petermr's blog

#oaweek

[This is a short post as I am testing whether I can post from my guest room (I probably can’t blog from the main lab)]. I shall explore this theme, probably getting even more angrier that I am.

We have ceded the homeland of Scholarly Publishing to the commercial closed access publishers. For me the only true goal is that we regain the ability to control our scholarship – authoring, publishing, reading, re-use. I don’t see many people actively formulating this goal and doing something about it. I don’t think many people, even in the OA community, actually care about this. I haven’t formulated it well, but that’s because there has been a 10-year vacuum of thought and action.

There are two intermediate positions: Green, which cedes the moral right of publication to the publishers and negotiates scrappy deals on the least profitable land. “You can grow hay on this plot as long as you continue to let us exploit the best land. You can only do this during these months (because we say so) and if you are too successful we’ll find another way to stop you”. Green OA is appeasement. It has no political force and is entirely dependent on the whim of the publisher. For me NO OA mandates should even think of green. (Hybrid is even worse, we pay the publishers twice to remain under their control).

Gold, which says nothing about the means of production. It gives the readers rights, and these are sufficient for readers if full CC-BY is applied. (It makes no concession to the innovation of the web.) It gives the authors no rights, other than to make their work available to the world. It does not allow them freedom of expression or freedom of innovation in the publishing process. That’s not to say it isn’t useful in the interim but the publishers are still occupying our homeland. Some publishers do understand this and are moving, but the OA offerings from major (closed) access publishers still treat authors as second class (or worse).

What we need for OA is a clear political manifesto (we don’t have one) and clear courses of action.

Where is the Open Access Salt March?

Where are the Open Access busses?

Where are the Open Access Suffragettes?

Where are the people who have gone to court and possibly to jail for their beliefs? Mumbly platitudes (such as the lamentable Florida State university cop-out) don’t change the world.

On odd days of the week (this seems to be one) I despair. On even days I think we are winning.

#oss2011

I have a brief window in SFO – I love airports with free wifi

The OSS was mindblowing. The advances since last year are spectacular. Simply put: OSS has arrived and will – I am sure – be mainstream for years to come until everything is Open.

The primary message I took away is :

“Science needs democratization and we now have the tools and vision to make it happen”

The point of “garage PCR” is not that it’s a fun hobby – it shows that science belongs to everyone. The advances in sequences were so tremendous that we can see everyone determining their own genomic information in their own home.

And they must control it. The technology is coming to the highstreet, so let’s make sure it’s OURS, not theirs. As David Rowan (WIRED) said two weeks ago at the Serpentine:

“If something is free, the YOU are the product”

Stick that on your bathroom mirror. It’s critical to remember that we must continuously fight for our democracy.

I was blown away by Biocurious – a warehouse lab that Joseph Jackson and others have set up. In it a FOUR-YEAR old is able to work with the Green Fluorescent Protein. (Yes they are very aware of safety regs – they have autoclaves, etc.). I’d love to have a Biocurious in Cambridge and I have suggested they should look into cloning it, though country and state regs are the main complication.

The Open Science movement is coming together , just like the Open Knowledge movement has and the Open Source and Open Access ones. There are so many economies of scale by pooling resources and meeting other people doing the same and different things. (Last night we went to a hackerspace in SF where they had things like a sewing area, a mushroom growing area, a woodworking area.

And a Scanning Electron Microscope.

If you get the culture right then almost nothing is impossible.

Science is for all of us, not just academia. Academia has recently made a very bad job of doing science on behalf of the community. Open Science shows that the vision is much larger.

After all public libraries are not just for academics.

So why shouldn’t we have public science labs?

No reason – and we will. If this catches anyone who’d like to help then just mail Joseph Jackson or contact the OSS page

#oss2011

Yesterday I made the assertion:

“Closed access means people die”

I have no doubt this is absolutely true. I put it in the negative form because I want to drive home the inequity of walling information that, if released, could save people’s lives. In #oss2011 we’ve now had clear proof of this.

