Searching PubMed®
NCBI, NLM Resources,
Micromedex -GSBS
TTUHSC Preston Smith Library
presents
Rev. 08/17/14
To begin...
Hover mouse over Databases
Click PubMed
• Biomedical & life sciences journal literature - @6,000 journals
PubMed Database
• International scope
• Developed and maintained by
the:National Center for
Biotechnology Information
at the U.S. National Library of Medicine
at the National Institutes of Health
Accessing PubMed
• Freely available over the Internet
@ www.pubmed.gov
• Also through library’s home page
Create a Search Strategy Plan
Identify the question and key concepts:
In the CFTR gene, how does
sequence deletion impact protein structure
and nucleotide metabolism?
Write the search program using
medical subject headings (MeSH)
PubMed Home Page
Gene Sensor
aa
Enter and click
cftr Search
Click See 1287 articles about CFTR gene function
Gene Sensor
Click the PubMed icon
Using MeSH Database
MeSH Database
Terms in the database are called
Medical Subject Headings or MeSH.
is a “controlled vocabulary list” of more than25,000 subject headings.
The 10-15 MeSH assigned to each articlein PubMed is like a keyword abstractof the article.
Click MeSH Database
aa
(Note: If there is a Boolean ORrelationship, start with the
“OR” statement first.)
sequence deletion Searchand clickEnter
Term Definition
terms arranged in
tree structure hierarchy
MeSH
Terms are listed from
broadest to narrowest.
If Sequence Deletion
yields zero results, try using a
broader term: Mutagenesis.
Click Add to search builder
a
protein structure and click
Enter Search
Click the underlined term
Note:PubMed automatically
OR’s indented terms
under a broader term…
Click Add to search builder
a
nucleotide and click
Enter Search
Click the underlined term
Sub-headings narrow the “meaning” of a
articles under the MeSH term: Nucleotides.
They are a “subset” of all the MeSH term.
✔
1) Check the box next to the subheadinga
2)Then click Add to search builder✔
Click Search PubMed
Click Advanced
Click Add next to the set for PubMed (GeneRIF) Links for Gene (Search cftr[gene]…
Click Search
and the set forSearch ((“Sequence Deletion”[Mesh]) AND “Protein Conformation”…
PubMed identifies
9 articles
Search Results
Limiting Filters
X
Select article #2.
Click Display Settings
Select Abstract, change to Pub Date to
sort to most recent articles appearing first,
Applythen click
Icons for full text.
Click for MeSH terms.∨∨
AND
ANDprotein structure
nucleotides/metabolism
sequence deletion
MeSH Databasesearches only
the MeSH terms for:
Look at subject headings in the
MeSH Terms Indexfor additional terms.
You may want to write a new search
program using:
Protein Binding
.
Click Send to: and select
File to save citations to a file on your computer or
Clipboard to temporarily store selected citations or
E-mail to send citations to self or colleague
Linking to
Full-Text Articles
in Electronic Journals
When Searching from Off Campus:
Enter the
Eraider username and password
assigned to you
by Information Services.
A
Problems with eRaider? Call: 806-743-1234 a
Icons for full text.
Click PDF
Full Text Article
Close Article
Online Tutorial
Click Training & Tutorials for hands-on learning.
NCBI
National Center for Biotechnology Information
Mission:create automated systemsstore and analyze information
molecular biologybiochemistrygenetics
facilitate use of databases by the research and medical community
Click DNA Helix to goto the NCBI databases
National Center for Biotechnology Information Databases
AssemblyBioProjectBioSampleBioSystemsClinVarCloneDBConserved Domain DatabaseDatabase of Genomic Structural VariationDatabase of Genotypes and PhenotypesEpigenomicsEST (short single-read transcript sequences)
GeneGenomeGEO DatasetsGEO Profiles
GSS (short single-read transcript sequences)
HomoloGeneNucleotide DatabaseOnline Mendelian Inheritance in ManPopSetProbeProtein DatabaseRefSeqGeneReference Sequence (RefSeq)Sequence Read ArchiveSNPStructure (Molecular Modeling Database)TaxonomyUniGene
Gene
Select Gene
Search CFTR
Click
Protein
Select Protein
Search brca1
Click Homo sapiens (1324)
Click BRCA1 Homo sapiens
Sequence Data
Structure
Select Structure
Search brca1
Click structure
View, zoom, highlight in 3D
Proteins and interactions
Nucleotide
Select Nucleotide
Search CFTR
Click Homo sapiens (858)
Select deletion
Sequence Data
Click graphics
Graphical Sequence Data
dbSNP
Click Advanced
Search
5 variants with sensitivity to Warfarin
Other NLM Databases
www.ttuhsc.edu/libraries
Click Databases
Scroll and click National Library of Medicine
Click “N”
Click All NLM Databases & API’s
Locate and Click Database Name
MICROMEDEX
• Authoritative drug information
• Entire US National Formulary
www.ttuhsc.edu/libraries
Mouse over Databases
Click MicroMedex
Begin entering drug name.
Select correct drug.
warfarin
Select links
or detailed
document
Drug Monograph
Special ToolsA
Select Drug Interactions
Interactions table includes:
MICROMEDEX – drug identification
MICROMEDEX: also includes
Alternative Medicines
Diseases & Acute Care
Patient Education
Toxicology & Product Info
The End
Aug 2014