PubReMiner

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Introduction

See also PubMed Alternative Interfaces | Semantic search | Semantic web

Today’s researchers have access to an increasing number of third-party, home-grown, and open-source tools with which to refine their literature searches in Medline, and PubReMiner is one of them.

PubReMiner is a front-end data mining tool and search overlay that generates metadata in the form of hyperlinked frequency tables after completing a statistical analysis of searches in PubMed - MEDLINE. This provides an interesting lens for focusing subsequent queries and optimizing results. As a simple text-based query building tool, PRM looks at information from a set of PubMed - MEDLINE abstracts and then displays results in frequency tables by journals, authors and textwords. For systematic review searching, health librarians often recommend scanning the most relevant abstracts for ideas about how to improve search strategies; PubReMiner may also be useful for this purpose.

Uses for PubReMiner

In addition to building and refining search queries, PubReMiner is helpful for:

• selecting journals for your research by scanning journals publishing similar research
• finding experts by viewing top authors associated with your query; ‘authors’ list can be used to locate experts in the field
• determining research interests of authors by viewing the keywords associated with them; locate experts in the field;
• locating relevant MeSH terms for a set of references in PubMed; text terms, most common authors, journals, countries and substances

• GoPubMed versus PubReMiner for analyzing PubMed search results: a head to head comparison

How to read frequency tables

• PubReMiner will query PubMed - MEDLINE with your specified search query, and retrieve all abstracts and generate frequency tables
• first table shows journals in which your query is published the most
• second table shows authors which are most active in the field of your search query
• third table shows you words that have been used most in the title and abstract of the articles

In addition, MeSH and publication years are displayed, and any new elements you deem important can be added to refine your query. When you are ready to rerun your search, move to PubMed - MEDLINE and view the results.

References

• Bradley S, Giustini D. GoPubMed versus PubReMiner for analyzing PubMed search results: a head to head comparison of two free web ‘data mining’ tools. CHLA/ABSC 2011.
• Connor E. PubMed® search interface alternatives: a descriptive comparison. J Electron Resour Med Libr. 2010;7(2):126-134.
• Dietze H. GoWeb: a semantic search engine for the life science web. BMC Bioinformatics. 2009;10:S7.
• Glynn RW, Kerin MJ, Sweeney KJ. Authorship trends in the surgical literature. Br J Surg. 2010;97(8):1304–1308.
• Lu Z. PubMed and beyond: a survey of web tools for searching biomedical literature. Database (Oxford). 2011;2011:baq036.
• National Network of Libraries of Medicine, Pacific Northwest Region. Third-Party PubMed Tools. Slideshare.net
• Text Mining and Finding Connections. Virginia Commonwealth University. VCU Libraries.