Pubmed and other Annoyances in the Paper Writing Process

Anna's recent post about her struggles with Pubmed searches reminded me that there is still a lot that could and should be done to improve the paper (or thesis) writing process. This is my personal list of major annoyances:

Pubmed. This topic has been extensively covered in Anna's post.

Bibliographies. The process from finding a paper in Pubmed to storing it into your bibliographic software to downloading and storing the PDF to creating a bibliography in a paper is extremely complicated. In my case this process involves a web browser, Endnote, Papers, a PDF viewer and Microsoft Word.

Writing a paper. The idiosyncrasies of Microsoft Word (the tool probably used by most people for paper writing) would make for a different blog post. Microsoft Word can do many things that are never needed in a scientific manuscript, but lacks features that are important. And it likes to crash on long texts.

Collective Writing. The process of having several people working on a manuscript and managing different versions is overly complicated.

Paper submission. The online tools such as Editorial Manager are nice, but there is still too much formatting work required (in a format that is probably different depending on the journal).

Interestingly, the way we do paper writing and paper submission has changed a lot between ca. 1985 and 1995. Basically the transition from analog to digital. Who still remembers Index Medicus, Current Contents, copying papers in the library, Letraset for figure numbering, mailing hard copies of manuscripts around, etc.?

But what has changed in the last 10-15 years? Probably not that much. Web 2.0 is an overused term, but there is so much potential for improvement in the area of manuscript writing. We should not be satisfied with what Pubmed, Endnote, Microsoft Word, etc. offer today. That is why I don't understand some of the discussion surrounding Anna's blog post, basically advising her to just sit down and learn her Pubmed stuff.

If that is not enough for you, some people have already taken the next step: Web 3.0 and health librarians: an introduction.

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10 Responses to Pubmed and other Annoyances in the Paper Writing Process

  1. Massimo Pinto says:

    I can see an immediate problem when using MS Word and collective writing with at least three authors. One merely hopes for one of the following
    # They correct your document at very different times, so that by the time you have received the second set of corrections, these are useless, as the document changed by a lot (and you think it’s better now)
    # One of the two collaborators makes many more changes than the other
    # At least one of them does not use _track editing_ mode
    # (special case of the latter) One of them actually comes to see you for a coffee and talks to you instead of contributing to translating your manuscript to Gibberish further
    Of course, if anyone has a better solution, I am all ears!!!

  2. Anna Kushnir says:

    it’s very very nice to hear that I am not completely insane, Martin. I was beginning to doubt myself after reading all the comments on the post. Yes, if we all devote time and energy to learning the quirks and intricacies of the current system (please don’t get me started on how poorly MS Word works with Endnote. _Gag_) we can make it work reasonably well. I just don’t see why we should have to. These applications should be made scientist-friendly.

  3. Bob O'Hara says:

    I was in a course yesterday where we were discussing web-based teaching, and one thing we discussed was using wikis for collaborative writing. They _almost_ work for scientific articles, I guess someone would have to format them at the end.
    I heard that OpenOffice will be releasing their own version of EndNote for OpenOffice. Whether this works better I’ve no idea. It also has some collaborative writing tools, but I haven’t tried them.

  4. Richard P. Grant says:

    Formatting? That’s what XML is for, Bob. Separation of content and format. You _know_ it makes sense.
    (And I will *slap* the first person who mentions LaTeX – _damn_. I’ll just step into the carpark now… )

  5. Heather Etchevers says:

    I remember Letraset! and how the precious photograph that had been developed JUST SO ended up with a comma smeared on it elsewhere as you were placing your letter B in the upper left corner, or you didn’t quite orient the letter over the little white dot that gave it contrast on the dark background {shudder}.
    Then again, I think I lose more time in pagesetting for my image-heavy figures than in text formatting. Images are seriously RAM-hungry. Perhaps I don’t use the right software, since I know a fair bit about Photoshop (6.0) and have not wanted to invest the equivalent time to learn PageMaker or any other equivalent. What’s hard, too, is the blind devotion any students who work with me have to Powerpoint, when you can NOT make figures on it! But perhaps if laying things out and adding text graphics is as easy in PageMaker, it might be a good compromise. I just need the flexibility that Photoshop offers me, as I often have to normalize background for dozens of _in situ_ hybridizations. I need those layers to tweak the settings as I add in new photos.

  6. Heather Etchevers says:

    By the way, I’ve been using Endnote since version 2.0 out in Berkeley, and I would hope they could get their own act together and make themselves an add-in for OpenOffice. There’s no rule that says they have to be used with Word.
    @Massimo: no solution for you, except to delegate a super-author who has override authority.
    @Anna: those of us who did already learn the quirks of the current system are grouchy old grumps who don’t want to have to put in the time again to learn a new one (witness me with Photoshop). So we have a vested interest in things not changing too dramatically, nor do we have the same fresh, critical eye you do.

  7. Richard P. Grant says:

    Photoshop’s about the best tool there is, Heather (well, there’s Illustrator, which is incredibly powerful, but more difficult to use and even more of a memory hog). I don’t understand why people use Powerpoint for figures. It’s foulness incarnate.

  8. David Crotty says:

    As someone pointed out in the comments for the original post, “GoPubMed”:http://www.gopubmed.org is vastly better for searching, really one of the few Web 2.0 implementations for scientists that I can wholeheartedly recommend.
    Also, as “a well-known author points out”:http://journal.neilgaiman.com/2007/10/simplicity-of-black.html , sadly Google Docs is far too “Beta” to solve any of these collaborative problems.

  9. Martin Fenner says:

    @David: I would hope that Google Docs, “Buzzword”:http://www.buzword.com or “Zoho Writer”:http://writer.zoho.com improve to the point they can be used to write a paper. We wrote 80% of our last paper with Buzzword, and the experience, especially the collaboration was positive. But in the end we had to switch to Microsoft Word to include the references.
    @Richard: Using Powerpoint for figures (or posters) is something I will never understand. My favorite tool for more than 10 years was Freehand, but now that Adobe has stopped further development, I have to try something else. The last poster was done with Indesign.
    @Bob: Wikis are a great tool, but I’ve never seen them used for paper writing. In my limited experience I found the MediaWiki software not the best tool for printing and exporting into different file formats – two important features for paper writing.

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