petermr's blog

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I don’t read enough blogs these days, and so I’m really happy to have come across by chance an article written by Richard Poynder:

http://poynder.blogspot.com/2010/08/university-of-ottawa-press-launches-oa.html

In this he analyses the important differences between the types of language used to denote various approaches to Open Access. Terminology is important, and the Open Access movement has been bedevilled by a variety of different approaches to describing what is on offer.

For instance, anyone who read UOP’s announcement [University of Ottawa Press] that it is providing its books on a “free and unrestricted access” basis who then downloaded one of the books would surely scratch their head when they saw the all rights reserved notice attached to it.

While they could be confident that they were free to read the books, they might wonder whether they were permitted to forward the book to a colleague. They might also wonder whether they were free to print it, whether they could cut and paste text from it, or whether they were permitted to create derivative versions.

Free and unrestricted access would seem to imply they could do all those things. All rights reserved suggests quite the opposite — indeed, a copyright lawyer might argue that even downloading a book infringes an all-rights licence.

It does not help that there appears to be no terms and conditions notice on the UOP web site clarifying what readers can and cannot do with the books — as there is, for instance, on PSU’s Romance Studies site.

In fact, UOP is only granting permission for people to read, download and print the books.

But it need not be that confusing. OA comes in different flavours, and what UOP is offering is what OA advocates call Gratis OA (that is, it has removed the price barriers); it is not offering Libre OA (which would require removing permission barriers too — i.e. relaxing the copyright restrictions).

I have missed recent discussions in Open Access but if this means that they now have the terms gratis and libre then that is a major advance. I have long asked for clarity in terminology and this has now arrived, since it models the usage in the Open Source.

Richard Poynder will be the first of our guests in the Panton Discussions, where we ask influential figures in the open movement to take part in an in depth discussion. Richard interviewed me some time ago and for this I am very grateful; this returns the favour.

The distinction between gratis and libre can be found in http://en.wikipedia.org/wiki/Gratis_versus_Libre

With Richard Stallman’s famous phrase:

“Think free as in free speech, not free beer.”^[1]

When Richard Poynder visits the Panton Arms we should be able to manage at least some gratis, if not libre, beer.

Typed/Scraped/dictated into Arcturus

On one of the great things about working in an open environment is that you can keep a complete record of everything you’ve done immediately. In the Open Knowledge Foundation we use a tool called Ether Pad (there is a similar one called Pirate Pad). Anyone just sets up a site and types on it; anyone else can edit anywhere in the document at the same time. You can see other people typing at the same time as you application you get clashes but it’s all quite good humoured. Different authors are marked with different colours.

To date we had our monthly meeting on open-science at the OKF and he agenda was created on the ether pad (http://okfnpad.org/science-20100804 ). We had a long agenda but were able to get through it in just about an hour despite real life fire alarms. One of the items discussed was the Panton Papers and I’m transcribing that item for the blog. As you can see the numbers of ideas have grown and will continue to grow. We are starting to get custodians, or editors, for each item.

As with all OKF activities anybody can join in. The best thing to do is to join one or more of the OKF mailing lists.

Panton Papers which are short outlines of critical issues in science   

  (no particular order yet) – ok, let’s not number them, then, but use keyword tags (freer sorting)

  These should help guide policymakers, scientists and everyone. They should try to pre-empt messy incomplete solutions from elsewhere. Examples that need clear guidance 

(and are increasingly topical).

   – PPaper WhatIs: What is scientific data? (as opposed to argument, creative diagrams, discourse, etc.) ACTION: Mike (Petermr may contribute from JISC-XYZ project which involves BMC and we would do analyses of BMC papers), Claudia

   – PPaper OwnAnyone: Who owns data? Anyone? [hm, this question implies that anyone does, maybe find a more neutral question without any such implication? maybe: “Are data owned by anyone?”] ACTION: Greg, Claudia, …

   – PPaper WhenShare: When can *I* have *”your”* data? Does this relate to (scholarly?) publication [what *is* “publication” – is this concept in any way different for “data” and “non-data”? (see PP WhatIs)] ACTION: 

   – PPaper Mining: Data-and text-mining from scholarly publications

       ACTION: PMR to catalyze this. 

