References & citations

The pieces you dropped or bookmarked into Nomima aren't just there to read — you can work with them. Open any source in a calm in-app reader, highlight the passages that matter, and turn a highlight into a proper citation in one of your notes: a verbatim quote with real bibliographic attribution and a live link back to where it came from. Every source you cite gathers in a top-level References library, so your reading and your writing stay joined up.

The reader with highlights

Open a knowledge source — a file, an RSS article, or any web page you've bookmarked — and it opens in a distraction-free in-app reader: real structure kept, none of the clutter of the open web. Select a run of text and a small menu appears with your highlight categories. Pick a colour to drop a highlight, or hit the cite action (the quote mark) to highlight and send that passage straight into a notebook as a citation — Nomima asks which notebook to put it in.

Highlights are persistent — they're saved against the source and come back every time you open it — and you can recolour or remove any of them later, or send an existing highlight to a note whenever you like.

• Colour = meaning. Each colour is a research category (Method, Key findings, Conclusion…), so the way you'd colour-code a printed paper carries through the reader, the library and your citations. You set the categories up yourself — see Highlight categories.
• Cite in one step. The cite action does two things at once: it saves the highlight and drops a verbatim citation block into the notebook you choose, carrying the source's attribution with it.

Citations in your notes

A citation lands in your note as its own block — a verbatim, non-editable quotation. That's deliberate: a citation must never quietly drift from what the source actually said, so the quote text is read-only (you can select and copy it, or delete the whole block, but not retype it). Its words are still folded into search, so citations stay findable by keyword.

• A "Source:" pill. Every citation carries an atomic Source reference chip. Click it and the in-app reader re-opens on that exact source. If the source is later removed from your vault, the pill greys out to a struck-through "source removed" tombstone rather than dead-ending.
• Research-grade metadata. Alongside the quote sit the details that make it a real citation — document type, author, publisher, the published date and the accessed date (when you captured it) — plus a clickable identifier for arXiv ids and DOIs.
• A lineage chip. A small coloured chip shows which highlight category the quote came from (e.g. Method), so a citation remembers why you flagged it. It snapshots the category name at capture time, so it survives later renaming.
• One-click copy. A copy button lifts a formatted citation — every author, the quote, publisher, dates and URL — onto your clipboard.

Quotes, whole-work references, and live updates

Under the hood a citation block comes in two shapes, and Nomima picks the right one for you:

• A quoted passage. The everyday case — you highlighted a run of text and sent it to a note. The block shows that verbatim quote with a quote-mark icon and a Source: row.
• A whole-work reference. When there's no highlighted passage — you're citing the source itself, not a line from it — the block instead shows a formatted reference line (author, year, title, publisher, link) with a book icon and a Reference: row.

Citations stay in sync. A quote in a note and its entry in the library are the same underlying citation, so editing a note keeps everything honest: delete a citation block and the source's Cited in list — and any open bibliography — update on the next save, with no manual refresh and no stale reference list left behind.

The References library

Everything you cite gathers in References — a new top-level item in the sidebar (the bookmark icon at the bottom). It's a two-panel library: a searchable list of every source down the side, and a detail view for whichever one you select. Filter the list with the chips along the top: All, Files, Web, Articles, Manual.

Add a reference from the + menu at the top of the list:

• By URL or DOI — paste a link, a DOI or an arXiv id and Nomima resolves the title, authors and date for you (DOIs via Crossref, arXiv ids via arXiv).
• Upload a file — pull in a PDF or document as a reference. It's stored privately for citing, without cluttering any notebook.
• Enter manually — type in a source that isn't a file or link: a book, a paper, an email, a message, a report. Per-type fields keep the form sensible (an email asks From and Mailbox, a journal article asks Authors and Journal).
• Connect an account… — jump to Connectors to hook up a private workspace so its pages resolve too.

Select any reference and its detail view gives you the full picture:

• Read it your way. Open the source in the in-app reader, read an attached PDF in a built-in viewer (uploaded PDFs and arXiv papers alike), pop it into a live in-app web view, or open it in your browser.
• Abstract & details. For papers and articles the abstract sits up top (expandable), above a tidy metadata panel — authors, type, venue, the published and added dates, and a clickable DOI.
• Highlights. Every highlight you've made on that source, each with its category colour. Add quote sends any one to a notebook as a citation; once it's been quoted, a Quoted link jumps straight to that block in your notes.
• A formatted citation in the style of your choice, with copy and BibTeX/RIS export — see Citation styles & bibliographies below.
• Tags & collections to file it away — see Organizing your library.
• "Cited in" backlinks — a list of every note that quotes this source; click one to land on the exact block.
• Edit, Refresh or Remove. Edit fixes up the title, authors, publisher or date; Refresh re-pulls metadata from the web for a link or DOI. Remove is a clean reset — it clears the reference's highlights so you can start fresh, while any citations you already dropped into notes keep their text.

Organizing your library

As the library grows, a handful of tools keep it in order — all in the References view.

Tags

Give any reference free-form tags. In its detail view, the Tags section shows the tags it already carries as removable pills; hit ＋ Add tag to type a new one. Nomima also offers a Suggested row of tags it derived from that reference's own title and abstract — the same local engine that suggests #hashtags in the editor — so click one to add it, or Add all. Tags read as #hashtag pills, and when you quote a tagged reference into a note its tags fold into that note too: the reference's tags make the notes that cite it findable and graph-linked, exactly like a hashtag you typed yourself. The library search box also matches tags, so typing a tag name filters the list to the references that carry it.

