Systematic Literature Search

(2nd week)
 Access to Biological Literature

• Google Scholar
http://scholar.google.com/

• NLM Medline
http://www.nlm.nih.gov/pubs/factsheets/medline.html

• PubMed
http://pubmed.gov/

• PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/
 Google Scholar provides a simple way to broadly

search for scholarly literature. From one place, you can

search across many disciplines and sources: articles, theses,

books, abstracts and court opinions, from academic

publishers, professional societies, online repositories,

universities and other web sites.

 Google Scholar
http://scholar.google.com/
 READ IT!!
http://scholar.google.com/intl/en/scholar/about.html
 READ IT!!
http://scholar.google.com/intl/en/scholar/refinesearch.html
 Set your preferences first!
http://scholar.google.com/scholar_preferences?hl=en&as_sdt=0,5
Example
Make your search more specific
Advanced Scholar Seach
 PubMed comprises more than 21 million citations

for biomedical literature from MEDLINE, life science

journals, and online books. Citations may include links

to full-text content from PubMed Central and publisher

web sites.
 U.S. National Library of
U.S. Department of Health Medicine
&
Human Services
National Institutes of Health
NATIONAL INSTITUTES OF HEALTH
world's largest medical library
 http://www.nlm.nih.gov/services/usemedline.htmll
o Medical literature (Medline) since 1950
o Abstracts since 1975
o Molecular biology since 1985
o5,600 journals worldwide in 39 languages, 60 languages for older references
o 19 million citations, 17 million abstracts, 670,000 / last year, 2,000-4,000 / day
o MeSH Medical Subject Heading Thesaurus
o Controlled vocabulary
o Indexing terms
o Search concepts
o PubMed Help
o PubMed QuickStart
o PubMed Tutorials
o Journal Database
o LinkOut to journal publishers and other Providers
o Abstract Neighboring and related articles
o My NCBI: Query Storage
o Current awareness
 PubMed Central

PubMed Central® (PMC) is a free archive of biomedical and life sciences journal literature at the

U.S. National Institutes of Health's National Library of Medicine (NIH/NLM).

PubMed Central
Journal List
 PubMed Entrez Databese
http://www.ncbi.nlm.nih.gov/gquery/
 MedLine Sample Records
• UI 9738458

• AU Xie T, Ding D

• TI Relationship between synonymous codon usage and protein structure.

• MH Codon*

• MH Protein Folding*

• MH Protein Structure, Secondary*

• MH Proteins/chemistry*

• MH Proteins/genetics

• MH Animals

• MH Humans

• AB The hypothesis that synonymous codon usage is related to protein three-dimensional structure is
examined by …

• PT Journal article

• SO FEBS Lett 1998 Aug 28: 434 (1-2) : 93-6

 Medline Fields
•All Fields[ALL] •MeSH Terms[MESH]

•Affiliation [AD] •Publication Date[DP]

•Author[AU] •Publication Type [PT]

•EC/RN Number[RN] •Subset[SB]

•Entrez Date[EDAT] •Substance Name [NM]

•Issue [IP] •Text Words [TW]

•Journal Title [TA] •Title [TI]

•Language [LA] •Title/Abstract[TIAB]

•MeSH Date[MHDA] •Unique Identifiers[UID]

•MeSH Major [MAJR] •Volume[VI ]

•MeSH Subheads[SH]
Search on PMC
MeSH is the National Library of Medicine's controlled vocabulary thesaurus.
It consists of sets of terms naming descriptors in a hierarchical structure that
permits searching at various levels of specificity.
Add to search builder
Search PubMed
Try with MeSH
Searching in all MeSH catagories

• Nuclear Proteins

• Antigens

• Tumor Marker
 AND
It adds X-ray crystallography to seach builder OR
NOT
 About MeSH
http://www.nlm.nih.gov/mesh/
• MeSH consists of sets of terms naming descriptors in a hierarchical
structure that permits searching at various levels of specificity.

• MeSH descriptors are arranged in both an alphabetic and a

hierarchical structure.

• There are 26,142 descriptors in 2011 MeSH.

• There are also over 177,000 entry terms that assist in finding the most
appropriate MeSH Heading, for example, "Vitamin C" is an entry term
to "Ascorbic Acid."
 Advantages of using MeSH
• Represent a subject concept & no synonyms needed

• Find relevant articles on a search topic that may not be explicitly

mentioned in a title or abstract

• Focus search specifically eliminate irrelevant records

• Increase search efficiency

• Get complete & reliable results

 Disadvantages of MeSH

• Thesaurus terms may not cover all concepts, especially

new concepts and jargon.

• Not every concept in abstract or article can get

thesaurus terms.
 TAIR
• The Arabidopsis Information Resource (TAIR) maintains a database of

genetic and molecular biology data for the model higher plant Arabidopsis

thaliana .

• complete genome sequence along with gene structure, gene product

information, metabolism, gene expression, DNA and seed stocks, genome

maps, genetic and physical markers, publications, and information about the

Arabidopsis research community

 TAIR
• The Arabidopsis Information Resource (TAIR) collects information and

maintains a database of genetic and molecular biology data for Arabidopsis

thaliana, a widely used model plant.

• TAIR Database Statistics

http://www.arabidopsis.org/servlets/processor?type=tablestats
 Some example
• Gene name: P4H, TAPG

• Metabolic Pathways: ascorbate biosynthesis I

(L-galactose pathway)
•
The end of the second week!!