Comments on: ChEBI release 56, now with SD file http://www.steinbeck-molecular.de/steinblog/index.php/2009/04/30/chebi-release-56-now-with-sd-file/?utm_source=rss&utm_medium=rss&utm_campaign=chebi-release-56-now-with-sd-file A molecular informatics weblog Tue, 22 Nov 2011 15:29:25 +0000 hourly 1 http://wordpress.org/?v=3.3.1 By: Christoph Steinbeck http://www.steinbeck-molecular.de/steinblog/index.php/2009/04/30/chebi-release-56-now-with-sd-file/comment-page-1/#comment-7222 Christoph Steinbeck Fri, 01 May 2009 09:35:12 +0000 http://www.steinbeck-molecular.de/steinblog/?p=167#comment-7222 Tony, this was me being imprecise. I corrected the post. We have 17842 annotated entities, which includes classes of compounds, roles, etc. So the SDF only contains those entities which are well defined chemical compounds with a connection table. Tony, this was me being imprecise. I corrected the post. We have 17842 annotated entities, which includes classes of compounds, roles, etc. So the SDF only contains those entities which are well defined chemical compounds with a connection table.

]]> By: ChemSpiderman http://www.steinbeck-molecular.de/steinblog/index.php/2009/04/30/chebi-release-56-now-with-sd-file/comment-page-1/#comment-7206 ChemSpiderman Thu, 30 Apr 2009 21:45:45 +0000 http://www.steinbeck-molecular.de/steinblog/?p=167#comment-7206 I've opened the full SDF of the DB from the FTP site and it has 13210 entries. Your post commented: "17842 annotated compounds". Is there a reason the other 4600 are not in the SDF file? I’ve opened the full SDF of the DB from the FTP site and it has 13210 entries. Your post commented: “17842 annotated compounds”. Is there a reason the other 4600 are not in the SDF file?

]]> By: ChemSpiderman http://www.steinbeck-molecular.de/steinblog/index.php/2009/04/30/chebi-release-56-now-with-sd-file/comment-page-1/#comment-7200 ChemSpiderman Thu, 30 Apr 2009 19:05:37 +0000 http://www.steinbeck-molecular.de/steinblog/?p=167#comment-7200 No error messages other than "will not import". In the past 8 years I've only seen two cases where SDF files will not import into ChemFolder...the last one was a long time ago and I cannot recall the issue. Hyleos ChemFolderBrowser is also very good at opening files. I downloaded the version from the FTP site the second time...this time it opened. No error messages other than “will not import”. In the past 8 years I’ve only seen two cases where SDF files will not import into ChemFolder…the last one was a long time ago and I cannot recall the issue. Hyleos ChemFolderBrowser is also very good at opening files.

I downloaded the version from the FTP site the second time…this time it opened.

]]> By: Christoph Steinbeck http://www.steinbeck-molecular.de/steinblog/index.php/2009/04/30/chebi-release-56-now-with-sd-file/comment-page-1/#comment-7194 Christoph Steinbeck Thu, 30 Apr 2009 17:08:09 +0000 http://www.steinbeck-molecular.de/steinblog/?p=167#comment-7194 Hm, that is bad. It parses nicely with the Bioclipse SDF import. Do you get any error messages? In the meantime, I'll find out what my software engineers use for make it. Hm, that is bad. It parses nicely with the Bioclipse SDF import. Do you get any error messages? In the meantime, I’ll find out what my software engineers use for make it.

]]> By: ChemSpiderman http://www.steinbeck-molecular.de/steinblog/index.php/2009/04/30/chebi-release-56-now-with-sd-file/comment-page-1/#comment-7192 ChemSpiderman Thu, 30 Apr 2009 15:27:51 +0000 http://www.steinbeck-molecular.de/steinblog/?p=167#comment-7192 I cannot open the SDF file in neither the Hyleos ChemFileBrowser nor ACD/ChemFolder. What are you using to generate and open the SDF file? I cannot open the SDF file in neither the Hyleos ChemFileBrowser nor ACD/ChemFolder. What are you using to generate and open the SDF file?

]]> By: ChemSpiderman http://www.steinbeck-molecular.de/steinblog/index.php/2009/04/30/chebi-release-56-now-with-sd-file/comment-page-1/#comment-7191 ChemSpiderman Thu, 30 Apr 2009 15:11:54 +0000 http://www.steinbeck-molecular.de/steinblog/?p=167#comment-7191 Great news on the SDF file release Chris! I just downloaded it. Thanks for doing that! Great news on the SDF file release Chris! I just downloaded it. Thanks for doing that!

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