Importing & Exporting

A bibliography manager is only as useful as the references you can get into it and the formats you can get back out. Bibliofile has grown a full set of get-references-in and get-references-out paths that sit alongside the in-app Online search: you can paste BibTeX straight from the clipboard, drag and drop files onto the publications table, import from a file in BibTeX, RIS, or EndNote format, export your whole library to BibTeX, RIS, CSV, a styled HTML bibliography, or an RTF reference list — and clone the whole library, attachments and all, into a copy you can experiment on.

This chapter covers every one of those paths in depth: exactly what each one accepts, how cite-key collisions are handled, what fields are mapped where, and what lands on disk. Because importing adds entries to whichever library you have open — and, like every other edit, does not touch your .bib file until you Save — it is worth knowing precisely what each method does before you reach for it.

7.1 The four ways in, at a glance#

The first three are covered here; online search has its own chapter. Whichever method you use, the same two rules apply: cite keys are kept unique (a clash gets a -1, -2, … suffix), and the import is in memory until you Save.

Every import also ends the same way, so you can see what arrived: the sidebar selection is cleared back to the whole Library (a new entry that didn't match your current group would otherwise be invisible), the table reloads, and the first newly-added entry is selected and shown in the detail pane. Any warnings from the import appear in the status bar.

7.2 Pasting BibTeX from the clipboard#

The fastest way to capture a single reference is to paste it. Most databases and search engines — Google Scholar, publisher pages, the ACM and IEEE libraries, arXiv — offer a "BibTeX" or "Export citation" button that puts an @article{…} record on your clipboard. Bibliofile turns that clipboard text into a real entry.

There are two ways to do it — a menu command and a bare paste — and both end up in the same place.

7.2.1 Edit → Paste Publication (the explicit way)#

1. Copy a BibTeX entry to your clipboard from wherever you found it.
2. With a library open, choose Edit → Paste Publication (⇧⌘V / Shift+Ctrl+V).

The app reads the clipboard, parses it as BibTeX, and adds every entry it finds, then selects the first of them so you can review and tidy it in the detail pane.

The same command also sits in the Publication menu as New Publications from Clipboard (⌥⌘L / Alt+Ctrl+L), where BibDesk users will expect to find it — right after the two New Publication items, since that is what it does: it makes new publications, just from text you already have. The two menu items are the same command with the same behaviour and either shortcut works; use whichever you remember. (Unlike BibDesk's version there is no ellipsis and no parsing sheet — it reads BibTeX from the clipboard and adds the entries immediately, with no further input from you.)

If the clipboard is empty — or the app can't read it at all — you get "The clipboard has no text to paste." in the status bar rather than a menu item that appears to do nothing.

7.2.2 Just paste (the quick way)#

If the publications table has focus — that is, you are not currently typing in a field, a search box, or a text area — you can simply press ⌘V / Ctrl+V. When the clipboard text looks like BibTeX (it contains something of the form @type{), the app intercepts the paste and imports it instead of doing an ordinary text paste.

7.2.3 What paste accepts and how keys are assigned#

• One or many entries. The clipboard may hold a single @article{…} or a whole block of several entries; all of them are imported in one go.
• Missing cite keys are generated. An entry with no cite key is given one, derived from its author and year using your cite-key format (the same generator as the Generate button — see Editing entries). If nothing usable can be derived, it falls back to a provisional imported key you should rename.
• Clashing cite keys are disambiguated. If a pasted entry's key already exists in your library, the app appends -1, -2, … until it is unique, so pasting never silently overwrites an existing entry.
• Attachment blobs survive. If the pasted BibTeX already contains Bdsk-File-N attachment fields, they are carried across intact.

If the clipboard text contains no recognisable entries, the app does nothing and records the warning "No BibTeX entries found in the pasted text." — a sign the text wasn't BibTeX (a common mistake is copying a formatted citation rather than its BibTeX source).

7.3 Drag and drop#

You can drop files straight onto the publications table — the middle column of the window, which is the import drop target. As soon as you drag files over it, an overlay covers that column reading "Drop .bib or files to import", confirming the drop will land. Release the files and the app imports them according to their type.

The drop target is that column deliberately, not the whole window, because the other panes take drops of their own: dropping a file on the detail pane attaches it to the entry you are looking at (and dropping an image on its journal cover sets the cover), while the groups sidebar takes entries dragged onto a static group. Aiming at the table is what tells the app you mean import. The overlay also appears only for files dragged in from outside — dragging a row out of the table doesn't raise it. With no library open, the welcome screen accepts a dropped .bib too, but there it opens that file rather than merging it.

This makes drag-and-drop the fastest way to build a library: drop a pile of PDFs at once and each identified paper is looked up and turned into a real entry with the PDF attached. While the lookups run, the status bar reads "Looking up references…"; when it finishes it shows a summary such as "Imported: 3 from identifier, 1 linked to existing, 2 to review."

Reviewing PDFs with no identifier#

A PDF with no DOI or arXiv id (e.g. an older scan, or a working paper that prints no identifier) isn't auto-added — that would litter a large library with empty, hard-to-find placeholders. Instead all such PDFs from the drop open a review dialog: the PDFs are listed on the left, with the normal entry editor on the right. Click a PDF to edit its entry (type, cite key, fields, notes — the title is pre-filled from the filename), then:

• Accept — creates the entry in your library and attaches that PDF (AutoFiling it only if you have AutoFile attachments when added switched on — see AutoFile).
• Discard — drops the PDF; no entry is created.

Nothing is added to your library until you Accept — the drafts live in a scratch area, so closing the dialog (or discarding) leaves no trace. Tip: fill in the Author, Title, and Year, then click Generate for a proper cite key.

7.4 Importing from a file#

When you want a tidy, dialog-driven import — choosing exactly which files to bring in — use the Import menu.

1. With a library open, choose File → Import → From File (BibTeX / RIS / EndNote)… (⇧⌘I / Shift+Ctrl+I).
2. In the file dialog (titled Import), select one or more files. The dialog filters to Bibliographies (.bib, .ris, .enw, .enl, .xml) by default; switch the filter to All Files if you need to.
3. The chosen files are imported by type — .bib files merge their entries, .ris files import their records, EndNote .enw/.enl/.xml files import their records, and any other file you force through the All Files filter is handled just as with drag-and-drop: a PDF is looked up by its DOI/arXiv id (no-identifier PDFs open the review dialog), and any other file becomes a stub with that file attached.

The same File → Import submenu also contains Search Online (CrossRef / arXiv)… (⇧⌘O / Shift+Ctrl+O), which opens the online-search window — the fourth way in, documented in its own chapter.

7.4.1 What survives a round trip#

A .bib you merge in — or open outright — is re-serialized when you next save, so it is worth knowing what that does and doesn't preserve. The layout is rewritten into the app's canonical shape (see Normalisations applied on save), but the content is meant to come back out exactly as it went in, including these cases that a careless parser gets wrong:

• % comments inside an entry are treated as comments, so a % line containing a stray ,, {, or " cannot knock the field splitting out of step and drop real fields. A free-text @comment{…} or @preamble{…} body is left alone instead, so a literal % in one (JabRef and Zotero emit these) survives untouched.
• A missing } damages only the entry it belongs to: the parser resynchronises at the next @type{ that starts a line, rather than swallowing every entry after it.
• Unmatched braces in a value — a title containing a lone { or } — are written out as the balanced TeX control words {\textbraceleft} and {\textbraceright}, which re-read as the same characters and are shown as { and } in the app. Values whose braces are already balanced (which is nearly all of them) are written through unchanged.