We’ve had a wonderful survey of the involvement of patients in their own diseases. I’ll exemplify this with Lorenzo Albanello, a scientist who suffered from a visual aura. His doctors all said it was migraine, but it wasn’t – he had main brain scans / MRI and it was due to a vascular anomaly. He visited specialist who gave him contradictory and varied advice.

So he went to the web and created http://lorenzosbrain.blogspot.com/ where he published his brain. You can see the anomaly

And he asked the world for advice:

What’s the best decision to make?

Hi there,
my name is Lorenzo, I’m a biotechnology researcher, I am 27 and I’m writing from Italy. Since I was a child I have experienced the occurrence of generalized seizures, however such phenomena were rather sporadic and resembling normal faintings, so I haven’t investigated the problem for long time. When I was 22 I went to see a neurologist after a new epileptic fit and she prescribed an MRI exam. So did I, discovering an arteriovenous malformation in the left frontal area of my brain. My reaction was rather careless about it, so I didn’t take care of the AVM nor did I want to take an anti-epileptic medication. I just continued my normal life without any trouble.

He also posted the six options he was given (some of which had substantial risks of death (15%)).

Happy to say he picked one that worked and he is fine. I salute his brave venture. But he also said

“because I am a scientist I was able to read the [closed access] medical literature”

If he had not been able to do this he might well be dead.

Access to the medical literature saves lives.

As patients said “we don’t care about privacy, we want to be cured”

Let’s try to make access to all scientific literature a human right.

#oss2011

Jenny Molloy and I have been representing the Open Knowledge Foundation at the Open Science Summit and we presented the Open Research Reports (ORR) project. The slides we used are at http://dl.dropbox.com/u/6280676/orr.pptx. I expect that at some stage we’ll be on the video record (last year’s was very useful and also there was a transcript!). Because what we say affects the understanding of the slides.

The slides came from several sources:

• The presentation by David Shotton and Tanya Gray at Science Online this September in London. ORR arose from ideas from David and others of us who met at “Beyond the PDF” where the idea of ORR emerged (idea don’t belong to people, they choose people). The SoLo presentation gave lots of detail on the Semantics, which wouldn’t have fitted into a 13-minute slot, but the WHY slides and some of the WHAT and HOW were included.
• Jenny’s overview of the London discussion and our further groundwork with JISC, OKF and SWAT4LS. See http://www.ukoln.ac.uk/events/devcsi/life-sciences-hackdays/index.html
• My thoughts on the WHY of Open Research Reports (many expressed in animalophoto-comics)
• Jenny’s overview of what we’re going to do in ORR and particularly the Hackathon in December
• Results of the Open Bibliography/Citations projects

The slides themselves tell only part of the story – what follows is my thoughts alone and (probably) what I said. I was somewhat provocative and any flak should be directed at me, not Jenny, David or Tanya.

Summary:

Open Knowledge saves lives

ORR is A community project to make disease data Open

We started with the (obvious) truth that information is a key component of health-care. That it’s critical for the poorest countries in the world. So isn’t it already catered for by the HINARI program http://en.wikipedia.org/wiki/HINARI which “was set up by the World Health Organization and major publishers to enable developing countries to access collections of biomedical and health literature.”

So the publishers make their electronic material freely available (presumably gratis not libre) …

The country lists are based on Gross National Income (GNI) per capita (World Bank figures). Institutions in countries with GNI per capita below $1600 are eligible for free access. Institutions in countries with GNI per capita between $1601-$4700 pay a fee of $1000 per year/institution

So isn’t this very commendable of the publishers to give their material freely to those most deserving? And when the countries become rich , they can pay. Well, this year Bangladesh became a richer country and the HINARI journals were cut off. There was outrage, reported by the Lancet (itself an Elsevier journal and closed access so presumably the Bangladeshis couldn’t even read the outrage). Read http://download.thelancet.com/flatcontentassets/pdfs/S0140673611600664.pdf – which appears to be gratis. And the LANCET argued that the HINARI should be re-extended to Bangladesh.

But I think that’s completely wrong. The HINARI program only exists because the publications are CLOSED. It costs nothing to make the journals available. It costs more technically to prevent people reading the literature than to make it available. Libre material gets copied at zero cost. HINARI is nothing more than the crumbs of charity that the kinds used to give out. HINARI perpetuates a morally unacceptable system. The publishers aren’t giving their content free, they are giving OUR content free (or rather restricting access to our content).

