How to collect articles, take notes and organize them..

I need help with something…

First, I want to collection information by scanning from books and collect articles from the web.

Second, I want to annotate/take notes on that information in a way that I can easily reference later.

I have found that the way I put information into DT changes how it is imported… The ideal way I have found is to highlight the text I want from the browser and then drag it directly into the DT database. This creates a webarchive of only what I selected and preserves the formatting (if you drag it onto the dock icon you get a text document and lose formatting OR if you use the bookmarklet you get everything on the web page including adds which makes the “see also” feature pointless. Who wants to index Google Adds?).

Then, I right click and turn the webarchive into a pdf so I can highlight and take notes using Skim. DT is aware of my Skim annotations (very nice) but there it doesn’t index them or make them search-able.

Is there a better way? Is there a way to take lots of notes and then refer back to them later in an organized way?

I used to use the app Notebook that let you assign labels to highlight colours and then flip through all your highlights in an index or do a search within your notes or highlights.

I tried the Devonwiki feature but this only works in text files so PDF’s are out…

I’d really appreciate it if anyone has an ideas here… DT really blows all other note taking/info organizer apps away but I need to figure this out…


I use a rich text note to comment on a referenced document, whether the referenced document is PDF or any other filetype.

A convenient way to to that is to select the referenced document, then choose Data > New with Template > and choose “Annotation”. This will result in a new rich text note, datestamped and with a hyperlink to the referenced document. The Name of the new note includes the Name of the referenced document, so that a Name search of the referenced document will also bring up the annotation note.

This is especially convenient, as there’s a keyboard shortcut to invoke the Annotation smart template, without needing to navigate the Data menu items.

If the referenced document is a PDF and the PDF display is set to show the sidebar with page thumbnails, one can Control-click on a page thumbnail and choose the contextual menu option, “Copy Page Link”. Then paste that Page Link into the rich text note and there’s a hyperlink to reference the location of an excerpt or quote that was copied from the PDF, or to document the source for a comment made in the note.

If I’m working on a project it’s likely that I’ll make more than one note about a document, or that I’ve mentioned that document in other notes and wojuld like to refer to them. In that case I’ll add hyperlinks to my annotation note that will instantly lead me to those notes, perhaps opening them as new tabs in the view or document window (so that I can move among the tabbed documents without losing my scrolling position).

When a search is performed in DEVONthink, for several filetypes a document selected in the search results list will automatically scroll to the first occurrence of a query term, and highlight that term. Although Page Llinks are primarily useful in PDFs, I can use “cue strings” that are likely unique to a particular page of one document among the tens of thousands of documents in a database. Copy that string of perhaps 4 or 5 words into the annotation note, enclose it in quotation marks, then do a Lookup search, “Command-/”, for the cue string (including the quotation marks). This results in an exact string search, so that I can quickly jump to the page in a rich text document or WebArchive or PDF that I’ve referenced in my annotation note.

I prefer using rich text notes to notes within PDFs because of the ability to use hyperlinks, and because the notes themselves are searchable. In the course of a project I’ll usually create a ‘spiderweb’ of interlinking notes to and about my references, and to the draft writing sections of the project.

Often, in addition to the primary notes about a reference document I’ll use See Also (or See Related Text on a selected section of a document) and include links and notes about related documents. This can be a powerful way to dig though the information content of a big database, and a wonderful way to break a writer’s block.

Finally, I’ll confess to an eccentricity. I hate to mark up my references with text notes, underlining or highlighting. I keep them pristine. :slight_smile:

Wouldn’t it be easier to just make PDF annotations searchable?


I’m not a developer, but that was a long-time problem for Adobe in Acrobat. :slight_smile:

From the perspective of a user, or maybe just me the user, it would be just great if you could search your pdf annotations.

Thanks for your comments,


@Bill Hey, I was just thinking about how you use an annotation note to collect multiple pages using a link back to them.

I think the real issue is remember which word or paragraph or section of a page that the annotation is referring to. You can only link a whole page, not a specific word in a page. Am I right?

