Iatul june1 2009


Published on

Published in: Technology
  • Be the first to comment

  • Be the first to like this

No Downloads
Total views
On SlideShare
From Embeds
Number of Embeds
Embeds 0
No embeds

No notes for slide
  • Quality through Innovation We, like other academic libraries have had to revise o r supplement our traditional information literacy initiatives and reference services as these approaches have become less effective or unsustainable in an increasingly online environment. (Library is no longer the starting point for academic research)
  • Impetus for introduction Other data repositories, patents
  • Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological information generated by the scientific community. These tools enable scientists to locate and analyze gene and protein data Combines the fields Biology, Mathematics and Computer Science-manages a vast amount of sequencing data GenBank core resource, 83 million sequence records and 86 billion pairs of nucleotides EMBL- The European Molecular Biology Laboratory DDBJ- DNA Databank of Japan Human diseases may nor be in same form as animals but usually sufficient data for researchers to make inferences about the process in humans
  • Bioinformatics provides access to the enormous amounts of data produced by genome researchers so that it can be analyzed and interpreted by researchers Excellent marketing tool for other Biology IL sessions-review IL skills
  • Perception that librarians have sufficient subject knowledge to provide assistance or have expertise with Bioinformatics Tools Need to develop fluencies, good marketing tool for other senior level biology classes Key is collaboration – librarian has knowledge of how databases function and effective pedagogies for using info resources Faculty knowledge of content-model assignment on real world experience
  • 14 questions
  • Detailed descriptions on over 80 genetically-inherited diseases are available in the Genes and Disease database
  • Inheritance pattern of the disease What is the name of gene(s) believed responsible for the disease What types of mutations have been discovered in this gene What chromosome is the gen located on
  • Bioinformatics are complex containing more information than students need Success breeds confidence – completing one task in a database means they will likely use or try another Using a database to ask “real world” questions lends credibility to exercise-make sure they are rewarded for use Read screens carefully-extract what they need and use built-in features to manipulate the data Questions will arise during the session with searching and interpreting the data that both experts may be required to help with
  • Learned more Developing closer partnership with faculty has provided insights how Biologists approach information so I am better able to understand their collection needs and IL requirements Librarian brings understanding of novice researcher this ensuring that explanations are clear and assignments are doable and IL builds on existing literacy skills
  • Iatul june1 2009