   – PPaper Repro: Reproducibility in scientific data analysis and calculations

       ACTION: Daniel

       Victoria Stodden wrote a relevant article on this? http://www.stanford.edu/~vcs/papers/ERROLSI03092009.pdf ACTION: ask Victoria Stodden in: Daniel

   – PPaper ReqFunders: Data sharing requirements by major research funders

       ACTION: Daniel

   – PPaper WhyShare: Why should *I* share *my* data?

       may fit well directly after PP WhatIs or OwnAnyone

       ACTION: Iain, Mike, Daniel

   – PPaper AchieveRepro: Why data sharing is not enough to achieve reproducibility (possibly to be combined with PPaper Repro)

       ACTION: 

   – PPaper BestWayto: What is the best way to share my data? Standards/ Platforms / Logistics / usefulness

       Related to repository question? possibly, but not necessarily, maybe SR/IR are the containers we can think of today, but next generation ideas might be helpful, too? so maybe keep the two papers separate for exactly this reason? ACTION: Mike, Claudia

       http://oad.simmons.edu/oadwiki/Data_repositories

   – PPaper DataSR/IR: (Subject)Discipline or Institutional repositories? (http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=2519)

       ACTION: Claudia, …

   – PPaper ChangeStart: Do my data collecting methods change when producing Open Data right from the start? ACTION: 

   – PPaper ChangeQA: “open data will probably be used to answer questions that are different to those for which the data was generated” (Andrew Treolar) http://ff.im/od9Wc

   ACTION: 

Example of a BMC article collection

http://www.biomedcentral.com/series/FANTOM4

BMC Research Notes would likely be the best venue to publish the PPapers (http://www.biomedcentral.com/bmcresnotes/) Bill Hooker, Donat Agosti and Andrew Vickers, for example, are on the Editorial Board and could be potential contributors. ACTION: Iain to discuss with them

   # <please insert more PP ideas here>

   PMR will blog this item and offer the world to read this Pad and contribute to it.

   See http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=2510 for current state of published PP draft-drafts. Some community feedback on where repos should be:

   http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=2505

   http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=2519

.NB: BMC (IanH) are tentatively offering to publish PPapers. Probably need OKF author(s)  for each topic. Also need to agree rough set of PPapers Huge field but we should lay it out before the bitwise messiness starts. More ideas for PPapers urgent.

On the condition that they will be peer reviewed BMC is keen to publish them in Research Notes.

You’ll see that we hope to get these formally published and this therefore represents a new way of authoring peer-reviewed publications. (Of course it doesn’t apply to those publishers who refuse manuscripts where any word has appeared in public beforehand).

Dictated into Arcturus

I have just been at #scifoo – a remarkable annual gathering created and run by Google (Larry Page), Nature (Timo Hannay) , and O’Reilly (Tim O’Reilly). I have been privileged to have been invited three times and without question this was the best #scifoo for me.

#scifoo is an unconference. That means that there is no set agenda and anything might happen. There is an approximate format that has been worked out over the years. The camp lasts for about two days and there are about 7 1-hour sessions per day. These can be anything from presentations to demonstrations to group activities to unstructured discussion. We start by introducing ourselves giving our affiliation and then three words to describe whatever is at the top of our mind. Mine was “reclaim our scholarship” and I also showed the flowerpoint. (as you can see #scifoo is extremely informal and there are many people who bring along all sorts of physical objects from fossils to puzzles to knitting to Lego, so the flowerpoint is perfectly in tune).

Then there is a mad rush for people to propose sessions. Although there has been considerable pre-discussion from some people, there is no priority and it depends a little bit on how hard you shove. Three of us (Carl Bergstrom, Johan Bollen and me) proposed a session on ” reclaim our scholarship” (RoS) and this took place on the Saturday (about 15 people came). But numbers are not important and if two or three people come that’s quite OK by #scifoo. Sometimes the sessions suggested have so much in common that they are collapsed and redesigned.

There’s lots of physical objects – a sailing machine that can go faster than the wind, Lego implementations of Babbage’s engines and the Antikythera mechanism, and a lot more. One session I went to was on three-d printers. There are lots of chairs , food and drink (Google is famed for its food). Any one can go up to any one and can talk about anything. One session I went to has involved Greg Bear, SF writer, talking about recent papers in Nature describing quantum coherence in photosynthesis. He was speculating that this might extend to neuronal activity and that this could affect our perception of time and causality. There was a mix of people most of whom did not understand the science but two or three who did. It was a very enjoyable and good humoured session without resolving anything very definitely.

