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