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 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 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 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

aaaa Enterand 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 M edical S ubject H eadings or MeSH. is a “controlled vocabulary list” of more than 25,000 subject headings. The MeSH assigned to each article in PubMed is like a keyword abstract of the article.

Click MeSH Database

aaaa (Note: If there is a Boolean OR relationship, start with the “OR” statement first.) sequence deletion Search and 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 subheading a 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 for Search ((“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, Apply then click

Icons for full text.

Click for MeSH terms. ∨

AND protein structure nucleotides/metabolism sequence deletion MeSH Database searches only the MeSH terms for:

Look at subject headings in the MeSH Terms Index for 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 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: 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 systems store and analyze information molecular biology biochemistry genetics facilitate use of databases by the research and medical community

Click DNA Helix to go to the NCBI databases Click DNA Helix to go to the NCBI databases

National Center for Biotechnology Information Databases Assembly BioProject BioSample BioSystems ClinVar CloneDB Conserved Domain Database Database of Genomic Structural Variation Database of Genotypes and Phenotypes Epigenomics EST (short single-read transcript sequences) Gene Genome GEO Datasets GEO Profiles GSS (short single-read transcript sequences) HomoloGene Nucleotide Database Online Mendelian Inheritance in Man PopSet Probe Protein Database RefSeqGene Reference Sequence (RefSeq) Sequence Read Archive SNP Structure (Molecular Modeling Database) Taxonomy UniGene

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

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 Authoritative drug information Entire US National Formulary

Mouse over Databases Click MicroMedex

Begin entering drug name. Select correct drug. Begin entering drug name. Select correct drug. warfarin

Select links or detailed document

Drug Monograph

Special Tools A Special Tools A 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