Iatul june1 2009

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


Contents

Introduction Why use Bioinformatics? Biology 311 Lessons Learned Conclusion Key Resources


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


Bioinformatics

What is Bioinformatics? Why use Bioinformatics? Challenges for Librarians Key Resources


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


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


Challenges for Librarians

Content Bioinformatics databases designed for

researchers Faculty perceptions Need to Collaborate


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)


Sample Genetic Diseases Hemophilia

Colon Cancer

Glaucoma

Diabetes, Type 1

Cystic Fibrosis


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?


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


Search for Disease topic


Cystic Fibrosis Gene


Detailed Gene and Protein Information


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)


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”


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


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


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/


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/


Thank You, Merci, Danke, Grazie…

Don MacMillanBiological Sciences, Physics & Astronomy

Librarian University of Calgary

email: [email protected]

Iatul june1 2009

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