I am delighted to congratulate Michael on his award as a SPARC innovator: http://www.arl.org/sparc/innovator/ Here are some bits of the citation (below) but my personal comments first.

Michael is a true 21^st century scientist. There aren’t yet many around, and academia stifles their growth. They change the rules of the organization, the community, the values. So, almost by definition, they have to work outside the system. Michael was/is a quantum physicist with an enviable track record but he has given this up to explore the 21C. We’ve met 2-3 times last year and he’s currently (I think) doing lecture tours having written his seminal bestseller Reinventing Discovery http://press.princeton.edu/titles/9517.html. If you get a chance, try to get to a lecture, though you can also see the TED lecture http://www.ted.com/talks/michael_nielsen_open_science_now.html.

Here’s SPARC…

Michael Nielsen

Michael Nielsen, a 37-year-old, Australian quantum physicist, just completed a 17-city tour in seven countries, doing a series of presentations to promote the open sharing of data and research to advance science. On top of that, he spent a month traveling to promote his book, Reinventing Discovery: The New Era of Networked Science (Princeton University Press, 2011). His talk of changing the culture of science has drawn audiences beyond typical academics. Nielsen’s passion, credibility as a scientist, and knack for storytelling has helped propel the issue of Open Science into the mainstream.

For being a thought leader and demonstrating how doing science in the open can promote change and bringing the discussion to a new level, SPARC honors Nielsen as the January 2012 SPARC Innovator. 

#semphyssci

I am editing the video material from our Semantic Physical Science symposium, and the first is my introduction (http://vimeo.com/35169794, ca 10 mins). This is partly because it’s short (so less technical hassle – though more editing) and partly because I can give myself permission, while I am still waiting for other speakers to give the OK. [All talks WILL be mounted, and all will be Open Knowledge Definition compliant (CC-BY 3.0, Creative Commons Attribution). This means that anyone can do anything with them, including cutting snippets and re-using them. Even (especially) for political purposes.] Here M.I.T.-bear strikes a blow for freedom (about 8 mins into the video)

NOTE: There are a few frame drops, interestingly on the titles. Maybe a more consistent background will help. (You haven’t missed anything)

My video is complex because it contains

• Hello Participants and Hello World
• The purpose of the symposium – to hand over 15 years of work to the world scientific community in an Open Manner
• Tribute to my colleagues and funders
• Context of semantic science
• Political barriers to be overcome (ca 8:00 mins into video). Here M.I.T-bear strikes a blow for freedom against RWA/HR3699. Also PMR expresses his views on the proposed legislation.

Here are some of the links I mention – it’s easier to follow them here

pmr.ch.cam.ac.uk/wiki/Presentations
pmr.ch.cam.ac.uk/wiki/Visions_of_a_%28Semantic%29_Molecular_Future
jcheminf.com/series/semantic_mol_future
jcheminf.com/content/3/1/37
pmr.ch.cam.ac.uk/wiki/Group_Members
pmr.ch.cam.ac.uk/wiki/Projects
blueobelisk.org
quixote.wikispot.org/
lbm2011.biopathway.org/index.php?p=keynote_speakers
lbm2011.biopathway.org/index.php?p=technical_program
pantonprinciples.org/
plus.google.com/u/0/109377556796183035206/posts/L6QNRbt4S8x
michaeleisen.org/blog/?p=846
guardian.co.uk/science/2012/jan/16/academic-publishers-enemies-science
poynder.blogspot.com/2012/01/mit-press-distances-itself-from.html
vimeo.com/34259668

and here is the programme. I am intending we post all of these, but it’s a lot of time experimenting with video conversion.

#semphyssci

We ran a most rewarding workshop and symposium on Semantic Physical Science last Tue/Wed/Thu (2011-01-10/12). The program is below. This is an interim post to keep the momentum going and to let others know that there will be in important continuing activity. There were about 25 for the workshop and another 10 for the symposium.

