Zotero video transcript & links
Zotero functionality demonstration, by S.Mok – Jan 2025 - [email protected]
On this page you'll first find a table with the most import links, then a topic index for the Zotero videos in the playlist, and finally a full transcript for all videos broken up into subsections.
Links
The videos can be found here: https://utwente.yuja.com/V/PlayList?node=4512850&a=2010311004
Zotero official
Zotero https://www.zotero.org/
Zotero official documentation https://www.zotero.org/support/
Register a Zotero account https://www.zotero.org/user/register
Your Zotero Library online https://www.zotero.org/mylibrary
Your Zotero Groups https://www.zotero.org/groups
Use with Google Docs https://www.zotero.org/support/google_docs
3rd party
Zotero Addon-Market Plugin https://github.com/syt2/zotero-addons
Better BibTeX manual https://retorque.re/zotero-better-bibtex/
How to link Overleaf w/ Zotero https://www.overleaf.com/learn/how-to/How_to_link_Zotero_to_your_Overleaf_account
How to dynamically cite in Overleaf w/ Zotero (just like in Word) https://www.overleaf.com/learn/how-to/How_to_search_for_references_in_an_Overleaf_project#How_to_use_advanced_reference_search_(premium_feature)
Topic Index
To find in which video (and optionally subsection) I mentioned certain terms.
Topic --> Video (+subsection)
ACS (Source) 3.1
Add-on Market 4.2
Adding Items 3
Annotations 5, 5.1, 5.2, 6.3
Better BibTeX 4.2, 4.3, 8, 8.2
Bibliographies 6.2, 8.1
BibTeX 3.2, 4.3, 7.1, 8
Browser Connector 1, 3.1
Citations 6, 6.1, 6.4, 8.1
Collections 7.1
Crossref 3.2
Deleting Items 4
Duplicate Items 3.1
Exporting 8, 8.1
Find Full Text 8.2
Google Scholar 3.1
Groups 7.4
Importing 3.2, 8.2
Linter 4.2, 4.3
Login 2a
Mendeley 3.2, 8
Metadata 2a, 3.1, 3.2, 4, 4.1
Notes 5.2, 6.3, 8
Open URL Resolver 2
PDFs 2a, 3.1, 3.2, 5, 8, 8.2
Plugins 4, 4.2, 4.3
Reading PDFs 5
RIS Files 3.2, 8
Save to Zotero 3.1
Scopus 3.1
Search 7.2
Shared Libraries 7.4
Sync 2a, 7.4
Tags 7.3
University of Twente library 2, 8.2
Unlink Citations 6.4
Transcripts per video (& subchapter)
1. Download & Install
Download Zotero from zotero.org. Press the download button, and then again the download button for the software. It will auto-select the right software for you.
If you want another version, you can find one down here.
Make sure to also install the browser connector; it's essential for using Zotero. You can also install it later, but why not do it now?
Once it's downloaded, run the installer and then open Zotero.
2. Initial Setup
When you first start up Zotero, you'll see this screen, and it should pop up a browser window that looks like this.
It mentions installing the Zotero connector if you haven't already, and then it points you to the registration process.
If you haven't done it already, I suggest doing it now, and then it says, "Start using it." Let's get back to Zotero.
This is what it looks like when you actually open the software.
The first thing I recommend to do is to go into the settings.
There are two things you should change when you initially start up.
One is here in general for the resolver. Select, of course, the University of Twente library. This will make sure it will use the library's Open URL resolver to find items.
(ignore) -Then, in sync here the account you made at Zotero.org enter your credentials here and set up syncing-
2a. Initial Setup - login & sync
The second thing I recommend to do is to head over to the sync tab, enter your credentials from zotero.org - so your username and your password that you just made - and then press "Set up syncing".
It will log in, and then it will show you a lot of options.
I highly recommend to not sync full-text content and do not sync attachment files.
This will make sure that Zotero will sync all the metadata that you save - so all the items actually in the library - but not the PDFs because that's limited to 300 megabytes standard.
We'll get back to that later.
