I am trying to understand how the “link” annotation tool for PDFs works in DT. Perhaps it’s too late in the evening for me to “get” it, perhaps it’s the lack of explanatory material in the user’s manual—at any rate I would appreciate some help.
Many thanks.
That’s the way Adobe invented them 
You can link any area but it doesn’t have any visual impact.
Scroll to the desired target page, then click the “Set” button.
Aha! I should have reckoned—how inexcusable of me!
Unbelievable (then again, it’s Adobe).
I wonder, would any of the AppleScript sorcerers wandering around in these forums would be able to make a script that would:
Place a graphic at a selected position on a PDF page (any graphic, e.g. a circle or an arrow);
Overlay a transparent “link” annotation over that graphic; and
Set the “URL” attribute of said link to the contents of the clipboard…
Is that technically feasible with the existing DevonThink dictionary for AppleScript?
I am only asking because the invisible links are virtually useless unless there is something to betray their presence…
Alternatively, perhaps the existing annotation tools provided by DevonThink could be enabled to do the same. At present, the URL attribute for all but “link” annotations is disabled.
Many thanks.
I think this is precisely why Bill De Ville of DT fame never tires of recommending another Rich Text document from and to which you can link visibly and clearly to the pdf.
Also, many people have learned the hard way that pdf annotations are somewhat volatile and may disappear under certain circumstances. Keeping your notes outside it may be the most stable solution in the long term.
HTH
Prion
The venerable Bill de Ville has a solid strategy for annotations, I am sure. But it is my impression that his method would not work as well with PDFs that are hundreds of pages long, because in such cases the “mediating” document containing links to the individual annotations be very long, having accumulated an entire book’s worth of annotations.
I would be perfectly willing to change my mind, though.
You are perfectly right about the volatility of built-in PDF annotations. They can easily evaporate, for instance, when performing OCR. To my knowledge, only the OCR facility of Acrobat Professional is able to salvage built-in annotations.
That said, I very much enjoy having my annotations on the actual PDF—and I realize that this is another difference with Bill, who prefers his original PDFs kept pristine. I admire his purism—and in principle his mode of reading is superior—yet I am not convinced that quitting my habit of scribbling on the margins would be more productive than otherwise.
Chacun à son goût – tastes vary, opinions vary and workflows vary; I think that’s a very good thing. I’ve learned a lot from the approaches other users describe on this forum, and I’ve often adapted them for my own use. 
Perhaps my reluctance to “deface” documents comes from having collected some rare books on topics that interest me. Some of them are hundreds of years old. They have passed through many hands, and probably will after my ownership of them, as well. I try to keep them in good shape, and will never take a highlighter pen to them.
I’ve still got a couple of textbooks from my freshman year in college. At that time I used a pencil to underline important passages. One of those old textbooks has underlining under almost every word in some chapters! Later, I found that my comprehension was improved if instead of mechanically underlining or highlighting material as I read it, I wrote my own notes in a journal book for the course, summarizing important facts and concepts and with page number references to the source. As I got better at that, my notes became shorter, easier to review and more effective in preparation for an exam. The trick is to distill the important stuff from the minutiae, and to only emphasize the minutiae when they illustrate the important stuff.
I was about 13 years old when Vannevar Bush’s article, “As We May Think”, appeared in the Atlantic Monthly. The article excited me then, and I never forgot it. Bush described his dream of a Memex machine, which would allow one to compile a vast collection of information and to add value to that information by adding to it, including finding new relationships among the items in the collection. The Memex machine as he described it was limited to the technologies available at that time, in the 1940s. But his vision translates very well to today’s technologies that include digitized information and the wide availability of digitized material via the Internet.
My DT Pro Office databases are my Memex machine. I think Bush would like those databases, as they allow incorporation of information in many forms, textual, numerical, image, video and audio.
I use rich text notes as they are searchable, can link to all of the various filetypes in my database, can include formatted text, lists, tables, hyperlinks and even embed or link to images, video or audio if desired. Those notes add value (to me) in the databases, and often are assimilated into drafts of a final writing project.
Even when making annotations and notes about a long and rich document, my notes are usually relatively short. If there are many facts or concepts I’ll “branch” a note into multiple documents, with a clear set of links to them, rather like an outlining approach, in which the primary annotation note includes an overview of important topics, each of which might become a separate linked note (and might, in turn, link to other sources or notes).