The event covered a lot of ground, with a lot that was new for many people and many different possible ways of tackling semantics. The immediate outcome is there was very good agreement on:

• The value of semantics
• What to do in the first instance
• Timescales
• Resources

The areas we covered were:

• Computational chemistry (participants included STFC (DL), PNNL, Cambridge (EarthSci, Chem, Chemeng, Cavendish), QMC, Bristol, Imperial (unfortunately Henry Rzepa had to miss the last day)
• NMR. Concentrating on 1-D NMR spectra (Bruker, Varian, JCAMP), mainly (CSIRO and PNNL). Unfortunately Christoph Steinbeck (NMRShiftDB) couldn’t come but we have a very good outline of what needs doing
• Crystal. Main interest in having a repository of published structures independent of any restrictions (e.g. Crystaleye)

The software is now clearly alpha or very close to it. We are particularly grateful to Andrew Walker for FoX and good prototype/proof-of-concept was made with NWChem and AMBER. To be successful we shall need the continuing support of the developers. JUMBOConverters is now distributable and straightforward to add new converters, validators and dictionary-lookup.

Chempound worked well and there is clearly demand for all 3 disciplines

We’ll try to get a fuller summary out in the next few days. Basically we have agreed that the immediate phase involves:

• Firming up some conventions, especially NMR
• Pulling the various CML websites and resources together
• Deciding on how to do dictionaries. There are two schools of thought:

1. One uber-dictionary for compchem. Anything that is program-specific isn’t important
2. One dictionary per program and an uber-dictionary for compchem

I am deliberately neutral on dictionaries, but I think the software has to support (2) [That make it able to support (1) as well]. I think during development phase it will be necessary to have a number of dictionaries, but we must be careful they don’t get set in concrete. For NMR I suspect we shall have to have instrument-specific dictionaries

• Firming up validator software
• Firming up commandline converters

Many thanks to Charlotte Bolton for organizing all sorts of things. As with last time Charlotte will continue to support with documentation and publication.

I am also working hard on editing the videos. They aren’t too hard sequentially in that everyone talked well and in a linear fashion, but I’m still not on top of WMV => ffmpeg => MP4. Anything 1280*960 is likely to drop image frames; half size is fine, but it’s hard to read the screen. In any case they need editing. I’m going to post them privately to the participants in case there’s anything they want to delete/add. We need to do this as MP4 [ca 100 Mbytes / 30 mins] because WMV is just far too big.

Cameron and I have some political messages about SOPA/RWA etc so those will probably be the first out.

More later. [Next week I have Open Biblio sprint, so not much time for relaxation! But it’s fun].

AnnMaria is a small business owner and writes passionately about the harm that HR3699 does to her: http://www.thejuliagroup.com/blog/?p=1932. I’ll quote extensively below. And I want you to get angry as well.

And start DOING something about it.

I’ve written before about the Scholarly Poor; small businesses are a major part of it. Every time I meet people in small business (and Cambridge is the UK centre of technology-based startups) I ask them whether they (a) want to read the scientific literature and (b) whether they can and (c) whether they suffer. And the answers are (a) yes and (b) generally no and (c) yes. Many businesses give up and only read freely accessible articles and do not re-use the data. There are illegal work-rounds:

• Ask on Icanhazpdf (it is illegal to send people copies of closed articles)
• Get a graduate student in your erstwhile to pipe through the articles (also illegal)

But ethical companies don’t do that. And also, as SOPA and RWA come nearer, we shall see prosecutions. If Wiley can threaten a graduate student for reproducing a single graph (an unethical and probably illegal act) are their hired guns in SOPA going to hold back? Because the scholarly publishers as well as the music industry are supporting SOPA. And SOPA won’t be policed by the nice people who we meet in publishers, it’ll be policed by professional enforcers. If you can sue a kindergarten child for pirating music you can also sue a small business.

Here’s AnnMaria:

Research Works Act: Latest Congressional Lie about Helping Small Business

I am pissed

ed.

As a small business owner, I am feeling very, very disappointed that there is certainly some law out there that would impose penalties if I drove on over to Riverside County and bitch-slapped [1] Darrell Issa. I’ve grown cynical enough in my old age and after having run a small business since 1985 that I am used to every politician under the sun spouting “Think of small business!” as a knee-jerk reaction to anything, whether their position is for it or against it. Usually, they are easy enough to ignore. Payroll taxes are not going to decide whether or not I hire people – business demand is. Health care – we’ve made that an option for our employees long before it was required by law.

This time, though, they are REALLY pissing me off. Let me tell you what the Research Works Act is and how it really does hurt my small business. As this succinct article by Janet Stemwedel on the Scientific American blog site explains well, not only does it require the American taxpayer (that’s me!) to pay twice for the same research, but also, the very people being protected and profiting are NOT those who produce the work to begin with.

Right now, if a person is funded by federal funds, say, the National Institutes of Health, they are required to submit the results of their research to PubMed’s repository within twelve months of publication. The idea is that if the public paid for this research then the public has the right to read it. Sounds fair, right?

In case you don’t know, rarely do authors get paid by journals.  I’ve published articles in the American Journal on Mental Retardation, Research in Developmental Disabilities, Educational and Psychological Measurement – to name a few. I’ve been a peer reviewer for Family Relations. For none of this did I get paid. That was fine. Almost all of the research I did was funded by federal funds and part of the grant proposals included dissemination – that is, publication of scientific articles. Fair enough. As a peer reviewer, I’m just repaying the service others have done in reviewing my work. Again, no problem.

Yet, in many cases, if I need a journal article for a grant or report I’m writing for a client, it is going to cost me $30 per article.  Contract research is a good bit of where the actual money comes into this company (you didn’t seriously think I made my living by drinking Chardonnay, spouting wanton programming advice and snarky comments, did you?)

The journal did not pay for the research to be conducted – the federal government did. The journal did not pay the author – the federal government did. The journal did not pay the reviewer – they volunteer.

SO WHY THE FUCK SHOULD I PAY $30 AN ARTICLE?

I just pulled up a random small project I had done recently for a client and there were seven articles in there that I would be charged $210 to have used. As I said, this was a small project, and I calculated it would have brought the price up 7.5%

Not long ago, there was a huge outcry about the city of Santa Monica adding a ten cent cost for a paper bag and banning plastic bags. “It will hurt small business!” people cried. Actually, I have always made a major effort to shop at our local businesses, I still do and it has not hurt any business anywhere that I can tell. You know what else I can tell you? That increasing the cost of a $3,000 project to $3,210 is a hell of a lot more significant than paying ten cents for a paper bag!

So what exactly is this bill doing? It is moving money from small businesses, like me,  and like my buddy, Dr. Jacob Flores, who runs Mobile Medicine Outreach and into the hands of large publishing companies, who not coincidentally gave a huge amount of money  to Democratic congresswoman Carolyn Maloney of New York. I’d like to bitch-slap her, too, but being on the opposite side of the country, it would be a lot less convenient for me.

You can read more detail in this article from the Atlantic, where Rebecca Rosen asks, “Why Is Open-Internet Champion Darrell Issa Supporting an Attack on Open Science? ”

As Danah Boyd points out on her blog, there is this new thing for sharing knowledge now, called the Internet and a major point of the Research Works Act seems to be to prevent it being used to share knowledge that I paid for with the approximately 50%  of my income (yeah 38% federal, 10% state) that I pay in taxes. And you know what, being a graduate from that great institution, the University of California, that enables me to make the money to pay these taxes, I don’t object to that.

What I DO object to is paying again for the same resources I already paid for once just because some lobbyists for large corporations lined Issa’s and Maloney’s pockets.

While it may not be legal for me to bitch-slap Issa it is certainly legal for me to go to the next California event where that lying-ass mother has the balls to stand up and claim to be helping California small business. Anyone who knows the next public event where he’ll be speaking, please hit me up.

One thing, though, I don’t think I’ll be going to any of his fundraisers. I think he’s gotten quite enough money from the publishing industry.

AnnMaria shows the very simple equation:

Supporting the scholarly publishing industry profits = draining opportunity and profits from new technology companies.

The scholarly publishing industry is making profits out of monopolistic restrictions. In so doing it is destroying other industries. We’ve heard in the UK that IP restrictions prevent companies like Google setting up here. If SPOA/RWA are passed it won’t be possible to set up new Googles in California either.