"Sync automatically," I recommend enabling, but for this demonstration, I'm not going to enable it because, otherwise, my Zotero will fill up with all my previous items.
Those are the two settings I recommend to change.
There are lots more. You could take a look yourself, but we'll get into a few others later.
3. Adding Items
The first thing you will want to do, obviously, is adding items to your library. There are many ways to go about this.
3.1 Adding Items - from your Browser
The most often, you will add items from your browser. You will find an article that you like, and you want to store it. Then you can use the browser connector, and you can see the icon here: "Save to Zotero." If I now click this item, it will save it. This icon will change depending on what is detected on the page. It says in brackets "Scopus," so it has found a Scopus item.
You can right-click the item and use "Save to Zotero" to store it in a different way if the automatically detected item isn't correct. Normally, this is fine, and you can just press the button. Let's do that.
Press it. It will store it in the folder you currently have open in Zotero. We will get back to that later. You can see it stores the item and also some extra information supplied by Scopus: a snapshot of this webpage and the PDF of this paper.
If we look at Zotero, we indeed see this item now in our library. We can open it to see the attachment, note the amount of times it's been cited, the PDF, and a screenshot of the page itself. You can, of course, open the PDF to read it. We will get back into that later.
The metadata here is pulled at the moment of import from however you import it. This can change depending on the source. If we now look up this article, instead of in Scopus, we look it up at the journal page in ACS. We can see here that it has detected that it's indeed a publication by ACS. Let's save that as well. It will store it. You can see it now doesn't take in the notes or a snapshot. That's something that Zotero only does with Scopus and not with ACS, apparently.
We can now see it twice in our library. We can see that the metadata is indeed different. Scopus, as you can see, for instance, has the initials, and ACS has the full names - at least the full first name. There are some other...for instance, Scopus doesn't include the ISSN, but ACS does. There are multiple other differences. Now both got the PDF, so that's great. But now you might see I have a duplicate. That's not what I'd want.
You can go to the folder "Duplicate Items," and you can see it's detected them. You can tell what the primary item is. ACS is better metadata, so let's choose that as the primary one and merge them. Now we can see we only have one left, and it updated the metadata. That's the primary way to import items.
There are some differences between sites, as you see, but you can also, for instance, like here, we have a search result on Google Scholar. You can see it has a folder icon. If we click that, it tells you, "Hey, we have multiple items found. Do you want to store them all?" And you can do that then. Not all are properly identified in this manner, but sometimes it works very well. But again, you can change how it stores it - not this, because you first need to select the items itself.
3.2 Adding Items - from other sources
For a random web page, you can, of course, store Wikipedia as a specific detection. There are Wikipedia articles, but also, you can grab the embedded metadata or other identifiers from pages like this. If we, for instance, save this page, this Wiki page, you can see it saves it as a Wikipedia article with the article itself, the abstract of the article. So that's one way.
Another way to do it is to paste an identifier here and look it up, and it will go search for that paper. And again, that's the same paper. And you can see, again, this is not entirely the same metadata as that we have imported from ACS. This, I think, uses Crossref as the primary supplier for information.
Finally, you can, of course, import files like RIS files, BibTeX files, as you can see here. So let's show that as well. If we have a BibTeX file, for instance, we can say, "Let's import this." And normally, it makes a new folder to store this import. And here, you can see it has imported this BibTeX file. So that's easy to do. This is a useful way to move from, for instance, EndNote to Zotero.
If you look at the import option, you can also see that it comes with a Mendeley online import. You can log in from here to directly import from Mendeley if you'd like. And finally, what you also can do is grab a PDF from a paper and drag that to your library, and it will add that as well. As you can see here, it's this article here. It started, of course, with the PDF, so it has it already, and it retrieved the information from both from the PDF and from Crossref. That's the numerous ways you can add items.
4. Metadata, Installing plugins
Now, of course, you can delete items again. If you don't want them in your library, you can select them, move them to trash. Okay, and if we have the trash, and you can see everything that we've removed, and we can empty it too and delete them.
