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 [...]
Entries Tagged as 'Open Standards'
ChEBI chemistry ontology development funded by BBSRC
May 19th, 2009 · No Comments · ChEBI, Chemoinformatics, Open Data, Open Science, Open Standards
Tags: ChEBI·Ontologies
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 [...]
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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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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 [...]
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Creating and Reviewing Patches in the Chemistry Development Kit (CDK)
September 1st, 2008 · 4 Comments · Chemistry Development Kit, Life of Chris, Open Source, Open Standards, Scientific Culture
In order to prevent major turbulences in the main source code development line of the Chemistry Development Kit (CDK), we decided a while ago to have separate branches in our subversion source code management system for each developer and each of his subprojects. Once a project has been finalized by a developer in her branch, [...]
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Linus on GIT on Google TechTalks
August 26th, 2008 · 8 Comments · Blue Obelisk, Chemistry Development Kit, Informatics, Open Standards, Publishing, Scientific Culture
I’m a big fan of Google TechTalks and watch a lot of them during flights. This week I enjoyed the recording of Linus Torvalds insulting all kinds of people including the whole SVN develoment team while introducing his distributed source code management system GIT. Egon had pointed me to GIT quite a while ago but [...]
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PAC on Graphical Representation Standards for Chemical Structure Diagrams
March 17th, 2008 · No Comments · Blue Obelisk, Chemistry Development Kit, Chemoinformatics, IUPAC CPEP, Open Standards
The February issue (V80, No 2, P 277-410) of IUPAC’s Pure and Applied Chemistry Journal has a 133 pages of IUPAC recommendations for the Graphical Representation Standards for Chemical Structure Diagrams. In the Blue Obelisk context, this material is both valuable for the development of our structure representation and editing tools (JChemPaint, JCPViewer) as well [...]
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Interactive Open Access and Collaborative Peer Review
June 3rd, 2007 · No Comments · Open Standards, Publishing
An interesting article by Ulrich Poeschl on Interactive Open Access Publishing and Collaborative Peer Review in the latest issue “Forschung & Lehre” describes a publication process practiced for example by “Atmospheric Chemistry and Physics” and sister publications. In a first step, a submission is immediately published as a “discussion paper” in the online discussion forums [...]
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Mathematical Formulae and HTML Slidy
November 29th, 2006 · 4 Comments · Open Standards, Publishing, Teaching
Last week I wanted to include some math into my lecture slides prepared with HTMLSlidy and found the fantastic ASCIIMathML tool which allows you to write your math formulae in a LaTeX-like manner in your regular text.
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