So – if you want wealth generation in the future, support 21^st century industries like Google, O’Reilly, and AnnMaria. And let the scholpub adapt or die.

[Peter Suber] Robert Heinlein responded to the [scholpub] position more than 70 years ago (Life-Line, 1939):  “There has grown up in the minds of certain groups in this country the notion that because a man or corporation has made a profit out of the public for a number of years, the government and the courts are charged with the duty of guaranteeing such profit in the future, even in the face of changing circumstances and contrary to public interest. This strange doctrine is not supported by statute or common law. Neither individuals nor corporations have any right to come into court and ask that the clock of history be stopped, or turned back.”  

[1] Bitch-slap f = http://www.urbandictionary.com/define.php?term=Bitch+Slap (AnnMaria – please send pictures when you do)

I have been blogging for a week about HR3699 (Research Works Act). I have been trying to take personal action – apart from blogging I have mailed OUP and CUP asking them to stand up and be counted on their membership of AAP.

Yet if I hadn’t been actively involved in open data I wouldn’t even have known anything was happening – that there was anything I should be concerned about. And no-one has tried to reach me and get me involved – even to sign a petition.

In contrast other Open movements such as F/OSS, Avaaz, 38 Degrees mail me every week asking me to sign on all sorts of issues. In the internet age it’s easy to reach out to people and provide means to get them involved.

I’ve searched for “stop HR 3699 petition” and the first site that comes up is

http://www.thepetitionsite.com/207/support-the-open-access-movement-stop-the-research-works-act/

This is a site (Care2, Jennifer P. – I’d never come across it) for “ordinary people” who care about access to information, especially health information. They are the “scholarly poor”. The people who – unlike rich Universities – actually feel the lack of access to healthcare information.

As soon as I heard about HR3699 I mailed the patent advocates I knew. And, of course, they have responded magnificently. Here’s Gilles Frydman, through the Society for Participatory Medicine. The Scholarly poor with real disease.

http://e-patients.net/archives/2012/01/open-knowledge-saves-lives-oppose-h-r-3699.html

Here’s Gilles:

Before reading further, remember the definition of Participatory Medicine:

a movement in which networked patients shift from being mere passengers to responsible drivers of their health, and in which providers encourage and value them as full partners.

How can you be a responsible driver of your health if you don’t have direct access to all information? That’s why Dave has been fighting for his damn data and similarly why ACOR has been engaged in multiple efforts to maximize the dissemination of any and all scientific publication that relates to an ACOR group condition.

Seeing a corrupt travesty of the democratic process used today to promote the interests of a few gatekeepers at the expense of millions of people is very disturbing. The NIH and other agencies must be allowed to ensure timely, public access to the results of research funded with taxpayer dollars. Please oppose H.R. 3699. You’ll be in great company!

And there’s lots more [I quote from Gilles]

Tim O’Reilly [PMR One of the great entrepreneurs and thinkers of this century] Please don’t write laws that protect 19th century industries against 21st-century disruption!

[Gilles: ]Tim’s […] sentence may need some explanation, which thankfully has been provided by Microsoft Researcher and grand guru of social media’s influence on the youth, danah boyd, in her December blog post Save Scholarly Ideas, Not the Publishing Industry (a rant):

The scholarly publishing industry used to offer a service. It used to be about making sure that knowledge was shared as broadly as possible to those who would find it valuable using the available means of distribution: packaged paper objects shipped through mail to libraries and individuals. It made a profit off of serving an audience. These days, the scholarly publishing industry operates as a gatekeeper, driven more by profits than by the desire to share information as widely as possible. It stopped innovating and started resting on its laurels. And the worst part about it? Scholars have bent over and let that industry continuously violate them and the university libraries that support them. [..]

WTF? How did academia become so risk-adverse? The whole point of tenure was to protect radical thinking. But where is the radicalism in academia? [PMR emphasis]

Ironically, of course, it’s the government who is trying to push back against the scholarly publishing’s stranglehold on scholarly knowledge. [..]

Please, I beg you, regardless of whether or not we can save a dying industry, let’s collectively figure out how to save the value that prompted its creation: making scholarly knowledge widely accessible.

