Zusammen

Today's stop on our continuing tour of free chemistry databases and Web services takes us to ChEBI, a searchable collection of biologically-relevant molecules. From the about page:

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

ChEBI is organized around the concept of small molecules that interact in biological systems. The entry for oseltamivir illustrates what ChEBI has to offer. The entry is divided into two tabs, "Main" and "Automatic Xrefs" (cross-references). The Main tab lists general reference information about the molecule, including SMILES, InChI, molecular mass, and IUPAC name. The cross references tab displays the interactions of this small molecule with various proteins. For example, the protein sequences heading lists five neuraminidases, and each hyperlinks to the UniProt database.

A unique feature of ChEBI is its chemical ontology. This can be found under the main heading of each summary page by clicking on the Treeview link. In the case of oseltamivir, the various categories under which this molecule has been placed can be viewed.

For selected molecules, ChEBI also displays known interactions with proteins. For example, ChEBI lists oseltamivir as a prodrug. Clicking on the link labeled prodrug takes us to a page showing other small molecules possessing this role.

ChEBI also offers an intriguing feature called "Entity of the Month" that highlights one ChEBI entry. For example, the entry for July discussed the newly-named element Copernicium. The entry for last month highlighted Capecitabine. Unfortunately it appears that no RSS feed dedicated to Entity of the Month is available.

The idea of cataloging known biologically-relevant small molecules and exposing their protein interactions is an excellent one, and something of significant potential use. Unfortunately, ChEBI contains too few pieces of data associated with its small molecule entries to be a broadly-useful research tool. In addition, the associations that are exposed offer no obvious citations to the primary source for the information.

Although ChEBI in its current form consists mainly of a catalogue of biologically-relevant molecules, increasing the level of cross-linking to other biological databases could result in a much more useful service. As chemical databases such as ChEBI and other databases containing intersecting information continue to proliferate, such cross-linking is likely to increase in importance.

Kudos

• Chemical Ontology.
• Entity of the month.
• Continuously updated data set.

Ideas for Improvement

• Reveal primary data supporting small molecule-protein interaction.
• Enable browsing of records by chemical structure.
• Increase number and variety of annotated links to other biological databases.