  Although non-canonical residues, caps, crosslinks, and nicks play an
important role in the function of many DNA, RNA, proteins, and complexes, we do
not fully understand how networks of non-canonical macromolecules generate
behavior. One barrier is our limited formats, such as IUPAC, for abstractly
describing macromolecules. To overcome this barrier, we developed BpForms and
BcForms, a toolkit of ontologies, grammars, and software for abstracting the
primary structure of polymers and complexes as combinations of residues, caps,
crosslinks, and nicks. The toolkit can help quality control, exchange, and
integrate information about the primary structure of macromolecules into
fine-grained global networks of intracellular biochemistry.