READ GILLES ARTICLE.

PMR: Yes “where is the radicalism in academia?” Where is the radicalism in the Open Access movement? The OA movement is playing pillowfights while the AAP hired guns play dirty with baseball bats. They spend their money on lobbyists. And the OA movement is not mobilising opinion.

[I acknowledge that there are people who are working hard to change opinion on Capitol Hill and I respect them. But it’s closed. It’s a small group of people who don’t tell the world what they are doing. Maybe this is necessary secrecy but it leaves the mass of people outside the OA movement uncoordinated. There’s Richard Poynder who has already mailed all the University Presses. But if there are other activities no one is publicising them sufficiently.]

As a result the activist response is either missing or fragmented. Some instances:

• Where is the OA petition against HR3699? I couldn’t find one.
• Where is the organisation of responses to Capitol Hill.? Am *I* (as a non-US citizen allowed to submit to OSTP? I asked on lists and got no reply. I tweeted (I have 1000 followers) – no reply.
• Where is the count of people who have signed or written against HR3699?
• Where is the communal Wiki for people to find resources for the protest?

Here’s a typical simple action – my avatar. I got the idea from Glyn Moody. YOU could do it. Don’t be afraid – it’s not illegal to protest publicly.

There are many more things that you could do, but I’ll use a separate post to give things that the Open Access movement could be doing now. All within the holy law of copyright. There’s hundreds of millions of dollars spent on OA (if you include Repositories) – there’s certainly enough resources to organize 21^st century protest activities.

Late last year I gave a slogan for the OA movement: “Closed access means people die”. It’s simple. It’s a political slogan. But I was severely criticized because it hadn’t been proved in a scientific manner. (Actually there is quite enough evidence supporting it). The point is that the OA movement has to use slogans to reach out beyond its narrow boundaries. I’ve offered the apparent double negative: “Open Access saves lives”. This is the sort of message we should be using.

Because it’s obvious that the Scholarly Poor – Jennifer P, Gilles, Tim O’Reilly, Dana Boyd are doing their own activities without the coordination of the OA movement. Their anger and passion comes through and it reaches out to the Scholarly Poor in a way that academia does not.

So, OA community – if there is one – start engaging with people outside – and that’s increasingly including me.

UPDATE: Recent tweet: @petermurrayrust @PublicAccessYAY round up of OA coverage connotea.org/tag/oa.rwa Place to vote against it https://t.co/JfGooTmp #rwa

Dear Nigel Portwood,

I am an alumnus of Oxford University (Balliol, BA, MA, DPhil) and write to urge OUP to repudiate H.R.3699 and the Research Works Act promoted by the American Association of Publishers of which OUP is a member.

The AAP has proposed a bill which effectively legislates the restriction of access to scholarly publication with the sole intention of raising the income of publishers. I and many others feel this is unethical, immoral and unworthy of any organisation committed to the dissemination of knowledge. Some commentators have described it as an act of war by the publishing industry on the scholarly community. Balanced and factual accounts are given by Richard Poynder (http://poynder.blogspot.com/2012/01/mit-press-distances-itself-from.html and related posts in his blog).

Already academic publishers are distancing themselves from this Act. MIT Press (link above) has stated:

“The AAP’s press release on the Research Works Act does not reflect the position of the MIT Press; nor, I imagine, the position of many other scholarly presses whose mission is centrally focused on broad dissemination.

I can see every reason why OUP should issue a similar, or even stronger, message repudiating the AAP’s position. I hope that you can assure me OUP was not involved in creating the AAP’s position and ask you to consider the downsides of belonging to an organisation such as AAP.

[This is not the first time that the publishing industry has created anti-scholarship initiatives – I wrote to OUP about the iniquity of the “PRISM” alliance in 2007. I doubt it will be the last.]

Yours

[PS. I do not have personal email addresses and assume that “press” will reroute this mail. In any case I have a heavily followed blog and will post this letter there – maybe someone at OUP will forward it if required].

