Polymer Markup Language Paper

December 3, 2008 6 Comments

Now i started this blog with the intention of writing about polymers, informatics etc.. Somewhere along the way, some advocacy, some ranting and a general critique of the scholarly publication process also crept in and, of course, there were long breaks. However, we have recently published polymer markup language, which has been in the making for a while and I am pleased to announce the paper, published in the Journal of Chemical Information and Modeling:

Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language

Nico Adams, Jerry Winter, Peter Murray-Rust and Henry S. Rzepa

Polymers are among the most important classes of materials but are only inadequately supported by modern informatics. The paper discusses the reasons why polymer informatics is considerably more challenging than small molecule informatics and develops a vision for the computer-aided design of polymers, based on modern semantic web technologies. The paper then discusses the development of Polymer Markup Language (PML). PML is an extensible language, designed to support the (structural) representation of polymers and polymer-related information. PML closely interoperates with Chemical Markup Language (CML) and overcomes a number of the previously identified challenges.

Many thanks are due to everybody who worked on this and everybody in the Unilever Centre who was available for discussions, comments and critique.

The paper can be found here

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Filed under informatics, paper, PML, polymer, semantic web, XML

Semantic Web Applications and Tools for Life Sciences – Afternoon Session

December 1, 2008 1 Comment

Tutorial: The W3C Interest Group on Semantic Web Technologies for Health Care and Life Sciences (M.S. Marshall)

“Scientists should be able to work in terms of commonly used concepts

The scientist should be able to ork in terms of personal concepts and hypotheses (not forced to map concepts to the terms that have been chosed for him)

Otherwise general overview over what the interest groups does and how it works….link to the webpage is here.

To participate email [email protected]

Task Forces:

  • Terminology
  • Linking Open Drug Data
  • Scientific Discourse
  • Clinical Observations Interoperability
  • BioRDF – integrated neuroscience knowledge base
  • Other Projects – clinical decision support, URI workshop

Paper in IEEE Software: SOftware design for empoweriing scientists

I stopped blogging after this mainly because my batteries were dry and there was a scarmble for the power sockets in the room I did not wishh to participate in. During the meeting some people said they were blogging this and that there was some discussion on Friendfeed….but I can’t find anything much on either. If anybody has a few links, please give me a shout and I will happily link out.

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