Zotero Tutorial: Working with PDFs

[@anton9004]

I never knew you could extract highlights. This is a game changer. Cheers

[@arielgerardo6475]

You all probably dont care but does anyone know of a way to log back into an instagram account?? I somehow forgot the password. I would appreciate any tips you can offer me!

[@bryannasir243]

@Ariel Gerardo instablaster ;)

[@arielgerardo6475]

@Bryan Nasir I really appreciate your reply. I got to the site through google and Im waiting for the hacking stuff atm. I see it takes a while so I will reply here later with my results.

[@arielgerardo6475]

@Bryan Nasir it worked and I now got access to my account again. I am so happy! Thanks so much, you saved my account!

[@bryannasir243]

@Ariel Gerardo happy to help :D

[@carolinespec]

Your videos are great. I looked at several explanations for different citation management sources and your explanation for each aspect is so clear that it made me really want to use Zotero. Your videos are just excellent. You speak slowly enough, describe aspects in a way that isn't more confusing than necessary, and make the whole process seem manageable. Thanks so much for your efforts!

[@anjalisrivastava5628]

Thank you for this well organized and very well presented tutorial. I have watched many an online tutorials and never was I motivated to express my gratitude about having benefited from one. Today, I am. I found your presentation content, advice, style and demeanor to be pleasant, sensitive, authoritative and knowledgeable - hope you teach somewhere in person as well. Thank you.

[@chrissmith3960]

Starting to write a masters thesis, and have been on the fence about using EndNote vs Zotero (have been using EndNote the last two semesters). Your videos have prompted me to switch to Zotero. Much appreciation for the time you've spent creating these very informative instructional videos.

[@NicholasCifuentesGoodbody]

Couldn't be happier to read your message, Chris. Thanks for compliment. You made my day! And you definitely made the right choice going with Zotero ;) If you're about to undertake a big writing project, you might also look into writing in Markdown. See my playlist: kzbin.info/aero/PLXt-tu7G1H3tLeZgbbUmYjE0_kvbjA4YU.

[@junhyeukshin3611]

I am learning Zotero before going to grad school. It was great source of learning for me! Thank you very much.

[@lukeace4921]

0:00 intro 0:30 Where pdfs are stored 3:51 Highlighting and annotating in PDFs 7:12 Extracting annotations

[@editaaksoy7576]

This is one one of the best tutorials I ever watched. I just can't thank you enough for your excellent work. Right now I am procrastinating ;-) but thats OK, because when I work on my final thesis I am super efficient. Zotero and your explanations of it, made my life so much easier and I can focus on the topic instead of f.e. sitting hours after hours to create a correct bibliography. THANK YOU!

[@NicholasCifuentesGoodbody]

Great to hear. Good luck on your thesis!

[@thinkfreeordiestupid]

Thank yo so much for this in depth tutorial. Very helpful to a new doctoral student.

[@NicholasCifuentesGoodbody]

Thanks, Bob. I wish I had known about Zotero when I started my PhD. This will save you TONS of time --- especially when you're doing your dissertation. Let us know how it goes!

[@stephenbaron]

Thanks for the presentation. Very informative.

[@PVCol]

Excelentes videos, muy didácticos, completos y la pronunciación clara del inglés para individuos como yo hispano hablante

[@NicholasCifuentesGoodbody]

Orlando Mora me alegra que te haya gustado 😊

[@Favoritsvid]

Thanks for the great tutoriel. I have a problem, when I right click on a pdf, I don't see the last two option "Attach new file" & "Manage attachements", so i cant extract notation.

[@Armando_Lara]

If "Manage Attachments" -> "Extract Annotations" does not show up for you, it is because you have not installed Zotero Add-on Zotfile. Get it from zotfile.com/. It worked for me. I'm using Foxit PDF reader but I guess it would work perfectly with other PDF readers as well. Thank you for the video BTW.

