Would be great to be able to add comments in specific locations in PDF, highlights, etc.
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Rest assured, we are working on that one. It’s probably the feature that’s requested most frequently. That’s not just a signal for us to put it high on our priority list it’s also a signal that this needs to be done right. So it will take a bit more time.
Edit 9/2/15: PDF annotation is now available for beta testing: PDF annotations are in beta. Please read this first
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While you are on it, would be great to also have a robust text selection tool for copy-pasting. I guess this might be qualified as a related feature.
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If you have an iPad see this tip:
I have yet to see a single reference manager whose PDF annotation features come anywhere close to those of GoodReader on the iPad, so for me these features are unnecessary bloat and a distraction from the app’s core functionality. But I understand why developers feel compelled to add these features within the app.
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Thanks Kerim. Personally, I would prefer not to use so many disconnected applications for this. Also, I am not looking for a super advanced annotation capabilities. What Mendeley can do is quite enough for me.
I was talking about a web based solution to add annotations. We definitely would use an existing solution if it existed. But everything out there turned out to be not good enough to recommend to our users or to license/integrate within Paperpile. And “not good enough” is actually a very friendly way to describe the other products available in this space…
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Although I have a tablet, I tend to use computers more. I’ve been looking for a browser (i.e. chrome) based PDF annotation tool for a long time.
I strongly prefer to have the annotation stay within the PDF. The way Mendeley does is not portable and is not good at all…
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We agree. PDF is an ISO standard and supports all kinds of annotations. That’s why our solution will save all annotations natively in the PDF.
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NotablePDF has some of these solutions. Why not implement in Paperpile something like that?
As I said above, we are implementing it right now 
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Being very lazy, could I add another feature in this area and that is that when I highlight in the pdf that the highlighted text appears in the notes section as notes. Then when I am checking through papers in the Paperpile main page I can quickly review the abstract and notes without launching the pdf viewer. Having the para and page number with each note would be paradise… Told you I was lazy.
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I’ve noticed that all the apps that allow you to highlight in chrome simply use an overlay that makes the text less readable because it reduces the contrast between the text and the background. I hope that you will be able to avoid this particular problem.
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You’re right. They simply add a layer with 50% translucency which makes the highlight color pale and the text gray.
That’s one reason why we don’t have released our PDF annotator yet, because getting these things right takes time and effort.
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Will the highlighted words or annotations be searchable in Paperpile? Or Google Drive? Would the annotations be visible if the file is opened in the Google Drive viewer?
Easy to answer for the things that are under our control: Yes. It is planned that the annotations will be extracted from the PDF and will be visible in Paperpile itself. Since we write the annotations (Highlight, Sticky Notes, …) into the PDF file itself, any PDF viewer that implements correctly the PDF specification will be able to display the annotations. For Google Drive, I do not think that it specifically allows to search in annotations only, but since Google extracts the full text and even does OCR on PDF files you should generally be able to search within PDF files in Google Drive.
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Will there be an option to export the annotations from a document as a text file?
Please, can I suggest something that goes beyond mere annotation? No one so far is offering a very simple thing : categorizing annotations. While you can do this in software like NVIVO and CITAVI, they are bloated and clunky, and disrupt the online workflow. I am amazed that no app has developped such a simple feature: highlighted text is transformed in annotations/notes, then can be categorized. It would be so useful!!
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I really like everything about it other than annotating pdf which is a big requirement for me. Is there any ETA on when the basic highlight and side annotation would be shipped?
We hope to start beta-testing soon, but we can’t really give an exact ETA. We’ll announce ways to early access the feature here.
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I think as soon as built-in annotation is added to Paperfile, this program will become indispensable to me. I would be very interested in participating in the beta testing. Thx