Simply, closed access publishers make money by restricting access to information.

That’s been a consistent theme through the discussion

Now we all agree, I think, that more and better information leads to better medicine, better health-care, better environment.

And

    The worse the medicine and healthcare, etc. the more people die.

Nothing controversial so far? But these are the premises of a syllogism, and when followed through you end up with the conclusion:

    Closed access means people die

I don’t think anyone can deny the truth of that conclusion. If a doctor, a patient, a planner, an engineer, cannot read the appropriate literature then they make suboptimal decisions. And that means people die.

So the balance is:

If we want a closed access publishing system then we have to accept that the price is people’s lives.

Well, isn’t that how the world just is? Engineering has fatalities, Transport has fatalities, leisure sports have fatalities, so why not scholarly publishing?

Because it’s completely avoidable. The more I write about Openness the more angry I get about the immorality of closed access and walled gardens. And even more angry about the lobbying, the politics that tries to close down open efforts. We heard today (not from me) about how the American Chemical Society had spent money and lobbied to have Pubchem (the repository of Open chemical structure information) shut down. So my language is now less nuanced

    Closed access means people die

And that’s not just me. In ORR we are having major contributions from Graham Steel and Gilles Frydman – patient champions for CJD and Cancer. Gilles told me of hundreds of people who die if their physicians don’t know about the latest literature. Remember these physicians cannot read the literature (there’s a blithe and stupid assumption that because they are professionals they don’t have to pay for the medical literature – the papers WE scientists give the publishers in return for our h-indexes). So misdiagnosis is common and avoidable by access to the literature. (And don’t dare try to tell Gilles he and his 65,000 community are not qualified to make this assessment).

So then we moved to WHAT can we do and how can we do it. The basic idea is to take the Open material – primarily libre material in (UK)Pubmedcentral – and collate it into annotated quality reports, one per disease. Collect the Open papers, and rank them by citation (yes I know that’s imperfect, but we aren’t trying to advance someone’s career, we are trying to save lives). Then we get the community to annotate them.

What? Get unqualified people to extract information from the papers? That’s junk.

No. here’s the sort of material that David has listed for an infective disease paper:

I am sure that no one reading this would be unable to extract SOME of this information reliably. You don’t have to be a medic to understand lat/long or dates or species. I personally would be able to extract all the drugs (and even our software can). So each person does what they can do well.

And as a result the community edits the report.

And we have a high-quality tool.

Hang about! You’ve omitted all the closed access stuff. That’s 90% of the literature.

So? For many purposes 10% is completely sufficient. For introductory material, for teaching, for a text-mining corpus, for diagrams, the list is endless.

And the quality of the annotation and extraction can be used for data-mining, mashups, all sorts of semantic stuff. Making it much more useful than the same amount of stuff in the closed literature.

And mightn’t this just jerk the consciences of some people? And continue to tip the balance to Open.

So join us for the Hackathon in London, UK on 2011-12-06/07. Because it’s a hackathon we don’t know in detail what we’ll do. But we’ll make a major start to establishing Open Research Reports.

And of course YOU can take part. The literature must be all Open, so everyone can read it. All tools will be Open. It’ll be great fun. Closed access publishers especially welcome as it will help them to adjust to the inevitable change taking place.

#oss2011

Jenny Molloy and I are representing the Open Knowledge Foundation at Open Science Summit in the Computer History Museum, Mountain View, Silicon valley(haven’t had time to look at ANY of the museum!). It’s a fantastic meeting, run by Joseph Jackson with huge dynamism and belief. Open Science is a forum bringing together a wide range of those interested in doing things Openly. See http://opensciencesummit.com/ for the programme.

But last night there was a party in Biocurious (the open science company that Joseph started) in a warehouse in Sunnyvale. Great atmosphere. Core Californian – young, enthusiastic people – each with their startup. Total faith in their success. (They contrast this with the east coast where everyone is cautious).