[@DuskAndHerEmbrace13]

@G. Naz HOW TO INSTALL & SET UP ZOTFILE To start using zotfile, make sure that Zotero is installed and follow these simple steps: Install ZotFile For Zotero 5, first download the extension file (follow the download link above, click on the .xpi file for the most recent release). Now start Zotero 5 and go to “Tool -> Add-ons -> Tools for all Add-ons (the small, drop-down wheel in the top right corner) -> Install Add-on From File” and select the downloaded .xpi file. Change the Source Folder for Attaching new Files To attach new files to Zotero items, zotfile looks for the most recently modified (e.g. just downloaded) file in a user specified folder. For Zotero Firefox, this option is set to the Firefox download folder by default. For Zotero Standalone, this option has to be changed on the ‘General Settings’ tab in the preference window (Tools -> ZotFile Preferences). The source folder can be set to any location but I generally recommend setting it to your browser’s download folder such as ~/Downloads on the mac for most browsers. Changing other Options (optional) ZotFile offers many other options that can be changed by the user. Most of them are located in the zotfile preference window under Tools -> ZotFile Preferences.

[@dimasgomez]

@@DuskAndHerEmbrace13 It worked for me. Thanks a lot! There is also a feature that I figured out just yesterday: Google Docs are able to fix line-breaks of copied quotations automatically.

[@elliscraft]

Thank you for putting these together! They are really helpful to my theological studies!

[@daniello2009]

Nicholas, Thanks for the Great Work! It has really helped. If possible, could I suggest that some of the FAQs could be compiled? That would save you answering them repeatedly through the comments. I was very tempted to ask the question but instead spent the time scrolling through the comments to find the answer. Anyway, THANK YOU. Really good work.

[@NicholasCifuentesGoodbody]

That's an excellent idea, Daniel. Thank you!

[@suresh93783]

Excellent session

[@Armando_Lara]

If "Manage Attachments" -> "Extract Annotations" does not show up for you, it is because you have not installed Zotero Add-on Zotfile. Get it from zotfile.com/. It worked for me. I'm using Foxit PDF reader but I guess it would work perfectly with other PDF readers as well. Thank you for the video BTW.

[@mehtayeb]

thank you, your instruction helped me a lot. I've been confused why it does not work for me? I use Adobe Acrobat for PDF reading. thanks again.

[@nehasingh3346]

Hi Nicholas, Thanks your video is very helpful. But I am not able to locate the extract annotation function in my windows version Zotero

[@jenmcg2499]

Hi, thanks for making this tutorial, very helpful! Definitely one of the clearest and easy-to-follow that I've come across!! 👍🏻

[@NicholasCifuentesGoodbody]

Glad to hear it helped!

[@csldc]

Extremely helpful! Thank you!

[@jacobgeorge7009]

Really helpful...thanks for sharing this and sparing your time for this.....

[@NicholasCifuentesGoodbody]

Thanks so much for the comment. Glad to help!

[@jacobgeorge7009]

I am learning zotero exclusively from your tutorial videos....thumbs up.....for your contribution.....

[@vigneshmoorthy5820]

Thanks for the tutorial. I couldnt find the options - "Open in internal viewer and Manage attachment" in my Zotero. What am I missing ?

[@sak9260]

Absolutely wonderful! Thank you so much for a clear and comprehensive explanation with a great summary. Can you kindly share the tool you use to actually create the video with the zoom features etc..?The sound is crispy clear. Thank you again.

[@NicholasCifuentesGoodbody]

+sak sak , Thank you for your comment! I use SceenFlow on the Mac.

[@craiglennox445]

Thanks for your video. its really useful. I am using the most recent version of zotero, 5.0.72 and when i right click it does not have the option to manage attachments and extract annotations. I am using a mac. any help would be warmly welcomed.

[@aliquot]

Very timely for me. Thank you for this!

[@hanydalees]

Thank you very much Dr. Nicholas

[@guoliangwang4826]

seems that the new version does not have extract annotation function

[@alanmac3931]

Excellent material - Thanks Alan

[@NicholasCifuentesGoodbody]

Glad it's helpful. Good luck with your work!

[@PeterOlin]

Thanks! This was great and very helpful. You could add a link to Zotfile in the link list of the video description and make it more clear that this Add-on is required.

[@NicholasCifuentesGoodbody]

Glad it was helpful! You can find all the info for installation in the first video of this series: kzbin.info/www/bejne/fZ6VfpWPd5ieatE.

[@frequencymanipulator]

Thanks so much, this has been so helpful.

[@tilakrohitha4074]

Thanks for the good explanation. I have a problem. I cannot see Referance Button.

[@lisabenjamin7130]

Thanks. This is a very useful video.

[@adc.super.t]

I tried to extract the annotations as described using the stand alone version of Zotero for Google Chrome. When I right click on the PDF I am not given the option to Manage Attachments as described. Is there any other way of making this feature work?

