Archive for the ‘Databases’ Category

Open Position for a Scientific Database Curator/Annotator in ChEBI team

We are looking for a Scientific Database Curator/Annotator to work on the ChEBI (Chemical Entities of Biological Interest) project within the Cheminformatics and Metabolism Team. The position is based at the European Bioinformatics Institute (EMBL-EBI) located on the Wellcome Trust Genome Campus near Cambridge in the UK. The successful applicant will work on the existing […]

Upcoming conference: Therapeutic Applications of Computational Biology and Chemistry (TACBAC)

Courtesy of Andres Rueda, Flickr There are still places available at the 2012 conference on¬†Therapeutic Applications of Computational Biology and Chemistry (TACBAC),¬†12-14 March 2012, at the Wellcome Trust Conference Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK This conference will bring together leading researchers investigating computational chemistry and biology techniques as applied to advancing our […]

ChEBI release 57, now with links to NMRShiftDB

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 […]

NMRShiftDB now with more than 12.000 proton spectra

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.

ChemSpider aquired by the Royal Society of Chemistry

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 […]

ChEBI behind the scenes

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. […]

ChEBI release 56, now with SD file

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 ( and Rhea ( This release contains 17842 […]

CDK Workshop 2009 Wrap-up

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 […]

CDK Workshop 2009 kick-off talk

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 […]

ChEBI at the Fall 2009 ACS meeting in Washington

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 […]