What’s Eating Scientific Data? – Google Tech Talk on the Chemical Semantic Web

July 9, 2009 Leave a comment

google

Jim and I recently visited Google, where we were invited to give a tech talk about our research and the work that the PMR group in Cambridge is doing. It’s now online and you can watch it on YouTube here:

We are discussing the semantic toolstack as applied to chemistry and show how CML, RDF and ontologies can be used to bring chemical data into the 21st century. Jim also talks extensively about Lensfield – our system for the generation, management and publication of semantically rich linkeed data. A big thank you also to David Konerding for hosting us during the day and for the great discussions!

(If the video doesn’t show up in your feedreader, please click through to the the webpage.)

Looking forward to your comments!

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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

The Cambridge Polymer Builder.

July 10, 2007 1 Comment

The first “proof of concept” product of the Cambridge Polymer Informatics Group is up on the web. It is a demo application of a polymer builder, which uses Chemical Markup Language, Polymer Markup Language and Jumbo to build various types of polymers.

The polymers are constructed from small fragments, such as CH, CH2, CO etc. groups with the associated connection table defined in CML. Polymer Markup Language (PML) then contains a set of instructions in terms of how these fragments are “glued” together, how torsions (in 3D representations) are dealt with etc and it can also deal with distributions (of torsional angles just as much as molecular weights) and probabilities (e.g. for random compolymerizations etc.). (More details in a forthcoming paper).
The polymer builder subsequently takes the fragments and the relating PML document as an input to enumerate a full connection table for a macromolecule in CML. (We have not implemented ensemble building in this demonstrator).

polymer-builder.gif

Right now we can build most structural motives, such as homopolymers, block- and random copolymers, dendrimers and branched systems. In this demonstrator, we have not currently implemented bump checking and a number of other controls, but we are working on them as I write. The demonstrator app is available as a webservice here. Please go out and take it for a spin. And, by the way, we are grateful for feedback….so let me have your thoughts and comments via the comments function on the blog.

Filed under CML, PML, polymer

Polymer Informatics Lecture

May 29, 2007 2 Comments

A while ago, I gave a lecture about our beginning polymer informatics work here at the Unilever Centre. We videoed it and have now permission to put it online from our sponsors, so here it is:

Thanks to Jim Downing and Dr Andrew Walkingshaw who were behind he camera.

The talk covers our vision for polymer informatics, namely being able to solve the “inverse structure-property relationship problem” and to develop technologies which allow the rapid development of design-rules for polymers.

Subsequently, there is a discussion of what, at the moment, is preventing us from achieving that ambition. The nature of current polymer information systems is discussed together with a brief discussion of the quality of polymer data.
The talk then goes on to introduce the notion of the semantic web and illustrates how semantic web technologies can be used to address some of the problems that were previously discussed. As a part of this, a markup language for polymers and a polymer ontology are briefly discussed.

The lecture also showcases a polymer builder which makes use of the markup language, together with an example of reasoning over the polymer ontology.

You can download the talk to your iPod directly from the Google Website (clicking on the little Google Video Icon on the bottom right of the player will take you straight there).

Filed under CML, informatics, ontology, OWL, PML, polymer, polymer property, RDF, semantic web