SteinBlog

ChEBI release 56, now with SD file

ChEBI Entity of the May 2009

We are pleased to announce release 56 of our database of Chemical Entities of Biological Interest (ChEBI).

SDF files are now available with ChEBI Release 56. They can be exported via the Downloads section or the search results page. We also have automatically generated links from IntEnz (www.ebi.ac.uk/intenz) and Rhea (www.ebi.ac.uk/rhea). This release contains 17842 annotated chemical entities (and not compounds, as I wrote earlier – we also have classes of compounds and abstract concepts) with 74 of them new submissions entered via the ChEBI submission tool. The next ChEBI Release will be on the 27 May 2009.

See our entity of the month, Ethyl formate.

All data are also available on the public FTP site:

ftp://ftp.ebi.ac.uk/pub/databases/chebi/


Categorised as: ChEBI, Chemoinformatics, Databases, Open Access, Open Science, Open Source, People, Scientific Culture


6 Comments

  1. Great news on the SDF file release Chris! I just downloaded it. Thanks for doing that!

  2. 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?

  3. 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.

  4. 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.

  5. 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?

  6. 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.

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