From owner-chemistry #at# ccl.net Mon Sep 19 15:04:21 2005 From: "CCL" To: CCL Subject: CCL: W:Disclose your data, or not publish ! Message-Id: <-29235-050919150347-3737-8ZOlMZqGwssFfsd6IptP8w!A!server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Mon, 19 Sep 2005 14:03:36 -0500 MIME-Version: 1.0 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