Web Tools For Searching Biomedical Literature

Have you heard of iPubMed, PubGet, Bablemesh, HubMed?  They are some of the many alternative interfaces to PubMed, offering different search and retrieval methods currently not available within PubMed.  With some many of these aternative interfaces how do you keep track of them?  When would it be better to use the alternative interface over PubMed or vice versa?

John Dupuis alerted me to this article, “PubMed and beyond: a survey of web tools for searching biomedical literature” (free full text) from Database (2011) Vol. 2011, doi: 10.093/database/baq036

The article looks at and reviews 28 web tools for searching the biomedical literature and compares them to PubMed and each other and has a website dedicated to tracking existing tools and future advances in the area of biomedical literature search tools.


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.

Not only does the article look at these 28 interfaces but it also looks at the recent changes to PubMed that were often influenced by these and other outside interfaces.

There is no way any library or librarian can teach or support every one of these interfaces, but this paper is free and is a nice resource to whip out when somebody asks about one of them.

4 thoughts on “Web Tools For Searching Biomedical Literature”

  1. Biological entities and processes has been acquired by thousands of scientists through some of experimentation and analysis. The latest need is the creation and quick dissemination of new information. Much of this information and knowledge, however, is represented only in text form–in the biomedical literature, lab notebooks, Web pages, and other sources. Researchers’ need to find relevant information in the vast amounts of text has created a surge of interest in automated text-analysis.

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