[I have sent the following letter to press@cambridge.org. If anyone knows better addresses for the addressees, please could you forward it. You might also wish to add messages of your own]

Dear Stephen Bourne,
Dear Andrew Brown,

I am a member of Cambridge University (Reader Emeritus, Chemistry and past Senior Research Fellow, Churchill) and write to urge CUP to repudiate H.R.3699 and the Research Works Act promoted by the American Association of Publishers of which CUP is a member.

The AAP has proposed a bill which effectively legislates the restriction of access to scholarly publication with the sole intention of raising the income of publishers. I and many others feel this is unethical, immoral and unworthy of any organisation committed to the dissemination of knowledge. Some commentators have described it as an act of war by the publishing industry on the scholarly community. Balanced and factual accounts are given by Richard Poynder (http://poynder.blogspot.com/2012/01/mit-press-distances-itself-from.html and related posts in his blog).

Already academic publishers are distancing themselves from this Act. MIT Press (link above) has stated:

“The AAP’s press release on the Research Works Act does not reflect the position of the MIT Press; nor, I imagine, the position of many other scholarly presses whose mission is centrally focused on broad dissemination.

I can see every reason why CUP should issue a similar, or even stronger, message repudiating the AAP’s position. I hope that you can assure me CUP was not involved in creating the AAP’s position and ask you to consider the downsides of belonging to an organisation such as AAP.

[This is not the first time that the publishing industry has created anti-scholarship initiatives – I wrote to you about the iniquity of the “PRISM” alliance in 2007. I doubt it will be the last.]

Yours [Peter Murray-Rust]

[PS. I do not have personal email addresses and assume that “press” will reroute this mail. In any case I have a heavily followed blog and will post this letter there – maybe someone at CUP will forward it if required].

Michael Eisen works in gene regulation and is a co-founder of the world-changing Open publisher PloS. Like many of us he strongly opposes the proposed US bills HR.3699 and RWA which will forbid public funders to require that published research is Open. Here’s his article in the NY Times

http://www.nytimes.com/2012/01/11/opinion/research-bought-then-paid-for.html Take a minute to read it.

And here is his blog:

http://www.michaeleisen.org/blog/?p=807

the US National Institutes of Health instituted a Public Access Policy:

The NIH Public Access Policy ensures that the public has access to the published results of NIH funded research. It requires scientists to submit final peer-reviewed journal manuscripts that arise from NIH funds to the digital archive PubMed Central upon acceptance for publication.  To help advance science and improve human health, the Policy requires that these papers are accessible to the public on PubMed Central no later than 12 months after publication.

…

The policy has provided access for physicians and their patients, teachers and their students, policymakers and the public to hundreds of thousands of taxpayer-funded studies that would otherwise have been locked behind expensive publisher paywalls, accessible only to a small fraction of researchers at elite and wealthy universities.

The policy has been popular – especially among disease and patient advocacy groups fighting to empower the people they represent to make wise healthcare decision, and teachers educating the next generation of researchers and caregivers.

But the policy has been quite unpopular with a powerful publishing cartels that are hellbent on denying US taxpayers access to and benefits from research they paid to produce. This industry already makes generous profits charging universities and hospitals for access to the biomedical research journals they publish. But unsatisfied with feeding at the public trough only once (the vast majority of the estimated $10 billion dollar revenue of biomedical publishers already comes from public funds), they are seeking to squeeze cancer patients and high school students for an additional $25 every time they want to read about the latest work of America’s scientists.

…

The publishers have written their case in deliberately misleading language – their “private sector” means anyone who isn’t a government employee

The term `private-sector research work’ means an article intended to be published in a scholarly or scientific publication, or any version of such an article, that is not a work of the United States Government (as defined in section 101 of title 17, United States Code), describing or interpreting research funded in whole or in part by a Federal agency and to which a commercial or nonprofit publisher has made or has entered into an arrangement to make a value-added contribution, including peer review or editing. Such term does not include progress reports or raw data outputs routinely required to be created for and submitted directly to a funding agency in the course of research.

They are using intentionally misleading language to distinguish works funded by the government but carried out by a non-governmental agency as “private sector research”. Thus, under this bill, works funded by the NIH but carried at a University would be “private sector research”.

