The EndNote is nigh

First of all, many thanks to all of you who commented on my last post. My mother-in-law isn’t out of the woods yet, but is taking baby steps in the right direction. We’re all gradually exhaling and trying to adjust to our “new normal”, which for me involves reclaiming at least some of my usual blogging and other online time, which I need if I’m going to retain my sanity!

And so, with no further ado, on with the usual grant deadline day software screenshots and rants!

EndNote, this time. (It’s not my fault; everyone uses EndNote at work, and so I have no other choice).

Now, when EndNote and Word both feel like playing nicely together, it’s not the world’s worst set-up. However, when hustling to consolidate all six latest versions of the proposal text in time for the 5pm deadline, playing nicely goes straight out the window and a full-on playground fight tends to break out.

I’ll spare you the details of EndNote crashing Word and thereby uninstalling its own macro (TWICE today), and of seemingly random recognition of some inserted references but not others, and focus instead on a bug in EndNote’s PubMed search feature.

Some of the PIs had peppered their versions of the grant with PMIDs to indicate which reference should go where, making my life extremely easy. However, others had inserted numbered references corresponding to a list from another document, which may or may not have been provided to me, and still others used references in the format “CA Dunn, Gene, 2005” (one of my own papers, not at all related to the grant, used merely as illustration, etc.).

Now, I could have searched each of these references in PubMed, grabbed the PMID, and used that to import the reference into EndNote. But I was rather hoping to be able to use the provided information directly, thereby skipping a step. But look what happened:

It took me a good three or four such failures to realise that the difference between “Dunn CA” and “Dunn, C.A.” was responsible for these failed searches.

Really, EndNote?


Is it so hard to ignore all that (ridiculous and unnecessary) punctuation and just import the damn reference?

It might not seem like a big deal, but when you’re dealing with well over 100 references, the time required to reformat those author names really starts to add up.

So, in conclusion:

EndNote can bite me.

(I feel much more normal now, thank you very much!)

About Cath@VWXYNot?

"one of the sillier science bloggers [...] I thought I should give a warning to the more staid members of the community." - Bob O'Hara, December 2010
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18 Responses to The EndNote is nigh

  1. Steve Caplan says:

    When I was a Ph.D. student, I used a primordial version of EndNote (I believe it was called “EndNote Dino”). For whatever reason, of the 196 references in my dissertation, EndNote decided it didn’t like the second author of every paper that had 2 or more co-authors.

    No matter what I did or tried, I could not solve that problem. As such, I manually entered 174 2nd authors into my dissertation (there were 22 papers with only 2 authors…).

  2. Steve Caplan says:

    Here’s hoping for continued recovery!

  3. abi says:

    I’m writing a paper and opened up word this morning to find that endnote has decided not to recognise half my references and messed up the reference list. Will have to re-input the references and hope that it behaves. I have no idea why and I don’t understand what I did to upset it either. Bad endnote!!!!

  4. SB says:

    I re-discovered the punctuation glitch just last week… how frustrating!!

    I don’t know a single person who is mostly or fully satisfied with EndNote. There were definitely days while I was writing my undergrad thesis when I wondered if it wouldn’t be easier to manually input EVERYTHING (high school style). Here’s to hoping there will be a less crashy version available by the time I’m in grad school!

  5. Grant says:

    (I feel much more normal now, thank you very much!)


    I’ve several posts I’ve left in the Drafts folder that run along similar lines… 🙂

    I’ve just been through trying a few bibliography options myself. In principle some of the other bibliography applications can read/write EndNote format bibliographies and I had hoped that might widen my options. The GUI for Papers2 appealed, for example, but I had to give up on it. Best as I could tell there was a conflict between Paper2 and EndNote as to how to deal with Unicode characters. (It’s possible I’m missing something. Also, they have since released a new point release, so it’s possible whatever was bugging it has now be fixed. Unfortunately the demo license has expired, so I can test if it’s been put right!) Thing is, I have some idea of how you feel!

  6. cromercrox says:

    Many years ago when the world was young (OK, it was 1987) and I was writing up my Ph.D. (we didn’t have things like endnote, we had to do it all by hand), I had recourse to my adviser’s thesis on a similar topic, and found that not all the citations in the text corresponded with a reference at the back. I questioned my adviser on said omission and he went all wistful and recounted this story.

    My adviser (we can call him AL) was having his thesis typed up by a typist, that is, a person who used a typewriter. The typist agreed to type the thesis in exchange for AL’s moped. It came to the point where AL had to take the references to be typed – these were written individually on large cards, several hundred of them, tied up with an elastic band, which AL carefully stowed in the pannier on the back of said moped. And so AL set off.

    It was quite a long way to the typist’s house. It was getting dark, and it had started to rain. AL went over a small bump in the road, the pannier sprang open, the elastic band snapped and all his references flew out like snow all over the dark, wet road. AL collected up as many as he could, but – he said – there were probably a few – those he didn’t manage to catch – still rotting under a Cambridgeshire hedge.

  7. Mike says:

    Henry, does that make you your supervisor’s bodyguard? (cue Seinfeld-esque bass solo)

    Cath, cough, <a href=""splutter; I’m amazed this was the problem you ended up blogging about. Srsly – so many different people actually using the same reference software? You were lucky. When I were a lad, all my co-authors insisted on eating reference gravel.

