a rapid publication framework, available on the web, archived by the British Library and indexed for searching by Google, therefore, is our main form of outreach.

¹⁵However, this process can be augmented. All content will be available and reusable under a Creative Commons license, making it reusable with citation outside of the KiB environment. We will maintain active “Social Web” streams through Twitter. We will solicit articles relating to the use of Twitter and the blogosphere from members of the scientific blogging community; as well as generating content, this will leverage their existing readership, raising awareness of KiB, both as a resource for readers and authors. We will maintain a well-advertised mailing list allowing requests for, or offers of, new articles either commissioned or otherwise.

¹⁶Finally, we will advertise the resource through normal academic channels of paper and poster presentation. Where possible, we will also propose micro-workshops (aka Birds of Feather meetings) at suitable meetings/unconferences.

2.4 WP4 – ‘In house’ article authoring

¹⁷The staff on the project will contribute a significant number of articles to the KiB k-blog. Stevens will produce 20 articles; Lord 10 articles and Swan 10 articles (WP4.1). Both Lord and Stevens have already contributed articles to the Ontogenesis k-blog and will further extend on Ontogenesis in the wider KiB topics. These topics will include articles on tips for modeling in OWL; using ontologies with linked data; converting data to RDF and linked data; On-line knowledge resources; using ontologies in over-representation analysis of microarray data; integration strategies; and so on. Some of these in-house articles will act as glue that draw together many of the other articles. For example, an article on the role of knowledge in biology will draw together the need for the k-blog and act as a pathfinder. Where appropriate, we will use tools such as “Anthologize” and “Web Trails” to facilitate these aggregation activities. In house articles will be reviewed (WP4.2) by an external reviewer, potentially from the pool of contributors sourced in WP2.

2.5 WP5 – Project Management and JISC Requirements

¹⁸Management of the project will use regular weekly teleconferences, to ensure that all aspects are proceeding according to the project plan. In addition, we will fulfill the legal requirements for collaboration agreements and the formal reporting requirements from JISC as part of WP5.

¹⁹To ensure maximum community and public engagement in this proposal, all appropriate documents will be posted using the k-blog environment in addition to those locations specified by JISC, except where that information is withheld under normal FOI rules.

²⁰Finally, we will gather and collate statistics on the use of these articles as measures of impact; directly in terms of page views from the underlying k-blog platform; indirectly from incoming links (both those using trackbacks, and those discovered using Web searching tools) and comments; and finally through secondary indicators such as Twitter and email communications. These statistics will also be made publicly available where appropriate.

2.6 Timetable

2.7 Deliverables

²¹A high-quality body of content, consisting of a series of articles from multiple authors; describing different topics fitting within the theme of “Knowledge in Biology”. 40 of these articles will be authored in-house. A further 200 will be sourced with consultancy payment. We anticipate many others will come from crowd-sourced, enthusiastic authors, engaged with the process.

²²A website, based on the k-blog platform, that delivers this content.

2.8 Project management arrangements

²³The project will be managed from Newcastle University; the primary management will be from Dr Lord, who will be responsible for:

    - Developing Project Management Plans;

    - Ensuring that the Project work package objectives are met;

    - Prioritising and reconciling conflicting opportunities;

    - Reporting and collaborating with JISC programme Manager;

    - Dissemination of community content.

²⁴Project progress will be evaluated through scheduled, short, “stand-up” meetings on a weekly basis, conducted face-to-face, via Skype or phone as appropriate. Primary unscheduled communication will be via public mailing list, ensuring maximum visibility and openness. User consultation will be via public mailing list. Close tracking of requests for content and payment of authors is essential, and transparent procedures will be put in place for this. All staff are associated with several other projects and duties (research, research support, teaching and training), and are responsible for managing these independent workloads. All have experience with the k-blog platform and process.

²⁵We have formed a small, unpaid advisory committee from recognised experts in the field. They will be invited to give feedback on the topics covered at 2, 4 and 6 months into the project; this will help to ensure an even and representative coverage of the area, that is not overly biased by the particular interests of the staff on the project.  Mark Musen (Stanford), Chris Rawlings (BBSRC Rothamsted) and David Shotton (Oxford) have all agreed to be our advisory board.

2.9 Risks

²⁶Staff Risk – as with all projects, loss of staff could negatively impact on this project; however, all staff are on permanent contracts, have long histories in research, so this is less likely. Additionally, the nature of the workload means all staff would be able to cover duties relating to sourcing and generating community content, we limit the risk should a single person leave.

