[Open-access] [GOAL] Re: Re: Fight Publishing Lobby's Latest "FIRST" Act to Delay OA - Nth Successor to PRISM, RWA etc.

Peter Murray-Rust pm286 at cam.ac.uk
Sun Dec 1 18:38:24 UTC 2013

I agree with what Bjoern and Mark have said. We have the imperative to
develop a new set of tools and most is in place.

For my part I am launching "the Content Mine" over these current days. The
goal is simple - to extract 100,000,000 million facts from the scholarly
scientific literature. See

https://vimeo.com/78353557 (5 minutes video).

and innumerable current blogs on

I would very much welcome help. I have been offered some from outside
academia - it would be nice to have some academics who also believed in

This is not vapourware. I demo'ed this at OKFN/Open Science in Oxford last
Wednesday. I am starting with "Open Access" papers, such as PLoSONE and
when tested there will move to other outlets. These papers can be queried
for a wide range of scientific facts such as species (where we start),
chemicals, sequences, geolocations, identifiers, phylogenetic trees, etc.
We have means of publishing this and means of capturing it. Everything -
code, protocols, extractions, stores, etc. are fully Open (OKD compliant).

This has the potential to act as a semantic current-awareness system and
also as a scientific search engine. At present there is no Open search
engine for science, except Wikipedia. As Bjoern and Mark have made clear we
must create one - and rapidly. Else we shall remain completely reliant on
the charity of mega-corporations - do we trust them?

I have applied for a personal grant to work on this. I will be delighted to
work with any others outside or inside academia - all my software is Open
for anyone to re-use without my permission. Only by making science
immediately Open (OKD-compliant) at the time it is published do we have
Open Access in the true (BOAI) sense of the word.

On Sun, Dec 1, 2013 at 2:27 PM, Bjoern Brembs <b.brembs at gmail.com> wrote:

> On Saturday, November 30, 2013, 12:30:54 AM, you wrote:
> > The technology to do all of this already exists. Most of
> > the STEM metadata you describe is actually directly
> > available in Medline, and the core parts can be used as
> > per the open biblio principles. Crawling the websites is
> > already possible using pubcrawler and other tools, and
> > finding out what their stated licence status is can be
> > done with howopenisit (although more often than not the
> > answer is "not properly defined").
> Precisely!!
> > However the hard part is not building or running these
> > things or collecting all the data, but sustaining it in
> > and imbuing it with credibility.
> Totally agreed!
> > For example I can run a server with all this on it at not
> > too much personal expense, but who would treat it as a
> > serious source? Scaling up to handle a large amount of
> > users and providing a good service does cost money, which
> > I (we) could probably find a way to fund - but even then,
> > we still have to solve that credibility problem. It has to
> > be known by those in or entering the field that "this is
> > where you go to find this stuff" - as opposed to the
> > current "go to the library and follow all the rules" approach.
> What we should be able to do right now (and for some of that we're
> applying for grants as I type this), is to start building the
> infrastructure for software and data. This will provide the opportunity to
> develop standards for how to make the databases for text (repositories),
> data and software interoperable.
> Simultaneously, these standards need t be communicated and adopted by a
> critical mass of institutions.
> But perhaps most importantly, the institutions participating in crawling
> and harvesting all our literature need to develop a way of searching,
> filtering and sorting not only the existing literature, but especially the
> incoming, new literature in a way that is superior to what we have now.
> Given that there isn't really a single place where you can exhaustively
> search the literature, the first part should be easy (existing literature).
> For the second part, (incoming, newly published literature), we're
> currently in the process of developing an RSS reader which is tailor-made
> for scientists.
> Thus, if there is a superior way to handle the literature, that
> outcompetes everything we have right now (again, not too difficult), people
> will go there, simple because they save time and effort that way.
> The next step will be an authoring tool that allows collaborative writing
> with scientific referencing and peer-review. there are currently several
> initiatives developing that environment. Once this is running, submission
> will be as simple as hitting 'submit'. Everybody who has ever submitted to
> a journal knows how people will flock to a service that allows submission
> with a single click.
> Thus, I agree, this will be the important part, but offering a superior
> way should do most of the work - just look at how quickly GScholar was
> accepted.
> Cheers,
> Bjoern
> --
> Björn Brembs
> ---------------------------------------------
> http://brembs.net
> Neurogenetics
> Universität Regensburg
> Germany
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Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
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