[@NicholasCifuentesGoodbody]

+Alice Clarke, sure. Regardless of whether you're using Zotero as an extension of Firefox or as a standalone, you have to install the Zotfile plugin in order to extract annotations. First, download the Zotfile plugin from zotfile.com/. Next, open the Zotero standalone and go to Tools > Add-ons. In the window that opens, click on the gear and select "Install Add-on From File." Then select the file you've downloaded from zotfile.com/. It'll then install the add-on and restart the application. Once Zotfile is installed, you should have no problem.

[@adc.super.t]

+Nicholas Cifuentes-Goodbody Thanks for your response. I did find the Zotfile plug in and install. Once Id set the source folder in the preferences it worked fine!

[@NicholasCifuentesGoodbody]

Great! Good luck with your research. If you have more issues, the Zotero support forums are an excellent resource.

[@abderahmanrejeb4423]

Thank you very much you really save my day

[@NicholasCifuentesGoodbody]

Abderahman Rejeb Great! Happy to help!

[@mahiteja5014]

How to remove those date and page numbers in zot file??

[@orkideizci406]

thank you very much this is very helpful!

[@CesarHarada]

Thanks a lot - that was super helpful.

[@joannas3799]

Hello! I have only experience with Mendeley and CITAVI. Both of them have a feature of viewing the PDF files in the software and organize the annotations (highlights and notes) not in one big chunk, as ZOTERO does, but in small "bubbles"/windows linked directly to the marked part in the PDF. Instead of post-processing the notes, already while reading I can make a significant distinction between the type of annotations and notes that I am taking. Imagine, I read a proceedings book, I mark the "methods" part in red and the "results" part in green in many different articles. This color distinction (red= methods, green= results), at least in Mendeley, allows me to filter out the marked parts with the linked content or what's even better, in CITAVI I can tag my comments and assign them with a customized label, which later on I can link to a part of my future article. Are there any similar features available in ZOTERO? Again, I'm sorry if it's a rookie question but I'm trying to see what advantages does ZOTERO have over the programs I'm currently using.

[@NicholasCifuentesGoodbody]

Sounds like you've put together a great workflow. Thanks for sharing!

[@bpeg88]

[PROBLEM WITH ATTACHMENTS EXTRACTION] - Dear Nicholas, when i try to extract my notes and marks made in the PDF file (after properly saving it in the same folder) by right clicking in the PDF file, it doesnt not show me the last two options to click in ('attach new file' and 'manage attachments'), it ends at "rename file" and "index item". (I am using a zotero version in portuguese). Any ideia of what might have happened? Thank you in advance (again)!

[@NicholasCifuentesGoodbody]

It sounds like you haven't installed Zotfile. You can find instructions here: github.com/jlegewie/zotfile.

[@bpeg88]

Dear Nicholas, thank you for your answer. You were right I hadn't installed the zotfile.xpi. I just corrected that but a little problem remains. Every time I left-click on a folder a small message appears: "ZotFile ERROR - the source folder is not valid. Please change the source folder under ZOTERO-Actions-Zotfile preferences. You might have to use a custom folder." I don't know what it actually means, as i have all my files dully saved in Zotero's standard folders. Do you know what it is and how to solve it?

[@NicholasCifuentesGoodbody]

Looks like a question for the Zotero forums. Good luck!

[@bpeg88]

Good idea. Thank you anyway Nicholas. =)

[@bpeg88]

Thanks Nicholas! =D

[@PVCol]

Gracias por responderme en español. Me lo imaginé. Hace como dos años conocí el programa y sus videos; pasé mucho trabajo logrando obtener las anotaciones de los PDF. a a Ahora retomé el programa y entendí la necesidad de bajar ZOTFILE. Parece que varias personas han tenido ese impuse. Sugiero, si es posible, presentar un video específico sobre este punto. Reitero mis agradecimientos por su esfuerzo. Gracias desde Bogotá

[@pauls7056]

Thank you Nicholas. Really good and so clearly explained. I'm using MAC and the stand alone version of Zotero - so the Manage>extract annotations option didn't come up when I right clicked. Do you think that I am missing something (say a plugin) or does it only work with the on-line version of Zotero rather than stand alone? Thank you, Paul

[@NicholasCifuentesGoodbody]

Hi Paul. Yes, I'm guessing you need to install the Zotfile plugin: zotfile.com/

[@pauls7056]

Hi Nicholas, thank you for coming back to me so soon. You were right! In fact, I did a word search on these comments and found that you'd already suggested this to another commentator. It worked. I had to go out for a few hours and was just about to update my comment to say I'd found your earlier suggestion - but you beat me to it :D. Thanks again, great video and I really wished I'd known about Zoltero when I was a student.