²⁷Lack of community engagement – the strength of this proposal depends on contributions from many different authors, generating new, novel and, currently, unavailable content. However, there is also a risk that the community will not wish to contribute. We have limited this risk by offering to pay people consultancy rates – an unusual reward within academic research; however, we will only need to commit funds following the submission of the content, so should authors not deliver, we will reallocate these funds. Should we still find it hard to solicit contributions, we will increase the rates per article.

²⁸Technology dependencies – Content will be disseminated in the form of k-blogs, and thus there is a dependency on the k-blog platform. It is already suitably developed and packaged. The k-blog platform is a publishing framework only; it is not essential for the authoring of articles. This limits the scope of the risk. Content could be published independently of the k-blog platform, with only a small loss in the feature set. Additionally, content could be relocated elsewhere at any time; it would retain its value outside of the k-blog platform. With the archival agreement under the Sustainability section, archives of the original KiB content will always be available.

2.10 IPR position

²⁹It is essential that content is released with as few restrictions as possible on re-use and re-purposing, but authors must be allowed to maintain credit associated with the original work, or they are unlikely to contribute. Project members agree to release their work under a Creative Commons Attribution-NonCommercial ShareAlike 3.0 Unported License (CC BY-NC-SA), which allows re-use and modification for non-commercial purposes with attribution. This is in line with the JISC Model Licence. Authors invited to submit articles will be allowed to choose a Creative Commons licence of their own but will be strongly encouraged to use as permissive a licence as possible. Choice is offered to allow considerations of different institutional policies on published content. Public domain submissions will also be accepted to accommodate US government employees; these submissions will be uncommissioned.

2.11 Sustainability

³⁰To maintain the persistence of the online resources beyond the end of the project, documents produced by project staff and KiB contributors will be publically available and clearly licensed. The k-blog site and sub-domains are already archived by the UK Web Archive, in which JISC is an active partner. The Digital Curation Centre will be asked to provide strategies for long-term database archiving.

2.12 Staff Recruitment

³¹All staff are already in post.

3 Impact

³²Our key beneficiaries are the community of researchers working to develop knowledge in biology. Specifically this focuses on groups involved in data standards, linked data, knowledge in synthetic biology and statistical analysis of biological data. The needs to this community are clearly demonstrated from our Ontogenesis experiment, which is currently receiving 1000 page views per month for a small number of articles. Simple question and answer websites such as http://biostar.stackexchange.com/, receive over 2k page views per week; however, there is a gap between this and more formal knowledge.

³³We will generate statistical information, using the k-blog platform as a clear metric of impact; for freely available, reusable and web-delivered content indicators such as page views are well recognised, and the main form of impact assessment. Both natively, and through tools such as Google analytics, the k-blog platform can provide comprehensive and detailed feedback on access of individual articles. We will also exploit secondary impact measures, including Twitter through appearance of suitable hashtags; comments and trackbacks to articles on KiB; and, finally, links to KiB as provided by web search.

³⁴We will seek to increase impact through a number of activities in addition to normal academic channels. First, we will invite contributions from well-known members of the scientific blogging community that should result in secondary readership. Second, we will invite contributions on relevant topics that have become of recent public interest. Thirdly we will monitor article popularity; for areas that prove to be of interest or are controversial we will seek to commission additional content.

4 Partnership and dissemination

³⁵Internal engagement of core project members, and the wider community of researchers crowd-sourced to supply content will be via the mailing list, after initial approaches are made. The plans for content generation are further outlined in WP3 and WP4. Content generation will allow further interaction with more disparate groups (content consumers), who will be encouraged to engage through the k-blog process and the project mailing lists. The advisory committee will be able to ensure that our engagement with the content-producing community is representative of the community. The nature of the k-blog process means dissemination is intrinsic to content generation.

³⁶Project members are on the existing JISC funded Knowledge Blog grant in the “Managing Research Data” programme. We will approach individuals with funding from this and other programmes, requesting articles describing the value of these projects to biologists. We will, of course, also be pleased if JISC programme managers wish to contribute articles to this knowledge in biology resource.