The RoS session went pretty well including some excellent presentations from Carl and Johann. One of the themes at #scifoo is trying to look beyond the immediate extension of our activities, and in this session (and another on the future of scholarly publishing) some of us are trying to jump to a future some years ahead where we can rely on the web, computers, AI and open collaboration giving us very different ways of working. It certainly confirmed me in my own determination to change the way we produce disseminate and evaluate scholarly material.

A major feature of #scifoo is the encouragement for people to expand their visions and to go to sessions that they know nothing about. So a constant theme was the changing nature of society both in terms of the collapse of current institutions and the potential of the new technologies. Andrew Marr from the BBC talked about the death of journalism, how this would affect political and social discourse and decision-making. It was great to have a chat with him after words about the way scientists think and behave at the sorts of things that we believe we can contribute to decision-making and information gathering. …

Hopefully more later

Typed/Scraped into Arcturus

Useful constructive feedback on my strawman PP4 for where scientific data should be stored:

Kenji Takeda says:

August 2, 2010 at 9:39 pm  (Edit)

Dear Peter,
Great discussion you have opened up! I believe that you are right, domain specilaists need to be involved. My personal hope is that a new type of data librarian may emerge, and that these people may come from a mixture of discipline specialists and librarians. This is what happened/happens in scientific computing, some scientists move into the computing arena, and some computing people move into the scientific arena – as demonstrated by the eScience programme.

I believe this will take around a decade, as open repositories have done. I also believe that a federated approach is the only sane architecture. You may be interested in reading Chris Gutteridge’s recent paper on the subject @ http://eprints.ecs.soton.ac.uk/20885/

The University of Southampton is committed to open data, and as such we hope to be in the leading wave of open institutional data repositories. eCrystals and our new Materials Data Centre (www.materialsdatacentre.com) projects, are examples of disciplines being the focus.

The whole point of our Institutional Data Management Blueprint project is to figure out how a whole institution can manage and openly publish its data. The genesis of this was that a bunch of us got together and realised that the institution is responsible for its data, and it therefore has the biggest incentive to manage, and publish it. Libraries have a role, as do publishers. I think forward-thinking libraries could jump right in here, as you suggest, but as always funding and priorities need to be matched.

We have a long way to go, but we’re starting down the road. We’re learning all the time!!!

Cheers,
Kenji

http://www.southamptondata.org

OK, I’ll set out the possibilities as I see them. I’d like to get agreement on what is being proposed, before discussing their merits

Federated Repositories

Here we conceive of a network of repositories worldwide (it has to be worldwide as disciplines are worldwide). The simplest model to conceive is one repository per research institution, funded out of central university funds (themselves top-sliced from grants). [There are somewhere about 1,000 – 10,000 institutions (I’d appreciate a better figure). This is what we have got.] They are used for certain disciplines for storing digital artefacts (mainly in arts and humanities) but not in science. There is variable compliance in repositing author manuscripts – either raw or final. Southampton and Queensland UT are very high, Cambridge probably near zero.

When an author has a data set they reposit it locally. The repository is federated to all 9999 other repos and immediately alerts them (RSS?) to a new data set. So now all repos can get the dataset.

Pros:

• Insts already fund repos so we “only” have to scale it
  
• Insts have a permanency
  
• Insts can interact directly with authors and help or beat them to submit.
  
• Authors have a one-stop for any type of data
  

   

Cons

• There is very little, if any, current federation of repos
  
• It will take years/decades for 9999 repos to get to a state where this federation is seamless
  
• All repos have to play. If some don’t, then their authors have nowhere to repo data
  
• The individual repos have no domain knowledge of the data and can only provide generic support
  
• Users have to have a portal into the system
  
• There is no simple mechanism for adding domain support for search, etc.
  
• Journals have to deal with 9999 different places to reposit
  
• Compliance will have to be monitored by Insts, will be highly variable and is unlikely to be acceptable to funders for some time.
  
