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Better Late Than Never: Report from MLA Professional Development Awardee, Jane Saxton

Submitted by Jane Saxton, Director of Library Services, Bastyr University, Seattle, WA

This year, the NN/LM PNR awarded funds to several Network Members allowing them to attend Continuing Education courses at the Medical Library Association 2012 Annual Meeting in Seattle in May.  The awardees were asked to write up their “thoughts and reflections” on these classes, which were published in the July 3, 2012 issue of the Dragonfly. Claiming “too busyness” at the time, I promised to send something along later.  Later it certainly is, but a perfect time to assess the lasting impact of the CE I attended: “New Generation Tools for Advanced Biomedical Literature Study.”  What exactly did I learn way back then?  Which new tools am I using today?

Dr. Yi-Bu Chen, Program Coordinator in the Norris Medical Library at the University of Southern California, discussed three categories of new resources that are designed to answer your scientific and clinical questions: Innovative information retrieval (IR) tools, information extraction (IE) tools, and text-mining (knowledge discovery) tools.  Here are three resources, one from each category, that are now part of my search repertoire.Thank you to the NN/LM PNR and to Dr. Chen for introducing me to them!

go pubmed

GoPubMed – – a sophisticated information retrieval tool, searches PubMed for a disease, compound name, or gene, then displays the results to help you visualize major biomedical concepts associated with your query.  I especially like the statistical features that show you how your topic is trending, e.g. Top Authors, Publications Over Time and a world map showing where publications originate.

For additional information, see this YouTube video, And also: Dietze, Hl, et al. (2009). GoPubMed: Exploring PubMed with ontological background knowledgeBioinformatics for Systems Biology, Part V, 385-399. DOI: 10.1007/978-1-59745-440-7_20


Quertle – – an information extraction tool, was a winner in the National Library of Medicine’s software development challenge: Show Off Your Apps: Innovation uses of NLM Information. I like the breadth of this meta-tool!  It uses algorithms to extract relationships from your query, searching not only in PubMed, but also in PubMed Central, TOXLINE, Biomed Central, NIH, FDA, and other agency grant proposals, as well as biomedical news sources.

For additional information, see this and other YouTube videos, and also Giglia, E., (2011). Quertle and KNALU: Searching PubMed has never been so easy and effective. Eur J Rehabil Med, 47,: 687-90.

FACTA+ –, – a PubMed text-mining tool created by the University of Manchester School of Computer Science, finds “hidden” i.e.  indirect, relationships between genes and biomedical concepts, thus leading to knowledge discovery.  I frequently use the Find Indirectly Associated Concepts button – how cool is that?

For further information, see: Tusruoka Y, Miwa M, Mamamota k, Tsujii, J, Ananiadou A. (2011). Discovering and visualizing indirect associations between biomedical conceptsBioiniformatics, 27 (13): i111-i119. PMCID: PMC3117364; DOI: 10.1093/bioinformatics/btr214

One Response to “Better Late Than Never: Report from MLA Professional Development Awardee, Jane Saxton”

  1. Hope Leman Says:

    Thanks so much for the write-up of those tools, Jane. Very edifying and interesting. I also got a kick out of, “how cool is that?” Pretty cool!