4.1 Changing Metadata
If the metadata that you received isn't correct, you want to change it. You can, of course, manually do that however you'd like. However, I do not recommend doing that. It's often not necessary.
Most of the time, the metadata that comes with the items is pretty good. If not, there is an extension that can really help you to fix that, and extensions are very powerful additions to Zotero.
4.2 Installing Plugins
Previously, for each extension, you had to download, find them on the web, and download them yourself. Now they have...there is an add-on market that you can install.
I'll send a link to you where you can download the file, and then in Zotero you can go to "Tools", "Plugins," and you'll see this window. Then you press "Install Plugin from File," you select the plugin you want to install, and in this case, it's "Zotero Add-ons," and it's installed it. And now we have a new button here, the "Add-on Market." This pulls in add-ons from a list.
Each add-on has the full source code available, so you can right-click and go to "Home Page" to look at the home page with more details of every extension that you can install here, and also the source code, so you can check that if you're a programmer. But that at least makes it a bit more safe. People can check what the code is, so it's more trustworthy.
There are two extensions that I really recommend everyone to install. The first one is this: "Zotero Linter." Let's install that. And the second one is "Better BibTeX for Zotero," and that's not only for people writing LaTeX. It's useful for everyone.
Now we've installed those. You can also mark this to automatically update all the extensions, including the Add-on Market itself, so I recommend marking that as well.
Now, once you've installed plugins, you can go to "Tools," and you can click "Plugins" to see what you've actually installed if you want. Most tools - most of these plugins - will have a settings menu added here in the settings. So you can see "Better BibTeX" and "Linter."
For most of them, the standard settings are fine, but for Linter, I would recommend disabling this if you get annoyed by all the pop-ups because every time you add an item now to your library, it will show you what it's doing, and it can be annoying, so you can disable that and then later activate it manually.
4.3 Using Plugins
But I'll show you what it does, the Linter. If you have an item, like, for instance, this one, the PDF that we added, we can right-click, go to "Linter," and press "Lint and Fix," and it will look up the metadata in the source and update it where possible. And same for this one. We can do that, and these ones were already quite good, so not much has changed, I think. But there are also other options, like, for instance, if the creator names aren't all in the same format, you can press this, "Fix that case," the capitals and lowercase letters, or the title, for instance. You can automatically fix all kinds of things: "Retrieve Fields from Identifiers," etc.
So it will fix up the metadata, and it's very useful. In the end, if you have a list of items you want to cite, you can select them all, lint them all in this, so they are all formatted in the same way.
"Better BibTeX" make sure that BibTeX keys are properly produced, and that's very useful of its own if you're using LaTeX. If not, that doesn't really do much for you, but it does in the back end add a lot of extras that are helpful that I won't go into at the moment.
5. Reading & Annotating PDFs
Now, another thing to do, of course, is to read PDFs. So if you have a PDF, you can open it in Zotero, and you can see it's just a PDF reader. The nice thing is that it directly integrates, of course, the rest of your library. So we can, of course, mark things here, give it a color, for instance. And here, we can see a list of all the things that we marked with the color that we picked.
5.1 Annotating PDFs
We can also add different kinds of comments, like underlines, or sticky notes, or just text, or whatever, drawings. We can do whatever we like, and you can see it saves it, stores it neatly. Included is the page number, so that's the page number as it is in the document, as you see, not of the PDF, but that's also very helpful for proper references because these notes can be stored in your library, and you can refer to them later when you're writing your thesis or document.
So if we now see this item, you can see that we don't really have anything extra added here. There's nothing - nothing has shown up yet, although we did make some notes. If we click the PDF itself, you can see that we do have the annotations, so they're not on the item, but they're on the PDF. If we want to link them directly to the item, you should press right-click and "Add notes from annotations." And then you can see that the things that we marked here - not the drawings, because it can't convert those to text - but the rest that we select or write down ourselves is written down here, including dynamic links. So these ones, we can go to this item directly. So in this way, you can link two items dynamically and go back.
