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NCBI Entrez Digital Tools and Utilities

NCBI Entrez Digital Tools and Utilities

The lecture will cover three related methods of accessing the information in Entrez.

The class will start with an overview of querying in the Entrez web pages and an introduction to some of the lesser known but highly useful aspects of Entrez.  That will including the use of MeSH to limit PubMed queries to a reasonable number of results, bounding the results by a date range, and exploring the precomputed sets of related articles and links to sequence database records.

Programmatic access to the Entrez data is provided by the Entrez Utilities (EUtils) set of URL-based services.  Simple programming languages (e.g., Perl, shell script) can be used to automate multi-step Entrez queries that can be repeated on a regular basis.  These services return results in XML format, which can be interpreted to construct subsequent EUtils queries or to generate summary reports.

Finally, the EBot service allows the user to design a query path using a web interface, and it generates a Perl script that performs the query.  EBot eliminates the need for laboratory scientists to do their own computer programming in order to use EUtils for automated queries.

Course Materials and Resources

Class Handouts:

School of Medicine