[@lordfallbar]

@@NicholasCifuentesGoodbody Thank you so much. This helped me a lot.

[@vince5474]

hey. how do i insert the complete extracted note with text and sources (with adding the authors into the bibliography) into word? thank you for your great tutorials!

[@JibHyourinmaru]

I've been using Mendeley and it has a built-in pdf reader which is great but lately, Mendeley doesn't work great. Should I change to Zotero?

[@NicholasCifuentesGoodbody]

I prefer Zotero, but all these tools are great. Why don't you commit to doing one research project with Zotero and then decide?

[@JibHyourinmaru]

@@NicholasCifuentesGoodbody I changed today. haha I found out that the latest Zotero beta has built-in PDF reader which is great news.

[@TheMaxJuni]

Hi !! Is this functionality available on Zotero 5.0? I'm not seeing this on mine ..

[@NicholasCifuentesGoodbody]

There's a plugin you need to install. Go to the first video in this series.

[@sashanealand8315]

when I save my pdf the notes do not get saved

[@Pete81Moore]

Hi thanks for the video but I have a question. How do I make sure that I save the annotated pdf in the exact same place that I got it from? Zotero seems unable to extract the annotations and I think it might be because I saved the pdfs in a new folder.

[@NicholasCifuentesGoodbody]

+Pete Moore Thanks for the question. If you're working with Windows, there is a tutorial on my blog: universitytalk.org/2015/10/15/using-zotfile-on-a-pc-extracting-annotations/

[@rebeccatheurich6397]

thank you for the video, I am a new user so its a bit difficult. I tried to add annotations but the manage attachment seems not to appear, don't know what the problem is. thank you

[@DuskAndHerEmbrace13]

zotfile.com/#how-to-install--set-up-zotfile Be sure to follow the instructions on how to install

[@petvek3355]

@@DuskAndHerEmbrace13 Thank you so much! It worked.

[@allanakatwijuka2291]

you are really good, so good; GOD BLESS YOU

[@NicholasCifuentesGoodbody]

Thanks!

[@futuristiclandscapes]

Hi, I don't have the option for managing attachments, any idea why?

[@riase]

It does not have those icons at all? You seem to have an entirely different zotero

[@linuskarlsson4823]

You need zotfile aswell a plugin for zotero

[@PalinuroRex]

HI Nicholas, I noticed in other videos that you use markdown plaintext in your Devonthink notes, and yet the Zotero annotations you show are all in RTF. I wonder what's you're workaround to this issue. I've been dabbling with the Highlights app, and while it outputs markdown natively, it's not very customizable. Thanks again for a great video :)

[@jorgearturochaveso.6270]

Excelente video, claro y pedagógico.

[@NicholasCifuentesGoodbody]

¡Mil gracias, Jorge Arturo! Espero que te haya servido.

[@jorgearturochaveso.6270]

sí, de hecho estoy viendo el resto de la serie.- Dos preguntas elementales, Nicholas, sobre dos cosas que no encuentro. Una, muy útil, en el pop menu sobre un pdf no me aparece "Manage attachements" y, tampoco entonces Extract annotations. Sería formidable si lo logro.- La otra, no logro que Zotero aparezca en la mitad inferior de la pantalla de firefox. Cuando hago clic en el icono de la Z, me remite a Zotero, standalone, como app, que instalé en mi escritorio. Olvidaba decirte que soy de Mac, y trabajo con una Macbook pro.

[@NicholasCifuentesGoodbody]

Una pregunta: ¿Estás usando Chrome o Safari? Si es el caso, te recomiendo que bajes Firefox y instales Zotero allí. El standalone está bien, pero la versión plugin de Firefox tiene la ventaja de que lo actualicen más en seguida. Una ves estés en Firefox, tienes que bajar Zotfile, otro plugin. Ése es el que te da el pop menu. Todo está en el primer video de esta serie: kzbin.info/www/bejne/fZ6VfpWPd5ieatE. Si tienes otra pregunta, avísame. ¡Suerte!

[@jorgearturochaveso.6270]

estoy en firefox y sí tengo instalado el complemento Zotfile y aun así no me funciona. Pero lo volveré a revisar con cuidado después de almuerzo. Gracias.