5.2 Working with Annotations
So if you make these notes, you can also directly type, of course, in these notes, add links yourself here, insert links and other things. So if you open it here, you have a full text editor. So you could write your entire document in here even, although I don't recommend this. The nice thing is that these annotations, these notes, can be directly imported into whatever software you're using for writing, and it includes those dynamic citations.
6. Citations & Bibliographies (in Word)
So, let me now move over to Words to demonstrate citing items. You will have a new tab in Zotero to automatically install this. For other writing software, you can also do this. You should look it up in the documentation.
6.1 Adding Citations
If we want a citation, we can add one. If you do it the first time, it will ask you what style you want to use. There are a couple of standard styles, of course, but if you want a different one, you can press "Manage Styles," and then "Get additional styles." And here, it will show you all the ten and a half thousand styles available directly in Zotero. So, you can look one up, and you can see there are quite a lot. Some of them are quite old, some of them are newer, but let's, for instance, pick this one here. And if you want to change it, or if you want to preview it, you can press "Preview." If you want to change things manually, you can press "Editor," etc. But for now, let's just stick with this.
So add the citation, use this one, and press "OK." Then it will pop up this window, a search bar, that you can use to search for through your library. And if we look, we want, for instance, to cite this one, press "Enter," and it will add the citation for us.
6.2 Adding Bibliographies
And if we then want to show our bibliography, we press this, and it will add it as well. You can, of course, then change the style to something else, and it will automatically update everything for you in whatever way you want. ACS is, I think, proper here.
6.3 Adding Notes
And what you can also do is insert a note, like the note we just made. You get another search bar, a yellow one in this case, and here you can select the annotation you want, press "Enter," and it will add it, as you can see here, that's what we selected. And you can see it automatically adds the correct citations in there as well. Those are dynamic. Of course, all of them are, so, for instance, now it's one, but if we add another citation here earlier, then it automatically updates this to two, and it's, of course, also included here properly. So that's how to do it.
6.4 Unlinking Citations
There's then a final option here, "Unlink citations." If you do that, it will ask you, "Are you sure," and you can press "OK." Now it's not dynamic anymore, now it's just text, and this can be useful for the final basis if you want to print or share the item, and you're worried that things will break. This is the way to go. However, in regular use, you will never want to press this button. You will never want to press this button.
7. Collections, Search, Tags, Groups
All right, now I have added some more items to my library again, and what I now want to show you is the collections, the groups.
7.1 Collections
So as you can see here, I imported this from a BibTeX file, and it already made a new map to store that, but you can also see that in my library, there are also...these submaps always are a subset of the primary map that's above it, and you can also make a submap inside a map. Initially, it's empty. If we want to add some things, we can do that, but you can see they don't disappear from the first folder; they only get added to the second one. So it's a refinement of the initial set, but it never gets removed from the top level - important to know.
Then you can - that's one way to order things and sort things. When you add an item to your library, you can select in which folder it should end up, and if you, for instance, add something to "Test," it will also add it in "Master," and also, it will show up in "My Library," of course. So all the folders above, but not the folders below.
7.2 Search
Then you can also search if you quickly want to find something. So for instance, searching for "microfluidics," you get this. But you can also do an advanced search, and then you can see a quite in-depth interface where you can set up a search exactly how you'd like. This can be very useful if you have a large library and you want to automatically sort things for you. So for instance, let's say I want everything with "microfluidic" in the title, search, yes, then we have this, and search for collections, show only top-level items, for instance. You can change all kinds of things. Maybe we also want then the date to be after 2020, for instance, and then we find nothing - 2010. You can see how it works.
If you do this, and we have a search and we're done, we can save it, and you can see that it adds a folder here. It's a "search folder," and this will automatically update the results. It will just run the search every time that something is changed in the library, and it will show you the results here. So that's a dynamic folder. This can be very helpful, very useful, of course.
7.3 Tags
Another thing that you can do is you can search, use tags. So an item can have tags, and see here, you can use whatever you like. So for instance, this is "important," or we can tag this "to read" or something, and you can see them listed here. You can immediately filter out all the items except the one with a tag, or search by tags, and then we can see only this item. So that can also be a useful way to manage and store your items.
