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MICB 405 Bioinformatics Mini-Lab #1 – NCBI’s Entrez

MICB 405 Bioinformatics Mini-Lab #1 – NCBI’s Entrez. Dr. Joanne Fox joanne@msl.ubc.ca. Objectives. By the end of today’s tutorial: You will practice searching the Entrez database retrieval system.

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MICB 405 Bioinformatics Mini-Lab #1 – NCBI’s Entrez

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  1. MICB 405 BioinformaticsMini-Lab #1 – NCBI’s Entrez Dr. Joanne Fox joanne@msl.ubc.ca

  2. Objectives • By the end of today’s tutorial: • You will practice searching the Entrez database retrieval system. • You will learn to recognize links between the different Entrez databases, and differentiate hard and neighbor links. • You will search PubMed using advanced techniques and tips.

  3. What is Entrez? • “The life sciences search engine” • text-based search and retrieval system at NCBI • Covers all major databases of NCBI

  4. Joanne Fox MICB 405

  5. Accessing Entrez Slide 5

  6. Example #1 – Searching for Sequences, Hard and Neighbor links • We will: • go to Entrez • do a search for “obesity genes” • view the GenBank flat file for the first nucleotide entry in your search results • investigate the hard links available from this nucleotide sequence record to PubMed • investigate the related articles (neighbor links) available for this PubMed record

  7. http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html Search Google for: “genbank sample record”

  8. Hard Links Neighbor Link

  9. Hard Links and Neighbor Links • Hard Links are: • direct connections between entries in different databases. • Example: a link between nucleotide and protein records at NCBI. • Neighbor Links are: • connections between entries in the same database. • based on criteria that can change between databases. • Examples: similar papers, related sequences, or similar 3D structures.

  10. Follow this link Slide 12

  11. The NCBI Bookshelf

  12. Example #2 – Searching PubMed • How many papers in PubMed are there: • about cancer? • about carrots? • Using Entrez PubMed, can you see if there are any scientific links between carrots and cancer? • How many papers are there about “carrots AND cancer”? • What is the active chemical substance in carrots that may play a role in cancers?

  13. Joanne Fox MICB 405

  14. Joanne Fox MICB 405

  15. Joanne Fox MICB 405

  16. Links • The About Entrez page at the NCBI http://www.ncbi.nlm.nih.gov/Database/index.html • PubMed Tutorial from NLM http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/

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