MICB 405 Bioinformatics MiniLab - PowerPoint PPT Presentation

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MICB 405 Bioinformatics MiniLab

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Title: MICB 405 Bioinformatics MiniLab


1
MICB 405 BioinformaticsMini-Lab 1 NCBIs
Entrez
  • Dr. Joanne Fox
  • joanne_at_msl.ubc.ca

2
Objectives
  • By the end of todays 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

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Accessing Entrez
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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

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http//www.ncbi.nlm.nih.gov/Sitemap/samplerecord.h
tml Search Google for genbank sample record
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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.

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The NCBI Bookshelf
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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?

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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/pubmedtuto
    rial/
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