Silke Schomburg briefly mentioned the #Wikidata talk by Markus Krötzsch at #swib14. See the slides at https://swib.org/swib14/slides/kroetzsch_swib14_53.pdf #swib23
@nev I used https://hypothesis.is in the past for social annotation of web content and PDFs. It is open source. However, it doesn't seem that people are encouraged to run their own server although it was advertised as decentralized in the past (see e.g. Dan Whaley's #swib14 talk: https://swib.org/swib14/slides/whaley_swib14_51.pdf ).