ChEBI User Workshop Summary

The first user workshop of the European Bioinformatics Institute’s (EBI) database and ontology of Chemical Entities of Biological Interest (ChEBI) is over. We had about 30 participants from industry, universities and research institutions. The user workshop started with three talks by ChEBI users reporting on their particular use of our resource. Colin Bachelor from the Royal Society of Chemistry described text mining efforts at the RSC Publishing Department and how the ChEBI ontology could be improved to better serve their purposes. He pointed out, for example, surplus overloading of ChEBI’s ‘is_a’ relationship and how this can be overcome. We’ll work on it.

Ulrike Wittig of EML Research in Heidelberg talked about ChEBI and their SABIO-RK database, which contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. Here, ChEBI helps to match lists of compound names from different databases via its synonyms feature.

Giles Weaver from Unilever presented a talk on the construction of Genome Scale Metabolic Networks and how ChEBI aids as a small molecule hub to genomic and other information.

The workshop continued with ChEBI group coordinator Paula de Matos presenting the “ChEBI story so far”, as well as new developments such our recently introduced substructure and similarity search and future plans. The following open discussion focused on the ChEBI ontology, its potential improvements and how a discussion with experts from OBO Foundry Ontologies would help in making the ChEBI ontology more useful them. Such a meeting is now projected as a parasitic meeting of the OBO Foundry Meeting here at EBI in July.

The first day ended with a very nice dinner at the George Inn in Babraham.

Kirill Degtyarenko started the second day explaining how the ChEBI curation process works and what we consider to be good annotation practice, followed by Janna Hastings giving a hand-on training on ChEBI. A lively discussion originated in the end, covering question on database growth, having an automatically annotated buffer database and cooperation/crosslinking with other resources.

The ChEBI team feel thoroughly enjoyed the feedback and thinks that the workshop was a great success. The analysis of questionnaires returned by our participants unanimously point into the same direction. The results and the feedback from this workshop will help us to shape the development strategies for the upcoming month and year.

We gratefully acknowledge the sponsoring of the ChEBI user workshop by the EBI Industry Programme.

Categorised as: Open Science

One Comment

  1. Duncan says:

    Hi Christoph, thanks for a great workshop, I had a great time. Wrote some notes up on day one and day two to add to your summary above. See you again soon, Duncan.

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