Transcript PubMed Advanced: Linking PubMed to NCBI Genetics Databases

PubMed Advanced: Linking
PubMed to NCBI Genetics
Databases
KTL Vaughan
Librarian for Bioinformatics & Pharmacy
UNC-CH Health Sciences Library
Welcome!
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K.T. Vaughan, instructor
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Topics:
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Nani Vaidhyanathan, assistant
Searching PubMed for genes (keyword and
MeSH)
Linking PubMed results to sequences
Linking Entrez Gene results to PubMed articles
60 minute class
Communicate via the chat
Practice using separate browser window
Opening PubMed MEDLINE
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Start at HSL Homepage (www.hsl.unc.edu)
Click on “PubMed (MEDLINE)” link
PubMed opens in a new window
Keyword Searching for Genes
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PubMed has difficulty with 3-letter codes
May need to use synonyms – gene code,
gene name, protein code, protein name
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Ex: ALS1, amyotrophic lateral sclerosis, SOD1,
superoxide dismutase 1
Use Limits to narrow to human/animal only
MeSH Searching for Genes
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MeSH = Medical Subject Heading
Used to describe the topics of an article
Not the same as keyword searching!
Ex: SOD1 becomes “superoxide dismutase
1[substance name]”
st
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Practice Opportunity
Find abstracts in PubMed using a gene of
your choice (human or animal)
1st: Keyword search
2nd: MeSH search
5 minutes to practice
Come back to chat about this search
Linking PubMed Results to Sequences
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NCBI makes direct links between articles and
the sequence(s), structure(s), SNPs, etc.
they published
Not all articles have these links!
In the aggregate:
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Find any linked sequence to any article in your
search
Use the “Display” pull-down menu to choose an
NCBI database
Ex: Find RefSeq curated sequences by choosing
“Nucleotide (RefSeq)
Linking PubMed Results to Sequences
(pt.2)
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For one specific article:
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Use “Links” to the right of the citation
Choose the NCBI database of interest
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Using the articles you found in search #1,
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Practice Opportunity
Find all the sequences that these articles are
linked to in RefSeq
Find sequences that one particular article links to
5 minutes!
Come back to the chat to discuss
Linking Entrez Gene to PubMed
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All NCBI databases use PubMed articles as
foundation
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Therefore, all NCBI databases include links to the
supporting research for all records
Entrez Gene is a great starting place for
genetic info: links to sequence, introns/exons,
GO & RIF statements, homologies, etc.
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All is backed up with PubMed article links
Either use the Display pull-down menu or the
PubMed link on the right
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Practice
Find your gene in Entrez Gene
Use the link to PubMed to get articles that
have supported the Gene record.
How does this list differ from what you found
doing your keyword & MeSH searches?
5 minutes!
Come back to chat to discuss
Key Points from Today
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PubMed has lots of articles on genetic topics
– not just human or medically relevant
Searching for literature on a gene can take
many routes:
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Keyword searching in PubMed
MeSH searching in PubMed
Entrez Gene / other Entrez databases linked to
PubMed
Combining all of these is the most reliable
method
For More Information
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NCBI Tutorials:
 PubMed tutorial http://www.nlm.nih.gov.libproxy.lib.unc.edu/bsd/pubmed_tutorial/m1001.html
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Entrez tutorial http://www.ncbi.nlm.nih.gov.libproxy.lib.unc.edu/Entrez/tutor.html
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This class will be available online at
http://www.hsl.unc.edu/Bioinformatics
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Please fill out our online evaluation! http://www.hsl.unc.edu/services/classes/evaluationform.cfm