Use Cases

From OBO Foundry

Contents 1 OBO Use Cases 1.1 ChEBI 1.2 GO 1.3 SO 1.4 PATO

OBO Use Cases

ChEBI

1. Describing substrate-specificity of gene products (very ontological)

   Consider the aminoglycoside-specific terms in GO. The definitions for these are written in terms of the chemical composition of the antibiotic, for example the deoxystreptamine ring in streptomycin and positions thereon. Unfortunately we can’t yet query ChEBI to find out which bit is the deoxystreptamine ring (it is the ring that contains such and such atoms disposed in so and so a way) or even verify that streptomycin contains a deoxystreptamine ring.

2. Describing binding modes of drugs to gene products (very ontological)

   We can already say Lys233 for the lysine residue at position 233 in a protein chain, but we can’t easily record which atoms in the drug molecule are binding to that residue because the canonical numberings are buried in some IUPAC document somewhere.

3. Structure to name conversion for new compounds (very ontological)

   If correctly set up, ChEBI will contain most of the rules needed for determining names from structures.

   For example the definition of a pyrrole should be that it is a compound that has as a part a mancude five-membered ring of four carbon atoms and one nitrogen atom. Further, it should contain the information that the nitrogen atom is at the 1- position.

4. Testing name to structure conversion (not especially ontological)

   If one runs all of the names (that have structures associated with them) in ChEBI through a name to structure conversion program, the InChIs provided by the name to structure converter should match those in ChEBI. Failing that, because of the layered structure of the InChI, partial credit can be awarded. (I have a more detailed document about this elsewhere.)

GO

SO

PATO