Workshop Chair: Peter S. Cooper, Ph.D.

The National Center for Biotechnology Information

Part 1 Using the Entrez System
 
In this workshop I will provide an overview of the NCBI integrated biomolecular databases that comprise the Entrez system and show how to effectively use the Entrez system to find and download data of interest. I will also provide  information on bulk download and automated access through the EUtilities. After  describing the types and sources of molecular data emphasizing the the importance of NCBI derivative databases (RefSeqs, RefSNPs), I will demonstrate effective use of  using the Entrez interface including filters, search strategies to collect and download a specific set of records, to narrow the search, and to find related sequences, proteins, pathways, expression information and structures. Those with laptop computers can follow the live examples on the NCBI website.

Part 2 Genes and Variations

In this workhshop I will use the mouse fig4 homolog and the human APOE gene as examples to navigate across the integrated databases to find literature, sequences (genome, mRNA and protein), and variations. I will then map those variations onto genes, transcripts, proteins, and structures. This workshop will emphasize the importance of the Gene database as the best way to access these data. Examples will also demonstrate additional tools and viewers associated with Entrez including BLink (BLAST Link), the Graphical Sequence Viewer, Map Viewer, and the Cn3D structure viewer. The workshop will emphasize the power of the pre-computed analyses and links across and within databases to uncover relationships. Those with laptop computers can follow the live examples on the NCBI website.