[@jorgearturochaveso.6270]

ya revisé y lo que encontré es que el Zotfile tiene sus propias preferencias. Le modifiqué el método de extracción, creo que solo eso y ahora se resolvieron las dos cosas: ahora abre Z en la mitad inferior de Firefox y puedo manejar los attachements. (Solo en algún caso me dice que "skipped the attachements" porque son "top level items" o "snapshots").. Gracias de nuevo por tu ayuda.

[@mji1967]

Dude - thank you so much

[@NicholasCifuentesGoodbody]

No problem, dude!

[@luisameyer00]

Hello Nicholas, Thanks for your video. I have a question. My Zotero seems to have different menus than yours. For example, at the minute 11:57 you show that when you right click on the PDF one of the options to select is: Manage attachments. I do not see this option. When I right click these are the options that appear on my pop-up: View PDF, View Online, Show File, Show in Library, Move item to trash, Export item, Create bibliography from item, Generate report from Item, Rename file from parent Metadata and Reindex item. Are there different versions for Zotero?

[@NicholasCifuentesGoodbody]

luisameyer00 thanks! You need to install an additional plugin for Zotero. It's called ZotBib. Check out the first video in this series.

[@HiteshMoryani]

How can I import PDF from Zotero to Mendeley?

[@TheJoshtheboss]

Hi Nicolas, I think there is an inherent problem. Let's on day 1 you make extract Annotations from PDF. You put Headers there to make it nice and tidy. The problem! Day 2 you read another 30 pages and make new highlights. You of course extract notes again. This create and new Child note with the new highlights, etc. But it doesn't contain the Headers you made the previous day :| P.S. Is there way to display the highlights with in their original colours?

[@derchor4685]

Hi - I cannot find "Manage Attachments" on the right click menu...I think I have the standalone version though. Is this the reason? Can I still extract annotations from pdfs?

[@NicholasCifuentesGoodbody]

You need to install Zotfile. See the previous comments about this below.

[@catalaineknell2389]

Hi trying to install the annotation manager . Its inbedded in Firefox and there is no install add on from file button? The add on is sitting on my desk top and says it doesn't know what to open it with... thanx

[@NicholasCifuentesGoodbody]

Sorry to hear that. You might search through the Zotero support forums to see if someone has faced a similar issue. www.zotero.org/support/

[@bmntech]

The explanation starts with "welcome to our SECOND video on doing annotations with Zotero". I searched and I could not find the FIRST video!

[@NicholasCifuentesGoodbody]

Check the playlist on my channel page

[@bmntech]

@@NicholasCifuentesGoodbody Thank you for your reply (and for a very well done video). However, This video title is "Understanding Zotero". On your channel there are TWO playlists, "Master Zotero 4" and "Zotero Quick Tips" and, by the title, this video belongs to none of them :(

[@lamin1979]

Hi Nicholas, could you be of help? when I highlight and make notes in PDF files I cant save them so that I could use Zotero to extract the annotations from a PDF file for later reference. when i click save it does not save automatically on zotero rather it gives me options in my computer.

[@emmadeheveningham5932]

I have the same problem, did you find a solution by any chance?!

[@NicholasCifuentesGoodbody]

My students figured out a solution: universitytalk.org/2015/10/15/using-zotfile-on-a-pc-extracting-annotations/

[@laniakande5318]

Hello Nicholas, and thanks for your helpful tutorial. A question, please: I followed the direction on how to download zotfile. However, when I click on 'Install Add-Ons from File', it doesn't give me the zotfile I just added as an option. Any ideas? Thanks.

[@NicholasCifuentesGoodbody]

Hi Lani. Thanks for your message. It's hard to know from what you've written, but I have two ideas. First, make sure you're using the plugin version of Zotero, not the standalone version. Next, when you go to the Zotfile webpage to download Zotfile, make sure you're using Firefox as your browser. If you prefer using the Zotero standalone version, then you need to remember the location you save the Zotfile. It probably your downloads folder. Look for the file that has an XPI extension. Good luck!

[@1969Mizori]

Thank you very, very much for these great videos. I have learned a lot! I have ONE question though: while trying to extract notes from a annotated PDF, I am unable to find MANAGE Attachment so that I am unable to access Extract Annotation. Can you please try to help me solve this problem? I am using PC in combination with Zotero 5. THANK YOU.