• It’s very difficult to run distributed communal projects
  

Domain repositories

These already exist, some for > 20 years. My guess is that there are in the region of 30-300. Again a figure would be useful. There is a single site for each discipline (there may be mirroring or some slight national/continental federation but it’s small. For example the world uses 3 genome sites (US, EU, JP). PubMedCentral uses 2 so far (PMC and UKPMC). The author finds the single repo for their discipline and submist the data. Increasingly the data are reviewed and validated by specialist personel and software. The world has a single point of deposition and a single search point.

Pros:

• One clear deposition point
  
• One clear search and retrieval point
  
• Specialist help for both
  
• Major interest in the community (e.g. special sessions at meetings)
  
• The system works in many cases and is very highly valued by the community
  
• Journals understand it and can manage the interaction
  
• Funders can easily monitor compliance
  
• It’s easy-ish to run distributed communal projects. For example Open StreetMap is sponsored by ULCC (Univ London Comp. Centre)
  

Cons

• A different repo needed for each discipline or subdiscipline
  
• Funding is highly discipline dependent and always difficult (unlike the current topslicing support for IRs).
  
• There is no guaranteed permanence.
  

Ultimately in the giant scientific semantic web the systems will converge (the domain experts could receive material from Insts as well as directly). But that is 10 years or more away.

To build a federated system of IRs for this will take at least 5 years and probably more (see the current rate of progress in IRs – this is not judgmental, simply good project metric practice). And even then it will not be complete and there will be many many gaps. But for this we need to tell people – for this period – hang on, federated IRs are coming and we can’t do discipline repos until they are here.

The alternative – which is happening whatever you feel about it – is that domains are scraping their pennies together, blagging space where they can find it. Journals are supporting it. Funders such as Wellcome are supporting it (UKPMC).

Pragmatically, therefore, I see that if we are to capture the drive for data we have to take it to the disciplines and not to the Insts. Of course there will be overlap and collaboration, but it will be by domain. Show me any scientist who is arguing otherwise – I haven’t found one. And scientists know it will cost money.

Typed into Arcturus

If you’re going to San Francisco,

Be sure to wear some flowers in your hair.

I have been at #scifoo (more later, hopefully much more) and have met Fabiana Kubke, an ardent contributor to OKF. She has taken to the Flowerpoint and has offered to create a web resource. So here’s the basis:

Flowerpoint is a natural language and there are relatively few rules other than it should symbolize Openness. It’s a vehicle where concepts can be carried on the petals. You can have any number of petals but I have eight, partly because that’s what I needed and what there was space for and partly because there is a lovely alpine flower called Dryas Octapetala (also grows in UK on limestone terraces). I have a spare petal if I need it.

If you want to make one, here’s my parts list: any number of petals, in my case cardboard but many plastics or thin plywood would do. Drill a hole and make them a nice set of colours (I stuck on coloured paper, but you could plaint them or use coloured card board). The card should be reasonably rigid. There’s then two hubs, one fixed (wood) and one removable. Both should have the OKF logo. I drew it in pen and then stuck it on but if you are brave you can write/paint directly.

The petals can carry OKF activities, concepts or other suitable material. I have chosen ones I am actively engaged with. If you want to “collect badges” and only create petals when you have made a significant contribution, fine, but this is not a “I’ve got more badges than you” activity.

You can write the concepts if you are brave but I often run out of positive or negative space so I write on Post-it notes and stick them on (use some transparent library tape to hold them down.) This means you can pull the concept off and add a new one without damaging the petal.

My flowerpoint is double sided and carries my mantra “Reclaim our scholarship”. Make sure that when people read it it makes sense. My talk got it garbled.

The petals are assembled in whatever order you like but it should be in order of fanning out. They are held in by an OKF boss and then a wingnut. By tightening or loosening this you can rotate or fix the petals. This is a critical design feature. You can, for example, fold them all down and release them one by one or group them together.

I reserved one petal for my notes (since I can’t see the other side of the flower). See bottom petal. (the green stuff in the picture is real grass – it’s what many flowers grow in, but you don’t have to take it with you).

Many thanks for the design and construction of the spindle and hubs by Ralph Bradshaw. This design is CC-BY. The petals are also CC-BY PM-R.