7.5 The RIS format#

RIS is a long-standing tagged citation format exported by EndNote, Zotero, Mendeley, PubMed, ScienceDirect, and many library catalogues. A RIS record is a list of two-letter tags, one per line, bracketed by a TY (type) line and an ER (end of record) line:

TY  - JOUR
AU  - Einstein, A.
AU  - Podolsky, B.
AU  - Rosen, N.
TI  - Can Quantum-Mechanical Description of Physical Reality Be Considered Complete?
JO  - Physical Review
PY  - 1935
VL  - 47
SP  - 777
EP  - 780
DO  - 10.1103/PhysRev.47.777
ER  -

When you import RIS (by drag-and-drop, by File → Import, or by dropping a .ris file), each record becomes a BibTeX entry. A trailing ER is optional — the last record is imported even if its ER line is missing. As with every other import, cite keys are generated and de-duplicated automatically, and the library is marked unsaved.

7.5.1 RIS type → BibTeX type#

The RIS reference type (TY) chooses the BibTeX entry type:

Any reference type not in the table is imported as misc. (You can correct the type afterwards from the Type dropdown — see Editing entries.)

7.5.2 RIS tag → BibTeX field#

Tags the importer does not recognise are ignored, so an unusual RIS file imports cleanly with its mappable fields and quietly drops the rest.

7.5.3 EndNote import#

Bibliofile reads the two EndNote formats you actually run into:

• Refer / tagged (.enw) — the line-oriented %X value format. This is what Google Scholar's "EndNote" download produces, and what many journal sites offer as "Download citation → EndNote". Records are separated by blank lines; %A (author), %E (editor) and %K (keywords) may repeat.
• EndNote XML (.xml, .enl) — EndNote's richer <xml><records>… interchange export. Text wrapped in EndNote's <style> runs is unwrapped to plain text automatically.

The reference type sets the BibTeX type (Journal Article and Electronic Article → article, Book and Edited Book → book, Book Section → incollection, Conference Proceedings/Paper → inproceedings, Thesis → phdthesis, Report → techreport, Manuscript and Unpublished Work → unpublished; anything else, including Web Page and Generic, → misc). Common fields map across as you would expect:

As with RIS, EndNote imports get fresh generated cite keys and are added as new entries (nothing is overwritten); unrecognised tags are ignored.

7.6 Exporting your library#

To get references out of Bibliofile in a different format, use the Export menu. Each format writes the whole library to a file you choose. (This section also covers the two neighbouring ways out that aren't file formats at all: printing and cloning the whole library.)

Choose File → Export → and then one of:

Each choice opens a Save dialog (titled Export) with a sensible default filename — your library's name with the appropriate extension. None of the export items has a keyboard shortcut; they live entirely in the File → Export submenu.

To export just some entries, select them in the table and choose File → Export → Selected Entries (BibTeX)…. This writes only the highlighted entries (or, if exactly one row is selected, that one) to a .bib file — handy for pulling the references for a single paper out of a large library. The default filename is your library's name with a -selection suffix.

If you have defined any export templates of your own, they appear at the bottom of the same File → Export submenu — each as a submenu offering Whole Library…, Shown Entries…, or Selected Entries…. That is the route to a layout of your own design, and the only export route that can write just what the table is currently showing. See Customizing panels → Export templates.

7.6.1 RIS export#

Each entry is written as a RIS record. The BibTeX type is mapped to a RIS TY (for example article → JOUR, book → BOOK, inproceedings → CPAPER, phdthesis → THES, misc → GEN; unknown types fall back to GEN), and the fields are emitted as their RIS tags — AU per author, A2 per editor, TI, T2 (journal or book title), PY, VL, IS, SP/EP split from Pages, PB, CY (from Address), SN (from Isbn/Issn), DO, UR, AB, a KW per keyword, and ID carrying the cite key. Values are de-TeXified on the way out so accents and braces export as plain Unicode text.