[@NicholasCifuentesGoodbody]

Thanks! I'm glad you like the videos. In order to do that, you need to install the ZotFile add-on for Zotero: zotfile.com

[@CatherineMeeson]

Thank you so much for your videos, great clarity and direction. I wonder the extracted annotations, can that also be done from online books or digital books? Thanks

[@NicholasCifuentesGoodbody]

Glad to hear you found them helpful! With digital books, there are a few factors to keep in mind: (1) what's the format of the ebook (epub, Kindle), (2) where are you reading them (iPad, Kindle), and (3) how you want the highlights saved. One service that I used to use was www.clippings.io. That might be a good start. If you find any other good tools, please let me know. Good luck!

[@PeterSchutte]

this is great thank you so much

[@TobiasDettinger]

Everybody knows how to edit a pdf but no one knows how to add a pdf to the zotero library. This is the importand point. I have a new pdf. Where i have to put it to work properly???

[@navidvirani3085]

Hey!! I am unable to extract annotations. the problem i am facing is that after highlighting and saving the PDFs' i am not getting to option to manage attachments. Please help me out with this

[@NicholasCifuentesGoodbody]

Hey, Navid! I'm guessing that you have not installed Zotfile yet. Watch the first video in this series, where I show you how to do it: kzbin.info/www/bejne/fZ6VfpWPd5ieatE

[@soniaperez9269]

Hello I just tried to highlight and annotate part of a pdf as per your tutorial. When I have gone to 'Manage Extractions' and then 'Extract annotations' I get a message saying "Attachments skipped because they are top level items, snapshots, or the file does not exisit'. Do you know what is going wrong and what I should do?? Many thanks,

[@NicholasCifuentesGoodbody]

Very odd! Do the PDFs in your Zotero library exist as child items? That is, are they attached to an entry for a book, article, or book chapter?

[@soniaperez9269]

@@NicholasCifuentesGoodbody Thank-you so much for your prompt reply! I had just dragged and dropped PDFs from my desktop into Zotero. I have just tried right clicking on the pdfs and selecting 'create parent item' and now I am able to extract annotations. Thank-you!!! Your videos are proofing incredibly helpful for me trying to learn Zotero as quickly as possible!!

[@hegeskaar2214]

@@soniaperez9269 I was having the same problem! Thanks for the explanation! :)

[@mmikemma]

This is awesome - thanks for this tutorial. There's so many functions that it's pretty confusing sometimes! I was also able to drag and drop PDFs into Zotero and the citation information appears - do you know how that's done? I just want to sanity check to make sure the method is reliable

[@maxkoghut2417]

Regarding the question below: there is no way to highlight any text in a secured pdf, as such, nothing to extract.

[@NicholasCifuentesGoodbody]

Make sure you install the Zotfile plugin.

[@srinjayadasa3862]

Great tutorial Fantastic feature regarding extracting annotations but when I did it the link to the original note only gave the page number not the citation in form of author and year as it shows in your video. Why is that? The document is a small book I had scanned in but the file has been renamed from the Metadata.Any ideas?

[@NicholasCifuentesGoodbody]

Many thanks! It's hard to say what the problem is based on what you've said. But, since you scanned this book yourself, I would make sure that you OCR'ed the text. If there's only the page image in your PDF with no text layer, Zotfile won't be able to extract annotations. Good luck!

[@ajnghamedsa]

THANK YOU for the videos!! very nicely presented and I appreciate the time you have put into this. THANK YOU! I am facing a problem with annotation extraction. I have the zotfile installed (I am working on mac, firefox and stand alone zotero both). Initially i could not see "manage attachments" but got around that and fixed if. However, when I "extract annotation" there is no "notes" created as you suggested at 7:45. Can you please assist?!

[@NicholasCifuentesGoodbody]

Glad you enjoy the videos, +an war! My first piece of advice is to choose either the Firefox or standalone version of Zotero and stick with just one. I recommend the Firefox version because it tends to be updated more often. Once you've chosen, uninstall and reinstall the Zotfile plugin. Also, keep in mind that it can take several seconds for Zotfile to create a note with your annotations --- especially if you're extracting from a large PDF file. Good luck!

