Pub med+
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  • 1. PubMed + Alternate Interfaces RETRIEVAL ANALYSIS, EASY PDFS AND DATAVISUALIZATION FOR THE MEDICAL RESEARCHER Ryan McComas, MLIS
  • 2. Introduction 2 PubMed: Public data source of biomedical citation information. Has its own search interface, pubmed.gov PubMed’s information retrieval model has certain shortcomings Advances in data storage capabilities, text mining, search and data linking technology, and human-computer interaction has enabled researchers to create applications for PubMed’s database
  • 3. Introduction 3 Problems with PubMed:  Difficulty with link resolver  Unranked results  NO statistics and analysis!
  • 4. Introduction 4 There are many tools, but today we are going to outline three that make searching, retrieving and understanding relevant literature easier and faster:  GoPubMed  MEDSUM  Quertlehttp://library.mskcc.org
  • 5. GoPubMed: stats and visualization 5
  • 6. GoPubMed: stats and visualization 6 Accepts PubMed query syntax [mesh], [au], etc. (called “tags”) Two major fields for concept searching: (MeSH) (Gene Ontology) ◦ Ontology=detailed relational and conceptual hierarchy.
  • 7. GoPubMed: stats and visualization 7 Sorting and refining results  Left-hand column – Sort, refine, and analyze results using filters.  View statistics in tabs above results.  Export PubMed citations without saving to a text file.
  • 8. MEDSUM: Results Analysis 8
  • 9. 9MEDSUM: Results Analysis
  • 10. 101) how PubMed translates Shows authors,the query journals, research2) the number of associated biases, and MeSHarticles categories and years Gives the top Major MeSH Returns the number of papers Headings for papers with broken down by year (going MeSH entries back to 1945 max) MEDSUM: Results Analysis
  • 11. Quertle: Semantic Search 11
  • 12. Quertle: Semantic Search 12 Quertle searches whole concepts rather than simply keywords or terms matching. Left-hand sidebar: filter and refine results. Power terms ($) allow you to search for classes of objects. Export citations to EndNote and RefWorks. Many libraries have partnered with Quertle to make links to full text available for subscription databases.
  • 13. Quertle: Semantic Search 13 Quertle Search Tips  SUBJECT-VERB-OBJECT model of searching  Find definitions  Use Power Terms to specify classes of topics  Search broadly with search terms in the then filter results.
  • 14. More Resources 14 David Rothman’s blog: http://davidrothman.net/category/technology/3rd-party / Lu, Z. (2011). PubMed and beyond: A survey of web tools for searching biomedical literature. Database. doi:10.1093/database/baq036 Email: ryanraymccomas@gmail.com