7.6.2 CSV export#

The CSV has a fixed header row and one row per entry, with these columns:

Cite Key, Type, Authors, Title, Year, Journal, Volume, Pages, Publisher, DOI

The Journal column falls back to the book/proceedings title when an entry has no journal, multiple authors are joined with ; , and cells containing commas, quotes, or newlines are quoted and escaped to standard CSV rules. The result opens cleanly in any spreadsheet program.

7.6.3 HTML export#

The HTML export produces a complete, self-contained web page — a styled bibliography you can open in a browser, email, or publish. The page has its own inline styling (so it needs no external CSS), a heading showing the library's name and the number of entries, and one formatted reference paragraph per entry:

Einstein, A., Podolsky, B., Rosen, N. (1935). Can Quantum-Mechanical
Description of Physical Reality Be Considered Complete?. Physical Review,
47, 777. https://doi.org/10.1103/PhysRev.47.777 [einstein1935]

Each reference shows the authors, the year, the title, the venue, volume and pages, a clickable DOI link, and the cite key in brackets — and any field an entry lacks is simply left out of its line. The page is generated from a Handlebars template, the same lightweight templating approach BibDesk's old custom .template language served, and every interpolated value is HTML-escaped, so titles with <, >, or & export safely.

7.6.4 Printing a bibliography#

File → Print… (⌘P / Ctrl+P) produces a printed, CSL-formatted bibliography — the same styled citations you see in the detail pane, one per entry, with a hanging indent and a heading. Choosing it opens your system's standard Print dialog, which on macOS also offers Save as PDF (a quick way to get a formatted PDF reading list without exporting a file first).

Unlike Export, Print follows what you are looking at:

• If you have two or more entries selected, only those are printed.
• Otherwise everything the table is currently showing is printed — the current group (the whole library, or a static or smart group's members) narrowed by whatever is in the live-search box.

The heading is your library's name, and — when a group other than the whole library is selected — the group name too (for example math-demo — To Read). The entries are formatted with your default citation style (set in Preferences), so switching styles there changes how the printout reads.

7.6.5 RTF export#

File → Export → RTF (formatted bibliography)… writes the same CSL-formatted references that Print produces, but to an .rtf file instead of the printer — one reference per paragraph, formatted with your default citation style, ready to paste into a manuscript or hand to a co-author who doesn't use BibTeX. The italics and bold the style asks for are carried into the RTF; links become plain text, since RTF has no clickable-DOI equivalent here.

Unlike Print, this is one of the whole-library exports: it writes every entry, not the current selection or view.

7.6.6 Cloning a bibliography#

File → Clone Bibliography… makes a complete, self-contained copy of the open library — including its attached files — and opens it in a new window. It exists for the moment when you want to try something drastic (a big Find & Replace, a re-run of AutoFile, OCR over a pile of scans) without risking the library you actually depend on.

1. Choose File → Clone Bibliography…. A Save dialog (titled Clone Bibliography) opens, defaulting to «your library» copy.bib beside the original.
2. Pick a name and location. The clone is written there, and every file the library links is copied into your Papers folder, named by your AutoFile format exactly as a freshly added file would be — see AutoFile. With no Papers folder set, the copies go into a «clone name» Papers folder next to the clone instead, and the summary tells you so.
3. The clone's attachment links are rewritten to point at those copies, and the clone opens in its own window.

A summary then reports what happened — "Cloned 412 entries to 'thesis copy.bib'" — along with how many attachments were copied and the folder they went into, and a warning list if anything could not be copied.

