Exercise 1: An introduction to searching the scientific literature.
I. INTRODUCTION
The most fundamental skill in bioinformatics is the ability
to carry out an efficient and comprehensive search of the scientific
literature to find out what is known about a specific subject. All
of you are familiar with web search engines and while they can
be useful, they also turn up many items that have never undergone
the test of scientific peer review. Thus, this exercise is NOT a search of the
world wide web, but will introduce you to searching the published scientific literature
using a database such as MEDLINE, Biological Abstracts or Chemical
Abstracts. This exercise will focus on the Entrez browser entry to
the national library of medicine database MEDLINE (PubMed). Other useful resources include OMIM (Online Mendelian Inheritance in Man) and
Books-on-Line, both available via Entrez
PubMed via Entrez Browser
We will access Medline directly
from the Library of Congress via the Entrez browser (http://www3.ncbi.nlm.nih.gov/Entrez/). It is also possible to access Medline or
Biological Abstracts or a number of other databases through the Tufts Library
system via OVID browser (Tufts University Libraries > Article Databases>
O>OVID). Each browser has its own advantages and disadvantages and I have summarized
these on a separate document
We will focus on Entrez browser since it is available to all
users. Some key features of the Entrez browser include:
-
Free and accessible to everyone (i.e.
you don't need a Tufts ID or access via an institutional library to
use this)
-
Clipboard feature allows for easy
generation of subsets of hits
-
Related articles can help broaden a
search to capture articles that would not appear in the initial
term
-
Links to full text of a number of textbooks
gives background information
- Allows easy
connection to nucleotide and protein databases via Entrez browser
II. An EXAMPLE OF AN ENTREZ
PUBMED SEARCH
This Linked Document is an example of a PubMed search that uses Boolean
Operators, the Clipboard, Limits, Related Articles, Books and Full Text on-line. Additional on-line help files and tutorials are available from the national library of medicine.
PubMed Tutorial and PubMed Help files
III. EXERCISE 1 (The Literature Search)
Pick one of the four exercises below. Once you have a
short list of articles, pick one and display it in abstract
display. Click on Books and you will see a number of terms in the
abstract are now links. Click on one of these to see what
information is available.
Exercise 1 (Uncoupling Protein
and Diabetes)
UCP2 is a protein found in the inner mitochondrial membrane
of some cells. It leaks protons back across the membrane, decreasing the
amount of ATP produced. Recently, a role for UCP2 in the development of adult
onset diabetes has been proposed. You already know that there is a correlation
between obesity and adult onset diabetes. Construct a literature search for
papers published on UCP2 which also deal with obesity and are limited to
research done with humans.
Exercise 2 (Telomeres and Aging)
The ends of chromosomes (telomeres) pose specific problems
for the replication of DNA. Recent work has suggested that a process as
fundamental as aging may be connected to telomere dysfunction. Construct a
search of the literature for those review articles that deal with
telomeres and aging. Note five review articles on this topic. Since it is
unlikely you know much about telomeres, do a quick search on telomeres in the
Books database and look at one entry. List the entry you looked at.
Exercise 3 (Glycolysis in the neonatal heart)
You have been studying glycolysis in biochemistry class and
are interested in learning what research has been done on this area that
specifically looks at glycolysis in newborn humans and is published in an
English language journal. You would like to focus your search on this pathway
in the heart since you know that each organ is slightly different in its
metabolic needs and capacities. Structure a search to pull this information out. Provide me with the
total number of hits your search brings up and a list of the titles of the five articles you deem most interesting
(based on a quick look through the abstracts).
Exercise 4 (matrix metalloproteinases and periodontal disease)
Matrix metalloproteinases are a family of extracellular
proteolytic enzymes that have been implicated in a variety of pathological
conditions including metastatic cancer. Recently, it has been suggested that
these enzymes could also play a role in gum disease. Find three articles that
address the role of this class of enzymes in periodontal disease.
These tutorials were developed by Dr. Ross S. Feldberg, Dept of Biology, Tufts University, Medford, MA 02155 with the assistance of a Teaching with Technology grant from the Academic Computing Department at Tufts. Thanks to Anoop Kumar, Abhra Verma and Scott Cordeiro for help in developing this resource. Suggestions, corrections and comments should be sent to Ross.Feldberg@Tufts.edu. (last modified Aug 2005)
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