Capacities (capacities.io) is a personal knowledge management (PKM) tool built around the concept of objects — typed items like books, people, concepts, and projects — rather than flat documents. Notes are structured around these objects and can be linked bi-directionally. It's popular with researchers and knowledge workers as an alternative to Notion, Obsidian, or Roam Research. Reading and annotating source material is a common first step before adding highlights to a Capacities space.

How do I add EPUB highlights to Capacities?

The most common pipeline is: convert PDF to EPUB → read and highlight in Readwise Reader → export highlights via Readwise to Capacities. Capacities has a Readwise integration that imports highlights automatically, tagged with the source metadata. Alternatively, copy highlights manually into a Capacities 'Book' or 'Article' object and link them to your notes. Capacities doesn't have a native EPUB reader, so Readwise Reader or a dedicated e-reader is the annotation layer.

Can I store EPUBs directly in Capacities?

Capacities supports file attachments on objects, so you can attach an EPUB to a 'Book' or 'Article' object for reference. However, Capacities doesn't have a built-in EPUB reader — you'd open the attachment in an external app. The primary workflow is to use an e-reader or Readwise Reader for reading and annotation, then import the highlights into Capacities as structured notes linked to a source object.

What PKM tools have the best EPUB and reading integration?

Readwise Reader has the deepest integration: it accepts EPUB uploads, lets you annotate, and exports to Obsidian, Logseq, Roam, Notion, Capacities, and other tools. Zotero supports EPUB natively in its built-in reader and can export annotations. Obsidian works well with the Readwise plugin. Capacities connects via Readwise. The common thread is: read and annotate in Readwise Reader or an e-reader, then let Readwise push highlights to your PKM tool of choice.

Is Capacities better than Obsidian or Roam for academic reading workflows?

It depends on your mental model. Capacities is object-centric (think: typed entities), which suits researchers who think in terms of 'this paper', 'this author', 'this concept'. Obsidian is file-centric with a flexible link graph — good for freeform note-making. Roam is block-centric with bi-directional references — good for daily notes and progressive summarisation. All three can receive EPUB highlights via Readwise. The EPUB conversion step is identical across all three workflows.

Capacities Workflow: Convert PDFs to EPUB for Annotated Reading Before Adding to Your Space (2026)

Updated June 2026 · Research

Capacities is a PKM tool built around typed objects — books, articles, people, concepts — and the connections between them. Most source material arrives as PDF. Converting to EPUB first, reading and annotating in Readwise Reader or on an e-reader, and then importing highlights into Capacities via the Readwise integration gives you a clean reading-to-notes pipeline. Here's how it works.

PDF-to-Capacities reading pipeline

Step	Tool	Output
1. Find source PDF	arXiv, PubMed, JSTOR, SSRN, or web	PDF file
2. Convert to EPUB	toolkit.bot	EPUB file
3. Read and annotate	Readwise Reader / Kobo / Kindle	Highlights + tags
4. Sync to Capacities	Readwise → Capacities integration	Highlights in source object
5. Write object notes	Capacities	Linked concepts, people, projects

Setting up Readwise → Capacities

Subscribe to Readwise (readwise.io)
Upload your EPUB to Readwise Reader, or connect your Kindle/Kobo account
In Capacities, go to Settings → Integrations → Readwise and connect your account
Highlights sync automatically into a Capacities 'Daily Note' or source object, tagged by document title
Link highlights to related concept objects, people, and project notes in your Capacities space

Why convert to EPUB before reading for Capacities

Better annotation in Readwise Reader — Readwise Reader accepts EPUB uploads and provides cleaner annotation than PDF (especially for two-column academic papers)
Source metadata preserved — toolkit.bot preserves document title in EPUB metadata; Readwise picks this up and uses it as the object name in Capacities
Comfortable long-form reading — read on a Kobo or Kindle with adjustable font and night mode before annotations flow to Capacities
Mobile reading — open the EPUB in Apple Books or Moon+ Reader on your phone; highlights from Readwise Reader sync to Capacities automatically

Frequently asked questions

What is Capacities?: Capacities (capacities.io) is a personal knowledge management (PKM) tool built around the concept of objects — typed items like books, people, concepts, and projects — rather than flat documents. Notes are structured around these objects and can be linked bi-directionally. It's popular with researchers and knowledge workers as an alternative to Notion, Obsidian, or Roam Research. Reading and annotating source material is a common first step before adding highlights to a Capacities space.
How do I add EPUB highlights to Capacities?: The most common pipeline is: convert PDF to EPUB → read and highlight in Readwise Reader → export highlights via Readwise to Capacities. Capacities has a Readwise integration that imports highlights automatically, tagged with the source metadata. Alternatively, copy highlights manually into a Capacities 'Book' or 'Article' object and link them to your notes. Capacities doesn't have a native EPUB reader, so Readwise Reader or a dedicated e-reader is the annotation layer.
Can I store EPUBs directly in Capacities?: Capacities supports file attachments on objects, so you can attach an EPUB to a 'Book' or 'Article' object for reference. However, Capacities doesn't have a built-in EPUB reader — you'd open the attachment in an external app. The primary workflow is to use an e-reader or Readwise Reader for reading and annotation, then import the highlights into Capacities as structured notes linked to a source object.
What PKM tools have the best EPUB and reading integration?: Readwise Reader has the deepest integration: it accepts EPUB uploads, lets you annotate, and exports to Obsidian, Logseq, Roam, Notion, Capacities, and other tools. Zotero supports EPUB natively in its built-in reader and can export annotations. Obsidian works well with the Readwise plugin. Capacities connects via Readwise. The common thread is: read and annotate in Readwise Reader or an e-reader, then let Readwise push highlights to your PKM tool of choice.
Is Capacities better than Obsidian or Roam for academic reading workflows?: It depends on your mental model. Capacities is object-centric (think: typed entities), which suits researchers who think in terms of 'this paper', 'this author', 'this concept'. Obsidian is file-centric with a flexible link graph — good for freeform note-making. Roam is block-centric with bi-directional references — good for daily notes and progressive summarisation. All three can receive EPUB highlights via Readwise. The EPUB conversion step is identical across all three workflows.