Victoria Stodden kicked off with Reproducible Research – it’s clear that a lot of people are committed to the importance of this – funders, (some) editors, researchers.

Then a session on Patents. Most interestingly a project involving people playing a game with real money and several different models of patents (conventional, conventional+”pantentleft”, and completely open). The completely open approach (i.e. no patents) brought in the most money and was at least twice as efficient in time and cost.

Awesome presentation from Beijing Genomics Institute. Non-profit, with as much output as the whole of the US (I think I got this right).

Several things I already knew about, but no less interesting for that – Mendeley (which has fully opened its content – I need the URL for that). Mathoverflow. Digital Ocean I didn’t know.

Jai Ranganathan promoting #crowdfunding. Great idea. (They raised 60K USD for a statue of Robocop – I thing average of 20 USD per donation). So they’ve moved to #scifund which is asking for science projects which can be exposed to the world for funding. You’ve clearly got to get your idea across rapidly – but, hey, that’s what it’s about. A great way of getting science into the community and getting the community driving science.

Alex Hodgson who I met in the Biocurious party runs a recommender company for antibodies. Many antibodies are crap (there’s a sticker saying – “Say no to crap antibodies”). So it’s like hotel reviews (“rude staff and bedbugs” translates to “complete crap” or “wasn’t what was on the label”). IN this way we get a system of trust created for different suppliers. Would that it happened for chemicals! Alex’s company has been invested by Digital Science.

There’s a great buzz. No doubt that Open Science Summit is here to stay (several people elsewhere indicated to me that they would have loved to come or would be coming next year).

The next post will describe what Jenny and I presented.

Yesterday I posted an analysis (/pmr/2011/10/21/open-access-works-articles-matter-not-journals/ ) of the accesses to the papers from our special symposium (“Visions of a Semantic Molecular Future). In it I claimed that it no longer matters where you publish but what you publish. It was a single anecdote, but I think a very important one. If anyone has similar cases then I think we can make a fairly strong case.

I reported that in SIX DAYS 1247 had accessed the article by John Wilbanks. Now “Accessed” != “read in total” but it means that at least a human has clicked on the link to the paper and presumably allowed some photons from it to be processed. (It’s a bit complex because these papers are still provisional and you have to click through to the full PDF whereas with a final (Open Access) paper you can read the whole thing.

How long does it take to “read” a paper? I’d guess between a minute and an hour. A minute?? Yes – because that’s what many of today’s readers do. I can’t give the link, but I recall Allan Renear describing a study of how young scientists read the literature skipping rapidly from here to there – perhaps 30 papers an hour. I certainly read some papers in a minute (unless the production is so awful that my brain hurts. Why do we have double-column PDF on screens devised for viewing movies. It’s grotesque – but that’s why we pay publishers to produce stuff we don’t want).

So let’s assume that 200 people a day have read John’s paper. Do we have any evidence?

Yes – from the twittersphere. Yesterday there were 40 tweets with the string “Openness As Infrastructure”.

40. Some were retweets (RT) but still people had taken the effort to tweet this. Why? Because they wanted to tell their friends and the world about this paper. They aren’t bots because you can see they are beautiful people, with real identities. Most simply RT’ed, but I fished out the comments:

“Science was like a wiki! ” [a quote from John’s text]

“A very interesting article for open data folk and others”

[Twitter only gives you this much after you have included the title and the @wilbanks]

If people had thought there was something wrong with the article then they’d have said so.

So I think we can conclude this is massive public interest and approval of the article.

In J.Cheminformatics!

The last place you would expect to see an article from John.

Now I frequently hear people say “Oh, don’t publish there – no one will read it and it’s not got a decent IF” (IF == Journal Impact Factor, remember). So here’s a very relevant comment from Mike Taylor, the sauropodovertebrologist:

Mike Taylor says:

October 21, 2011 at 8:42 am

VERY interesting analysis. I wonder if there is a way to move this beyond the anecdotal, and somehow quantify the relative importance of writing a good article and placing it in a good journal.