6 Previous experience of the Project Team

³⁷Dr Phillip Lord is a Lecturer of Computing Science at Newcastle University. He has a PhD in yeast genetics from University of Edinburgh, after which he moved into bioinformatics. He is well known for his work on ontologies in biology, as well as his contributions to eScience beginning with his role as a RA on the myGrid project. Since his move to Newcastle, he has been an investigator on there more eScience projects; CARMEN, ONDEX and InstantSOAP, as well as maintaining an active engagement in standards development (OBI, MIGS, MIBBI), and publishing on the fundamentals of ontology design. He was an active participant in the Ontogenesis network, and is currently leading the JISC funded Knowledge Blog project. He is an active blogger and developer.

³⁸Dr Robert Stevens is a reader in Bioinformatics in the Bio and Health Informatics group at the University of Manchester. His main areas of research are in the development and use of semantics within the life sciences. This is blended with the use of e-Science platforms to gather and manage the data and knowledge of the life sciences. He was PI on the Ontogenesis network that ran the meetings for the first Knowledge Blog. He is or has been a co-investigator on the myGrid and myExperiment grants that will provide both content and technical input to this project. As well as the JISC funded myExperiment project, Stevens was an investigator on the JISC funded CO-ODE project that developed Protégé 4. On the back of this, Stevens has led the OWL training activities at Manchester that has directly fed in to the Ontogenesis Knowledge Blog. Stevens currently leads content development for the JISC Knowledge Blog grant.

³⁹Dr Daniel Swan has a PhD in developmental biology and continued to work in developmental biology as a post-doctoral researcher before moving into bioinformatics in 2001. Subsequent positions included working for Bart’s and the London Genome Centre and the Centre for Hydrology and Ecology in informatics driven roles dealing with large, distributed biological datasets generated by large user communities. Currently the manager of the Newcastle University Bioinformatics Support Unit, he leads a small team aiding biological researchers generate, capture, store and analyse their digital data. His interdisciplinary background means he has grounding in both computer and biological sciences and is comfortable working on CS focused projects (CARMEN, InstantSOAP, Bio-Linux). He has been most recently involved in the JISC Knowledge Blog grant, providing technical support and engagement with microarray community.

I was delighted recently to discover Greyhole. Essentially, it’s a system that allows you to configure a Samba share at one end, and a bunch of disks at the other. The disks get the data shared between them, with a configurable level of duplication. It’s aimed mainly at the home user, who wants a higher degree of data security than the single drive approach provides, but is not going to go the expensive and poorly scalable RAID approach.

The implementation is fairly straight-forward and elegant. The Samba share is provided by a customised Samba virtual file system. This augments the standard process by logging to a spool region (one file per file operation). A daemon consumes these files, stuffing them into a database, then consumes the entries in the database. Essentially, if anything has changed, greyhole rsyncs the change to one or more of the backend disks.

It’s a really nice system. I must admit that PhP wouldn’t have been my first choice, but that is horses for courses. Likewise, the dependency on Samba is unfortuante — I always found it a pig to configure, besides which I’d like to use this internally on a linux box. I had a discussion with the author Guillaume Boudreau, who confirmed my initial feeling that the Samba VFS could be easily replaced with another, such as FUSE. I’d like to have a go at doing this work, and it’s very possible — basically, it requires a big merge between Guillaumes VFS and the FUSE based loggedfs. If I had written any C, I could probably do it in a day or so, but as it stands, it is likely to take longer.

As well as home usage, though, this could also be good for the researcher. While a small lab could pay for managed storage, this tends to come in at £1000 per TB, per annum. Most labs don’t need 24/7 recovery though, and the data is often write once, read occasionally. Greyhole would work out for 1TB at 200 quid (for a low-wattage PC server), 100 quid two 1TB discs which would cost, say, 40 quid to power for a year (say, 15W for the computer, 10W for the hard drives, and a bit more for networking, adaptors, USB hubs and so). For lab usage, the drives would probably last 2-3 years at least, while an all solid state computer might last twice this long. More storage space could be added as needed, dropping the cost per TB substantially, although how scalable greyhole is I don’t know.

The general approach could be used more widely, though. As well as JBOD spanning, what about:

I’m buying a low power consumption PC to try out greyhole in it’s current form, to see how it goes.

I was entertained by a couple of articles recently, one from PLoS Blogs and one from Ed Yong both bemoaning the low social status of bloggers at least in some peoples minds. As the front page of the PLoS blog says:

Blogging is just one of the outlets science journalists use. It’s about time we separate the person from the medium.

