Literature Resources for Bioinformatics

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

Presentation for the Computational and Systems Biology Summer Institute (CSBSI)
Friday, June 20, 2008

Last updated 6/19/2008

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. Collections ----> Indexes & Abstracts - listing of databases available from ISU Library

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

4. Electronic books - electronic books about bioinformatics, genetics, genomics

Research 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

Types of databases by scope http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/Databases/databases_scope.html

Types of databases by level of curation (Archival vs curated) http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/Databases/databases_curation.html

Useful links available from the homepage

II. Entrez

What is Entrez?

From the NCBI homepage, click on "All Databases" on the toolbar ----> Entrez Cross-Database Search Page

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

Example: Search for this record, L42110 (all sequence records are given accession numbers)

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

From the L42110 record, click on "Links", select "Related Sequences" and look at the second record, NM_000021. Note the number of references that include publications about this sequence and the comments field.

RefSeq records have distinct accession numbers - 2 characters followed by an underscore character ('_').

RefSeq FAQ: http://www.ncbi.nlm.nih.gov/RefSeq/RSfaq.html

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

Where can you find information about the human HTT gene?

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

IV. Taxonomy

What is the scientific name for the honeybee?

TaxBrowser - link on the NCBI tool bar

V. PubMed

MEDLINE database

PubMed http://www.pubmed.gov/

VI. Using PubMed

VII. Additional Resources - all of the following resources are listed under "Indexes & Abstracts"

Questions?

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