Ontologies such as PROV-O manage the provenance of the resources in an RDF Graph at an instance level, but I need to manage the provenance of each triple, is there any good reference to do this?
As you will need to reify at some point anyway, why not directly create a provenance individual for each triple and then use PROV-O for that individual?
Example:
for triple: s p o .
add new provenance individual i:
i a tripleProvenanceIndividual;
tripleProvenanceSubject s ;
tripleProvenanceProperty p ;
tripleProvenanceObject o .
and then use i to manage provenance information of s p o.
In particular, Nanopublications (http://nanopub.org/guidelines/working_draft/) allow you to specify both provenance of triples and provenance of provenance statements.