Collections

Collections are named folders of references — a reading list, a project's sources, a literature review. They live in the Collections section of the left rail: click ＋ and type a name to create one, and each row shows how many references it holds. Click a collection to filter the list to it; hover a row to rename or delete it. On a reference, its own Collections section lists the collections it's in as chips, and an Add to collection menu lets you toggle membership or spin up a new collection on the spot. Collections are pure organisation: delete one and its references stay in your library.

Saved searches

Filtered the library down to just what you want? Save that view. Whenever a filter is active — search text, a kind chip, or a collection — a Save search chip appears; name it and it's pinned as a chip under the filters. Click a saved search to re-apply its whole filter in one go, or × to remove it. Saved searches are stored on your Mac.

Merge duplicates

Added the same paper twice — once by DOI, once by arXiv link? Open the + menu and choose Find duplicates…. Nomima groups references that look like the same work — a shared DOI, a matching title, or the same arXiv id, even when they were added different ways — and opens a review modal. For each group, pick which copy to keep (it defaults to the most-cited one) and hit Merge: the others' quotes, highlights and collection memberships move onto the one you kept, its tags and any missing metadata are folded in, and the duplicates are removed.

Citation styles & bibliographies

Nomima can format any reference in the scholarly style you work in, and roll a notebook's sources into a ready-to-paste bibliography.

Pick a citation style

Every reference's detail view has a Citation block with a style switcher — APA, MLA, Chicago and IEEE. Pick one and the formatted reference re-renders in it, with the DOI or link shown as a clickable in-place link. Below it, quick actions copy the reference in that style: Copy (the full reference), In-text (a short parenthetical like (Vaswani et al., 2017)), BibTeX and RIS (for LaTeX or a reference manager). Your style choice is remembered and shared everywhere citations are formatted.

A notebook's bibliography

Any notebook that cites sources can produce a bibliography of them. Open the notebook's header menu and choose Bibliography…. Nomima gathers every source you've quoted in that notebook, sorts them by author, and lists them formatted in your chosen style (the same APA/MLA/Chicago/IEEE switcher sits in the modal's header). Copy a single entry, Copy all as plain text, or export the whole list as BibTeX or RIS. The list stays live — add or erase a quote in the notebook and the bibliography updates with it.

Note: styles format from the metadata Nomima captured — authors, year, title, journal or publisher, DOI/URL. A missing field is simply dropped rather than left as an empty bracket, so keeping a reference's details tidy (or hitting Refresh to re-pull them) gives the cleanest output.

Search your whole library

Every reference is full-text searchable — its title, its abstract, and the full body Nomima captured — even a paper you've saved but never quoted. Two places surface those hits:

• The command palette. Press ⌘K and start typing. Matching references appear in their own References group, listed below your note matches so a long PDF never outranks your own writing. Pick one and Nomima jumps to the References library with it open.
• Summon. When the assistant searches your vault to answer a question it now reads your references alongside your notes — a relevant passage is folded in tagged · reference, with a share of the results reserved for references so a saved-but-never-quoted paper still reaches the assistant.

Smart Add

The By URL or DOI field is smarter than it looks — it takes more than plain web links. Paste any of these and Nomima resolves it into a typed, populated reference:

• a URL — the page is read for its title, byline and article text;
• a DOI — full metadata comes back via Crossref;
• an arXiv id — resolved against arXiv;
• a Slack, Confluence, GitHub, Notion or Jira permalink — recognised by its host and typed accordingly (a Slack message, a Confluence page, a Notion page…), so it files itself under the right kind.

Tip: for private workspace links — a Confluence page or a Notion doc only your account can see — connect that account first (below) so Nomima can actually read the page rather than just recognising the link.

Connectors

Some of the things you'll want to cite live behind a login — a private Confluence page, a Notion doc, a GitHub issue or PR. Connectors (in Settings → Connectors) let you paste a personal access token for each so those links resolve properly. Nomima supports:

• Atlassian — Confluence and Jira (needs your site URL and account email alongside the token);
• Notion;
• GitHub — also what powers the GitHub repo block below.

Your tokens stay on your Mac. Each token is stored in your macOS Keychain, never in Nomima's database, and requests go straight from your machine to that service — nothing routes through any Nomima server. Disconnect an account and its token is wiped from the Keychain.

Highlight categories

The colours you highlight with aren't arbitrary — each one is a research category, the way you'd colour-code a paper by section. You manage the set in Settings → Highlights, and it's shared everywhere colour carries meaning: the reader's picker, the References library, and each citation's lineage chip.

Nomima ships with a sensible section-based scheme you can keep or reshape: Introduction, Method, Key findings, Results, Discussion, Conclusion and Future research. From the panel you can:

• Rename any category;
• Recolour it from a fixed eight-colour palette (each colour is used by at most one category, so meanings never collide);
• Reorder them, so your most-used categories sit at the top of the reader's menu;
• Add or remove categories (up to the eight palette colours);
• Reset to defaults at any time.

Note: a highlight stores only its colour; its label is read from the current category list. Rename a category and every existing highlight of that colour re-labels with it — but citations already in your notes keep the label they were captured under, so their lineage stays true.

The /github block

A related trick for anyone tracking code: type /github, drop in a repo (as owner/name or a GitHub URL), and Nomima renders a live status card for it — stars, forks, open issues and PRs, the latest release, default branch, language and license, the latest CI result from GitHub Actions, and a graph of recent commits. It refreshes on its own, with a manual refresh button in the header.

Heads up: the card reads GitHub through your connected GitHub account, so connect one in Settings → Connectors first. There's a fuller entry for this block on the Advanced blocks page.

Where to go next. To get sources into the reader in the first place — dropping files, bookmarking pages, folding articles into your knowledge — see Capture & reading. For how tokens and reading stay on your machine, see Settings & privacy.