Polymer Markup Language Paper

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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6 Responses to Polymer Markup Language Paper

  1. I’m very interested in reading the paper and was quite surprised to see that it was published in a “closed access” publication considering the enormous advocacy for Open Access publishing. That said, would you be willing to send me one of the “free copies” that you likely are allowed to issue from publishing in JCIM. Thanks

  2. Dr Nico Adams says:

    Antony,

    you are completely right to remark on this. We have debated this long and hard internally and my personal preference would have been not to publish with JCIM. Apart from being closed access, JCIM, as you know, doesn’t even allow self-archiving. The main reasons for publishing there were (a) it is the 8th paper in a series and we did not want to break that, (b) there is currently no good open access journal of chemical informatics (at least to my knowledge) or polymer science, though I hear interesting noises coming from the EBI at the moment and hope that situation will change and (c) (and probably most indefensibly) I am not an established academic at the moment and have to tread a fine line between advocacy for a better way of doing things and giving an institution a chance to employ me. And in my particular context that means having to satisfy the “traditional metrics” of publishing in journals with high impact factors etc.. I do appreciate that it is a much less principled stand than some of my peers take and much more pragmatic. It will be the subject of a forthcoming blog post and I will value and welcome any thoughts you might have on the matter.

  3. Ahh…pragmatism. MUCH needed in this area. It has been very necessary when directing the development of ChemSpider through the torturous paths of criticism about what we’ve been doing. But I think we have shown ourselves worthy now. You might have seen the RSC announcement about us working with them on an InChI resolver now?

    I understand the need for your decision. I personally publish in JCIM and many other mainstream journals very regularly. I am now on the editorial board for the new Journal of Cheminformatics coming our from Chemistry Central (http://blogs.openaccesscentral.com/blogs/ccblog/entry/journal_of_cheminformatics_now_accepting) so consider there for the future…Christoph Steinbeck from EBI is involved.

  4. Fore! says:

    Nico,

    Is there a publicly accessible PML schema (.xsd) available for download somewhere?

    That would make your work the de facto standard, like the MatML one for materials

    http://www.matml.org/schema.htm

  5. Dr Nico Adams says:

    Dear Fore,

    PML is a subset of Chemical Markup Language (CML) and thus part of the CML schema. You can find everything related to CML on the CML sourceforge site: http://sourceforge.net/projects/cml/.

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