Pubmed and other Annoyances in the Paper Writing Process

Anna's recent post (https://web.archive.org/web/20120612090300/http://network.nature.com/blogs/user/U2929A0EA/2008/03/22/i-am-not-yelling-not-out-loud?) 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 (https://web.archive.org/web/20120612090300/http://www.endnote.com/?), Papers (https://web.archive.org/web/20120612090300/http://mekentosj.com/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 (https://web.archive.org/web/20120612090300/http://www.editorialmanager.com/homepage/home.htm?) 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 (https://web.archive.org/web/20120612090300/http://pubs.nrc-cnrc.gc.ca/jchla/jchla29/c07-035.pdf?).