BIT 410: Manipulation of Recombinant DNA
Databases for Biotechnology
and Cloning
PubMed
(and NCBI)
PubMed is the primary molecular biology database and includes articles
on human diseases and conditions and clinical and basic research.
It is also part of the National Library of Medicine's collection of
biotechnology tools, the National Center for Biotechnology Information
(NCBI). You can link from articles in PubMed to nucleotide and protein
sequence information and to many other NCBI tools (e.g., genomic maps,
protein structures, etc.). See the description of NCBI in the next
section for more information.
SciFinder
Scholar
Covers chemistry, biochemistry, and related fields. Includes articles
on molecular biology, contains some sequence information, and articles
on methods and protocols. SciFinder Scholar also searches Medline
simultaneously. (Note: This database requires special software to
access, and is not available off-campus. Use the link above for more
information.)
Subject-Related Databases
The Database
Finder organizes databases by subject area. Use it to locate and
link to databases on subjects from Agriculture to Zoology.
These databases will include information about genes and molecular
biology, but with a focus on specific areas, such as plant science,
microbiology, etc. Here are some examples of subject-related databases.
Subject Coverage
Agricola
Agriculture and related sciences, including plant and animal
sciences.
BIOSIS
Previews (Biological Abstracts)
All areas of the biological sciences.
CAB
Abstracts
Agriculture and related sciences, including plant and animal
sciences.
Cambridge
Scientific Abstracts
A collection of databases on topics including microbiology,
plant science, environmental sciences, agricultural and environmental
biotechnology, biotechnology and bioengineering, ecology, entomology,
genetics, etc.
Web
of Science/Science Citation Index
All sciences. Especially useful for interdisciplinary subjects.
Also a citation database, so you can track who has cited important
papers in your area.
Zoological
Record
Zoology
Tips for Searching Databases
A. Get ready to search by analyzing your topic to identify:
The main concepts or ideas and their relationships.
- If you are unfamiliar or new to a topic, locating a review
article in a journal or overview in a book or textbook can be
helpful in clarifying relationships between concepts and identifying
terms.
- Appropriate terms and synonyms to use for each concept.
- Use the MeSH
Browser to search for terms. The MeSH Browser can give you
definitions (or scope notes) for terms, the relationships between
terms, alternate terminology, scientific names for organisms,
etc.. MeSH stands for Medical Subject Headings, a system of terminology
used in PubMed.
- Use online or print dictionaries to check the meanings of unfamiliar
terms. This
site links to several online biotechnology glossaries.
Using a Search
Strategy Worksheet can be helpful when analyzing your topic and
planning your search.
B. Use appropriate database searching terms and methods to enhance
results:
Boolean Operators
Note: In PubMed Boolean operators must be typed in all caps.
- Use AND to include two or more concepts or ideas in a search. For
example: insulin receptor AND gene AND human
- Use OR to account for synonyms, word variants, or to include at
least one of a set of terms in a search. Example: (gene OR genome
OR clone). Words linked by OR are usually enclosed in parentheses
to indicate that they should be treated as a single search concept.
Truncation
Use truncation to account for variations in word endings, including
singular/plural word forms. Many databases, including PubMed, use
an asterisk * as the truncation symbol. Example: regul* for regulatory,
regulate, regulation, etc.; gene* for gene, genes, genetic, genetics,
etc.
Controlled Vocabulary
PubMed (and several other databases) use a "controlled vocabulary"
of terms, with detailed definitions and relationships. This controlled
vocabulary (often referred to as "subject terms" or "descriptors")
can help obtain very specific and focused results in your searching.
For more information see this description
of MeSH.
Limits and Field Searching
Each database record is divided into sections, called fields.
These include title, author, journal name, year, subject terms, organism,
etc. You can limit your search to retrieve records that have designated
terms in a specific field.
- Limits are another way of narrowing or focusing your search. Some
examples of ways to limit a search are to restrict your search to
certain years, specific organisms, specific types of data or molecules,
etc.
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