It is my duty today to review a patch for some piece of CDK code again. I blogged about this process earlier. This particular patch was submitted by Mark Rijnbeek in my team via the CDK patch tracker. I first go to the patch page, assign the patch to myself and set the patch status […]
If the pompous title caught your attention, and you are ashamed of that: Don’t worry. It is all true. My cheminformatics and metabolism group at the European Bioinformatics Institute (EBI) is looking for a phd student this year and all you need to do is apply through the regular route. The range of possible topics […]
I’m giving my quartly report on progress in my area for the EBI industry programme. Here is what I will elaborate on: We received a ChEBI BBSRC grant for ontology development. We are in the process of hiring five new ChEBI team members at the moment – one, our new curator Steve Turner, has arrived […]
NMRShiftDB is a database of organic compounds and their nuclear magnetic resonance (NMR) data. At present, we hold 30.000 compounds and 1D NMR spectra for carbon, proton and some other nuclei. NMRShiftDB developer Stefan Kuhn, in collaboration with the EBI systems group, has now established an NMRShiftDB node at the European Bioinformatics Institute (EBI), which […]
Congratulations to the ChEBI team for publishing ChEBI version 57. ChEBI Release 57 now contains links to NMRShiftDB. Search ChEBI for “caffeine” PuTTY quit command , 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 […]
We received our official award letter from BBSRC Tools and Resources Fund today for the ChEBI ontology development grant. Needless to say, we are thrilled. We are now going to work together with Michael Ashburner’s group at the University of Cambridge to align ChEBI with other OBO Foundry ontologies by adoption of the Basic Formal […]
The number of structures and spectra in NMRShiftDB now exceeds 31.000 and 35.000 puttygen ssh , 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 […]
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 […]
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. […]
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 […]