Need pdf organizer + annotator - please help (not obvious!)

Discussion in 'iPad Apps' started by nayakan88, Jul 4, 2014.

  1. nayakan88, Jul 4, 2014
    Last edited: Jul 4, 2014

    nayakan88 macrumors newbie

    Jul 4, 2014

    Please read this detailed message and help. It is a bit long because I have tried very hard to get what I need - and failed. So I am being very specific in my query.

    I recently bought an ipad with one express purpose - to read, organize, and annotate my large collection of scientific pdfs. I have the following requirements, and I have tried a number of solutions, and none of them have worked for me. I would like to know if ANY app can fulfil my need - else my ipad purchase is a waste.

    (BTW, this is my first foray into the Mac world; I have only used PCs so far, and a good friend persuaded me to get into the Mac Universe. But this first experience is very frustrating. So, relevant information here is that my desktop machine where I have also loaded itunes is a windows machine.)

    So, here are the requirements:

    1. I need to be able to organize - sort and search by TAGS - my entire collection of scientific papers so that I can retrieve a paper very quickly in a search.
    2. I would like full-text search on my pdfs.
    3. I would like to search multiple pdfs simultaneously in full-text search.
    4. I would like to annotate my pdfs, more the better - handwriting, etc.
    5. I want to be able to use iTunes to upload and save documents from the app. I DO NOT WANT TO USE DROPBOX, etc. I see absolutely no sense in spending $10/month on online cloud storage (of 100 GB) when I have an external hard drive for 1 TB that I bought for $100. (as an aside, I find it amusing that on various websites, ipad owners complain so much about a "pricey" app that sells for $7 (one-time cost) but are willing to happily fork out $10 a month to store their data on the cloud. Well, I am not happy paying for this. I think the entire dropbox/etc. move is a scam.) Plus my iPad has 64 GB, so it can easily store whatever I want to store on it.

    I should point out that my collection of pdfs is quite large - a total of more than 10 GB. That means that with most services like dropbox, etc., I will exceed the free storage limit of 2 GB or 5 GB or whatever (most apps only have dropbox connectivity, some have other options too), and I cannot store my files on cloud servers.

    Now let me tell you what I have already tried: Documents 5, PDF Express 5, GoodReader, Sente, Papers, colwiz, Evernote, and Mendeley. None of these satisfy all the requirements stated above. For example:

    Documents/PDF Expert 5 have a wonderful multiple file search, but they don't seem to have a proper tagging system where you can assign text tags to individual papers and search by tag. For example, I may have different papers dealing with "bubble columns", "stirred tanks", "computational fluid dynamics", "chemical reactions", etc. - and more than one tag may apply to each paper. I would then like to be able to search the papers by searching for these tags. In addition, I would also tag the papers by the authors, etc., so e.g., search for "Smith" "stirred tanks" "mixing" tags and get all the papers dealing with these. I could try to manage with multiple file search, but searching on 500 or 1000 papers is not easy. Folders will make it easier, still, I prefer tags to folders because folders are too limited. For instance, what if a paper concerns both "stirred tanks" and "bubble columns"? Which folder would I put it in?

    Many of the "reference management" softwares, like Sente, Papers, colwiz, etc., can do parts of what I want - for instance, all of them will allow you to categorize papers by authors, journals, subject, etc., but most of them are tied to the cloud, which will make them expensive options for me. colwiz, for instance, uploads whatever you import to their cloud storage - and you only get 2 GB. If you refer some friends to their service, you can bump that up to 3 GB. Right now there isn't even an option to get more storage by paying, but I can bet it will be expensive - at least $5 per month - and I don't wish to plonk down $60/year. Besides, the main function of reference management software is citations, and I am not particularly interested in citing, more in reading. I work in industry and we rarely publish - though we read a lot.

    And I don't mind manually inputting authors' names as tags - something the reference managers do for free for me - if I can get the other functionalities I want - sync with iTunes, tag-based sorting and searching of pdfs, full-text searching of pdfs, and some annotation at least, if not the best - the last I can negotiate a bit on.

    I looked at a few reviews of software such as DevonThink, that seem quite interesting, but apparently it is useful only if you already own a mac, which I don't (yet). Also, I searched a lot for file managers, and a few, like OrganiDoc HD, seemed like they may be good for file organization, but did not have enough PDF annotation capabilities.

