Congratulations to the ChEBI team for publishing ChEBI version 57.
ChEBI Release 57 now contains links to NMRShiftDB. Search ChEBI for “caffeine”, for example, and you find the link to the carbon NMR spectrum of caffeine on the “automatic XREFs” page of ChEBI, in the “Small Molecules” section.
ChEBI now contains just under 17,963 manually annotated entries [...]
Entries Tagged as 'Databases'
ChEBI release 57, now with links to NMRShiftDB
May 27th, 2009 · 1 Comment · ChEBI, Conferences and Meetings, Databases, Open Access, Open Data, Open Science, Publishing
Tags: Add new tag·ChEBI·NMR·NMRShiftDB
NMRShiftDB now with more than 12.000 proton spectra
May 14th, 2009 · 2 Comments · Databases, Open Access, Open Data, Open Science, Open Source, Publishing, Scientific Culture
The number of structures and spectra in NMRShiftDB now exceeds 31.000 and 35.000, respectively. The number of proton spectra alone is now 12.934. This is due to NMRShiftDB developer Stefan Kuhn in my group importing a recent donation from our collaborators Reinhard Dunkel and Heinz Kolshorn. Thanks to Heinz and Reinhard for their generosity.
Tags: NMR·NMRShiftDB·Open Access
ChemSpider aquired by the Royal Society of Chemistry
May 11th, 2009 · 4 Comments · Databases, Open Science, People, Scientific Culture
It’s going to be all over the place soon anyway, so I’ll make it short: The Royal Society of Chemistry has announced that it has aquired ChemSpider. This is great news and I’m confident that it will be a move to even more openess in chemistry and cheminformatics. It will also allow the RSC to [...]
Tags: ChemSpider·RSC
ChEBI behind the scenes
May 8th, 2009 · 2 Comments · ChEBI, Databases, Open Data, Open Science, Open Standards
With ChEBI release 56 behind us, I thought I’d share some insight into how ChEBI is created and what we do to prepare a release. In the last years, the ChEBI team on average consisted of two software engineers maintaining and improving the software and two to three curators doing the data entry and curation. [...]
Tags: ChEBI·Curation·Ontologies
ChEBI release 56, now with SD file
April 30th, 2009 · 6 Comments · ChEBI, Chemoinformatics, Databases, Open Access, Open Science, Open Source, People, Scientific Culture
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 [...]
Tags: ChEBI·Curation·Ontologies
CDK Workshop 2009 Wrap-up
April 23rd, 2009 · No Comments · Bioclipse, Blue Obelisk, Chemistry Development Kit, Chemoinformatics, Conferences and Meetings, Databases, Fun, Life of Chris, Open Science, Open Source, People, Scientific Culture, Teaching
The CDK workshop 2009 is over and what is left is a bad cold. But I’ll get over it.
The workshop itself was phantastic – we had 40 participants with well balanced contributions from industry and academia. The first half day was dedicated to tutorials on various aspects of CDK, basic installation, our CDK and Oracle-based [...]
Tags: CDK·Cheminformatics·Open Source
CDK Workshop 2009 kick-off talk
April 20th, 2009 · 2 Comments · Blue Obelisk, Chemistry Development Kit, Chemoinformatics, Conferences and Meetings, Databases, Fun, Life of Chris, Open Science, Open Source, People, Scientific Culture, Teaching
I’m collecting some thoughts for my CDK workshop kick-off talk on Monday and I guess I’ll go for the boring regular version, with an introduction to CDK history, followed by some statistical figures and ending with an explanation of the format for the developers workshop on Tuesday afternoon.
As anyone can read on our CDK homepage, [...]
Tags: CDK·Cheminformatics·Open Source
ChEBI at the Fall 2009 ACS meeting in Washington
March 27th, 2009 · No Comments · Conferences and Meetings, Databases, Life of Chris, Open Data, Open Science, Open Standards, Publishing, Scientific Culture
I’ve been invited to present our ChEBI ontology at the 2009 Fall Meeting of the American Chemical Society. Here is our abstract:
ChEBI – An open ontology for Chemical Entities of Biological Interest
Paula de Matos (1), Kirill Degtyarenko (2), Marcus Ennis (1), Janna
Hastings (1), Inma Spiteri (1) and Christoph Steinbeck (1)
(1) European Bioinformatics Institute, Hinxton, Cambridge, [...]
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Open Access Journal of Cheminformatics now live!
March 17th, 2009 · 1 Comment · Blue Obelisk, Chemoinformatics, Conferences and Meetings, Databases, Informatics, Life of Chris, Open Access, Open Science, Open Source, People, Publishing, Scientific Culture, Structure Elucidation, Teaching, Uncategorized
I’m delighted to announce that the first open access journal of our field, the Journal of Cheminformatics, is now live and has published its first articles. Journal of Cheminformatics is a new open access journal from Chemistry Central publishing peer-reviewed research in all aspects of cheminformatics and molecular modelling. It is run by Editors-in-Chief [...]
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Beilstein Symposium on Systems Chemistry, Day 2
May 28th, 2008 · 1 Comment · Chemoinformatics, Conferences and Meetings, Databases, Hot Science, Informatics, Life of Chris, Open Science, Scientific Culture
The Wednesday morning session is about to start. Paul Labute chairs it.
Tom Blundell of Cambridge starts with “Exploring Biological and Chemical Space with High-Throughput Crystallographic, Biophysical and Computational Methods: The new Dimensions of Drug Discovery”. Tom starts with a view on a cell, stating its complicatedness or complexity. He points out the large number [...]
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