The flower has a effective power measured as [ED50]10, meaning that at a range of about 10 metres (better lettering makes it more effective) it will open 50% of closed minds. It has a lower power against corporate groupthink but we are worker on large versions with parabolic petals to focus the power.

Fabiana will be creating a web version. This should allow you to author your own flowers (she has ideas on tools) and to create PNGs or whatever to embed in your pages. Watch the OKF lists. I guess there will be a Flowerpoint page and that the flowers will hyperlink back there.

Oh, Deep in my heart,

I do believe,

We shall overcome some day.

Typed into Arcturus

Rapid update for #solo2010.

What’s emerged from talking with Jean-Claude Bradley, Mat Todd, Cameron Neylon and others doing Open Science / Chemistry is that we are going to do an open experiment starting now and in full view until #solo2010 at the start of Sept.

We shal use the Open Access (chemistry) literature to answer the question:

“Do industrial chemists use different (or fewer) chemical reactions that academia?”

This will be a data-driven experiment relying on the Open Access (CC-BY) literature and extracting reactions both manually and automatically (using the Cambridge OSCAR/ChemicalTagger software). The results will be put into an Open RDF repository (CML +RDF) where all data will be Open Data according to Panton (CC0 or PDDL).

Current sources will be:

• European patents (i.e. industrial) – PD
  
• Acta Crystallographica E (ca 10,000) CC-BY
  
• J-C’s open notebook (Drexel)
  
• Mat Todd’s theses. (Sydney)
  

Anyone can take part. All resources must be Open. We’ll probably coordinate through OKF or Unilever Centre.

More later. We’ll expect to do this on a daily basis.

Dictated into Arcturus

This post is a first outline – not even a draft – of a proposed Panton Paper on “Semantic Open Scientific Data”

The vision of the Semantic Web 2.0 (If I’ve not lost count) includes Linked Open Data. We’be dealt a lot with Open and somewhat with Data but not about links. The rules of Linked Open Data (http://en.wikipedia.org/wiki/Linked_Data ):

• Use URIs to identify things.
• Use HTTP URIs so that these things can be referred to and looked up (“dereferenced“) by people and user agents.
• Provide useful information about the thing when its URI is dereferenced, using standard formats such as RDF/XML.
• Include links to other, related URIs in the exposed data to improve discovery of other related information on the Web.

The technologies for doing Semantic Web are therefore HTTP/URI, HTML, various XMLs, and RDF. The linking technology is can be through HTML link, href, or Xlink (or others).

LOD does not say much about documents, and most scientific data is published in document format. Most documents such as theses and scientific papers contain headers, abstracts, sections, paragraphs, embedded tables, images, attached data, etc. Common formats are Word, LaTeX and HTML. These provide more or less semantics according to the authoring tool, the diligence of the author, etc. So, for example, several publishers has very well marked up HTML.

PDF, PNG, Powerpoint as commonly used have effectively no semantics. (There are areas in some of these allowing the inclusion of semantics but these are not used and are so variable between releases that they are effectively useless.) in the average PDF it is impossible for a machine to tell where a sentence or paragraph start and another begins. Superscripts, styling are also incredibly difficult to interpret.

Most authors author in a (semi)semantic form. Most publishers will accept this, then print it out and scan it or de-semantify it as PDF. Many have the manuscript retyped.

Many graduate theses are required as PDF even though the authoring is in Word or LaTeX.

So here are my recommendations

• Authors should be provided with incentives and tools to create documents with as much semantics as possible.
  
• Publishers must become aware of the value of semantics and retain it during their processing
  
• Theses should always preserve the original born-digital document and data. It should always be available alongside any PDF.
  
• Repository owners should present their content as Linked Open Data (RDF) wherever possible. This may require managing identifier systems and ontologies
  
• Readers should have access to semantic readers supported by repositories and publishers
  
• There should be converters from common semi-semantic forms to fully semantic where possible (e.g. as in Chemistry), supported by repositories and publishers
  
• Tools should be available for human and machine semantic annotation. This may not always be completely accurate, but it will be useful.
  

   

Typed into Arcturus

Current state of play for Panton Papers. My contribution to the Panel on Open Access and Open Data this afternoon at #oss2010.