[@chrisguttler7897]

Hi Nicholas, thank you for your great videos! I have one question. I've Zotero standalone version 4.0.29.15 running on MAC and would love to extract those notations I've made in the PDF files, but unfortunately I don't have the "manage attachments" and/or "Extract Annotations" option, when I right-click on the PDF-entry. Do I do something wrong? thank you

[@chrisguttler7897]

problem solved, I didn't have ZotFile addon installed yet. thanks again

[@NicholasCifuentesGoodbody]

Great! Glad to hear it all worked out.

[@chrisguttler7897]

it work's really fine, great tool , but even better tutorial!

[@NicholasCifuentesGoodbody]

Thanks!

[@jyotithelightnew]

Thank you for sharing this with us, I do take sessions on Zotero for PG students and teachers, and this new feature is awesome

[@maxkoghut2417]

Hi Nicholas, thanks for your work. I was wondering if the extract annotation function would work with a SECURED pdfs?

[@NicholasCifuentesGoodbody]

Good question! Honestly, I don't know. If you do some experiments, let me know how they work out. Good luck!

[@maxkoghut2417]

Will do!

[@manuelcamassa2567]

Dear Nicholas, I have a problem with the "attachments extraction". Not only I'm not able to modify directly the pdf (I'm using a Mac and Preview saves automatically a copy of the pdf I'm highlighting, telling me that the original one cannot be modified), but, as many other users wo had the same problem, Zotero doesn't show me the last two options 'attach new file' and 'manage attachments' (I'm using Zotero for Firefox). I read that you suggested to use zotfile, but when I go to the webpage in order to download it, it says that it's not compatible with the Firefox version I'm using... I've been struggling with this issue for days and I can't find a solution. I really hope you can help me. And thank you so much for the tutorials: they are masterly done.

[@NicholasCifuentesGoodbody]

Hi Manuel. Thanks for watching the video! If order to extract annotations, you need to install Zotfile. If you're using Zotero inside Firefox, that means that your running Zotero version 4. So you have two options. (1) Upgrade to Zotero version 5 or (2) install an older version of Zotfile. You can find instructions for installing the older version of Zotfile here: github.com/jlegewie/zotfile. Good luck, and happy writing!

[@manuelcamassa2567]

Hi Nicholas. As you see, I've wited for days before replying to you. In facts, I tried to find a solution for my problem in the Zotero Forum, but to no avail. The issue is: Zotfile is apparently not compatible with my version of Firefox, that's why I was forced to use Safari, download the .xpi file of Zotfile and then I tried to to install it in Zotero by clicking on "Tools", "Add-ons" and "Install add-on from file". The problem is that I see this thing: imgur.com/Fzqlk8W and Zotfile is still not working. By the way, I have a Zotero version 5. I've been struggling with this issue for days, so I would be very much obliged if you could help me solve this problem. It's so frustrating! Thank you in advance!

[@NicholasCifuentesGoodbody]

Sorry to hear you're having trouble. My advice would be to post your question to the Zotero forums. You'll get a whole slew of answers. You might also tweet @zotero and @adam42smith. Both excellent resources. Good luck!

[@MirkoRuf]

Very apprehensive video! I just can't find the option to extract annotation in Zotero 5 (Windows). Is it not available anymore?

[@Sport-shooting]

"That's a function of ZotFile zotfile.com/, not Zotero itself, which you'll need to add to Zotero separately." you can read it here forums.zotero.org/discussion/68854/cannot-extract-annotations-from-pdfs-with-zotero-5 and then read " Instructions to Install ZotFile" so you can add this plungin to Zotero.

[@adif7542]

Great tutorials, very helpfull as I am new to Zotero. However, I am having a problem with extracting notes from PDF's; Acrobat Pro DC is my default PDF software on a Mac. In Zotero when I right click on a PDF I do not get the option to 'manage attachments'. Am I missing something i.e. a setting in preferences or a plug in?

[@NicholasCifuentesGoodbody]

Hi Adi. Glad you like the videos! Yes, you're missing a plugin. I'm guessing you need to install ZotFile. Go to the first video in this series for more info: kzbin.info/www/bejne/fZ6VfpWPd5ieatE. If you're using the standalone version of Zotero, see my answer to +Lani Akande below.

[@adif7542]

All works now. Thank you.

[@NicholasCifuentesGoodbody]

Great!

[@jenniferlindwall1309]

Hi Nicolas, thanks for these videos! Just finished up my first year of my PhD and trying to get a good system in place this summer before things get out of control on the article front. I am seeking to use zotero with papership, because I do a lot of reading on my ipad. I have done some experimenting but wondering if you have any good resources or tips. I still am working through how to actually save notes and categorize things so they sync back and forth.

