Since every nanopublication has a stable, resolvable identifier, nanopublications can reference each other just like web pages link to each other — and these references are themselves machine-readable. An assertion can build on a concept or claim introduced in another nanopublication, the provenance graph can declare that an assertion was derived from earlier ones, and comments, reviews, or disputes can point to the nanopublication they are about. The result is a growing, decentralized network of interlinked small knowledge units.

Some combination patterns have dedicated support. Indexes are nanopublications that list other nanopublications as elements, turning a set of them into a citable collection, such as a dataset. Superseding and retraction links chain versions of the same content together, so the history of a claim stays navigable. And shared reference points, expressed with properties like is part of, let independent nanopublications jointly form a larger resource: this FAQ, for example, is simply the set of all nanopublications declaring their entries to be part of the FAQ page.