Highlights v1.4 is available from today in the Mac App Store. It’s a pretty good (not perfect) upgrade to the annotation features, including the new optional ability to export each annotation into a separate file, with tags and commentary, into DEVONthink. The link-back in these files opens the PDF to the relevant page, but in Highlights, not DEVONthink.
Nevertheless it is a very good alternative to “Make an Annotation with Links, Notes, Tags”
Excellent news! I requested (or maybe seconded a request) this on twitter a while back. I get similar functionality via papers and applescript, but it’s a little messy (comments are not attached to highlights). This is a very promising development. But, as you note, I’d really prefer some control over the link back to the pdf.
In view of the recent, abrupt demise of CircusPonies, this appears to me to be a non-starter.
I checked this out: The link is of type “highlights://OSX_filepath”. For users like us, typically, there would be a high likelihood that the original pdf is also inside DT. Since DT moves files around inside its DB package at will, wouldn’t that shoot down the ability for Highlights to find the file? As far as I understand, inside DT, the only safe reference mechanism is using those x-DT-item:// descriptors. Maybe I’m missing something.
It seems to me that generally one would want to stick to one overarching management system. For us, that would be DT. We would use tools for annotating etc., but not ones that try to create their own ecosystem.
Hi, I am the developer of Highlights. The links are not really an attempt to lock you into my app, I have just not had the time to implement support for DT-links yet. Personally I think of Highlights as a PDF reader that actively avoids lock-in by supporting embedded annotations and letting you export to standard formats and common shoebox applications 
I have a beta version with support for DT-links you can test here: http://highlightsapp.net/download/Highlights_beta_255.zip
This is a demo version of the app, meaning it only extracts annotations from every other page, but it is otherwise feature complete. For the DT-links to be fetched the app will install an AppleScript into ~Library/Application Scripts/net.highlightsapp. Highlights will prompt you to install this the first time you try to export to DT. This script checks if the current PDF-filename is found inside your DT library and fetches the DT-UUID for it. Highlights then replaces the highlights:// link with a x-devonthink-item:// link.
Let me know what you think!
Thanks for the visit and the input, Jonas! 
Wonderful! I was not trying to imply any intended lock-in, simply tried to warn that inside DT, these systems (Highlights and DT) would not happily co-exist. With introducing x-DT-item URLs, this is of course changing everything.
I wish that Microsoft would be as flexible and quick to introduce an “open in” function to return Office docs to DTTG…
Warning: TL;DR alert. Some general comments and concerns about PDF annotation, searchable highlights and DevonThink links.
I have been trying to find a workable combination of tools that will support this for some time now and have moved through various combinations of tools, without real success. I am hoping that Jonas Ribe’s Highlights tool may provide part of the solution. I am wondering how other DThinkers have solved this.
Several parts to this problem:
The biggest problem is finding a combo that addresses both of these. This seems to be a common issue (common as in frequent, not common as in shared unfortunately) in apps that purpose to help you with collating references, research work, readings etc. So for example, I have tried Sente, which is nice to use as an annotation tool but making these annotations searchable is awkward and not possible in DThink. I am currently using Mendeley for reference management, partly because the annotations are searchable. But Mendeley uses a non-standard annotation format which does not show up when the annotated PDF is viewed in other apps such as Preview, DThink etc.
This is a known and documented compatibility issue. The author of DocEar is particularly strong in voicing opinions on this, noting that if you want to combine, for example, Mendeley with other apps, you should follow a split work process of using another app, such as DocEar (or Highlights?? ) for annotation but use Mendeley to manage the metadata.
DThink obviously could have a powerful role to play in all this, since it has powerful database functions and Scripting accessiblity. I have seen a few workarounds to this but they appear to be highly local/specific to that user’s machine or setup.
On top of this, I have an ongoing bugbear with the DThink x-DT-item URLs, which I have raised a few times before and am curious that no solution has been forthcoming. That is, it is very hard to make x-DT-item URLs active outside of DevonThink. Most other app makers seem to have fixed this. So if I create a sente:// reference, Sente is launched and the correct item is opened. If I create a brain:// URL to a PersonalBrain item, again the app is launched and the item is opened.
There is a Mac OS utility called RCDefaultApp by rubicode which helps to activate some of these URL type links and I recommend as being very useful to tweaking such things. But it seems to have no effect on how x-DT-item URLs are handled.
All very frustrating. One app cannot do everything. In a complex knowledge management environment, it would be great to have a suite of apps that can work together to achieve a good workflow… but I’m still searching.
Suggestions from anyone? Is Highlights the answer?
I rarely have an issue with DEVONthink x-devonthink-item URLs – the only problem that I haven’t resolved is with ConnectedText in a Windows 10 VM. That’s rather an edge case, so I can dismiss it.
Is there a particular app on OS X that you have trouble with recognizing x-devonthink-item URLs?
My own view of annotation is that everyone does what they want, based on the material they have, and the result they want to produce. It’s like note taking – there’s no standard way of taking notes, and no one will ever define one. It might be too much to expect any developer to solve a problem when no one agrees on the problem.
Is this reproducible and in what apps? I haven’t had any issues from my experience.
Concur with Korm (edit: and Bluefrog). I have not encountered issues with x-Dt-item, but I always have DT open, so I can only speak to displaying or revealing the file in DT when it is already open. So we need examples.
