Defrosting the digital library: bibliographic tools for the next generation web

Abstract

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.

Figure 1. A mind map summarizing the contents of this article in a convenient manner.

Figure 2. The approximate relative coverage and size of selected digital libraries described in the section Digital Libraries, DOIs, and URIs, and summarised in Table 1.

Of all the libraries described, Google Scholar probably has the widest coverage. However, it is currently not clear exactly how much information Google indexes, what the criteria are for inclusion in the index, and whether it subsumes other digital libraries in the way shown in the figure. Note: the size of sets (circles) in this diagram is NOT proportional to their size, and DBLP, Scopus, and arXiv are shown as a single set for clarity rather than correctness.

Figure 3. Google Scholar search results, identified by http://scholar.google.com/scholar?q = mygrid.

Google Scholar links out to external content using a number of methods including OpenURL , shown here by the “Find it via JRUL” (JRUL is a local library) links. Unlike, e.g., WoK, it is relatively easy to create inbound links to individual authors and publications in Google Scholar; see text for details.

Figure 4. A typical workflow for using a digital library representing a subset of the literature.

Tasks represented by white nodes are normally performed exclusively by humans, while tasks shown in blue nodes can be performed wholly or partly by machines of some kind. The main problematic tasks that make digital libraries difficult to use for both machines and humans are “GET” (publication) and “GET METADATA”. These are shown in bold and discussed further in the Identity Crisis section of this paper.

Figure 5. Mekentosj Papers can organize large collections of locally stored PDF files, with their metadata.

It looks and feels much like the popular iTunes application, allowing users to manage their digital libraries by categories shown at the top. It is presently available only under Mac OS/X.