I recently wrote (http://svpow.wordpress.com/2011/10/17/collateral-damage-of-the-non-open-reviewing-boycott/#comment-11558) that “If you work in an institution where they count up the IFs of the journals where your papers are published, then it may be advantageous to forego actually getting read and cited, for the benefit of rubbing up against other papers that, despite the disadvantage of being in a walled garden, still accumulate many citations. Promotion by the company that you keep rather than by your own achievements.” I’m hugely encouraged to think that we may be further along to road to fixing that system than I’d realised.

I think that for younger scientists this is tragically true. If it had been someone less well known who submitted the article would people have tweeted and read it? I don’t know. Possibly, but slower and in smaller volume. But unfortunately the great-and-the-good of science (with honourable exceptions such as PloS people) are generally saying “you must publish in the highest impact journals.” I hear this all the time. It’s a massive demonstration of the mediocrity of current academic morality.

Because people who cannot read the literature – the Scholarly Poor – suffer. Some die because of it. We don’t know who, but I am certain this is true. I want to see how we can measure this and expose this gross abdication of social responsibility.

Meanwhile, what about peer-review? In @wilbanks we can ask the questions:

• Is it in scope for the journal? Conventional thinking would say no, and some of the reviews for the other papers were somewhat conventional. I didn’t see John’s reviews. But we had agreed with/as editors that all the material was “inscope”. And the readership has confirmed this!
• Is it sound? The twittersphere thinks so, and so do I.
• Is it interesting. Same answer.
• Is it novel? I think we’d have heard “same old stuff” if it wasn’t.
• Was it plagiarised? As before

The point is that “peer-review” isn’t a single dimension. If I am reading a clinical trial I want to know that the stats are valid and the methodology sound. If I am seeing a crystal structure I want to know it wasn’t a duplicate of work published a year ago by the same authors. Although I DO want to see independently repeated scientific experiments as they calibrate the discipline. But for much of the rest the twittersphere is often hugely better than the conventional peer-reviewers.

As part of our Open Biblio project Jim and I were looking for lists of journal references to turn in BibJSON. I thought that I’d take some of our article listing from “Visions of a Semantic Molecular Future” (http://www.jcheminf.com/series/semantic_mol_future ) in J. Cheminformatics, an Open Access journal published by Biomed Central. To make clear, an Open Access journal is one where all the articles are individually OA, usually under a CC-BY licence so free to read and re-use and do whatever you like with.

So VoaSMF had 15 articles and they’ve just been published a few days ago. I was looking for a way to emit them as an RDF / RSS feed so that we could turn them into BibJSON. It would contain records for each article with name/title/journal etc. and we’d see how they fitted into the BibJSON schema. Anyway the RSS isn’t ready yet, but I did find one for heavily accessed articles (which would include one of our groups – ChemicalTagger).

So I went to http://www.jcheminf.com/articles/top/browse.asp and started to read down:

 Top 10 most accessed articles for last 30 days / past year / all time         [more info]

1367 accesses in … wow! 20Oct – 7 Oct = 13 days = 100 hits/per day. Well done the Open babel team. Of course OB is a wonderful program, open source and part of the Blue Obelisk. Wow!

2.
Accesses
1329 Preliminary communication    
Linked open drug data for pharmaceutical research and development
Matthias Samwald, Anja Jentzsch, Christopher Bouton, Claus Stie Kallesøe, Egon Willighagen, Janos Hajagos, M Scott Marshall, Eric Prud’hommeaux, Oktie Hassanzadeh, Elgar Pichler, Susie Stephens

journal of Cheminformatics 2011, 3:19 (16 May 2011)

That’s presumably hits for the month = 40/day. Extremely good. And the subject is about OPEN drug data. People must really want open data.

3.
Accesses
1247 Commentary    
Openness as infrastructure
John Wilbanks
Journal of Cheminformatics 2011, 3:36 (14 October 2011)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]

WOW! That’s only 6 days old, and from our symposium! 200 hits/day! These hits are not because of where it appeared. John has no connection with Chemistry. The point is that people want to read John’s work. And they will find it in DAYS regardless of where it’s published. It’s the top article in our symposium.