    Any hope for me?



    Is there anything out there for me?? Or should I just toss the ipad??
  2. jenn.y, Jul 4, 2014
    Last edited: Jul 5, 2014

    jenn.y macrumors newbie

    Jun 20, 2014
    Ok so, for your requirements, iAnnotate works - you can use text tags do a full search (of tags as well) and annotate, export to iTunes etc.

    But personally - I'm trying to figure out if I want to move to PDF Expert 5, simply because iAnnotate has been a little ... Glitchy for me. As in to me, it's annotation skills aren't the best - they're very customisable, but I really don't like the eraser and for me (not sure this is a universal issue) I sometimes get jagged lines when highlighting - but this might be my gosmart 200 stylus. iAnnotate does have its benefits however which is why I'm still hesitating.

    I don't know, iAnnotate might work for you, but yeah. :)

    And as a side note, I haven't figured out how I even delete tags in iannotate - it doesn't display my tags.
  3. AlphaHel1X macrumors newbie


    Jun 17, 2014
    I use iAnnotate for most of my work/school stuff.

    Biggest PDF I've annotated with was ~450 pages, but was only 50 Mb. Has worked great for my needs; i.e, no lag, handwriting/highlightin, etc.. Total, I have about 5 Gbs worth of docs, but I am stuck with a poverty 16 Gb air :mad:

    iAnnotate has been able to search most of my PDFs without problem, pairs with Google Drive well, and can store files locally. Not sure about using iTunes to sync docs though, I haven't tried before.

    Btw, I don't know anybody that pays $10 for that little of storage... Google Drive/OneDrive is 15 Gb for free, or 100 Gb for $1.99 a month. Heck, OneDrive is moving to 1 Tb soon (up to 5 Tb for free) if you subscribe to Office 365. And if you have a .edu email address, you can buy 4 years of OneDrive for ~75 bucks.


    @jenny: I thought the same thing at the beginning, but iAnnotate just seems to have a slightly weird learning curve. A stylus (Bamboo here) helps a bunch too.
  4. jenn.y macrumors newbie

    Jun 20, 2014
    Yeah I use a stylus - a gosmart, but I get these jagged lines when I highlight (freehand). E-E
  5. AlphaHel1X macrumors newbie


    Jun 17, 2014

    When I highlight with a stylus, or freehand, the lines are smoother than a baby's bottom...
  6. jenn.y macrumors newbie

    Jun 20, 2014
    I've attached the kind of things I get.

    Attached Files:

  7. AlphaHel1X macrumors newbie


    Jun 17, 2014

    Smooth as buttah, just randomly highlighted and used the free marker

  8. nayakan88 thread starter macrumors newbie

    Jul 4, 2014
    Hi Jenny,

    Thanks very much for that! Sorry for the slow acknowledgment - not because I don't appreciate your help, but because I wanted to first try it out and report on the experience!

    So, I took your advice and installed iAnnotate on my iPad, and you are right, it ticks all the boxes. I am just 2 days into using it (and not all day), so there might be stumbling blocks, but at least this is the closest fit to what I want. No deal breakers yet. Works with iTunes, no dropbox compulsion, tagging, sorting, full file search with multiple files, annotation.

    I only am having one issue with it so far, which maybe you may have an answer for - and again it is related to the scale of what I want. The app has tagging for files, and searching for those tags. Great so far. Only thing is, when you want to apply a tag to a new file, you have to remember what tags you may have used in the past. I am not able to see a list of all previous tags so I can decide which tag to apply, or whether I should create a new one. Ideally, there would be a drop-down menu of previous tag plus a "New" option, where I would enter a new tag. This would ensure that I don't have problems because of spelling errors or, say, spaces or something like that. E.g., "Fluid Mechanics" v/s "FluidMechanics". I've sent an email to Branchfire support; but if you already have encountered this, do let me know.

    But this is not a dealbreaker, only an inconvenience, and I hope they will remedy it in a future release. I think I can now safely import my entire pdf collection into my iPad Air and enjoy reading, organizing, and annotating!

