Bionano Summer Symposium August 22nd, 2013 Andrea Miller-Nesbitt

andrea.miller-nesbitt@mcgill.ca

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)

Questions?

Andrea Miller-Nesbitt

andrea.miller-nesbitt@mcgill.ca 514-398-1663

http://www.slideshare.net/andreaemn