Yearly Archives: 2008

Why PubMed is so important in the NIH mandate – cont.

Posted on January 5, 2008 by pm286

In Why PubMed is so important in the NIH mandate  – which got sent off prematurely – I started to show why the NIH/PubMed relationship was so important. To pick up… The difference between PubMed and almost all other repositories … Continue reading →

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Do the Royal Society of Chemistry and Wiley care about my moral rights?

Posted on January 5, 2008 by pm286

In a previous post I asked Did I write this paper??? because I had come across something like this: (click to enlarge). Take a long hard look and tell me what is the journal, and who is the publisher. Note … Continue reading →

Posted in publishing | Tagged , , | 3 Comments

Learning RDF and RDFS – help!

Posted on January 5, 2008 by pm286

I’m getting myself up to speed on RDF (and RDFS) and building molecular repositories as an example. I’m using  the Jena Semantic Web Framework (Open Source , Java, HP-inspired) and so far like it. But I have only done a … Continue reading →

Posted in programming for scientists | Tagged , , | 3 Comments

Open Data: Datument submitted to Elsevier's Serials Review

Posted on January 5, 2008 by pm286

I have just finished writing an invited article for Serials Review – Elsevier (I’m making an exception and submitting to a closed access publisher because (a) this is a special issue – from the invitation from Connie Foster *Serials Review* … Continue reading →

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Why getting information from publishers is soul-destroying

Posted on January 5, 2008 by pm286

I’m reprinting parts of a post from Bill Hooker. The point here is not just the message, but also the meta-medium. To get the message Bill has had to do some messy, boring, unsatisfying, incomplete research. Here’s how he did … Continue reading →

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Why PubMed is so important in the NIH mandate

Posted on January 5, 2008 by pm286

Some us of know the following phrase by heart: all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine’s PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for … Continue reading →

Posted in Uncategorized | 5 Comments

Does the semantic web work for chemical reactions

Posted on January 4, 2008 by pm286

A very exciting post from Jean-Claude Bradley asking whether we can formalize the semantics of chemical reactions and synthetic procedures. Excerpts, and then comment… Modularizing Results and Analysis in Chemistry Chemical research has traditionally been organized in either experiment-centric or … Continue reading →

Posted in chemistry, data, open notebook science | Tagged , , | 8 Comments

Did I write this paper???

Posted on January 4, 2008 by pm286

I just looked for one of my papers using Google (not Google Scholar) and found : (Click to enlarge) Hmm – don’t remember publishing something in “Cheminform” in  2005? I normally check who my co-authors are before they send a … Continue reading →

Posted in publishing | 4 Comments

Open Data: I want my data back!

Posted on January 4, 2008 by pm286

var imagebase=\’file://C:/Program Files/FeedReader30/\’;   Although I am mainly concerned with campaigning for data associated with schoilarly publishing to be Open, the term Open Data has also been used in conjunction with personal data “given” or “lent” to third parties (see … Continue reading →

Posted in open issues | Tagged , | 4 Comments

How to create interactive maps (and graphs?)

Posted on January 2, 2008 by pm286

Peter Sefton at USQ has developed the ICE system – a carefully thought out and engineered system for authoring compound documents in a scholarly environment based largely on XML. He has no illusions about the difficulty of this and the … Continue reading →

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