Workflows/Research a document

• Research a document
  • The short path: drop a PDF onto a page, read it in Tine's side pane, and highlight as you go. Each highlight becomes an ordinary bullet you can write under, quote anywhere, and follow back to the exact spot — so a paper turns into linked, searchable notes without leaving Tine. The precise highlight and storage rules live in Features/PDF annotation.
• Bring the document in
  • 1. Drag a PDF from your file manager onto any page and drop it on a block — or paste one you copied, or run the /Upload an asset slash command. Tine stores the file in your graph's assets/ folder and inserts a link where you dropped it.
  • 2. Click the inserted link. The document opens in the reader pane beside your notes; drag the pane's edge to resize it, and Tine remembers the width on this device.
  • What you should see: the PDF in its own pane, with a toolbar holding a page-number box, a find button (Ctrl+F searches inside the document), zoom controls, an Area highlight toggle, a Notes button, Outline, and a ⋯ menu.
• Read and highlight
  • 1. Select a passage with the mouse and pick a color in the menu that appears — that's a highlight. Click an existing highlight to reopen its menu: recolor it, or remove it with ✕.
  • 2. To clip a figure or table instead, toggle Area highlight in the toolbar (or hold Shift on Linux/Windows, Command on macOS) and drag a rectangle over the region, then choose its color. Dismiss the color menu and nothing is written.
  • 3. Long document? Outline navigates its table of contents, the page-number box jumps straight to a page, and the ⋯ menu offers a persistent Light, Warm, or Dark reader theme — remembered on this device, not written into your graph.
  • What you should see: colored marks on the document — and, behind each mark, a bullet on a notes page named after the PDF.
• Turn highlights into notes
  • 1. Press Notes in the reader toolbar. Tine opens the document's highlights page — listed under the document's plain name (its page name starts with hls__, like Logseq) — where every highlight is a bullet marked with a colored dot.
  • 2. Write under a highlight bullet: a summary, a question, your own structure. These are ordinary bullets on an ordinary graph page — edit, nest, tag, and search them like any others.
  • 3. Click the colored dot on a highlight bullet (or the highlight itself back in the PDF) to jump between the two: each note goes straight back to its spot in the document.
  • What you should see: your notes and their source passages stay connected in both directions, and recoloring a highlight updates its dot on the notes page to match.
• Quote a passage in your ordinary notes
  • 1. Click the highlight and choose Copy ref (on desktop), then paste into any bullet in your own notes. The pasted ((…)) renders as link-styled text quoting the highlighted passage, and clicking the quote opens the document at that page.
  • 2. Keep source and words visible while you write: the PDF sits in its resizable side pane next to your notes page, and Shift-click on any bullet's dot parks that note in the right sidebar. On a phone the reader instead fills the width of the screen and the sidebars open as overlays — the two-up layout is a wider-window pattern.
  • 3. Choose Linked references on the highlight's menu (also on desktop) to list every note that quotes it — the trail from one passage to everywhere you used it.
  • What you should see: your note cites the source live, not as a copied excerpt — touch nothing, and the quote still opens the PDF at the right page tomorrow.
• Share the result
  • 1. From the notes page title's right-click menu (or its ⋯ menu): Copy page as Markdown puts a clean outline on the clipboard, Copy / export as… offers a rendered copy, and Export to PDF… prints the whole page through your OS print dialog — always on a light background, whatever your theme.
  • 2. Publishing on the web? Pages marked public:: true are included in the static HTML export (Settings → Graph → Export graph to HTML).
  • Your annotations are stored Logseq-compatibly — the hls__ page with your notes, an .edn sidecar and any clipped area images under assets/ — so launch snapshots cover your notes, config, and PDF highlights (not media files), and another Logseq-compatible tool reads the same annotations.
• Where next
  • The exact highlight, merge, and storage rules are mapped in Features/PDF annotation. For quoting anything else with ((…)) and the reference panels, see Workflows/Find and revisit; for snapshots and backups, Reference/Files, external edits, and backups.