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
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Online Tutorial
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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