SteinBlog » ChEBI

What do we expect from a chemical structure editor applet?

Christoph Steinbeck — Sat, 11 Jul 2009 15:54:46 +0000

My team at the EBI maintains a couple of databases [1,2,3] dealing with various aspects of (bio-) organic chemistry. All of them need chemical structure editor applets where users can specify queries for substructure searches and which are used by our curators for data entry.The development of these databases is funded by the European Union and the BBSRC. We have a long-standing history of promoting open access to scientific publications and data, and of publishing our software as open source projects [e.g. 4,5] and we are therefore delighted that our funding agencies now promote these principles and support us in our goal to make all of our tax-payer funded research and development openly available. In all of our recent grants we have promised to deliver the software infrastructure of our databases as open source software to the scientific community.

Now, this does of course include the chemical structure editor mentioned above. As a pure coincidence , I had started a chemical structure editor in the late 1990s, called JChemPaint, which was later influenced a lot contribution from Egon Willighagen and others. JChemPaint experienced several rounds of re-architecture but for some reason it was never really considered to be production-ready.

We are now taking another go at it, at its applet version to be precise. And this time my charming profession team will give it a try and I’m confident that this time we’ll get it right. The fact that we are not alone in developing JChemPaint is both boon and bane. Everyone in an open source project is happy about harvesting the man-power of others but on the other hand you loose some control. While we, for example, are looking at the applet from a usability and GUI perspective, Egon and Arvid at Uppsala do a re-architecturing of the controler (the piece of software dealing with the user input) in order to make it maintainable through modularization.

So, in order to get an idea of what we actually need, we decided to do an analysis of a) existing structure editor applets and what they to well and not so well and b) how our curators do their work. For the latter, we did a screen recording of our curators’ work and looked at the type of functionality they used and how they did this (keyboard shortcuts, mouse, buttons, menus). The preliminary results are available on the JChemPaint wiki and we are more than happy to receive input from the community about this.

New ChEBI team members

Christoph Steinbeck — Sat, 20 Jun 2009 20:58:15 +0000

Welcome to our new team members

I’m glad to announce that the recent round of recruitment for the ChEBI team has been completed. We have two new colleagues, Steve Turner, our new Chemistry Curator, and Adriano Dekker, our new Software Engineer. Both will work with us to make ChEBI fit for the inclusion of more then 500.000 new ChEBI entries. Those chemical structure were brought to EBI by my esteemed colleague John Overington as part of the ChEMBL database, formerly known as Starlite, Candistore and Drugstore. ChEMBL obviously contains much more than chemical structure, namely their activities against around 4000 biological targets and other properties, and the ChEMBL resource will be manage by John and his team. ChEBI will provide the chemical structure, substructure and similarity searching for the ChEMBL structures and we will soon report on our recent advancements in this field.

For now, I wish Steve and Adriano a good start in my team. I’m sure we are going to have a good time together.

ChEBI release 57, now with links to NMRShiftDB

Christoph Steinbeck — Wed, 27 May 2009 12:29:09 +0000

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 annotated entries of which 108 entries have been submitted via the ChEBI Submission tool (www.ebi.ac.uk/chebi/submissions). The next ChEBI Release will be on the 24 June 2009.

See our entity of the month, Oseltamivir.

All data are also available on the public FTP site:
ftp://ftp.ebi.ac.uk/pub/databases/chebi/

ChEBI chemistry ontology development funded by BBSRC

Christoph Steinbeck — Tue, 19 May 2009 11:30:45 +0000

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 Ontology and the Relationship Types Ontology.
This will include extensive annotation of the ChEBI ontology required after adoption of BFO and RO. The adoption of the BFO will require a major reorganisation of the upper levels of the ChEBI ontology in order to allow it to align to the BFO. This
reorganisation can only be achieved by manual annotation although some semi-automatic means will be employed to aidthe curator. In addition to the reorganisation of the upper levels, new relationships will be introduced semi-automatically but as the ChEBI ethos requires that all data is manually checked to maintain ChEBI’s high standards of data quality, we expect a major annotation task. The project is funded for three years. Stay tuned. We’ll report on our progress on a regular basis.

ChEBI behind the scenes

Christoph Steinbeck — Fri, 08 May 2009 08:12:37 +0000

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.

ChEBI release 56, now with SD file

Christoph Steinbeck — Thu, 30 Apr 2009 10:31:52 +0000

We are pleased to announce release 56 of our database of Chemical Entities of Biological Interest (ChEBI).

SDF files are now available with ChEBI Release 56. They can be exported via the Downloads section or the search results page. We also have automatically generated links from IntEnz (www.ebi.ac.uk/intenz) and Rhea (www.ebi.ac.uk/rhea). This release contains 17842 annotated chemical entities (and not compounds, as I wrote earlier – we also have classes of compounds and abstract concepts) with 74 of them new submissions entered via the ChEBI submission tool. The next ChEBI Release will be on the 27 May 2009.

See our entity of the month, Ethyl formate.

All data are also available on the public FTP site:

ftp://ftp.ebi.ac.uk/pub/databases/chebi/