** WHERE IS THE BEST PLACE TO REGISTER MASS OPPOSITION TO THESE BILLS? The OA community doesn’t seem to be lobbying for support – at least not at high visibility. We have to become activists. Our freedoms – and we don’t have enough of them – are being taken away. When I tweeted a request for action no one answered.

I need a simple site where I can point people at and they can take 5 mins to protest.

Our workshop in Cambridge got underway yesterday – early arrivals met for dinner in the Maypole pub. I am really excited about the people who have agreed to come – there is a shared vision and a commitment to making things happen. There are 2 days of hackfest and then we present our results to the world in a symposium on Thursday (there are places if anyone wants to come for a day). We thank EPSRC Pathways to Impact for supporting the workshop which allows us to bring people from 3 continents. Although it’s about individuals we are delighted that there are 3 national laboratories represented as I think they are the best growing points for semantic science:

/pmr/2011/11/01/open-data-why-i-love-national-laboratories-sftc-pnnl-csiro-ebi/

and we are delighted to have participants from PNNL, STFC, and CSIRO .

In Melbourne at eResearch Nico Adams (CSIRO), Alex Wade (Microsoft Research) and I ran a 1-day workshop on the semantic web and physical science

/pmr/2011/11/15/anyone-can-run-their-own-semantic-repository-chempound-quixote/

and got a very good turnout and showed that people could install and run the software. We are continuing this today .

There is no set program to the workshop. We are running this as a hackfest and planning that self-forming groups will identify areas of common interest, create tools, examples, documentation, protocols, policy, whatever is most urgent, important and useful. Each group will present this on Thursday afternoon and we shall record this on video for transmission to the web. It’s based on:

• Our common agreement on the need for semantics in phys sci (especially chemistry and materials)
• Existing practice (e.g. IUCr’s CIF data and dictionaries)
• A common toolset (FoX, CML/JUMBO, Quixote/Chempound, Avogadro/Kitware)

I presented an approximate workflow at PNNL in 2011-11. (For NWChem you can substitute your own compchem program – e.g. GULP, DLPOLY)

The earlier blog posts cover much of the existing technology

/pmr/2011/11/16/multiple-metrics-for-%E2%80%9Cvisions-of-a-semantic-molecular-feature%E2%80%9D/

/pmr/2011/11/02/jumbo-components/

/pmr/2011/11/02/searchable-semantic-compchem-data-quixote-chempound-fox-and-jumbo/

An additional feature is that we have added NMR spectra to JUMBOConverters and expect that one of the groups will concentrate on semantifying and validating NMR data.

I’ll hope to be posting fairly frequently during these three days.

I’ve already blogged about the proposed Bill in congress (HR 3699) but it is one of the most serious threats to scientific liberty. YOU must challenge this. I suspect you can only do this formally if you are a US citizen as the mechanism to is write to your representative. [Any info on this would be useful.] Here’s how SPARC puts it:

A new bill, The Research Works Act (H.R.3699), designed to roll back the NIH Public Access Policy and block the development of similar policies at other federal agencies has been introduced into the U.S. House of Representatives. Co-sponsored by Darrell Issa (R-CA) and Carolyn Maloney (D-NY), it was introduced on December 16, 2011, and referred to the Committee on Oversight and Government Reform.

Essentially, the bill seeks to prohibit federal agencies from conditioning their grants to require that articles reporting on publicly funded research be made accessible to the public online.

The bill text is short and to the point. The main point reads:

“No Federal agency may adopt, implement, maintain, continue, or otherwise engage in any policy, program, or other activity that — (1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher of such work; or (2) requires that any actual or prospective author, or the employer of such an actual or prospective author, assent to network dissemination of a private-sector research work.”

Supporters of public access to the results of publicly funded research need to speak out against this proposed legislation. Contact Congress to express your opposition today, or as soon as possible.

For contact information and details on how to act, see the Alliance for Taxpayer Access Action Center at: http://www.taxpayeraccess.org/action.

It’s a bit difficult for non-US citizens to interpret but basically “the private sector” covers most organizations which are not US government. It certainly covers universities such as Stanford, Harvard, etc. (In Europe we tend to class Universities as the “public Sector”).

