Web Tools for Searching the Biomedical Literature – part II

Web Tools for Searching the Biomedical Literature – part II

Ten days ago I mentioned a paper by Zhiyong Lu that gives an overview over the available web tools to search the biomedical literature. Most of these tools enhance the PubMed service, and Zhiyong Lu in fact works for the NCBI, the developer of PubMed. In this post I want to take a more detailed look at the available tools.

A good starting point is the companion webpage to the paper, listing 28 services. One of the most painful shortcomings of PubMed is the sorting of results by date. Zhiyong lists 8 tools that can present search results sorted by relevance. Semantic search, seeking relevant concepts, and visualization of search results are all offered by several tools. Three tools will identify similar publications, and three tools will find potential experts, reviewers or collaborators. It is a good sign that there are so many tools that integrate with PubMed – in addition to the reference managers (e.g. Endnote, Papers) that do the same.

The analysis has one important shortcoming: only tools that specifically cover the biomedical literature are discussed. General purpose search tools such as Web of Science, Scopus, Google Scholar or Microsoft Academic Search are therefore not covered, neither are online bibliographic tools such as Mendeley and CiteULike. All of them also include biomedical literature – although the coverage at the fairly new Microsoft Academic Search is still limited. They all offer unique features not found in Pubmed or the 28 tools discussed in the paper.

When I think about how I find interesting articles, then it is increasingly through my social networks - including this paper by Zhiyong Lu. His paper unfortunatel fails to discuss this important search strategy. Twitter, FriendFeed, science blogs, etc. are strange places to find interesting literature, but they work for me. This April 22 post on the wonderful Massgenomics blog alerted me to two interesting papers published in JAMA on April 20 that describe the use of whole-genome sequencing in the care of two patients with acute leukemia. I presented the paper by Welch et al. in a journal club last Friday and we had a very interesting discussion.

The paper has also been discussed in the following places: Dragonfly, Center on Media and Child Health, Bernard Becker Medical Library, Medical Information Matters, Friendly Fire (German), Usalbiomedica (Spanish). This post is my much-delayed contribution to the medlib’s round blog carnival. Unfortunately I haven’t received any submissions since my call on April 29, but I probably didn’t do enough advertising.


Lu Z. PubMed and beyond: a survey of web tools for searching biomedical literature. Database. 2011 Jan;2011. doi: http://doi.org/10.1093/database/baq036.

Welch JS, Westervelt P, Ding L, Larson DE, Klco JM, Kulkarni S, et al. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. JAMA : the journal of the American Medical Association. 2011 Apr;305(15):1577-1584. doi:  http://doi.org/10.1001/jama.2011.497.

Copyright © 2011 Martin Fenner. Distributed under the terms of the Creative Commons Attribution 4.0 License.