Monthly Archives: April 2013

#ignorantchemist Typographical amusement #ami2

We are doing well at reconstructing semantic material from PDFs (#AMI2) but the challenges we are thrown are considerable. Here's today's amusement: #AMI2 can reconstruct most of this perfectly, but she doesn't know what to do with a hyphenated-subscript. Nor … Continue reading

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#openaccess: American Chemical Society charge additional 1000 USD for Creative Commons Licences

From the start of this month all RCUK-funded researchers will have to publish "Open Access". Exactly what this means has been the subject of a messy set of polemics. But on the assumption that authors wish to publish under a … Continue reading

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Update: The struggle continues… #ami2 would like alpha testers

A quick update. I've been spending most of my time on #ami2 which is now at raw alpha (see below). Other items of note include: Mendeley is now owned by Elsevier. I shall blog this. If you care about Open … Continue reading

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#animalgarden Bottom-up Ontologies in Physical Science

On Thursday (2013-04-11) I was invited by Fiona McNeill to give a 5-minute talk on ontologies at Edinburgh (http://dream.inf.ed.ac.uk/events/ukont-13/2013_workshop_program.html ). The workshop aims included: Amongst other areas of interest, there will be a particular focus on creating and using open … Continue reading

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#ami2 #ukont2013 15-min demonstration of AMI2 (and maybe OPSIN and ChemicalTagger)

I'm demoing after lunch to the 2nd UK Ontology Network Workshop in Edinburgh and it's billed as AMI2 (our content-mining software for #scholpub and related documents). Why content-mining at an ontology meeting? Because many ontologies are created "bottom-up" from the … Continue reading

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#openaccess Who owns the Law? Who owns scholarship? You must listen to Ed Walters

IF YOU HAVE ANY INTEREST IN OPENACCESS spend 15 Minutes on http://vimeo.com/63123518 "Ed Walters - Who Owns The Law?" It's worth the time.   In a chillingly precise, researched piece Ed shows how US states have handed over the ownership … Continue reading

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Teaching #ami2 to recognize biological names (binomial)

  Erithacus rubecula (Wikimedia Commons) "the Robin"   #ami2 can now read the text of scientific articles as HTML (she has a little trouble with bold letters and strange fonts but we'll teach her how to manage). Here is how … Continue reading

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#ami2 Can only academics understand scientific papers? Or can the #scholarlypoor be scientists as well? We need us

  A FORB (Wikipedia) One of the arguments scholarly publishing is that it is for "academics to publish to academics". Even Open Access advocates such as Stevan Harnad have stated this publicly. I find this arrogant and unacceptable – I … Continue reading

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#ami2 and @tabula : collaboration vs competition; #scholrev

Oreina gloriosa from Wikipedia (you'll see why) I've read 25+ academic papers about extraction of information from PDFs and only 1 of those makes any mention of availability of code. These papers are published to announce a new (usually incremental … Continue reading

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The Lancet’s new #openaccess policy. Do they/Elsevier take me for an (April) Fool?

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