I have been releasing a new Panton Paper pre-draft every 1-2 days. These are nuclei for communal editing to work towards “rough consensus and running implementability”. They are not, naysayers, cast in stone. You are welcome to hack them through the OKF Open wikis, Etherpads and other tools.

Panton Papers on Open Data

Already published:

• Open Data: The concept of Panton Papers
  
• PP1_0.1: What is Scientific Data? (we need to know what we are Opening!)
  
• PP2_0.1: Why Scientific Data should be Open (we need clear arguments)
  
• PP3_0.1: Who owns Scientific Data? Anyone? (a very complex topic)
  
• PP4_0.1: Repositories for Scientific Data (already generating different views)
  

Not yet published (the numbers may vary)

• PP5_0.1 When should data be released? (absolutely fundamental and a lot of hard work)
  
• PP6_0.1 Access to text- and –data-mining. (Firewalled publications are often contractually barred from this. The data must be minable)
  
• PP7_0.1 Reproducibility. The data must cater for being used in reproducible science (cf. Victoria Stodden)
  
• PP8_0.1 Semantic data. Linked Open Data – the dream of many of us – depends on semantic data
  
  

Readers an #oss2010ers, please add other topics and comments.

Typed into Arcturus

I’ve been invited (and accepted) to talk at Science Online 2010 (#solo2010). In previous years this was called “Science Blogging” and I’m currently wearing the T-shirt from one such. And they were held in the Royal Institution where you could lecture from the same place as Michael Faraday and Lawrence Bragg.

This year it’s in the British Library.

Recently Duncan Hull has highlighted that I am the only scientist. (http://duncan.hull.name/2010/07/26/solo10/ ). This has caught traction in the twittersphere. Help!

What shall I do? I had probably planned to talk about how to make science data Open. That’s my current rage. Should I change? Should I try to carry out some research before the meeting? Should I try to crowdsource some research before the meeting. Should I (like Lawrence Bragg) demonstrate a soap-bubble raft. (I don’t think the BL would like me bringing Bunsen burners into their hallowed racks.

Seriously – is there any exciting and new we could communally do before in the next month? My guess it would have to be in the area of data-driven chemistry. I was talking with Jean-Claude Bradley at breakfast about liberating chemical reactions from the literature. There will be new science in that. Not world-shattering, but worthy.

Thoughts?

Typed and edited into Arcturus

Sitting in the Free Speech Movement Cafe in Berkeley (see picture) it’s impossible not to get the sense of cataclysmic change. It’s doubly nostalgic in that it was followed a few years later by a similar rejection of the University status quo in the UK. I was warden of a hall of Residence in the University of Stirling when (in 1972) it publicly exploded its angst across the pages of the world. I was young (30) and although a lecturer was critical of the University administration and admired the drive for the students to Free Speech. I can’t remember the exact title but there was essentially a free speech forum where the students invited speakers with a wide range of views, often outside the pale and guaranteed their message would be heard politely, though not unchallenged.

This is echoed by a comment ( I’ll attribute if given the OK) to one of my posts on “Reclaim our Scholarship”:

Cue RATM: we gotta take the power back! 🙂

[RATM = http://en.wikipedia.org/wiki/Rage_Against_the_Machine ]

Listening to the presentations here I sense the same rage as in the sixties when that was against the Military-Industrial complex http://en.wikipedia.org/wiki/Military%E2%80%93industrial_complex

This term was and is widened to Military-Industrial-Scientific Complex (e.g. http://www.counterpunch.org/grossman01152009.html ). This is a sad condemnation of much scientific endeavour – whether in industry or academia – and is caused both by rapaciousness of individuals and institutions . (Just listening now to Tim Hubbard on the failure of Bayh-Dole and the tech-transfer departments – essentially the model has failed to generate significant wealth and has inhibited the use of science for the general good.

So what are we raging against now?

The Publishing-Industrial-(Scientific) Complex.

Of course not all publishers are implicated and not all industries and not all scientists. But there is a core of corporate resistance, gatekeepers, micro-control, which holds our endeavour back.

If this doesn’t change rapidly the PIS-Complex will fracture. Whether it will be deliberate action or whether it will be the amorphous forces of the zeitgeist and technology I can’t foretell.

But I am conscious that my current actions and attitude are a constant drip of water onto the congealed mass. There are many other erosive forces. Change is in the wind.