PubMed and beyond: a survey of web tools for searching biomedical literature

Abstract

The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search.

Figure 1.

Growth of PubMed citations from 1986 to 2010. Over the past 20 years, the total number of citations in PubMed has increased at a ∼4% growth rate. There are currently over 20-million citations in PubMed. 2010 is partial data (through December 1).

Figure 2.

Overview of general user interactions with PubMed (or similar systems) for searching biomedical literature. Adapted from Islamaj Dogan et al., (3).

Figure 3.

A diverse set of use cases in which different tools may be used.

Figure 4.

Technology development timeline for PubMed (in light green color) and other biomedical literature search tools (in light orange color). For PubMed, it shows the staring year when various recent changes (limited to those mentioned in ‘Changes to PubMed and looking into the future’ section) were introduced. For other tools, we show the time period in which tools of various features were first appeared.