A Blog Around The Clock

Duncan Hull and colleagues just published an excellent, must-read article – Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web:

Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.

The paper goes through each of the services, one by one, explains the pros and cons of each, and makes suggestions for the future development, as well as pointing out barriers and possible ways to overcome those. A couple of listed services are almost there – but are you using them? If so, why? If not, why not?


  1. #1 travc
    November 1, 2008

    I was all ready to respond by saying that anyone not using bibtex (and latex) is inferior… but the article is talking about a higher level I see (which makes mentioning EndNote odd, but whatever).

    I’ve recently run into an odd problem. My work is very interdisciplinary and using web tools and colleagues is the only sensible way to do a literature search. My sources/refs are split between CS, EE, behavioral Bio, and specialized signal processing sources. Even being able to understand papers on the same topic from different disciplines is a real challenge… but that is a different topic.

    Anyways, now that I’ve finally got a draft paper to the point of trying to figure out where to submit it (and edit it for that target), I realize I have no feel for any of the journals! I haven’t looked at an actual journal (even an online table of contents) for literally years (other than the general stuff like Nature of course).

    Quite frankly, no journal is a ‘good fit’, which is why the related paper/refs are from all over the place and web searches are so damn useful in finding them.

    Gets me thinking that the days of the journal as they exist today are probably numbered. The really general journals will be persist… almost everyone likes skimming those and they allow us to maintain some general literacy in the broader scientific community. The very specialized journals will be ok too, though will probably go online only. However, journals catering to broader topics or entire disciplines make less and less sense… the landscape changes too fast.

    So how do we do peer-review when everyone is looking at cross-refs and keyword searches (and blogs) of papers stored in general repositories (arXiv sort of things) instead of journals? How will “publish or perish” get transformed? I’m thinking that the next generation of journals may basically be wikis (with moderators and editors) linking and organizing papers (and more) which may well never be ‘published’ in a traditional sense. Hell, as part of my dissertation work (which requires some organizing collaborators and others in my field) I may well end up starting one myself.

  2. #2 Kevin Z
    November 2, 2008

    Zotero rocks! Works very well with NeoOffice on my mac. The browser interface with Mozilla works excellent, although it is a bit slow. Nonetheless, worth using. Importing 3000+ refs from endnote was simple although I lost all links to pdf files of the paper. But when you save a link in Zotero it downlads the paper (if available) in addition to the reference information.

  3. #3 Cassandra
    November 3, 2008

    I was struggling with Endnote until Zotero came along and that was so much easier to use. But I agree with Duncan that Zotero needs to offer more socialization features.

    I’m now trying WizFolio, a web-based reference manager. It’s very fast and worth using. Have u tried it?

  4. #4 Cassandra
    November 19, 2008

    Hi all,

    Learnt that WizFolio has a new feature which can search the publisher’s website for a PDF for your collected references. Even grabs free PDF automatically.

    You may wish to try it.

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