Bibliomics gone wild

I have an embarrassing confession to make. I must spend tens or hundreds or thousands or perhaps even millions of hours online per week and the first time that I heard the term “bibliomics” used in a sentence was earlier this week.

In an article published in Database earlier this year, one of NCBI’s bibliomics experts Zhiyong Lu, reviewed 28 Web tools that have been developed to help researchers quickly and efficiently search and retrieve relevant publications. According to Lu, the massive amount of data that now exists in NCBI’s pubmed database has become a monster to mine and currently available PubMed tools are insufficient for retrieving accurate and user-friendly search results.

28 web search tools reviewed by Lu

Some advantages offered by the supplementary systems include:

  • a variety of search result display formats (list-based, clustering, graphical, tabular and semantic relation based)
  • users can define how they want to see their search results (instead of simply by reverse chronological order)
  • including concept categories in search queries
  • taking into account the user’s click-through history and recency when returning relevant search results
  • determining text similarity based on word alignment
  • clustering results into topics
  • enriching results with semantics and visualizations
  • Improving search interface and retrieval experience

Lu has established a website for keeping track of developments in the bibliomics search field which can be found at

In an interesting commentary on this article, Martin Fenner at PLoS Blogs writes that Lu neglected to include social media search tools in his analysis and suggests that there is an increasing number of scientists that utilize social media as a tool for finding interesting papers.

With so many “traditional” search engines out there, I never considered social networking to be an important tool in my literature search arsenal. While I do click on interesting links that come across my desk via twitter and rss feeds, I would never consider that to be my primary method for searching the literature. Nonetheless, in the name of completeness, it would be interesting to see social media tools incorporated into the world of “traditional” search.

Lu Z (2011). PubMed and beyond: a survey of web tools for searching biomedical literature. Database : the journal of biological databases and curation, 2011 PMID: 21245076

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