Literature Resources for Bioinformatics

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

Presentation for the Computational and Systems Biology Summer Institute (CSBSI)
Monday, June 22, 2009

Last updated 6/19/2009

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.

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/ - 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

Useful links available from the homepage

• NCBI Site Map http://www.ncbi.nlm.nih.gov/Sitemap/index.html
• Resource Guide http://www.ncbi.nlm.nih.gov/Sitemap/ResourceGuide.html Provides brief descriptions about all of the NCBI resources.
• About NCBI http://www.ncbi.nlm.nih.gov/About/index.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, click on "All Databases" on the toolbar ----> Entrez Cross-Database Search Page

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

Entrez Nucleotide - collection of sequences from several sources, including GenBank, RefSeq, and PDB.

How do I interpret the information shown in the sequence record?

• Sample GenBank Record http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html (Can also link to this from the NCBI Resource Guide)

III. Genome Biology Resources

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

Click on "Genomic Biology" in the left-hand sidebar

• On the right-hand side, click "Genome Projects Database". On the left-hand sidebar note the following links: Statistics, Sequencing Centers.

Where can you find information about the human HTT gene?

Genomic Biology http://www.ncbi.nlm.nih.gov/Genomes/

• Click on "Gene" in the left-hand side bar. Search for: HTT [sym] and use the Limits tab to limit to: homo sapiens
  
  
• 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?

TaxBrowser - link on the NCBI tool bar

V. PubMed

MEDLINE database

• Produced by the National Library of Medicine
• Indexes the health sciences and life sciences literature

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
  • Most functionalities accessed through tabs: Limits; Preview/Index; etc.
  • Recommend using Boolean operators, AND, OR, NOT. Must be in capital letters!
    • Sample Search: bees AND social behavior AND genetics
      • Click on author name for "AbstractPlus" view.
      • Publisher-provided links to full-text and "Get it@ISU" button.
• Limits Tab and Field Tags
  • Can limit a search by various parameters, e.g. dates, language, etc.
  • Field tags can be very useful. For example,
    • signal transduction AND science vs.
    • signal transduction AND science [ta]
  • Complete list of tags available in the "Help" document. Search "field tags" ->Search Field Descriptions and Tags
    • Affiliation tag [ad]
    • PubMed ID [pmid]
• 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

VII. Additional Resources - The BCB Resource guide has additional databases listed under the "Find Articles & Conference Proceedings" tab. Because of the interdisciplinarity of this field, researchers in this field should search multiple resources.

VIII. Google Scholar

• 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

Questions?

Feel free to email me at: adinkelm@iastate.edu