Anot8 was built to work as a local server for annotating your PDFs, and to allow you to publish those annotations, for example like this. See here for instructions on how to run Anot8 locally.
Anot8 now also supports loading any PDF by a URL and searching Unpaywall.org by DOI for free copies of articles.
"Temporary" annotationsWhen you load a PDF in Anot8 via a URL, Anot8 allows you to add, edit and delete "temporary" annotations that are only stored in the URL of the page. This means Anot8 never stores your private data, and you have no hard dependency on this Anot8 server, but can still embed links to other annotated documents in to your own documents for others to use.
This allows you to use perma links like anot8.org/r/1772.1/1 in your internal documents, whilst keeping your PDFs and annotations private but allowing all your team to access the PDFs and annotations from a local server (faster & privacy) or password protected public server (privacy).