  8. Cath@VWXYNot? says:

    Steve: GAAH! Nightmare. I remember in the final stages of thesis writing spending a few hours manually adding all the accents and other non-English letters to foreign authors’ names in the bibliography, as EndNote hadn’t been able to format them properly. This exercise lasted until my PhD supervisor realised what I was doing and told me not to be so stupid that there were probably better uses of my time 🙂

    abi, sorry that it wasn’t just me suffering EndNote rage yesterday. Did you manage to fix the formatting?

    Part of the problem with our grant was that we had to format the references before it was ready for the final proofreading, to make sure we were within the page limit. This meant adding new references after the original formatting was done. I usually wouldn’t even touch the references until everything else is done, but we didn’t have much wriggle room this time.

    I just got buy-in from two senior PIs to try Google Docs for the next collaborative grant, rather than having multiple people editing and then circulating their own versions of the Word document, with unique reference and other formatting in each version… fun! I’m sure it’ll come with its own problems (as Heather just pointed out on Google+, actually), but at least they’ll be exotic and interesting new problems…

    SB, I’ve wondered the same thing myself, usually in the days or hours leading up to an imminent deadline! EndNote’s still definitely so much better than doing things manually, though. I think.

    Grant, sounds frustrating! If you find a good solution, please do let me know about it!

    Henry, that hilarious story is eerily similar to the one I heard (straight from the horse’s mouth, although I won’t identify the PI in question) about the PI, back in his postdoc days, cycling (drunk) into a canal with the lab’s communal stock of reference cards, carefully compiled and curated over decades, in his bag.

    The same PI later rode a different bike into a different canal, in a different city – also drunk, but with no collateral damage this time. At least he learned one lesson…

    Mike, I did format and unformat all references several times, uphill both ways, while living in a box in t’middle of t’road…

  9. ricardipus says:

    Of course, PubMed ain’t all it’s cracked up to be, either.

    I too am one of those who used much earlier versions of both EndNote and Reference Manager. For added fun and games, I even imported a database from one into the other on one occasion. Guess how well that worked.

    But more recently, I feel your pain… I am currently filling out a report for a Certain Funding Agency With Which You Are Familiar(TM), using an online system for a Certain Regional Organization That Administers The Funding Agency’s Funds In This Region (More Or Less, E&OE, etc.). Said online system has, in fact, a “reference lookup” feature similar to the one you describe. Putting a plain-vanilla PMID into it and clicking a couple of buttons results in a satifying SLURP of the data into all the relevant fields (author, title, abstract, etc.).

    Except when it doesn’t.

  10. ScienceGirl says:

    LaTeX user here, feeling like a minority… Not sure I could survive automagic to the likes of Word, sorry you have to deal with it!

  11. DrugMonkey says:

    Sounds like the real problem here is not EndNote but rather your antiquated scientists who can’t manage to use a reference manager and insert their own citations properly.

  12. Mike says:

    I think Google Docs has even less reference software support that Word. Whether that makes things easier for Cath or not is open for debate.

    But following on from ScienceGirl’s comment, I would love, love, love to see a bunch of life scientists trying to collaborate on a Latex document :D. Assuming of course that I wasn’t the one doing the final format.

  13. Grant says:


    They could use LyX 😉 I keep meaning to put up a review of version 2 on my blog sometime. One day…

  14. Cath@VWXYNot? says:

    Ricardipus, how remarkably helpful of the Certain Funding Agency With Which I Am Familiar(TM)! (Except when it’s not).

    ScienceGirl, one of the PIs I work with has a background in computer science and uses LaTeX for his papers (but not collaborative grant applications). I was hoping to teach myself LaTeX this summer, but then I got involved with this massive team grant with an August deadline (which should be illegal IMO) and didn’t have the time. I just don’t see persuading up to ten people (PIs and others) per grant to use it, though…

    DM, well, some of them managed it just fine, but it was the stitching together of multiple versions, filtered through various OSs and versions of Word, that seemed to do the damage. There were, let’s see, seven PIs on this grant, many of whom had their trainees also look the text over and edit it, plus me and a couple of other wrangler types, using work PCs, work Macs, work Linux machines, and personal MacBooks of various vintages…

    Mike, maybe I can make it happen, for your amusement, if not mine 🙂

    If/when we go the Google Docs route, I would still import the final version into Word for the final reference insertion and other formatting.

  15. Frank says:

    Those commas have caught me out too. I know it has to be either with or without comma but I can never remember which. And it is different in Web of Science, I seem to recall.

    These day software seems to get outdated/updated very rapidly. And when you have two lots of software that have to work together then you have a good chance of chaos ensuing. It’s good for us support types though, keeping some of us in a job!

  16. Grant says:


    If you want to dabble in LaTeX, LyX might be worth looking at – ? You can do most things without learning LaTeX itself and just pick it up as you dig deeper. It’a a GUI-based document processor, with familiar buttons for all the usual things – tables, images, different types of lists, citations, etc.

    If the option were reasonable (it may not be!) you could have collaborated around a plain text file, then once that is complete have one person format it in Word (like your google docs suggestion). I can’t speak for all the bibliographic software, but some (most?) work on plain text files.

  17. Verity says:

    Ah, yes, Endnote. When I was writing my thesis (started 2001, died 2006), I looked at the versions of Endnote which existed at the time. I decided it was less pain to do it by hand – I had a set of filing cards, a Word file (I had not yet learned of LaTeX) with the full references as my Bibliography, and an obsessive mindset. I think it was less pain than Endnote. Just.

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