CCL: W:Disclose your data, or not publish !
- From: "Ivanciuc, Ovidiu I."
<oiivanci!A!UTMB.EDU>
- Subject: CCL: W:Disclose your data, or not publish !
- Date: Mon, 19 Sep 2005 14:03:36 -0500
Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci!A!UTMB.EDU]
--Replace strange characters with the "at" sign to recover email
address--.
>> A simple solution for publishers would be to ask for
>> mandatory deposition of such data as supplementary materials.
>1. If publishers hold the data, would we not have to check
> with each publisher in turn to get the information?
> And if so, how much would it cost?
A search engine, such as Google Scholar, should be able to
find these data.
Many publishers already offer free access to supplementary materials,
such as American Chemical Society; many QSAR datasets (including
chemical structures) are deposited as supplementary materials
to the ACS journal Journal of Chemical Information and Modeling.
Of course, the chemical community (editors, reviewers, authors)
should ask for open access to computational data, because otherwise
the Publishers will not do it.
>2. We are, err, blessed with a wide range of file formats,
> many of which aren't described, or even readable.
> Whose formats would be supported, and would the vendors
> and other authors provide the necessary conversion routines?
A good starting point is CML - Chemical Markup Language
(http://www.xml-cml.org/).
See a recent paper on large-scale calculations (250000
compounds from the NCI database), which is a nice application
of CML and the new InChi chemical code:
A global resource for computational chemistry
Peter Murray-Rust1, Henry S. Rzepa2 , James J. P. Stewart3 and Yong Zhang1
Journal of Molecular Modeling (in press)
Regards,
Ovidiu
####################################
Dr. Ovidiu Ivanciuc
Sealy Center for Structural Biology,
Department of Human Biological Chemistry & Genetics,
University of Texas Medical Branch,
301 University Boulevard,
Galveston, Texas 77555-0857
USA