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Read, annotate and collect evidence

In short: Open a publication, get its PDF with View PDF, Fetch PDF or Upload PDF, then select text and choose Highlight, Comment or RIF it. Highlights and comments are saved to the project's notes automatically. RIF it adds the passage as evidence to a research object in Research in Formation, where you arrange your ideas and turn them into a working note with Expand into Working Note.

1. Open the publication's PDF​

  1. Click a publication in the Library tab, or click a publication node on a map.
  2. Use the one PDF action SciNodes offers:
ButtonWhen you see itWhat it does
View PDFSciNodes already holds a copyOpens the PDF viewer
Fetch PDFAn open-access copy can be foundFetches it in the background. You'll see "PDF fetched." when it's ready.
Upload PDFNeither of the aboveLets you add your own copy (up to 64 MB)

You can keep working while a fetch runs. If it fails, you'll get a "PDF unavailable" notification. Upload your own copy instead.

Details: Fetching and uploading PDFs

2. Read in the PDF viewer​

The toolbar has page navigation, zoom, Fit width, Download PDF and Open original. Click Annotations to list your highlights and comments on this publication. Once you've annotated, Download PDF saves a copy with your annotations.

Details: PDF viewer

3. Highlight, comment and RIF​

  1. Select a passage of text.
  2. Choose an action:
    • Highlight: marks the passage in the color you pick. Right-click a highlight later to change its color.
    • Comment: adds your own remark to the passage.
    • RIF it: adds the passage as evidence to a research object (see step 5).
  3. Highlights and comments are saved to the project's notes automatically. A highlight appears in Notes as "Highlight (p. N) — Title".

Details: Highlights and comments

4. Review your notes​

  1. Open the Notes tab.
  2. Switch between Sticky notes and Graph views. The graph shows notes, comments, highlights and folders.
  3. Open a note to edit it. The Sources bar shows what it's attached to, such as a publication, map node or cluster.
  4. Organize notes into folders and give them colors.

Details: Notes · Note editor

5. Collect evidence in Research in Formation​

Research in Formation (RIF) holds research objects: the concepts, theories, methods, publications, authors and other things your argument rests on. Each one gathers its evidence.

  1. Click RIF it on a PDF passage, a publication, a map node or a chat answer.
  2. In the Add to RIF dialog, either:
    • search under "Search existing Research Objects" and add the evidence to one, or
    • click + Create New Research Object.
  3. Click Create Research Object, or Save for Review to decide later.
  4. Open the Research in Formation tab. Items you saved for review wait in the Pending review queue. Click Review to file them.

Details: Research in Formation

6. Shape your argument​

  1. On the RIF stage, pick a layout: Concentric circle, Box or Pyramid.
  2. Place objects at the Focus, Secondary or Background level.
  3. Open an object's Research Record to see its type, origin, evidence (highlights, quotes, AI answers) and links. Use "Link an object…" to connect related objects.
  4. When an object has enough evidence, click Expand into Working Note to start writing from it.

Then turn your notes into text with citations. See Write with citations.

Ask about what you're reading​

Click Chat about this on the publication. The research assistant reads the PDF text if SciNodes holds a copy, plus your notes and highlights on it. The first question about a publication can take up to about 20 seconds while the assistant reads it. Long full texts use more credits.

Details: Ask AI about your research

Tips​

  • By default, fetching or uploading a PDF, writing a note or adding to RIF also files the publication into My references. Change this in User Preferences. See Preferences.
  • Use RIF it for the passages that support a claim and Highlight for everything else you want to find again.
  • SmarterPDF, a clean text-and-tables view of each PDF that you can annotate too (coming soon). See SmarterPDF.

FAQ​

Can SciNodes find the full-text PDF for me?​

When an open-access copy can be found, SciNodes shows Fetch PDF. Click it and SciNodes fetches the copy in the background. Otherwise, upload your own copy with Upload PDF.

Where do my highlights go?​

They stay on the PDF and are saved to the project's Notes automatically, titled "Highlight (p. N) — Title".

Can I download a PDF with my annotations?​

Yes. Click Download PDF in the viewer toolbar. The downloaded file includes your annotations.

What is a research object?​

A research object is an idea your research rests on, such as a concept, theory, method, publication or author. It collects evidence from PDFs, maps and chats so you can see what supports it.