Bionano summer symposium: Finding information for your research

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Bionano summer symposium: Finding information for your research

  1. 1. Bionano Summer Symposium August 22nd, 2013 Andrea Miller-Nesbitt andrea.miller-nesbitt@mcgill.ca Finding information for your research Yang, H. et al. (2009)
  2. 2. Objectives By the end of this presentation, you will be able to: • Identify appropriate resources for your research • Understand how to create and execute an effective literature search • Manage your searches and keep up to date
  3. 3. Accessing resources McGill users Non-McGill users Electronic access on campus • Connect to the McGill network • Access the Internet on your own mobile device using the eduroam network (more information: https://www.eduroam.org/) • Use a library computer and sign in as a guest (more information: http://www.mcgill.ca/library/services/conne ct/passwords/databases) Print material • Use your McGill ID card • Obtain a CREPUQ card from your home institution, bring it to McGill along with your student card Interlibrary loan • Request books and articles through Colombo • Request books and articles through your home institution’s ILL system
  4. 4. Bioinformatics resources Type of information Repositories One stop shop • NCBI • EMBL-EBI Genomics • UCSC Genome Browser • Genomes Online Database (GOLD) Proteomics • ExPASy • Protein Data Bank • UniProt Visualization • Cn3D https://www.mcgill.ca/library/find/subjects/health/bioinformatics
  5. 5. Other Bioinformatics resources • Nucleic Acids Research • Annual database issue (published every winter) • Annual web server issue (published every summer) • Protocols • Cold Spring Harbor Protocols • Current Protocols series • JoVE (Journal of Visualized Experiments) • Nature Protocols • Nucleic Acids Research Methods Online
  6. 6. To the rescue!
  7. 7. Organism specific information http://flybase.org/ http://www.informatics.jax.org/ http://www.arabidopsis.org/ http://zfin.org/ www.wormbase.org/
  8. 8. Database Subject areas Dates covered Types of information indexed MEDLINE Biomedicine and health care 1946 to present Journal articles NCBI Entrez A series of linked bioinformatics databases 1980’s to present Biological data, linked to PubMed SciFinder All aspects of chemistry 1907 to present Journal articles, patents, regulatory information, commercial information, chemical data Web of Science Multidisciplinary 1899 to present Journal articles, patents Scopus Multidisciplinary 1960’s to present Journal articles, theses, trade journals ProQuest Dissertations and Theses Multidisciplinary 1861 to present Masters and Doctoral Theses Database Comparison
  9. 9. Research question How is DNA used in the self-assembly of discrete nanotubes?
  10. 10. Finding the literature 1. Identify database(s) to search 2. Develop a search strategy and run your search 3. Apply limits to results 4. Evaluate results and modify strategy
  11. 11. Web of Science
  12. 12. Research question How is DNA used in the self-assembly of discrete nanotubes?
  13. 13. 1. Start with your first concept DNA 2. Combine any synonyms with OR DNA OR “Deoxyribonucleic Acid” 3. Repeat for your second, or any subsequent concepts Nanotube* OR Nanostructure* “self-assembly” 4. Group your concepts with brackets and combine with AND (DNA OR “Deoxyribonucleic Acid”) AND (nanotube* OR nanostructure*) AND “self assembly” Developing a search strategy
  14. 14. MEDLINE
  15. 15. Keyword Subject Heading “natural language” “controlled vocabulary” Database will search multiple fields Database will search descriptor field May not be the focus of the article Process involves humans, so results will be more relevant Does not take the meaning of the word into account Meaning of the word is considered ex. mouse (rodent) vs. mouse (computer mouse) Can yield irrelevant results Standard list of terms defines related synonyms Necessary if database does not have a controlled vocabulary, or if subject heading does not exist for your term Different in each database Keyword vs. Subject Heading
  16. 16. Cancer Tumor Tumour Neoplasm Neoplasms Neoplasms/ 25,588 MeSH terms Medical Subject Headings (MeSH)
  17. 17. Summary quiz 1. Combine synonymous terms with ________ 2. Web of Science uses subject headings (T/F) 3. Use the ________ database to construct your search in PubMed 4. PubMed is part of the _______ suite of resources 5. One way to limit your results is by _______ Bonus! If you are having trouble finding the information you need you can contact a librarian for help (T/F)
  18. 18. Questions? Andrea Miller-Nesbitt andrea.miller-nesbitt@mcgill.ca 514-398-1663 http://www.slideshare.net/andreaemn

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