What the clone guarantees, and why it is not just "Save As":

• The original is untouched. Its file, its unsaved-changes state, its undo history, and — crucially — every file it links are left exactly as they were. Your open window keeps pointing at the original, not at the clone (that is what Save As does instead).
• No existing file is overwritten by the copies. An attachment copy always gets a fresh, non-colliding name, even when a file of that name is already sitting at the target — so a clone can never end up sharing a PDF with the original. And cloning onto a .bib that is currently open (the source itself, or another window) is refused outright. (The save dialog will still ask before replacing some other, closed .bib you point it at, as usual.)
• Unsaved edits come along. The clone is written from what is in memory, so you needn't save the original first.
• Files it can't copy are reported. If an attachment is missing from disk or can't be read, the clone keeps that link pointing at the original file — a live link beats a broken one — and the summary says so. Those particular files are shared with the source library, so treat them as read-only in the clone.
• The encoding is preserved. The clone is written in the source's text encoding; if a rewritten path contains characters that encoding can't hold, the summary warns you rather than silently mangling it.

7.7 Quick reference#

7.8 Troubleshooting#

"Paste Publication did nothing / 'No BibTeX entries found.'" The clipboard didn't contain BibTeX. Make sure you copied the BibTeX source (@article{…}), not a formatted citation or an HTML snippet. Re-copy from the source's "BibTeX" / "Export citation → BibTeX" option and paste again.

"A plain ⌘V didn't import — it pasted text instead." The bare-paste import only fires when the table (not a text field) has focus and the clipboard looks like BibTeX. If your cursor was in a field, the search box, or a text area, ⌘V pastes there as normal. Use Edit → Paste Publication (or Publication → New Publications from Clipboard, ⌥⌘L), which imports regardless of focus.

"I dropped files on the window and nothing happened." Only the publications table — the middle column — is the import drop target. A file dropped on the detail pane is attached to the entry you are looking at instead, and one dropped on the groups sidebar does nothing. Watch for the "Drop .bib or files to import" overlay: if it isn't showing, the drop won't import.

"I dropped a PDF but the entry has no real title/author." If the PDF prints a DOI or arXiv id in its first pages, the entry is built from a real online lookup. If it doesn't (e.g. an older scan), the PDF opens the review dialog instead of being auto-added — fill in the fields there before you Accept, or look the paper up with Online search and copy the fields across. (Anything you Accept with only the filename title can be edited later, too.)

"My import isn't in the file after I quit." Imports are unsaved edits. Press ⌘S / Ctrl+S (or click Save) after a batch of imports. There is no autosave unless you enable it in Preferences.

"The RIS import dropped some fields." Only the RIS tags in the mapping table are imported; unrecognised tags are ignored. Add any missing fields by hand in the detail pane.

"My export looks reformatted / lost my Markdown." The CSV, RIS, HTML, and RTF exports de-TeXify and flatten values for their target format, so braces and TeX accents become plain text and Markdown in abstracts is not rendered. This is expected — those formats can't carry BibTeX/Markdown markup. Your .bib library itself is untouched by exporting.

"Clone Bibliography wouldn't write where I asked it to." A clone is refused if the file you picked is a bibliography that is currently open — including the original itself. Close that window (or pick another name) and try again. The refusal is deliberate: the open library's in-memory state would overwrite the freshly written clone the next time it saved.

"The clone says some attachments couldn't be copied." Those files were missing from disk or unreadable, so there is no copy to link. The clone keeps those particular links pointing at the original files, which means editing or re-filing them from the clone will affect your real library — the summary lists exactly which entries are affected. Fix the links (see Find Broken Links) and clone again if you want a genuinely independent copy.

See also#

• Online search — the fourth way in: pull references from CrossRef, OpenAlex, PubMed, arXiv, or a DOI/ISBN lookup.
• Editing entries — clean up an imported entry, and the Copy as BibTeX / Copy Citation clipboard commands.
• Attachments — how dropped PDFs are stored, and AutoFile (which decides where a clone's copied files land).
• Customizing panels — writing your own Handlebars export templates, which then appear in File → Export.
• Scripting with JavaScript — import, export, and transform entries programmatically (doc.import, doc.export, doc.save) when the menu commands aren't enough.
• Shortcuts & reference — the full menu and keyboard reference.