If you are US citizen, make your voice known. And tell others.

If you aren’t a US citizen, blog, tweet, mail.

The NIH information resources are one of the marvels of the modern world. I’ve had the privilege of working alongside NCBI and NCI for many years. Their innovation and commitment has been remarkable and the edifice of Pubmed provides a unique resource not only for the US but for the world. I’m on the advisory board of UK PubmedCentral (UKPMC) which draws (and hopefully contributes back) to the enormous resource provided by the NIH/NLM/NCBI.

Very simply, modern medicine draws heavily on access to information.

Put simply: “Open Information saves lives”.

And what the current bill is proposing is that access to information should be reduced so as to preserve the profits of publishers. Read it for yourself: http://www.publishers.org/press/56/. I’ll highlight some bits (some omitted for brevity)

Washington, DC; December 23, 2011— The Association of American Publishers (AAP) and its Professional and Scholarly Division (PSP) welcomed the introduction of the bipartisan Research Works Act, H.R. 3699 as significant legislation that will help reinforce America’s leadership in scholarly and scientific publishing in the public interest and in the critical peer-review system that safeguards the quality of such research.

The legislation is aimed at preventing regulatory interference with private-sector research publishers in the production, peer review and publication of scientific, medical, technical, humanities, legal and scholarly journal articles. This sector represents tens of thousands of articles which report on, analyze and interpret original research; more than 30,000 U.S. workers; and millions of dollars invested by publishers in staff, editorial, technological, capital and operational funding of independent peer review by specialized experts. North American-based science journal publishers alone account for 45% of all peer-reviewed papers published annually for researchers worldwide.

“America’s PSP publishers are making more research information available to more people, through more channels, than ever before in our history. At a time when job retention, U.S. exports, scholarly excellence, scientific integrity and digital copyright protection are all priorities, the Research Works Act ensures the sustainability of this industry.”

The Research Works Act will prohibit federal agencies from unauthorized free public dissemination of journal articles that report on research which, to some degree, has been federally-funded but is produced and published by private sector publishers receiving no such funding. It would also prevent non-government authors from being required to agree to such free distribution of these works. Additionally, it would preempt federal agencies’ planned funding, development and back-office administration of their own electronic repositories for such works, which would duplicate existing copyright-protected systems and unfairly compete with established university, society and commercial publishers.

Journal articles are widely available in major academic centers, public libraries, universities, interlibrary loan programs and online databases. Many academic, professional and business organizations provide staffs and members with access to such content.

More information about the impact of federal regulations on professional and scholarly publishing can be found at http://publishers.org/issues/5/9/

At least this is very clear. Vote either for profit or for access to knowledge. The argument that the quality of research depends on protectionism of an industry is unsupportable. Remember the cry of the publishers in PRISM “Open Access means Junk Science”. Tell that to the Nobel Laureates that run PLoS and the new eLife journal (Wellcome, HHMI, MaxPlanck).

Almost everyone is Scholarly Poor. They have no access to medical articles other than paying 40 USD per day for each one. They are denied access to life-saving knowledge for the greater good of preserving the publishing industry. (In case you didn’t understand the AAP blurb – the industry aren’t being subsidized – they are highly profitable – not surprising, as academics give them the knowledge and then pay them to get it back).

Ask Gilles Frydman (Kosher Frog and creator of American Cancer Online Resources). ACOR has 65000 members. They WANT access to the literature. The free resources are now being taken away from them. Can they just go down to their local university?? Or public library?

And the NIH itself cannot lobby. I’ve been through this before, where the ACS tried to restrict the scope of Pubchem (sic) as it threatened the ACS’s revenues. The NIH had to remain mute. It was up to US to protest, and we did, and we just saved Pubchem. This is even more serious.

We are in the middle of one of the great struggles of human knowledge. Every day we see example sof those trying to widen our horizons and those dragging it back.

For one motive only – profit.

It’s very easy to spread knowledge in the information age. And it’s very easy to build systems that prevent it. It involves money, lobbying and technological control.

Sometimes I think we are winning; other times I think we are losing. If we lose the tensions will become unbearable. Society will fracture.

You have to decide where you stand and make it clear.