SteinBlog

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. It is remarkable, that, by now, the question of which chemical compounds make it into ChEBI is completely community driven. Requests to enter compounds are submitted by users and other database maintainers via the ChEBI curator request tracker on SourceForge. Besides increasing the public knowledge of mankind, the biggest benefit and driving force for submitters is the assignement of a stable ChEBI identifier which then can be cited and linked to from other resources.

With ChEBI release 55 we have introduced the new submission tool which now allows our submitter to create ChEBI datasets themselves which a) gives our users more control over what they want to see in ChEBI and b) saves our curators some duplicate work.

In preparation for a release, here is what the ChEBI team does.

• Create automatic cross-references to PubChem, UniProt, IntEnz, BRENDA, SABIO-RK, ArrayExpress, IntAct, Patents etc…These are all run a week before the release and are based on ChEBI identifier matching or text matching.
• Annotation of entity of the month
• Submissions deposited directly into the database by users are processed by our annotators.

On the release day:

• Data is exported overnight into multiple formats, OBO format, SDF, Oracle data dumps and PostgreSQL/MySQL dumps.
• Public web site updated with the entity of the month.
• Statistics generated and stored.
• Sitemaps are generated to be used by search engines like Google for indexing.
• Finally data is deposited into PubChem and the EB-eye search engine is updated.

Tagged with: ChEBI, Curation, Ontologies

Categorised as: ChEBI, Databases, Open Data, Open Science, Open Standards