SteinBlog

Archive for the ‘Open Data’ Category

Open Positions in PhenoMeNal project (Metabolomics e-Infrastructure)

We are seeking to recruit a number of experienced people for our PhenoMeNal H2020 grant, to create an international e-infrastructure for large-scale computing and analysis of medical metabolomics data. You will join the Cheminformatics and Metabolism team at the European Bioinformatics Institute (EMBL-EBI) located at the Wellcome Genome Campus near Cambridge in the UK. We […]

Job offer: Bioinformatician in Metaspace project for untargeted spatial metabolomics

We are looking to recruit a talented bioinformatician to work within the MetaboLights team at the European Bioinformatics Institute (EMBL-EBI) located on the Wellcome Trust Genome Campus near Cambridge in the UK. You will work closely with a consortium of 8 European partners on the METASPACE project. METASPACE will enable untargeted spatial metabolomics for translational […]

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 […]

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 […]

ChEBI chemistry ontology development funded by BBSRC

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 […]

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.

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. […]

3rd International Biocuration Conference in Berlin

I’m attending the 3rd International Biocuration Conference in Berlin, which looks like a pretty successful meeting in terms of numbers of participants. Seems like somewhere between 100 and 200 participants. It looks like the time for recognition for biocuration and curated biological resource has come. The International Society for Biocuration has been inaugurated yesterday. People […]

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 […]