    1. 1. Letting the Genes out of the Bottle: Making the most of free bioinformatics information Don MacMillan University of Calgary Libraries and Cultural Resources Calgary, Canada
    2. 2. Contents <ul><li>Introduction </li></ul><ul><li>Why use Bioinformatics? </li></ul><ul><li>Biology 311 </li></ul><ul><li>Lessons Learned </li></ul><ul><li>Conclusion </li></ul><ul><li>Key Resources </li></ul>
    3. 3. Introduction <ul><li>Maintain credibility and relevance with users and partners </li></ul><ul><li>Need to add value beyond standard bibliographic sources </li></ul><ul><li>Bioinformatics - free, high quality scientific data </li></ul><ul><li>Subject knowledge - Collaboration – Student benefits </li></ul>
    4. 4. Bioinformatics <ul><li>What is Bioinformatics? </li></ul><ul><li>Why use Bioinformatics? </li></ul><ul><li>Challenges for Librarians </li></ul><ul><li>Key Resources </li></ul>
    5. 5. What is Bioinformatics? <ul><li>Analysis of genes and proteins using genomic databases </li></ul><ul><li>Provides greater insights into the biology of organisms </li></ul><ul><li>National Center for Biotechnology Information (NCBI) </li></ul><ul><li>Comprised of GenBank, OMIM, BLAST and PubMed and 26 other databases </li></ul><ul><li>Changing the nature of genetics research </li></ul>
    6. 6. Why use Bioinformatics? <ul><li>Students get to use free, real life tools to study genes, proteins and diseases </li></ul><ul><li>Primary source of gene & protein information </li></ul><ul><ul><li>Can be used for gene therapy, biotechnology and agriculture </li></ul></ul><ul><li>Easily incorporated into library instruction </li></ul><ul><li>Core competency for students in genetics and biochemistry (American Society for Biochemistry and Molecular Biology) </li></ul><ul><li>Enhances subject knowledge and collaboration </li></ul>
    7. 7. Challenges for Librarians <ul><li>Content </li></ul><ul><ul><li>Bioinformatics databases designed for researchers </li></ul></ul><ul><li>Faculty perceptions </li></ul><ul><li>Need to Collaborate </li></ul>
    8. 8. Biology 311 <ul><li>Introduction to Genetics </li></ul><ul><ul><li>500 2 nd and 3 rd year students </li></ul></ul><ul><ul><li>Previous knowledge of BIOSIS and Web of Science </li></ul></ul><ul><ul><li>Students located bioinformatics information on specific genetic disorder (e.g. gene and protein details) </li></ul></ul>
    9. 9. Sample Genetic Diseases <ul><li>Hemophilia </li></ul><ul><li>Colon Cancer </li></ul><ul><li>Glaucoma </li></ul><ul><li>Diabetes, Type 1 </li></ul><ul><li>Cystic Fibrosis </li></ul>
    10. 10. Sample Questions <ul><li>What is the inheritance pattern of this disease? </li></ul><ul><li>What is name of the gene that causes the disease? </li></ul><ul><li>On which chromosome is the gene located? </li></ul><ul><li>What is the calculated molecular weight of the protein? </li></ul>
    11. 11. Online Mendelian Inheritance in Man (OMIM) <ul><li>Database of human genes and genetic disorders – 19,000 entries </li></ul><ul><li>Used by researchers to determine inheritance pattern and clinical features of genetic diseases </li></ul><ul><li>Links to related genes and proteins </li></ul><ul><li>Entrez interface links to other NCBI databases </li></ul>
    12. 12. Search for Disease topic
    13. 13. Cystic Fibrosis Gene
    14. 14. Detailed Gene and Protein Information
    15. 15. BLAST-Basic Local Alignment Search Tool <ul><li>Set of Programs designed to compare gene sequence data </li></ul><ul><li>Check similarity between human and non-human species </li></ul><ul><li>Determine the structure and function of selected protein(s) </li></ul>
    16. 17. Assessment <ul><li>“ I learned how to use PubMed….find a specific protein…coding sequence…” </li></ul><ul><li>“ If I use OMIM again in the future it will be for any extra genomic information I need about a disease” </li></ul><ul><li>“ OMIM is quite complicated but the instruction really helped make this website useful” </li></ul>
    17. 18. Lessons Learned <ul><li>Focus on most useful aspects of resources </li></ul><ul><li>Develop sequential steps and links to an assignment </li></ul><ul><li>Create exercise that replicates expert use </li></ul><ul><ul><li>Ask “real” targeted questions </li></ul></ul><ul><li>Provide hands-on practice with assistance </li></ul>
    18. 19. Conclusion <ul><li>Librarian expanded subject knowledge, skill sets and relevance </li></ul><ul><li>Developed productive collaboration with faculty </li></ul><ul><li>Innovative learning experience for Students </li></ul><ul><ul><li>They learned more about genetics! </li></ul></ul><ul><li>May see greater relevance in using Bioinformatics tools </li></ul>
    19. 20. Bioinformatics Links <ul><li>NCBI http://www.ncbi.nlm.nih.gov/ </li></ul><ul><li>Genes and Diseases http://www.ncbi.nlm.nih.gov/books/bookres.fcgi/gnd/tocstatic.html </li></ul><ul><li>OMIM http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM </li></ul><ul><li>BLAST http://blast.ncbi.nlm.nih.gov/Blast.cgi </li></ul><ul><li>EMBL Nucleotide Sequence Database (Europe) http://www.ebi.ac.uk/embl/ </li></ul><ul><li>DDBJ – DNA Data Bank of Japan http://www.ddbj.nig.ac.jp/ </li></ul>
    20. 21. Related Links <ul><li>Link to the 30 th IATUL Conference Presentation, Handout and Lab Assignment </li></ul><ul><ul><li>http://tinyurl.com/ppydmz </li></ul></ul><ul><li>Link to getFAST (Free Assessment Summary Tool) </li></ul><ul><ul><li>http://www.getfast.ca/ </li></ul></ul>
    21. 22. <ul><li>Thank You, Merci, Danke, Grazie… </li></ul><ul><li>Don MacMillan </li></ul><ul><li>Biological Sciences, Physics & Astronomy </li></ul><ul><li>Librarian </li></ul><ul><li>University of Calgary </li></ul><ul><li>email: [email_address] </li></ul>