Microsoft OneNote is a brilliant tool for visual thinkers, with the ability to position notes anywhere on the infinite page. Furthermore, it provides rich organization capabilities with pages arranged in sections and notebooks. And OneNote for Mac seamlessly syncs all your content across Macs and iPads, and is even editable on the web at onenote online.
With today's update to OneNote, it now supports hyperlinks. PDFoo users can now copy from PDF and paste into OneNote to get a working PDFoo URL. Use the layout flexibility in OneNote for Mac to arrange the content in a way that makes sense to you. For example, the screenshot below shows my quick reference guide to best features in Scrivener for Mac. The blue URLs are pdfoo:// URLs and prefix "scrivmanv25" was assigned in PDFoo to the Scrivener 2.5 Letter-sized user manual in PDF format (available from the Scrivener support website).
It's a good idea to run OCR on the scanned PDF BEFORE you start adding a table of contents (TOC) to the PDF. This is because OCR apps usually create a new PDF, and may not know how to preserve the table of contents from the original PDF when writing out the new PDF. Your hard work in creating the TOC would then be wasted. Moreover, PDFs with OCR text allow text to be selected which can be used to build the TOC quickly as described below.
Note that PDFOutliner comes with an automatic TOC feature which parses the fonts used in a PDF - such as larger fonts used for chapter headings - to build a TOC hierarchy. However this "AutoTOC" feature doesn't work on a scanned PDF (which contain no text) or even an OCR PDF (which do not assign different fonts to chapters/body text etc.) In such cases, you have to "walk" through the PDF page by page, and add TOC entries. Here's how:
When you want to read and digest the content in a PDF thoroughly, PDFoo provides an efficient way to do so. The PDFoo app makes it possible to create a link to a specific location in the PDF, which allows you to focus on understanding the big picture while the details are just a click away.
Zengobi's Curio app has an amazing "lists" feature which allows you to position several list boxes on an infinite canvas (known as "idea space" in Curio.) If you select such a list box, and hit CMD+V to paste the clipboard contents, it gets automatically appended to the list. This makes it very convenient to use Curio with PDFoo: copy text from PDFoo, select a list box in Curio, and paste the content with a PDFoo URL appended to the text. The figure below shows a Curio idea space used to work through the OmniGraffle 6 user manual, and includes several "see also" links to detailed content in the PDF. In a similar manner, you can efficiently work through any important PDF using idea spaces in Curio and PDFoo copy-paste.
PDFCombo is a free app for Mac OS X 10.6 and later, available from the Downloads page.
Annotate PDFs in Evernote for Mac
What are PDFoo URLs?
When you click on a pdfoo:// URL, the PDFoo app responds just like when you click on a http:// URL, the Safari app responds (or rather, your default web browser). But the similarity goes further. In a http URL, there is a "server" on the Internet that Safari connects to based on the URL clicked. In the example below, the server is "onekerato.com". The rest of the URL conveys which page on the server should be displayed by Safari.
Similarly, a pdfoo URL has a "prefix" which identifies the PDF that PDFoo should connect to, and the rest of the URL identifies which page or location in the PDF should be displayed. In most cases, the rest of the URL is just numbers which corresponds to page numbers & locations on a page. However, when you drag out a TOC entry from the PDF, you will get a readable URL. When you click on a pdfoo:// URL, PDFoo figures out which page or TOC entry to open. Moreover, just like every website is a unique "server", similarly each PDF on your Mac must be assigned a unique "prefix" in PDFoo before you start dragging or copying out URLs.