OK, actually, there is a problem, but I don’t think it can be addressed on DT’s end: In MS Office documents, if I insert a hyperlink to other apps, such as x-DT-item, it will not work, because MS fiddles in odd ways with the link. Not so pretty solution there: I just past the plain link and don’t make it a hyperlink. I then select the URL and use the OS X service “open URL” and I’m good to go. Unfortunately, on the iOS side of things that does not work well, because even just selecting the link is painful, and there is no “open URL” service.
Whenever there is something non-standard in my ecosystem, it is typically caused by MS or Adobe.
Sidenote to Topps’ sidenote on comments: I hear you. There is is massive infrastructure in pdf to do all sorts of annotations, and then under OS X and iOS, the annotation part of the pdf is not searchable. That’s really unbelievable. Two ways out for me:
Many DT users make separate annotation files in rtf with backlinks. Tons of discussion on this forum. My problem: the annotations don’t migrate automatically with the pdf, so it is somewhat a DT lock-in.
Flatten the annotation. This works particularly well for me, because I annotate pdfs almost exclusively on my iPad(Pro), using iAnnotate. It has a nice feature, where you can save/export a version of the pdf that contains links to the comments, which are listed in the back of that flattened version. Importantly, everything is plain pdf, so it is all searchable. Another bonus: you can ask it to only export/flatten the pages that have annotations. So you can for example read a huge document and get a condensed, annotated version out at the end. Of course, you keep the original and the flattened version.
Well, that’s interesting and may explain the previous lack of response to my queries. Thank you.
It has improved recently but still fails more often than not. Having originally come from a Windoze environment, where such things more often work (or fail) across the whole range of apps, maybe I am expecting too much.
But there is hope that there may be something weird in my set up that is blocking this. Or maybe you have just been lucky with the apps you have been linking together.
I dug up my notes that I have made over the years about this and have added them as an attachment (‘More hyperlink testing.rtf’) so as not to flood the forum with lengthy posts. The most problematic area seems to be Microsoft apps - but kinda hard to avoid using them.
If you have any observations or suggestions about this, they will be much appreciated.
I will agree with @gg378 on the hyperlink issue. Not all apps are hyperlink aware. For example, pasting into Pages does not create a link. You have to specifically define the link and even then it always resolves to “http://x-devonthink…”. So your mileage will vary, app to app.
Thanks for the replies, people. Very helpful. Prompted by these comments I went back in and retested my previous problems… and yes indeed x-devonthink-item:// links now work much better across a range of apps. MS Word remains the recalcitrant standout. As gg378 noted, Microsoft and Adobe, the two companies who should be most vested in cross-app compatibility, remain the worst in this regard. Well that largely solves one side of the problem.
As BlueFrog noted, not all apps handle hyperlink pasting very well, but you can usually work around it (except with bl**dy MS Word).
Ok, back to the main focus of this thread… searchable annotations. Will try Highlights 1.4
My approach to annotations of PDFs (as well as all other document filetypes) is to do so using one or more rich text notes linked to the referenced document (and perhaps linked to other references or notes, as well). My notes are searchable, and can include text formatting, images, clickable links, tables and lists if desired. This approach isn’t limited to PDFs, but can be used with documents of any filetype.
I usually use the Annotation template, which has a keystroke shortcut to create a new Annotation note for a selected document. The Annotation note is linked to the selected document, and a link from the selected document to its Annotation note is created.
When I was a freshman in college (approaching 70 years ago), I was in the habit of underline or highlighting my text books, and often underlined whole pages. One of my professors observed me, and offered some good advice. He said that I would improve both understanding and retention of knowledge if I were to summarize information in my own words. He was right.
That’s also the premise of Cornell Notes, a simple tabular way of composing notes about a topic. As many of my references that I’ve annotated contain multiple topics, I often create Cornell Note tables in my Annotation notes for each topic.
In the case of annotation of PDFs, I’ll include Page Links to the page to which I’m referring. For other document filetypes I’ll choose a 5, 6 or 7 word string near the area to which I’m referring and save that string in my notes, enclosed in quotation marks. A phrase search in DEVONthink will (for many document filetypes) result in opening the document and scrolling to the desired position. It’s surprisingly easy to pick such text strings that will be unique, even in my Main database which holds some 30,000 documents!
Although a document can have only one Annotation note, I’ll often turn the Annotation note into a tree with branches – links to other notes or documents.
As I’m an old geezer and had to learn how to format source/citation information as required by various publications (long before citation manager software appeared) , I don’t use software for that purpose. I do try to make sure that all my documents contain source information.
This approach to annotation also satisfies my desire to keep my references virgin, without vandalizing them with highlights and note blobs. 
As far as I can see, they are vested and hence interested in cross-platform compatibility, but only as far as their product line is concerned. They believe that they offer everything you need, and don’t want to encourage you to venture to potentially greener pastures. Unbelievable how long MS held out trying to ignore the pdf format.
This works for me in Word 2016 (v15.18). The link launches the document in DEVONthink.
Works also in PowerPointer 2016 and Excel 2016 – though in those cases you need to use “Open Hyperlink” from the contextual menu. But, that’s the same as Pages 5.6 – click the link and a teeny menu opens where you have to click “Go to Page”.
Great! I’m still on Office 2011, and there it definitely does not work. Now if they only added “open in” to the iOS Office apps, the sky would be the limit.