[@NicholasCifuentesGoodbody]

So glad the videos are helpful! PaperShip is the best solution I've found so far for syncing between the Zotero library on my desktop and my iPad. To do this, you'll need to have an account with Zotero, and you'll have to sync your PDFs using Zotero's storage or something like Box.com. You can watch my video on syncing for tips. I would suggest paying the extra for PDF annotation in PaperShip. Then, take your notes and make highlights in the PDF on your iPad, sync with your library, and then extract your annotations and notes using Zotfile. I cover Zotfile in my video on installation and the one on notes, links, and cross-references. Good luck!

[@jenlindwall745]

Thank you for this reply! I do already have Papership and the annotation pack, I love using it. I am a bit confused about if I need zotfile though. Even after watching the syncing video. Is having Zotero and Papership enough to get all my annotations and notes synced up? Or do I need to do something else to be easily able to move between these two things. I tend to read and highlight on my ipad and then use my laptop for writing and organizing my library.

[@NicholasCifuentesGoodbody]

All good questions! First, my syncing video is more about backing up your library, so don't worry about it in the context of this conversation. Second, if you're using PaperShip, you don't need Zotfile to sync PDFs between your computer and your iPad. But Zotfile will still be a big help because it allows you to extract the highlights and annotations you make on your iPad into separate notes in your Zotero library. To give it a try, mark up a PDF on your iPad. Once it's synced back to your desktop library, right-click on the item. Go to "manage attachments," and then "extract annotations." Good luck!

[@muofherophuluswa5599]

Thank you very much

[@maxkoller4461]

Thanks for your videos! Maybe you can help me with this: It appears that when I right-click a pdf in zotero, I do not have the last two options ("Attach new file" and "Manage Attachments"). Do you have any Idea what I can do about that? I really like to use the "extract Annotations" tool. Cheers

[@maxkoller4461]

I found the solution to my problem. For the Zotero STANDALONE you need an Addon: zotfile.com/index.html#install-zotfile Read carefully how to install it for the Standalone version

[@maxkoller4461]

I found the solution to my problem. For the Zotero STANDALONE you need an Addon: zotfile.com/index.html#install-zotfile Read carefully how to install it for the Standalone version

[@NicholasCifuentesGoodbody]

Glad you figured it out. Good luck with your writing!

[@orkideizci406]

@@maxkoller4461 thank you very much this is very helpful!

[@guoliangwang4826]

New skill get, thanks

[@Sthenel]

Isn't it possible for Zotero standalone to extract PDF notes?

[@NicholasCifuentesGoodbody]

You'll need to download the add-on Zotfile: zotfile.com

[@RP-xs5ff]

Hi Nicholas, Thanks for this very useful video. I am facing problem in extracting annotations. I'm trying to do so on Zotero Standalone on my Windows laptop. I have installed the Zotfile 4.2.6 extension as well. So I can now see the option of extracting annotations. However, when I try to do it, I get the following error message: "Attachments skipped because they are top level items, snapshots or the item does not exist". Can you please explain why this is the case and how I can rectify it? Also, in the Standalone version, I am currently unable to see any option (when I right click on the PDF file) to rename it as parent metadata. Could you please also help to rectify this issue? Please help!

[@NicholasCifuentesGoodbody]

Appreciate your kind words! I'm guessing you need to install ZotFile. See my answer to +Lani Akande below, where I talk about installing it in Zotero Standalone.

[@SVGrokzero]

THANK YOU VERY MUCH!

[@NicholasCifuentesGoodbody]

Thank you for watching!

[@SVGrokzero]

I like how you explained things clearly about zotero and yes sir your series of videos is of great help! Hope i can see the same for an NVivo tutorial :)

[@kanewilliams1653]

godsend!

[@paucalderon8326]

So I can't read PDF files with Zotero? I'm sticking with Mendeley lol. But thanks for the video, it was helpful.

[@RaihanJamil]

Not clear what you mean. Zotero allows you to use your laptop's own pdf reader and uses it.

[@quintoncarroll1083]

If you are having problems loading Zotfile this video is very helpful. kzbin.info/www/bejne/nJK8e2edeqyNapI

[@monsieurayala]

Funny voice. Good video tho - thank you.

[@mahiteja5014]

How to remove those date and page numbers in zot file??