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Sometime back @ShreyaTrivediMD crowdsourced Ref Managers here:
Then more recently she asked #Academic Twitter with updates wherein I heard that some of us are entering citations manually. This blew my mind. So I took the challenge posed by @VirenKaul and will do my 1st #Tweetorial on reference managers.
First…a poll. How do you manage/enter your references?
1/I’m not going to try not to be judgy in this tweetorial, just gonna break down the facts and styles that might appeal to various of you. Hopefully its just a matter of “I didn’t know…” driving the manual entry of references.
2/First: What systems/devices do you plan to use? OS (Mac, Windows, Linux)? Will you be using your phone/ipad and need iOS/Android? Preferable browser Chrome/Firefox etc. Details matter for platform integration. Your optimal ref manager may be different than mine.
3/Next, what are you using this for? Maybe you just want to save Pubmed searches, get email updates on a saved search on a weekly/monthly basis, and save some refs for personal use. Pubmed MyNcbi may be sufficient. ncbi.nlm.nih.gov/account/?back_…
4/If you’re writing manuscripts solo and want to save/share articles for #MedEd purposes then you need a library.
5/Can be a desktop version/downloaded e.g. Endnote, but you have to know the platform isn’t clunky and won’t drive you crazy esp if you’re spending $$ on it. Personally, I don’t like exporting files, or electronic libraries that one person holds or has to share.
6/Speaking of exporting files, if you choose this route for sharing of libraries you need to make sure that the libraries your collaborators are using can handle what your favorite manager can export in (e.g. BiBTex, RIS etc).
7/Same with importing. You read this and want to change your current approach & your institution supports another program…check the importing so you can move your current refs to the new program. Many will use Pubmed, Ovid etc. for importing which will make life easier.
8/Desktop platform or Web-Based: #AcademicTwitter influencer-types with the @JAMA_current perspectives or @nature papers, that collaborate on 100+ projects across institutions will definitely need a web-based platform (e.g @F1000Workspace, @mendeley_com, @paperpile @zotero)
9/Even if you’re not that big time, I still think web-based platforms are the way to go due to space.
10/Which reminds me, check space given with free platforms as those 1940s PDFs that you asked the librarian to find on microfiche will take up space eventually. 200MB vs. 2GB vs. unlimited might mean you pick a different platform
11/What about citation styles, does that matter? Well…it can. Most of the platforms have enough that its no biggie, but those in a niche field that submit to obscure journals, internationally should check the number and types of styles supported by the ref manager you choose.
12/The extension method (CSL, BiBTex) will also vary though most of the big players will, again, be fine.
13/Speaking of academic fields, one other thing to ensure is that the ref manager you use retrieves references from databases and search engines that matter to you.
14/This isn’t a problem for PubMed, but those in the computer science and engineering fields capture information from IEEEXplore or CiteSeer which are not compatible with all the platforms.
15/Alright, now let’s get to the nitty gritty. You’d like to create lists, projects, move things around, maybe you even want to tag things or mark-up notes in PDF’s you’re reading while you’re saving references. Yes this is possible.
16/You want to work on references simultaneously with others, restrict access to collaborators to some content (user specific access). Many programs let you do this, but for e.g. EndNote doesn’t.
17/Word Processor integration is another key issue as @ShreyaTrivediMD pointed out. She uses GoogleDocs so @paperpile works well, as of this writing there doesn’t appear to be ability to use in MS Word on their webpage. Pick one that fits your #workflow.
18/Which reminds me, don’t take anything I’ve said here as gospel, these programs continually change, some platforms even get discontinued.
19/Which brings me to the next point. How transportable are these web-based libraries anyways? Does the company have a policy of what happens when you go from fellowship @KashlakHospital to FancyU that doesn’t have a license with your fav. reference manager? Check the websites.
20/Now I’m going to show some real examples of what I’m using now, @F1000Workspace. My institution has a license, its free, and I can invite collaborators outside of my institution to my projects and they can use it that way for free (on those projects). Win-Win.
21/So this is what it looks like, the organization of the projects, some shared, some private, sub-projects are possible (not shown). 
22/You can highlight PDFs, (I do this for old papers that I had to request) or for things I refer to often (practice parameters e.g.), and have marked up. Highlighted areas then appear in notes for that particular article.
23/There’s a tool section for the plugins that you’ll need to be able to import your references. This is what that looks like.
24/And I guess the main reason that spurred this #tweetorial was me cringing upon hearing of people manually entering references. Seriously there’s no reason for that. Its this easy to insert a reference on… say consensus criteria for #EoE(Spergel et al. 2018) #EGID
Okay that’s about all I’ve got energy for today, there’s probably much more. I’ve probably forgotten something big. Please feel free to add to this thread, or unroll it, share it. Just don’t manually enter references anymore, please? Thanks! Bye! Fin.
For this purpose, see these screenshots
