Annotate research papers offline — for literature review, peer review, and embargoed work

The moment you reach for this guide

You are three weeks into a lit review on 60 papers, or you have a peer-review assignment due next week, or a colleague has sent you an embargoed pre-print and asked for marginalia. Your reference manager's PDF reader handles highlights but you want more — sticky notes for marginal questions, freehand circles around figures, stamps for READ / CITE / Q1 / NULL-RESULT as a personal classification system. You also do not want to upload the embargoed pre-print or the peer-review draft to a cloud annotator. This guide walks the offline workflow on a desktop app.

The 13 annotation primitives, in research-workflow terms

Same primitives the lawyer-cluster sibling uses for contract review, relabeled for the lit-review job. Map your reading intent to the right primitive before you start — it makes the marked-up paper easier to scan months later when you come back for the thesis chapter.

• Highlight

  Color the background of a text selection. Standard use: highlight a key claim worth citing, a numerical result you want in the chapter, or a sentence you intend to quote.

• Underline

  Draw an underline beneath selected text. Useful for marking methods-of-interest, defined terms, or instrument/dataset names that recur across the lit review.

• Strikethrough

  Draw a line through selected text. Use sparingly — in research markup, strikethrough is for claims the paper itself retracts in a later section, or for sentences you disagree with strongly enough to flag.

• Sticky note

  The marginalia primitive. Single positioned note with optional body text — your own marginal questions, links to related papers, or 'TODO: re-read after I finish Bartlett 2019'. No comment-thread replies; FileHop is not Hypothes.is.

• Text box

  Inline typed text on the page. Use for longer marginalia that does not fit a sticky note, or to type a citation reminder next to a passage you want to come back to.

• Freehand drawing

  Stylus or trackpad freehand strokes. The 'reading on a Mac with the Magic Trackpad' primitive — quick scribbles, circles, arrows that do not fit a geometric shape. Strokes are preserved as vector points.

• Rectangle and circle

  Filled or outlined shapes with adjustable stroke width. The figure-circling primitive — outline a panel of a multi-panel figure, box a row in a results table, group a paragraph as 'the methods passage that matters'.

• Line and arrow

  Point at a value, connect two parts of a figure, draw a vector across the page. Useful for marking up a methods schematic, or for visualizing a citation chain across the paper.

• Stamp

  Customizable stamps with template, rotation, and optional top/bottom arc text. The personal-classification primitive — READ / CITE / CITED / Q1 / Q2 / NULL-RESULT / DOI?-NEEDED / METHOD-FOR-CH3. Apply by hand; FileHop does not parse stamps and there is no auto-classification.

• Whiteout (non-redaction)

  Paint a rectangle to hide content visually. NOT destructive — the underlying text is still in the PDF and would be recoverable. For destructive removal of participant identifiers in qualitative transcripts, use the separate Redact tool, not this primitive.

• Image

  Embed a PNG or JPG on the page. Useful for pasting a small reference diagram from another paper, a hand-drawn diagram from your notebook, or a screenshot of a related figure you want side-by-side.

• Signature

  Hand-drawn vector, typed text, or uploaded image. Researchers rarely sign in the reading pass — keep this primitive in mind for signing review-completed forms, co-author sign-off pages, or thesis-committee approval sheets.

• Text emphasis modes (combined)

  Highlight, underline, and strikethrough share an underlying selection model — you can apply them to the same text run in sequence and they layer cleanly on export. Pick a per-color convention (e.g., yellow=claim, green=method, pink=question) and keep it consistent across the lit review for fast skimming later.

Two practical consequences for the reading pass: (1) you can close the PDF and reopen it without losing marks-in-progress — annotation state is held in memory and rendered with tap-dot markers as you place them; (2) when you export the marked-up PDF, the wizard asks whether to overwrite the source or create a new flattened file. The default is 'create a new file', which keeps the source PDF clean for your reference-manager library.

Workflow B — Multi-reviewer consolidation (co-authors, peer-review panels)

When several people need to mark up the same manuscript without uploading it to a shared cloud workspace. Each reviewer annotates their own copy on their own machine and flattens; one person merges the flattened marked-up PDFs into a single review packet. The editorial wedge: the SERP does not walk this asynchronous-merge pattern, but it is the right answer for confidential peer review (where the journal's confidentiality clause prohibits uploads) and for embargoed-material co-author review.

1. 1

   Distribute the manuscript to each reviewer

   Send each reviewer their own copy of the same source PDF — encrypted attachment, secure file-share inside your institution, or a USB drop if the confidentiality obligation is strict. Each reviewer keeps their copy local. They do NOT share-link via a cloud annotator. There is no shared file and no concurrent edit — that's the trade against cloud collab, and it's the trade you wanted for this draft.

2. 2

   Each reviewer marks up their own copy

   Reviewer 1 reads and annotates in FileHop on their machine. Reviewer 2 does the same on theirs. Reviewer 3, same. Each reviewer is using the 13 primitives independently — there is no live cursor presence, no comment threads, no shared workspace. Convention: ask each reviewer to use a distinct annotation color (Reviewer A in red, Reviewer B in green, Reviewer C in blue, lead reviewer in orange) and to include initials in the filename of their flattened export so attribution is obvious at a glance. This convention substitutes for the per-comment attribution that cloud-collab tools provide automatically.

3. 3

   Each reviewer flattens and sends the marked-up PDF back

   Each reviewer exports a flattened _annotated.pdf via the export wizard (Workflow A, Step 4). They send the flattened PDF to the lead reviewer (or to the article's first author) via the same secure channel the source was distributed on. The flattened PDF renders identically in any PDF reader — the lead reviewer does not need FileHop to see the markup, which matters when the lead is on a managed institutional machine where they cannot install new software freely.

   Open the Merge PDF tool →
4. 4

   Lead reviewer merges the flattened PDFs into a single review packet

   Open FileHop's Merge PDF tool and combine the flattened marked-up versions in reviewer order — typically the clean draft first, then Reviewer A markup, Reviewer B markup, Reviewer C markup, then your own consolidated markup last. Page numbers run continuously through the packet, and you can scroll to see every reviewer's annotations on each section side-by-side. The merge operation runs locally; the PDFs do not leave your machine for the merge step. Distribute the packet to the article author or the panel chair via the same secure channel.

How offline annotation compares to the alternatives

Workflow comparison only, not a complete product comparison. Many researchers run a reference manager AND a desktop annotation tool AND an iPad reader — each for a different step of the reading pass. Pick the tool that matches the privacy posture of the specific paper or manuscript in front of you.

FAQs