4.
Accesses
1168 Software    
PubChem3D: A new resource for scientists
Evan E Bolton, Jie Chen, Sunghwan Kim, Lianyi Han, Siqian He, Wenyao Shi, Vahan Simonyan, Yan Sun, Paul A Thiessen, Jiyao Wang, Bo Yu, Jian Zhang, Stephen H Bryant
Journal of Cheminformatics 2011, 3:32 (20 September 2011).

Well done Pubchem. Pubchem is an OPEN data base of 30 million structures. Some closed organization some years ago tried aggressively to close it down as unfair competition. But Openness prevailed (ca 40 hits a day)

5.
Accesses
868 Research article    
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
Noel M O’Boyle, Rajarshi Guha, Egon L Willighagen, Samuel E Adams, Jonathan Alvarsson, Jean-Claude Bradley, Igor V Filippov, Robert M Hanson, Marcus D Hanwell, Geoffrey R Hutchison, Craig A James, Nina Jeliazkova, Andrew SID Lang, Karol M Langner, David C Lonie, Daniel M Lowe, Jerome Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L Tenderholt, Kevin J Theisen, Peter Murray-Rust
Journal of Cheminformatics 2011, 3:37 (14 October 2011)

Zowie! Another from the VoaSMF. (and I’m an author). 6 days = 140 hits/day. Fantastic. But, as they say, there’s more

6.
Accesses
672 Research article    
Open Bibliography for Science, Technology, and Medicine
Richard Jones, Mark MacGillivray, Peter Murray-Rust, Jim Pitman, Peter Sefton, Ben O’Steen, William Waites
Journal of Cheminformatics 2011, 3:47 (14 October 2011)

ANOTHER from our symposium! 110 hits/day. And nothing directly to do with chemistry. So people have discovered this article because of what it is rather than where it is!

… and …

7.
Accesses
598 Editorial    
Semantic science and its communication – a personal view
Peter Murray-Rust
Journal of Cheminformatics 2011, 3:48 (14 October 2011) – 100 hits/day

So what’s the message from this? It’s that journals are no longer relevant to discovery. If they were, no one would have discovered John’s article and probably not the Open Bibliography. There are other mechanisms. I don’t know what they are, but I suspect John’s has been blogged or tweeted. Because it’s OA people know they will be able to read it. It’s also clear that article metrics are real. This isn’t robot activity. Of course John might have written a fleet of bots to knock up his accesses but since the bean-counting-weenies don’t count accesses there wouldn’t be any point (and of course John wouldn’t even think of doing it).

So it’s real. People will find articles of value regardless of where they are published as long as they are Open.

Don’t get me wrong – I am not arguing against editors. The scientific editors and the technical editors have done a great job. But it doesn’t need to be done in a journal.

And although article metrics – like any metrics – can be gamed they are far more valuable than the mindless citations. After all, all the papers have ZERO citations – which would make them worthless.

Here’s a secret not many people know. The way to find out how good a paper is, is to read it. Try it.

I am spending 4 wonderful days working at Berkeley with Jim Pitman on Open Bibliography and BibJSON having met Jim and Karen Coyle IRL for the first time.

Bibliography? Boring…

No. Bibliography is the Map Of Scholarship. It tells us who has created what when and where. Traditionally it’s been seen as a library subject, managing the books and the catalogue, but in the electronic era it’s relevant for anyone and everyone. Books are changing, and research and its publications / communications is changing. So the way we communicate this is vital.

If you are a scholar or researcher your career is measured by bibliography. Your “H-index” is bibliography. The university’s “REF” or other research assessment is bibliography. It’s the formalization and characterization of scholarly output.

Isn’t it just books and papers / articles?

No longer. There’s many people (including me) who feel that there are a whole lot of outputs and inputs that are just as important:

• Online accesses
• Collaborations
• Software
• Blogs
• Twitter (What??? – what a lot of rubbish – only citations in peer reviewed papers matter. No, the twitter and blogospheres have excellent records of post-review of papers – finding errors and even forcing retractions and rewrites).
• Datasets
• Online resources

For example the Altmetrics group has some very exciting indications of how publications have an impact.

