PDFs and the study window

The 3 Library tab keeps one PDF per article, named after its citation. The app's reader shows a PDF, lets you highlight it, and lists the highlights with a checkbox each, to tick when the passage is in your article. The study window shows that reader next to the Radiopaedia page you are editing.

Adding a PDF to the library

There are two ways to add a PDF. In both, the file is renamed:

Author Year - Journal - Title [PMID 12345678].pdf

The author is the first author's surname. The journal is the abbreviation PubMed gives (J Oral Maxillofac Surg), and a long title is shortened. The PMID makes the name unique, and lets the file be matched to its article again if the database is lost.

Saving an open-access copy

When Unpaywall or Semantic Scholar has a link to a free copy, the card in the Screening tab shows ⤓ Save free PDF, which downloads the file. Many free links lead to the publisher's web page and not to the file. In that case the app shows a message, and you download the PDF from that page yourself and add it as described below.

Adding a PDF you downloaded

LibKey uses your library's login in your browser, so you download these PDFs in the browser as usual. Then drag them onto 📎 Add PDFs (drop them here) at the top of the Library tab, one or several at a time. For each file the app looks for the article in two places:

1. In the archive. It looks for a DOI in the text of the PDF, then a PMID, then the title of an archived article on the first page. The button is Add to library.
2. On PubMed, if the article is not in the archive. It searches by DOI, then by title. The title is taken from the PDF's metadata or from the line in the largest type on the first page. A title search is accepted only when exactly one PubMed article has the same title. The button is Add to archive and library, which imports the PubMed record first. This also works for an article that you marked read and that was deleted from the archive.

A PDF that matches no article gets a field where you can type the PMID. With more than one matched file, Add all N recognised PDFs adds them together. The file you dragged stays where it was. The library keeps its own copy.

Only a DOI or a title is sent to PubMed. A title is sent only when the first pages look like a paper, meaning that at least two of Abstract, Keywords, Introduction, Received and similar words appear. PubMed is asked about each file once per run of the app, and only if the NCBI email is set.

Managing the library

Each PDF in the tab has these buttons:

• 📖 Read opens it in the reader.
• Show in folder shows the file in the system file manager.
• Rename to the citation appears when the file name differs from the citation name, and renames the file.
• 🗑 Remove deletes the file from the library, after a confirmation.

The fields above the list filter it by text (title, author or PMID), by reading list, and by the draft that cites the article.

An article that has a PDF is not deleted at startup when it is marked read. The same applies to articles in a reading list.

To change the library folder, set PDF library folder under ⚙️ Settings in the sidebar. The default is PDFs inside the data folder. The database stores only the file names, so you can move the folder to another disk and then set the new location.

Reading and highlighting

📖 Read in the Library tab, or 📖 Read PDF on a Screening card, opens the PDF in the app's reader, in a separate window. The study window uses the same reader.

The reader has two views. PDF shows the document, fitted to the width of the window. Highlights shows one box per highlight, in reading order, with its page, its colour and its note.

To highlight, select text in the PDF view. A bar appears under the selection, with four colours (yellow, green, blue, pink) and U for underline. The keyboard shortcuts are 1 to 4 for the colours, U for underline, and Esc to cancel.

The highlight is written into the PDF file as a standard annotation, so other PDF readers, such as Preview or Acrobat, show it too. A highlight is on one page. A selection that continues on the next page is highlighted on the first page only.

These actions are on each box of the Highlights view, and in the bar at the bottom of the PDF view:

• Note writes a note into the PDF. Other readers show it as a comment.
• Delete removes the highlight from the PDF.
• Copy copies the text to the clipboard.
• Show in PDF goes to the highlight in the PDF view.
• The checkbox marks the highlight as done. Hide done hides the ticked ones.

The ticks are stored in the database and not in the PDF. Highlights made in other programs are also listed: the app reads them again whenever the file changes. It reads highlight, underline, squiggly and strike-through annotations, with their notes. A tick is kept when the file is saved again. A highlight deleted from the PDF is removed from the list.

In the PDF view the current highlight is outlined and the done ones are marked ✓. The bar at the bottom moves between them:

Key	Action
J or →	Next highlight
K or ←	Previous highlight
Enter	Mark as done and go to the next one that is not done
X or space	Tick or untick
H	Highlights view
P	PDF view

In the Library tab, each PDF with highlights has a section such as 🖍 12 highlight(s) · 3 done, with the same checkboxes. A tick made there appears in the reader within about 4 seconds, and a tick made in the reader appears in the tab when it is redrawn.

The study window

In the 4 Write tab, open 🪟 Study window: the Radiopaedia page next to a PDF and set three things:

• Radiopaedia page: choose it from the article list, from Radiopaedia's search, or by pasting a URL. The page of a Radiopaedia article is saved with the draft.
• PDF next to it: a PDF from the library, or none. The PDFs cited in the draft are first in the list and marked ★.
• Layout: ◫ Side by side or ⬒ One above the other.

🪟 Open study window opens two windows. One is Radiopaedia in a browser window of its own, where you can sign in and edit. The login is kept between sessions and is separate from your usual browser. The other is the reader described above.

The Radiopaedia article list

The article list is a CSV file exported from Radiopaedia's article search, with the columns Title, URL, Systems, Sections and the date of the last edit. Put it in the data folder that radiowriter --where prints. Name it radiopaedia-articles-<date>.csv (it can be gzipped) or search.csv. If there are several radiopaedia-articles files, the last one in alphabetical order is used. search.csv is used only when there is no radiopaedia-articles file.

The file is not included with the app. Without it, you can still choose the page from Radiopaedia's search or by URL.