Putting this Exercise into Context

Over the course of the term we will be looking at a variety of databases representing sequence and structural information in bioinformatics. Perhaps not surprisingly, there is a similar wealth of resources available to look at scientific literature. Librarians were among the first to use "informatics" as a description for the science of information retrieval and analysis, and it's no surprise that the NCBI is housed at the National Library of Medicine.

Think of NCBI as a tool shed.

• Good tools should not weigh down a worker too much
• A good worker will need to know how tools work to take the greatest advantage of the resources

The lesson is no different for the literature than it is for sequences or structures: there are easy ways to get answers, but they may not always be the best ones. A careful worker will know how to use available tools build comprehensive libraries of information (data or literature) and then be able to retrieve and organize the most relevant pieces of that mass of information.

The Challenge

• The databases are huge and growing
• The nature of the databases and their interconnections frequently change.

Our Definitions

• The Tools
  • The Entrez interface to the NCBI/NLM databases
  • The Voyager system for the UMDNJ library
  • EndNote bibliographic software
• An Index
  • You probably will never see an index
  • In the print context, an index was used to locate particular subject matter in a book or journal series; computers use Indices to locate data
• Content
  • Literature
    • Citations, often including abstracts, to journal articles, reviews, etc.
      • These citations and abstracts make up the content of the PubMed database.
      • You may elect a select subset and organize those locally using EndNote
    • Full-text linked from those citations
      • PDF documents
      • Links to unpublished data supplemental to cited articles
  • Data
    • Raw data including
      • GenBank Sequences
      • Trace Archives
    • Curated data including
      • RefSeq Data

What do the tools do? They permit you to...

1. Find the right pieces of data or literature
2. Retrieve the content (sequence? article?) you need
3. Keep data, full-text articles, and references organized on your end.

What you will learn

1. Growth and extent of the literature and data resources.
2. Starting points into these resources on the web.
3. Interconnecting data sets and the literature
4. Techniques for searching the literature
5. Tools you can use for searching the literature
6. Opportunities (and limitations) on retrieving full electronic text
7. Indexing - the role of an index in keeping everything in order
8. Libraries, and how are changing
9. Bibliographic software : Good (free, to us) tools to manage and use your private literature database

Page last updated on October 24, 2008