Literature Resources for Bioinformatics

Andrea Dinkelman, Assistant Professor and Science & Technology Librarian
Iowa State University
Email: adinkelm@iastate.edu

Presentation for the Computational and Systems Biology Summer Institute (CSBSI)
Tuesday, June 22, 2010

Last updated 6/21/2010

Goals of the session

1. To provide a brief introduction to the ISU Library.

2. To provide a brief orientation to the NCBI web site.

3. How to use PubMed effectively to search the scientific literature.

4. Briefly mention other major research literature databases useful in bioinformatics research.

ISU Library Website - http://www.lib.iastate.edu/

Useful links:

1. Classes & Tours --->Instruction LibGuides, Bioinformatics & Computational Biology (BCB) Resources, (http://instr.iastate.libguides.com/bcb) - Recommend using this as your starting point for finding information. Be sure to check out the list of electronic books related to bioinformatics, genetics, and molecular biology!

2. Collections ----> e-Journals & e-Books - listing electronic journals available from ISU Library

3. Library catalog - search for books, journals, CDs, & DVDs owned by ISU

By the end of class, you'll be able to answer the following questions:

1. What is the status of the genome sequencing project for the tomato?

2. What is the scientific name for the honeybee?

3. Where can you find information about the human HTT gene?

4. Your professor has asked you to retrieve the following articles, and all you have is a list of numbers: 17384733; 16886994; and 16216716. Can you find these?

5. You've been asked to locate some review articles about the swine genetics published within the last 3 years.

6. You want to be alerted via email when new articles are published about the evolution of turtles.

Answers will be revealed using the NCBI website and PubMed!

I. National Center for Biotechnology Information (NCBI) - http://www.ncbi.nlm.nih.gov/guide/- Created in 1988 as a part of the National Library of Medicine at NIH

What does the NCBI do?

•NCBI accepts submissions of primary data (e.g. GenBank). Original research data submitted by researchers.
•NCBI develops tools to analyze these data. (e.g. BLAST)
•NCBI uses these tools to create derivative databases based on the primary data (e.g Refseq).
•NCBI provides free searching, linking, and retrieval of these data, primarily through the Entrez system.

Data Domains http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/Databases/datadomains.html

Science Primer http://www.ncbi.nlm.nih.gov/About/primer/index.html A good resource for learning about bioinformatics, microarrays, SNPs, etc.

II. Entrez

What is Entrez?

• A system of linked databases (e.g. literature, sequence data, etc.)
• A text search engine
• A tool for finding biologically linked data
• Provides a quick view of the content of most NCBI databases.

From the NCBI homepage, the default search is "All Databases"

• Example: presenilin 1 (Shows number of records in each resource.)
  

III. Genome Biology Resources

What is the status of the genome sequencing project for the tomato?

Click on "Genomes & Maps" in the left-hand sidebar

• Under "Quick Links", click "Genome Project". To get the most precise results specify the organism field when searching with an organism name, for example: human[orgn]. Accepted common names usually give correct results. Use the scientific name if no results are obtained.

Where can you find information about the human HTT gene?

Click on "Genes & Expression" in the left-hand sidebar

• Under "Quick Links", click on "Gene". Search for: HTT [sym] AND human [orgn]
  
  
• Genetics Home Reference http://ghr.nlm.nih.gov/ (easy-to-understand about genes and genetic conditions)

IV. Taxonomy

What is the scientific name for the honeybee?

Click on "Taxonomy" in the left-hand sidebar. Under "Quick Links", click "Taxonomy".

V. PubMed

MEDLINE database

• Produced by the National Library of Medicine
• Indexes the health sciences and life sciences literature, Coverage: 1940s - present

PubMed http://www.pubmed.gov/

• Freely available web site - However, you'll want to access PubMed via the "Indexes & Abstracts" list on the Library's website. Choose "PubMed -- ISU Affiliate" link. This has the "Get it@ISU" link on every record. (Or, click on the PubMed link on the BCB Resources guide.)

VI. Using PubMed

• For additional information:
• PubMed Basics - 2 page handout (PDF) that highlights features. URL: http://nnlm.gov/training/resources/pmtri.pdf
• PubMed Tutorials and Quick Tours - http://www.nlm.nih.gov/bsd/disted/pubmed.html
  
  
• Search Tips
  • Recommend using Boolean operators, AND, OR, NOT. Must be in capital letters!
    
    
    • Sample Search: bees AND social behavior AND genetics

   

  • Search term selection: Are there scientific names, popular names, or abbreviations associated with your topic?

  (For example, lou gehrigs disease, ALS, amyotrophic lateral sclerosis)

  • Can limit a search by various parameters, e.g. dates, lanaguage, etc.
    
    
  • Use Advanced Search if you want to limit a search to specific fields (e.g. journal, affiliation, author, etc.) Example: Who is doing research at ISU related to swine genetics?
    
    
• Other Features
  • Journals Database: locate complete journal titles from abbreviations and vice versa
  • My NCBI: can set up searches to run automatically and have results emailed to you
  • PubMed Bookshelf: collection of full-text searchable textbooks

• will retrieve citations to book chapters, journal articles, conference proceedings, meeting reports
• is NOT as up-to-date as any of the above mentioned resources
• access via the Library website (listed under Indexes & Abstracts) for "Get it @ISU" linkage