Transcript
IATUL 2009 - Leuven, Belgium
Letting the Genes out of the Bottle: Making the most of free
bioinformatics information
Don MacMillanUniversity of Calgary
Libraries and Cultural ResourcesCalgary, Canada
IATUL 2009 - Leuven, Belgium
Contents
Introduction Why use Bioinformatics? Biology 311 Lessons Learned Conclusion Key Resources
IATUL 2009 - Leuven, Belgium
Introduction
Maintain credibility and relevance with users and partners
Need to add value beyond standard bibliographic sources
Bioinformatics - free, high quality scientific data
Subject knowledge - Collaboration – Student benefits
IATUL 2009 - Leuven, Belgium
Bioinformatics
What is Bioinformatics? Why use Bioinformatics? Challenges for Librarians Key Resources
IATUL 2009 - Leuven, Belgium
What is Bioinformatics? Analysis of genes and proteins using genomic databases
Provides greater insights into the biology of organisms
National Center for Biotechnology Information (NCBI)
Comprised of GenBank, OMIM, BLAST and PubMed and 26 other databases
Changing the nature of genetics research
IATUL 2009 - Leuven, Belgium
Why use Bioinformatics? Students get to use free, real life tools to study genes,
proteins and diseases
Primary source of gene & protein information Can be used for gene therapy, biotechnology and agriculture
Easily incorporated into library instruction
Core competency for students in genetics and biochemistry (American Society for Biochemistry and Molecular Biology)
Enhances subject knowledge and collaboration
IATUL 2009 - Leuven, Belgium
Challenges for Librarians
Content Bioinformatics databases designed for
researchers Faculty perceptions Need to Collaborate
IATUL 2009 - Leuven, Belgium
Biology 311
Introduction to Genetics 500 2nd and 3rd year students Previous knowledge of BIOSIS and Web
of Science Students located bioinformatics
information on specific genetic disorder (e.g. gene and protein details)
IATUL 2009 - Leuven, Belgium
Sample Genetic Diseases
Hemophilia
Colon Cancer
Glaucoma
Diabetes, Type 1
Cystic Fibrosis
IATUL 2009 - Leuven, Belgium
Sample Questions What is the inheritance pattern of this disease?
What is name of the gene that causes the disease?
On which chromosome is the gene located?
What is the calculated molecular weight of the protein?
IATUL 2009 - Leuven, Belgium
Online Mendelian Inheritance in Man (OMIM)
Database of human genes and genetic disorders – 19,000 entries
Used by researchers to determine inheritance pattern and clinical features of genetic diseases
Links to related genes and proteins
Entrez interface links to other NCBI databases
IATUL 2009 - Leuven, Belgium
Search for Disease topic
IATUL 2009 - Leuven, Belgium
Cystic Fibrosis Gene
IATUL 2009 - Leuven, Belgium
Detailed Gene and Protein Information
IATUL 2009 - Leuven, Belgium
BLAST-Basic Local Alignment Search Tool
Set of Programs designed to compare gene sequence data
Check similarity between human and non-human species
Determine the structure and function of selected protein(s)
IATUL 2009 - Leuven, Belgium
IATUL 2009 - Leuven, Belgium
Assessment
“I learned how to use PubMed….find a specific protein…coding sequence…”
“If I use OMIM again in the future it will be for any extra genomic information I need about a disease”
“OMIM is quite complicated but the instruction really helped make this website useful”
IATUL 2009 - Leuven, Belgium
Lessons Learned
Focus on most useful aspects of resources
Develop sequential steps and links to an assignment
Create exercise that replicates expert use Ask “real” targeted questions
Provide hands-on practice with assistance
IATUL 2009 - Leuven, Belgium
Conclusion
Librarian expanded subject knowledge, skill sets and relevance
Developed productive collaboration with faculty
Innovative learning experience for Students They learned more about genetics!
May see greater relevance in using Bioinformatics tools
IATUL 2009 - Leuven, Belgium
Bioinformatics Links NCBI
http://www.ncbi.nlm.nih.gov/
Genes and Diseaseshttp://www.ncbi.nlm.nih.gov/books/bookres.fcgi/gnd/tocstatic.html
OMIMhttp://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM
BLASThttp://blast.ncbi.nlm.nih.gov/Blast.cgi
EMBL Nucleotide Sequence Database (Europe)http://www.ebi.ac.uk/embl/
DDBJ – DNA Data Bank of Japanhttp://www.ddbj.nig.ac.jp/
IATUL 2009 - Leuven, Belgium
Related Links
Link to the 30th IATUL Conference Presentation, Handout and Lab Assignment http://tinyurl.com/ppydmz
Link to getFAST (Free Assessment Summary Tool) http://www.getfast.ca/
IATUL 2009 - Leuven, Belgium
Thank You, Merci, Danke, Grazie…
Don MacMillanBiological Sciences, Physics & Astronomy
Librarian University of Calgary
email: macmilld@ucalgary.ca
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