Scientific Literature, PubMed, & UA Library Lesson Date: 08/25/04 – W Created by: Angela M. Amoia 08/19/04

Lesson Objectives Recall what a reference tree is and how one is created Distinguish between primary article and review article Summarize how to obtain a full text article Recall key journals which contain primary structure articles and review articles Apply search skills (both PubMed and UA Library) to topic of choice.

Reference Tree 1° or R R or 1° R1° etc… R - Review Article 1 ° - Primary Article Trunk = Cornerstones Branches = ‘Complete the story’

Types of Scientific Literature Ambiguity to newcomers! Primary Article –A publication in which new research findings are presented, interpreted, and placed in the context of existing scientific knowledge. Review Article –A publication which provides broad perspective and insight into an area of scientific investigation, primarily by summarizing and comparing past research findings. Thanks Matt Cordes

Primary Article Presents novel data produced from an experiment(s) for a reader to evaluate Usually contains a large amount of graphical material (i.e. tables, figures) compiling data Reflects the individual viewpoint of an investigator(s) Usually has references

Review Article Does not present any novel data Summarizes the conclusions of current literature (within 10 years) on a specific system, a general topic, or whole field; may interpret and/or analyze in addition to summarizing. Is mainly text-based; contains minimal graphic material unless summarizing a compilation of data of illustrating an overall concept. Usually has over 100 references.

How do I get the full text of an article? Electronically –PubMed –Biochemistry Journals Online (UA subscriptions) –UA Library; full offering of electronic journals Hardcopy (Yes, a little exercise involved here!) –Science & Engineering Library –Med School Library Interlibrary Loan

How do I get the full text of an article? Electronically –PubMed –Biochemisty Journals Online (UA subscriptions) journal_pages/biochemjournals.html –UA Library; full offering of electronic journals (S & E Library) (Med School Library) Hardcopy (Yes, a little exercise involved here!) –Science & Engineering Library –Med School Library Interlibrary Loan

Let’s go book mark these pages! Use Netscape! All the links can be found on the Helpful/Useful Links page accessed from the course homepage: edu/classes/bioc462/462aH/ index.htm in the future you have to use Netscape to download structures so I would stay consistent

PubMed PubMed is a data base catalogs all ‘bio- scientific’ articles that are written. Maintained by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM), located at the National Institutes of Health (NIH) Access to bibliographic information: –MEDLINE (mid 1960’s to present) –OLDMEDLINE ( ) –4,800 biomedical journals: over 14 million citations

Key Journals Primary Structure Nature Science Biochemistry J. of Biological Chem Protein Science Nature Structure Bio PNAS Structure and Folding Review All listed under Primary Annual Rev of Biochem Current Opinion in Structural Biology Ann. Rev of Biophy & Biomolecular Structure Nature Rev of Mol & Cellular Biology

Pub Med Exercise Example: Searching for articles about the structure of HIV proteins and the viral RNA genome itself. We’ll learn some search tricks while doing so, since you’ll see how much stuff is out there on this topic and you can’t look at it all! LET’S DO IT…