    What I like about the organization is that it allows for both folders and tags, and when you do a tag search it searches everywhere, in all the folders as well, to see if there is anything relevant. This helps with the above limitation of not being able to see the tag list - because now I try to create a folder for each tag so that I remember that name - but I am not limited by that, because the tag search will find a file even if it has been filed away in another folder because it has two or more tags associated with it.

    Once I am really using it in full flow, maybe I will also be annoyed at some of the glitches you mention - but given that there are no alternatives to iAnnotate for my use case, I will have to live with them!

    Thanks for giving me a reason not to toss that 64 GB iPad Air (would have been a pity, really! :))

    Best regards,


  9. nayakan88 thread starter macrumors newbie

    Jul 4, 2014
    Hi AlphaHel1X,

    Thanks for your response. Yes, I am liking iAnnotate (see my response to Jenny as well), nothing more to add there.

    As far as storage costs, I am basing my numbers on dropbox. See

    Their free plan gives you only 2GB. The next level up is 100 GB for $9.99 a month. I understand Google drive is much cheaper, but not all apps have Google drive connectivity. Papers, for instance, one of the most popular apps for reading scientific papers and reference management, ONLY has dropbox connectivity. colwiz, another reference management software, doesn't have options for even dropbox, only their own servers - and they have a limit of 2 GB. They don't yet have an option to increase storage by paying, but it probably is in the works. Their competitor, Mendeley, also doesn't use dropbox or google drive, but uses their own storage. Users get 2 GB of free storage; if you want more than that, they have plans that are worse than dropbox - $ 5 a month for 5 GB storage, $ 10 a month for 10 GB storage, and $15 a month for unlimited storage. See here:

    So yes, evidently people pay that much for even less storage than what I first said.

    I agree that PDF expert 5 has a wide range of options for syncing - but hey, if I can do it for free using my own storage, why pay?

    Thanks again for responding.

    Best regards,


    One request: to you as well as Jenny as well as anyone else who knows and is reading this. You mentioned styluses. Any recommendation for which one I should buy?

  10. jenn.y macrumors newbie

    Jun 20, 2014
    Glad I could help. :)

    I can't find a way to view all the tags etc either. Branch fire should seriously do something about that. :/

    As for styluses, I personally use a GoSmart 200 stylus (I got mine for $26? - depends on where you live) for its precision tip (because I heard people tend to find Adonit Jot Pros etc becoming unresponsive after a few months) and I love it - there's just one thing, I get those jagged lines (see attached pic from earlier) every now and then - I'm guessing it's my stylus. But given the precision of this stylus - I'm staying with it. :) A note though - if you get one of these, make sure you have a screen protector. I've got scratches on my (cheap) screen protector thanks to it.

    There's also others with a big rubber tip - e.g. The Wacom Bamboo Stylus. And some have a microfibres tip - e.g. Truglide Pro. I tried one, not sure if it's the same brand, and it was really smooth - but for me, the tip is just too big in comparison. You can get these from anywhere between $10-30 depending on brand and quality. These ones don't scratch, but I prefer the precision of my GoSmart.

    And lastly, there's electronic styluses such as the Hex3 Nota ($40-50?), Truglide Apex /Apex Rechargeable ($60-70?), Adonit Jot Script ($75?), Adonit Joy Touch with Pixelpoint ($119?), and Adobe Ink ($200 bundled with the ruler). Basically these have very small tips made possible by some electronic impulse that stimulates touch or something - I'm not very familiar with how they work, but this means it feels a lot more like pen and paper accuracy wise. Some like the Adonits have palm rejection built in with certain apps (if the app isn't compatible, they just work like a normal stylus). And the Adonit Jot Touch has pressure sensitivity, but that's really for if you want to use it to draw. These connect via bluetooth generally. But if you want one of these - be warned, diagonal lines become jagged. Detailed here :

    It really depends on what you like. If you're willing to spend the money, one of the electronic ones might be worth it if you don't mind the diagonal lines, otherwise, it depends on whether you want something precise or something soft that won't require a screen protector.
  11. nayakan88 thread starter macrumors newbie

    Jul 4, 2014
    Thanks for those recommendations!

    Realized that there is another shortcoming in iannotate as far as tagged search...cannot do booleans ... E.g., "fluid mechanics" AND "reactor" ; nor can you do a nested search, viz., search once with one criterion, then perform a second search with different criteria on the results of the first search. So it is still very limited.


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