And citations – well they tell you something about what you did five years ago. Useful for historians of science, perhaps. Although look at the h-index of Galois (it’s 2 as he only published two papers before getting shot)

So we need a new approach to bibliography. Perhaps a new name. Something where we can record our outputs in detail. And where we are able to determine what is important – not some distanced commercial company which “measures” our value.

Didn’t you know that? Your value isn’t measured by your peers in the discipline or the university. It’s determined by what large commercial companies can make money out of. They only measure the easy things.

And they build walled gardens – they control us. The bibliography and metrics need to be Open. So we can actually verify what is being calculated. (Didn’t you know? The algorithms for determining the value of a scholar/researcher are commercial secrets – often created through tricky commercial deals).

What are we doing in Berkeley? We are continuing the JISC project on Open Bibliography. We are creating a universal language – BibJSON. Open source servers (BIBserver). Open tools for editing and creating bibliography. Reading lists. Reports, etc.

Aimed at individual scholars, departments, subject groups. To let them tell the world what they have done, what resources they think others would be interested in.

It’s all Open. But we are very happy to work with commercial and other organizations. To look at interoperability. To look at making bibliographic data Open.

I’ll be posting regularly on this.

We’ve finished our session on Walled Gardens at the Serpentine Gallery Marathon – great fun (and a lovely day)

Here’s the human team: L-R PM-R, David Rowan (who brought this together), Emer Coleman

David gave a powerful presentation of how walled gardens had the seeds of their own destruction – Facebook would disappear like AOL and MySpace. “If something is free, then you probably are the product”

Emer showed how opening government data allowed innovative apps to be made by independent developers. There were apps for Boris Bikes (London’s very own Boris’s answer to Amsterdam) . How if you had the map of London Transport and train times you could have real-time knowledge of exactly what train you would catch.

Here’s the “goodies” on the animal team… Bertie has been blinded by the evil HADOPI.

Gulliver Turtle (from BMC) being shown to the audience as an example of how you could be Open Access and profitable.

x

And my final thoughts for where hope and help comes from. Apologies if you aren’t on it.

I am delighted to say that the special issue of the PM-R symposium (Visions of a Semantic Molecular Future in January) has now been published by Biomed Central in J. Cheminformatics (http://www.jcheminf.com/ ). There’s fifteen papers and I hope that you’ll find many of them interesting. YOU DON’T HAVE TO BE A CHEMIST TO UNDERSTAND THE OVERALL IDEAS OF MOST OF THEM. Several are about Open Scholarship, others about semantics.

One of the broadest papers is on Open Bibliography:

Open Bibliography for Science, Technology, and Medicine
Richard Jones, Mark MacGillivray, Peter Murray-Rust, Jim Pitman, Peter Sefton, Ben O’Steen, William Waites
Journal of Cheminformatics 2011, 3:47 (14 October 2011)
[Abstract] [Provisional PDF]

Conventionalist: Hang on – why are you publishing an article on Bibliography in a Journal of Cheminformatics?

PMR: Because it’s Open access. (and because the editors have been very constructive in processing the symposium output)

Conv: But shouldn’t you publish it in a library journal.

PMR: Why?

Conv: Because it’s about bibliography.

PMR: Doesn’t matter where I publish it.

Conv: But the people who need to read it won’t find it.

PMR: You’ve found it – by reading my blog.

Conv: But that’s just chance.

PMR: Not really. People have many ways of finding information. In fact Open Bibliography is all about new ways of finding scientific information.

Conv: But that’s the point of journals.

PMR: No longer. We use all sorts of search engines, links, robots, etc. Journals are outdated.

Conv: They’re needed for all sorts of things – editors, impact factors.

PMR: No, it WHAT I write that matters. Not WHERE I publish. It means people will actually have to read papers to determine whether they are any good. Try reading this one for a start.

Conv: Hmm.

PMR: No, read it. There’s lots of ideas on how we can make bibliography simple for scientists. And we’ve got the software already written.

Conv: Hmm, Hmm.

PMR: I’ll be writing more about the articles in this issue. But the Bib one is a good one to start with. I am off to visit and collaborate with Jim Pitman next week.