Representing a DAG (directed acyclic graph)

Answer 1

I think the upcoming version (beta at the moment) of the Ruby bindings for the graph database Neo4j should be a good fit. It's for use with Rails 3. The underlying data model uses nodes and directed relationships/edges with key/value style attributes on both. To scale read-mostly architectures Neo4j uses a master/slave replication setup.

Answer 2

You could use OrientDB as graph database. It's highly optimized for relationships since are stored as link and not JOIN. Load of bidirectional graph with 1,000 vertices needs few milliseconds.

The language binding for Rails is not yet available, but you can use it with HTTP RESTful calls.