Category Archives: XML

funding models for software, OSCAR meets OMII

Posted on May 16, 2009 by pm286

In a previous post I introduced our chemical natural language tools OSCAR and OPSIN. They are widely used, but in academia there is a general problem – there isn’t a simple way to finance the continued development and maintenance of … Continue reading →

Posted in "virtual communities", nmr, open notebook science, Uncategorized, XML | 2 Comments

Chem4Word – why semantics are necessary

Posted on April 6, 2009 by pm286

I was asked to explain how Chem4Word and CML could encode ferrocene. I’ll start by using Wikipedia to give a clear and accurate picture. Sorry for the cut-and-paste mess. WP: Ferrocene is the organometallic compound with the formula Fe(C5H5)2. It … Continue reading →

Posted in "virtual communities", Uncategorized, XML | 1 Comment

"should theses be Open?"

Posted on March 29, 2009 by pm286

Until now most theses reside in a dusty basement or on a supervisor’s shelf, but we are in transition to a world where all theses are -potentially – Openly visible to anyone. Surely this is a good idea. In principle, … Continue reading →

Posted in "virtual communities", Uncategorized, XML | 6 Comments

The library of the future – Guardian of Scholarship?

Posted on March 19, 2009 by pm286

I am still working out my message for JISC on April 2nd on “The library of the future”. I’ve had suggestions that I should re-ask this as ““What are librarians for?”” (Dorothea Salo) and “what can a library do?” (Chris). … Continue reading →

Posted in semanticWeb, Uncategorized, XML | Tagged | 3 Comments

Closed Data at Chemical Abstracts leads to Bad Science

Posted on March 17, 2009 by pm286

I had decided to take a mellow tone on re-starting this blog and I was feeling full of the joys of spring when I read a paper I simply have to criticize. The issues go beyond chemistry and non-chemists can … Continue reading →

Posted in semanticWeb, Uncategorized, XML | 3 Comments

Working with the NCI

Posted on February 4, 2008 by pm286

I was intending to blog about our collaboration with Dan Zaharevitz and colleagues at the National Cancer Institute in the DTP (Developmental Therapeutics Program). Dan beat me to it: in a CMLBlog comment (February 4th, 2008 at 5:02 pm e) … Continue reading →

Posted in chemistry, XML | Tagged , , , , | 2 Comments

XML, Fortran and Mr Fox at NESC

Posted on January 18, 2008 by pm286

Toby White (“Fantastic Mr Fox@) has developed a superb system for enabling FORTRAN programs to emit XML in general and CML specifically. He and colleagues are presenting this at Edinburgh as part of the NESC programme: Integrating Fortran and XML … Continue reading →

Posted in Uncategorized, XML | 1 Comment

CML Blog and Update

Posted on January 6, 2008 by pm286

Henry [Rzepa] and I are planning a major facelift for the public face of CML this year.  CML is about 13 years old and has gone through several revisions and relocations, so that information is somewhat scattered. CML is now … Continue reading →

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Why publishers' technology is obsolete – I

Posted on January 6, 2008 by pm286

I have just finished writing an article for a journal – and I suspect the comments apply to all publishers. To create the Citations (or “references”) they require: CITATIONS Citations should be double-spaced at the end of the text, with … Continue reading →

Posted in publishing, XML | Tagged , , | Leave a comment

Exploring RDF and CML

Posted on December 30, 2007 by pm286

I’ve taken the chance pf a few days without commitments to investigate how we shall be using RDF. We’ve got several projects where we are starting to use it – CrystalEye – WWMM, eChemistry, SPECTRa : JISC and other ORE-based … Continue reading →

Posted in semanticWeb, XML | Tagged , | 5 Comments