7.4 Groups
The other way - another thing to do, of course, is to use group libraries and shared libraries. And for that, you will need to make sure that you're logged in, so that you have sync, and use your logged in with your account. Otherwise, this won't work. Now, I haven't synced everything yet at the moment because, otherwise, it will take a long time because I have quite a lot of items in my account, so I won't do that here. But if you want a group library, it's all done through the web.
So here, you can see, you can make a new group, and that's like a shared library. If you click that, it will point you to your browser, and you will need to log in, and then you can make a group. There are all kinds of options. You can look for that yourself, and you can see the other groups. You can open them here on the web as well, and if you enable the sync in Zotero, these will show up for you as well in Zotero itself. And from then on, it's just the same as it always was, except everything that you do will also be visible for the others, and so then you have a shared library that's separate from your own. There's nothing to do with each other, so it's just a completely separate library.
If you want to work together in a single document in Word dynamically, make sure that you're both using the same group library, then it will work properly. So if you just share this with anyone else, and you work together, you go live editing both in the same document, if you both have Zotero installed, you both are using the same library, this will work fine. That's it.
8. Exporting (+ advanced import)
You might also want to export, of course, your library to somewhere else. You can do that in multiple ways again.
8.1 Exporting
If you press "Export Library," you will get this menu. And the options available here will depend. Because I've installed Better BibTeX, you can see a lot of extra options here. That's one of the reasons that I highly recommend installing Better BibTeX, if you're using it or not, because BibTeX is often used to interface between different types of software, like, for instance, Confluence or something else.
If you want to export your library, BibTeX is a quite well-defined, standard format for that. So you can select the format here. And, for instance, let's use RIS - RIS file. You can choose to include notes or not, and files or not, and include the annotations of your PDFs, yes or no. So this is something that is very nice. This is something that, for instance, Mendeley does not have directly. You cannot export anything that you write down in your PDF, so Zotero has that built-in. If you select this, press "OK," then you can store it as a RIS file. And if we now open that file, for instance, in Notepad, you can see that it has indeed created a RIS file with all the references in my library. Okay, that's easy to do.
If you want to only select the subset, you can, of course, select whatever you want, press "Export Items," and do that. Do whatever you like. Sometimes you just want a quick citation of an item, and you don't want to use Word or whatever. For instance, I want to cite this paper. You can then press "Create Bibliography," select your style that you want to use, and use this bibliography mode, and then "Copy to clipboard," and press "OK." If we now paste somewhere, you can see that it has a nicely formatted citation for this item. We can, of course, do that for multiple as well. Do this, paste it. We get a nice quick bibliography. And even, I believe this should also work, we can just drag it. So if we have one and we drag it somewhere, you can see it uses the standard settings that you have somewhere to create the citation as well. You can see that it does that here as well. I'm not sure what the standard setting is here. It looks a bit weird, but we can change that.
You can also generate reports and other things, so you can explore these options yourself.
8.2 Advanced Import
Additionally, I didn't mention this yet, but if you haven't got the PDF for an item, but you do have the reference, you can press "Find Full Text," and it will try to find it for you using the DOI, and I think the library link as well, and open access sources. Sometimes it works great, sometimes it works less great. I think this works the best if you're actually at the UT because I don't think it properly identified the library access at the moment; and it does need a DOI. And there are some plugins that can help you do this and do this better because in the basic application, it's not that great, but there are some plugins that can help you. Normally, however, this is done when you find an item, and then it uses the connector to actually find the proper PDF for you. So that's how to do that.
If you want to import items, we already mentioned that by "Import" here, but you can also import from clipboard, so if you have something under your copy-paste, you can press this and it will paste it in here and see if it can add it. You can also do a scan of a document here, and with Better BibTeX, you can also scan files for references. So there are multiple ways to add references from various sources. And of course, you can change the styles and everything that you'd like in Zotero, but that's beyond the scope of this video.