This approach accommodates my personal foibles and preferences and works for me. It may or may not fit the workflows of others, and there are many and varied approaches that are possible.
I admit I still haven’t found my ideal workflow. I have given up on annotating pdfs directly unless the purpose of that is short-term, e.g. when reviewing somebody else’s manuscript which after sending it off to the editor will soon be replaced by the printed paper for me.
I would not trust my own notes about my own work to a workflow that I consider inherently unstable but I wonder what my preference would be if the technical aspects played no role: one condensed document full of notes (remember that you can link to specific pages inside the pdf, not only to the pdf document on the whole) or the annotated book itself?
Looking at my bookshelf next to my desk, it seems I am facing the same dilemma when dealing with real books. There are some textbooks which I annotated extensively when working through them as a grad student and others bristle with extra pages (one per chapter) of my notes. There are advantages to either approach but one thing is for sure. These notes carry a lot of meaning but not in and of themselves, they do for me because I spent a lot of effort in working through these books. Some pages I still have visual representations of in my mind even after decades and my notes refer to these connections in my mind.
To someone who has not read the book (or the ones I read before it) the notes would be interesting at most but not elucidating, and realistically mostly meaningless. No note-taking system, paper or computer based, will replace the effort of sitting and reading for hours and trying to grasp the essence of something.
Sorry for the long post and back to work for me
Prion
Doubtlessly, there are countless ways to keep notes. As I wrote earlier, Bill, I admire your method because it exudes maturity. There is something hysterical (or obsessive, to be more precise) in underlining and highlighting original texts to the point of saturation, and a concomitant illusion that knowledge is ‘objective’, that it is ‘there’ and readily available should you ever ‘need’ it. For many, especially inexperienced undergraduates, I venture to say that annotating serves as a deferral mechanism for the more painful (but irreplaceable) process of learning.
All that said, I would have been much less reluctant to try your approach (which, again, I do find superior in principle) if it were possible to create hyperlinks to the annotations on the PDF page itself: nothing extravagant or visually distracting, but perhaps a clickable asterisk or something discreet along these lines. In your system, it is this ‘bridge’ document containing all links to your annotations that I perceive as an intimidating layer of complexity at the moment, largely because I am now too preoccupied with my scholarly work to adapt to such a radically different workflow.
Also, in my case, there is a question of legacy: I have countless PDFs with important (and, yes, also many obsolete or even unfortunate) annotations. It could be distracting to have to use two different annotation systems.
But I do have a question: I thought that PDF annotations are indexed and searchable. Are they not!?
They are not, unfortunately, at least not in DTPO, see http://www.devon-technologies.com/scripts/userforum/viewtopic.php?f=3&t=11243&p=52808&hilit=pdf%2A+annotation%2A+index%2A+search%2A+#p52808
Aha! Very disappointing but good to know. Thank you, Prion.
PDF annotation notes are not part of the “text layer” or PDF, nor are they included in the properties or attributes metadata of PDFs. This goes back to Adobe’s design of the Portable Document Format.
Back in the year 2 BD (2 years before DEVONthink appeared in 2002) I was managing a project that involved hundreds of PDF standard operating procedure documents, which were in development for final approval for use in a governmental agency. I was the Black Hat guy who forced documentation of all technical procedures in the agency. That tends to rapidly draw the hatred of hundreds of people, of course.
Acrobat allowed one to designate a collection of PDFs and index them for searching. One could then run queries across the entire collectioin. But text note annotations were not indexed and so were not searchable. I devised a linked note system then to add additional information in the collection about problems with specific SOP (standard operating procedure) PDFs. The notes had to be incorporated in PDF form and the collection reindexed for inclusion in searches, which required more effort than my current approach in DEVONthink, and such notes couldn’t be dynamically modified, so that considerable effort and time was required to handle revisions of documents.
During the development phase, the indexed collection was available to a team of reviewers, as in many cases the SOPs for different groups required consistency among areas of their procedures. Indeed, that was one of the major reasons for the project.
I was delighted by the release of DEVONthink in 2002! It let me handle the final wrap-up of the project with ease, as it was far less cumbersome than Acrobat’s indexed collection.