Of course, I agree with this. There is some excellent material floating around the blogosphere. But at the same time, there is a subtle irony in all of this. Both of these authors, I think make a similar confusion about the medium. For instance,

my point is that the world of science blogging is populated with some of the best journalists I know.

PLoS Blogs
— Deborah Blum

At the moment, within science, blogging is still see as an appropriate place for Journalism about science, or in some cases scientists describing their personal experience within science. I don’t denigrate this in anyway, but I think to some extent it misses the point. Science blogging should be about scientists. Many of use now use blogging as part of doing science itself; take Allyson Lister’s excellent and extensive meeting or seminar notes. Or Simon Cockell’s experience sharing. Or my own move to just blogging my own papers and grants. And the occasional technological rant.

The blog is not the point here, it is just the tool that we are using to advance our science. This is also the point of my knowledgeblog project; it is not about adding to the blogosphere, it is not about using WordPress for science. It is about better, faster, cheaper scientific communication.

Ironically, it would help to solve Ed Yong’s problem as well. In future, maybe he won’t have to ask for the paper, because it will be on the web, with all the data, for all the world to see.

After this diversion into journalism, this blog will now resume normal service, as a place to describe my science.

I’ve just got around to installing the magnificient kcite plugin that Simon Cockell wrote for knowledgeblog. It’s actually a really simple plugin, but it’s tremedously useful. For instance, I can now cite my own papers on reality (doi:10.1371/journal.pone.0012258) , function (doi:10.1186/2041-1480-1-S1-S4) or protein classification (doi:10.1093/bioinformatics/btl208) and all the metadata will be gathered and cited for me in a nice reference list at the end.

Of course, I am used to the good life, and this is still all a bit clunky for me. I wanted support from my text editor. For this blog, I use a tool-chain of Emacs, asciidoc and blogpost. But for references I use reftex mode and bibtex. Now I realise that this is a pretty minority tool-chain, but it seemed to me that it should be possible to get it working. And it is, actually, pretty easy. Very rough and ready, but the lisp is below. Obviously, this will need fiddling with for each user, and I will improve it over time.

But it demonstrates the point, I think. A little bit of glue can produce a pretty good publishing tool chain, relatively quickly.

(add-hook 'adoc-mode-hook
          'phil-asciidoc-reftex-support)

(defvar phil-reftex-citation-override nil)

(defun phil-asciidoc-reftex-support()
  (reftex-mode 1)
  (make-local-variable 'phil-reftex-citation-override)
  (setq phil-reftex-citation-override t)
  (make-local-variable 'reftex-default-bibliography)
  (setq reftex-default-bibliography
        '("~/documents/bibtex/phil_lord_refs.bib"
          "~/documents/bibtex/phil_lord/journal_papers.bib"
          "~/documents/bibtex/phil_lord/conference_papers.bib"
          )))

(defadvice reftex-format-citation (around phil-asciidoc-around activate)
  (if phil-reftex-citation-override
      (progn
        (setq ad-return-value (phil-reftex-format-citation entry format)))
    ad-do-it))

(defun phil-reftex-format-citation( entry format )
  (let ((doi (reftex-get-bib-field "doi" entry)))
    (format "pass:[(doi:)
%s[/cite\\]]" doi)))

Bibliography

This article was jointly author by Phillip Lord and Simon Cockell.

Rhodopsin is a protein found in the eye, which mediates low-light-level vision. It is one of the 7-transmembrane domain proteins and is found in many organisms including human.

Rhodopsin has an number of identifiers attached to it, which allow you to get additional data about the protein. For instance, the human version is identified by the string “OPSD_HUMAN” in uniprot. If you wish, you can go to http://www.uniprot.org/OPSD_HUMAN and find additional information. Actually, this URI redirects to http://www.uniprot.org/P08100.html. P08100 is an alternative (semantic-free) identifier for the same protein; P08100 is called the accession number and it is stable, as you can read in the user manual. If you don’t like the HTML presentation, you can always get the traditional structured text so beloved of bioinformatics; this is at http://www.uniprot.org/P08100.txt. Or the Uniprot XML (that is at http://www.uniprot.org/P08100.xml). Or http://www.uniprot.org/P08100.rdf if you want RDF. If you just want the sequence, that is at http://www.uniprot.org/P08100.fasta, or http://www.uniprot.org/P08100.gff if you want the sequence features. You might be worried about changes over time, in which case you can see all at http://www.uniprot.org/uniprot/P08100?version=*. Or if you are worried about changes in the future, then http://www.uniprot.org/uniprot/P08100.rss?version=* is the place to be. Obviously, if you want to move outward from here to the DNA sequence, or a report about the protein family, or any of the domains, then all of that is linked from here. If you don’t want to code this for yourself, there are libraries in perl, python and java which will handle these forms of data for you.

So this might be overkill, but the point is surely clear enough. It’s very easy to get the data in a multiple variety of formats, through stable identifiers. The history is clear, and the future as clear as it can be. The technology is simple, straight-forward both for humans and computers to access. The world of the biologist is a good place to be.

What does this have to do with DOIs. Let’s consider a section of publications from one of us. Of course, one of the nice things about DOIs is that you can convert them into URIs. But what do they point to? Well, a variety of different things. Maybe the full HTML article. Or, perhaps an HTML abstract and a picture of the front page. Or more links. Or, bizarrely, a list of the author biographies. Or just another image of a print out of the front page of a identified digital object.

These are a selection from our conference and journal publications. Obviously, this doesn’t cover many of our conference papers, as most don’t have DOIs unless they are published by a big publisher. Or our books. These are published by big publishers, but obviously they are books which is different. I’ve also organised or been on the PC for a number of workshops. They don’t have DOIs either. All of them do have URIs.

In no case, can we guarantee that what we see today will be the same as what we get tomorrow, even though DOIs are supposedly persistent. The presentation of the HTML on those pages that display HTML is wildly different; in many cases, there is no standard metadata. Given the DOI, there doesn’t appear to be a standard way to get hold of the metadata. If you poke around really hard on the DOI website, you may get to http://www.doi.org/tools.html. At this point, you probably already know about http://dx.doi.org, which allows you to resolve a DOI through HTTP. The list of links doesn’t take that long to work through, so you might eventually get to http://www.crossref.org. From here, you can perform searches, including extracting metadata for articles; obviously, you need to register, and you need an API key for this. It doesn’t always work, so if that fails, you can try http://www.pubmed.org, which returns metadata for some DOIs that CrossRef doesn’t, but doesn’t hold a DOI for every publication it lists (even those that have them), so it also fails in unpredictable ways.

The difference between the two situations couldn’t really be clearer. Within biology, we have an open, accessible and usable system. With DOIs, we don’t. The DOI handbook spends an awful lot of time describing the advantages of DOIs for publishers; very little is spent on the advantages for the people generating and accessing the content. It is totally unclear to us what use case DOIs are trying to address from our point of view; what ever it is, they certainly seem to fail of their purpose.

So, why do we care about this? Well, recently, we have been implementing a DOIs for kblogs. Ontogenesis articles now all have DOIs. When we were originally thinking about kblogs, our investigations on how to mint new DOIs came to very little. If DOIs are hard to use, creating them is even worse, you need a Registration Authority; setting this up within a university would be a nightmare. Compare this to the £9 credit card transaction required for a domain name (even this can be quite hard in a University setting!). In the end, we have managed to achieve this using DataCite. Ironically, they are misusing technology intended for articles to represent data; we are misusing DataCite to represent articles again. We also have to keep a hard record of our own of the DOIs we have minted, because, despite the fact all this information is stored in the Datacite database, there is no way of discovering if a DOI points at a given URL using the Datacite API, so we have no way of doing a reverse lookup from a blogpost to discover its DOI.

We’ve also created a referencing system for WordPress. This does DOI lookups for the user, currently using CrossRef, or PubMed. We are not sure yet whether we can retrieve DataCite metadata in this way also.

The irony of this is that it is all totally pointless. WordPress already creates permalinks, based on a URI. These URIs are trackback/pingback capable so can be used bi-directionally. We have added support so that URIs maintain their own version history, so that you can see all previous versions. If you do not trust us, or if we go away, then URIs are archived and versioned by the UK Web archive. Currently, we are adding features for better metadata support, which will use a simple REST style API like Uniprot. Hopefully, multiple format and subsection access will follow also.

So, why are we using DOIs at all? For the same reason as DataCite which has as one of it’s aims “to increase acceptance of research data as legitimate, citable contributions to the scientific record”. We need DOIs for kblog because, although DOIs are pointless, they have become established, they are used for assigning credit, and they are used as a badge of worth. For us, we find it unfortunate, that in the process of using DOIs, we are supporting their credentials as a badge of worth, but it seems the course of least resistance.