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 [...]
Entries Tagged as 'Open Data'
Open Position for a Scientific Database Curator/Annotator in ChEBI team
April 11th, 2012 · No Comments · ChEBI, Chemoinformatics, Databases, Open Data, Open Standards, Publishing, Scientific Culture
Tags:
Do a cheminformatics PhD thesis at a world-class institution
June 16th, 2009 · No Comments · Chemoinformatics, Hot Science, Open Access, Open Data, Open Science, Open Source, People, Scientific Culture, Teaching
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 [...]
Tags: cheminformatics research·EBI·PhD
ChEBI release 57, now with links to NMRShiftDB
May 27th, 2009 · No Comments · ChEBI, Conferences and Meetings, Databases, Open Access, Open Data, Open Science, Publishing
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 [...]
Tags: Add new tag·ChEBI·NMR·NMRShiftDB
ChEBI chemistry ontology development funded by BBSRC
May 19th, 2009 · No Comments · ChEBI, Chemoinformatics, Open Data, Open Science, Open Standards
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 [...]
Tags: ChEBI·Ontologies
NMRShiftDB now with more than 12.000 proton spectra
May 14th, 2009 · 1 Comment · 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
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
3rd International Biocuration Conference in Berlin
April 17th, 2009 · No Comments · Conferences and Meetings, Life of Chris, Open Data, Open Science, Open Standards, People, Publishing, Scientific Culture
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 [...]
Tags:
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 [...]
Tags:
“new open source era … for better drugs”
March 3rd, 2009 · No Comments · Chemoinformatics, Conferences and Meetings, Open Access, Open Data, Open Science, Open Source, People, Publishing, Scientific Culture, Teaching
As we learn from a rather poorly written article over at xconomy, “Biology has never really had a social-networking movement like open-source computing, where thousands of loosely-affiliated people around the world pool brainpower to make better software”. If you translate that into what was needed for biology (or chemistry) according to the xconomy author, it [...]
Tags:
Industry-funded medical research will double your impact factor
February 16th, 2009 · No Comments · Open Access, Open Data, Open Science, Open Standards, Publishing, Scientific Culture
The Guardian has a nice piece by Ben Goldarcre reporting about a study published by the British Medial Journal entitled “Relation of study quality, concordance, take home message, funding, and impact in studies of influenza vaccines: systematic review”. Both the newpaper article and the study are worth reading and seem to be open. Besides many [...]
Tags: