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Bionano Summer Symposium August 22nd, 2013 Andrea Miller-Nesbitt
Finding information for your research
Yang, H. et al. (2009)
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
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/connect/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
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
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
To the rescue!
Organism specific information
http://flybase.org/
http://www.informatics.jax.org/
http://www.arabidopsis.org/
http://zfin.org/ www.wormbase.org/
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
Research question
How is DNA used in the self-assembly of discrete nanotubes?
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
Web of Science
Research question
How is DNA used in the self-assembly of discrete nanotubes?
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
MEDLINE
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
Cancer Tumor Tumour Neoplasm Neoplasms
Neoplasms/
25,588 MeSH terms
Medical Subject Headings (MeSH)
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)