Yes, the Page Link to a PDF links to a page, not to a specific word or phase on that page.

My large collections of references include a variety of filetypes. Probably 99%+ of some 15,000 scientific papers and journal articles in my main database are rich text. There are thousands of PDFs (books, reports, and some non-paginated PDFs), a number of Powerpoint presentations, HTML, WebArchive, Excel, Pages, and Word documents, depending on the source.

My database is not a monoculture of PDFs only. I want to make notes and annotations referring to an important reference regardless of its filetype.

In most of my documents I can establish an indirect link to the location of a phrase within the document by selecting it, enclosing it in quotation marks and pasting it into my rich text note about that document. A Lookup search, “Command-/”, will display the target document in the search results and when it is selected (in my most commonly used filetypes) the display will scroll to the first occurrence of the Lookup string.

It’s surprisingly easy (assuming that the author wasn’t excessively redundant) to select a few words for the Lookup string so that even in my database with about 30,000 documents only two results are displayed in the Lookup search results — the target document and my rich text note that also contains the ‘cue’ string. Click on the target document in the search list and there’s the exact location I wanted to see.

These approaches work for me. There are tradeoffs. Yes, using Lookup strings is indirect and takes a few seconds. But I save time with my rich text annotations in other ways, as I’m not limited to plain text. They can contain character formatting, hyperlinks, tables, diagrams and other images. Whenever possible I make notes that will end up as draft elements in my project article or report, so I actually save a lot of time in moving to the final article or report in this way. I don’t have to go back and pick out URLs, images, formatting within a quotation, and all those other little things that would be missing in plain text notes such as PDF text notes. I include in my notes footnote and/or endnote fodder, so that when I do the final editing it flows faster. But in case I forgot something that I’ll need for the final edit, my rich text notes have sufficient “bread crumbs” to lead me back to the section of a referenced document that I need to check again.

Certainly, I’ll be pleased by any new features in DEVONthink that allow me to associate notes and references more quickly and easily. For example, in DEVONthink 2.x new features such as Item Links and Page Links and the ability to search for multiple exact strings (phrases) for Lookup searches (“cue string A” AND “cue string B”) provided new or more precise “bread crumbs” for my notes. The recently added ‘Annotation’ smart template with its keyboard shortcut “Shift-Option-Command-A” quickly produces a new rich text note already linked to the selected reference document. If I’m going to make multiple rich text notes about a document, I’ll link to them from that “master” annotation note. In the case of PDFs, when the ‘Annotation’ note is created a link to it is added just above the text pane that displays the PDF, e.g., in the Three Panes view (this cross-reference link also appears for Pages documents). So I can jump to the Annotation note from the referenced PDF, and thence to any other notes I’ve made about that PDF. Likewise, I can jump from the Annotation document to the referenced document by a hyperlink.

The approaches described have let me develop workflows for associating searchable rich text notes to documents of any file type and I get a lot of work done by using them.

This sounds brilliant - but I don’t see a “New with Template” option in my Data menu. There’s a Data > New > With Clipboard but I haven’t found any templates anywhere.

I have DT Pro 1.5.4 unregistered (evaluating, looks good so far although it doesn’t play nicely with camino and I have to use safari to drag partial web pages in and maintain formatting and URL)

Where would I find such a template?

You will need version 2.0 to use the ‘New from template’ feature. Unless you have a compelling reason to evaluate 1.5.4, such as being stuck with Tiger with no option to update to Leopard, DT 2.0 is the way to go. DT 1.5.4 is just so far behind 2.0 in features and usability that reading forum posts from the last 1 1/2 years and trying to apply the information in them to help you understand how to use 1.5.4 will be frustrating at best.

Hm, my version tells me it’s up to date. I guess it doesn’t check across major versions.

I downloaded it a while a go, and I must say I’m glad for the “hours actually used” trial, because I was unable to test it for several months and just got back at it.

I’ll go look for version 2 then.

Thanks :slight_smile: