Notes and reference managers

What you highlight and write in Skyreader can follow you into the tools you write with. New highlights and notes arrive on their own, each with the article’s citation details: its link, author, dates, and a DOI or arXiv id where a paper has one.

Syncing is part of the Supporter plan. Downloading everything once, as Markdown or BibTeX, is on every plan: see Exporting.

Obsidian

The Skyreader plugin keeps one note per article in your vault.

1. In Obsidian, open Settings → Community plugins, choose Browse, and install Skyreader. Turn it on.
2. In Skyreader, open Settings → Notes & references and choose Create a password for Obsidian. Copy the password: it’s shown once.
3. In Obsidian, open the plugin’s settings and paste the password.

The plugin syncs when Obsidian starts and every 30 minutes after, or when you run Sync highlights now from the command palette.

What to sync

• Everything highlighted. Every article you highlight or write a note on gets a note, whether you saved it or not.
• Chosen collections. Every save in the Shelf collections you pick gets a note, highlighted or not, and one you add to a collection later arrives on the next sync. Articles outside them stay out.

Your notes stay yours

Each note has a part Skyreader keeps up to date, between two markers that reading view hides: the title, citation details, and your highlights and notes in reading order. Write anything you like above or below it, and add your own properties: a sync never touches them. Edit inside the markers and the next change in Skyreader replaces it.

Rename or move a note and it stays synced. Delete one and it comes back the next time that article’s highlights change.

The note’s properties carry title, author, url, doi, arxiv, published and saved, ready for a Dataview query or a citation plugin.

Zotero

Skyreader adds your saves to your Zotero library as references, and keeps your highlights and notes in a note on each.

1. At zotero.org/settings/keys, make a new key with Allow library access and Allow write access turned on. Copy it.
2. In Skyreader, open Settings → Notes & references, paste the key under Zotero, and choose Connect.

Skyreader syncs about every 15 minutes, or when you choose Sync now.

What to sync

• Everything. Every save, and every article you highlighted without saving.
• Chosen collections. Only the saves in the Shelf collections you pick, highlighted or not.

What arrives

Each article becomes an item in a Skyreader collection: a preprint for an arXiv paper, a journal article for anything else with a DOI, and otherwise a web page, document or book. It carries the title, authors, publication date, link, and the day you saved it as the accessed date.

Your highlights and notes go in a note on the item, titled Skyreader highlights, and that note is updated when they change. Write your own notes in a note of their own: Skyreader rewrites only its note.

If a paper is already in your library with the same DOI, the note goes on that item instead of a second copy.

An item is yours once it’s in Zotero. Edit it as you like: Skyreader doesn’t change it again. Delete it and it isn’t added back. Removing a save in Skyreader leaves its item in Zotero, and so does disconnecting. Removing a highlight takes it out of the note.

The Obsidian password

The plugin signs in with an app password, like other reader apps. It’s listed with your other app passwords in Settings → Other reader apps: revoke it there to stop the sync.