Low priority, as we only have a single example, which is currently in "misc"
misc, RNA trimethylguanosine capped (ter1)
Suggestions:
http://code.google.com/p/rnao/
http://rnao.googlecode.com/svn/trunk/rnao.obo
other alternative is RNAmods
http://s59.cas.albany.edu/RNAmods/
Chris also very briefly mentioned SOM - the SO Molecule ontology. I don't know much about it but we could ask Colin Batchelor ...