PubMed Advanced: Linking PubMed to NCBI Genetics Databases

1
PubMed Advanced Linking PubMed to NCBI Genetics
Databases

• KTL Vaughan
• Librarian for Bioinformatics Pharmacy
• UNC-CH Health Sciences Library

2
Welcome!

• K.T. Vaughan, instructor
• Nani Vaidhyanathan, assistant
• Topics
• 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

3
Opening PubMed MEDLINE

• Start at HSL Homepage (www.hsl.unc.edu)
• Click on PubMed (MEDLINE) link
• PubMed opens in a new window

4
Keyword Searching for Genes

• PubMed has difficulty with 3-letter codes
• May need to use synonyms gene code, gene name,
  protein code, protein name
• Ex ALS1, amyotrophic lateral sclerosis, SOD1,
  superoxide dismutase 1
• Use Limits to narrow to human/animal only

5
MeSH Searching for Genes

• MeSH Medical Subject Heading
• Used to describe the topics of an article
• Not the same as keyword searching!
• Ex SOD1 becomes superoxide dismutase
  1substance name

6
1st 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

7
Linking PubMed Results to Sequences

• 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
• 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)

8
Linking PubMed Results to Sequences (pt.2)

• For one specific article
• Use Links to the right of the citation
• Choose the NCBI database of interest

9
2nd Practice Opportunity

• Using the articles you found in search 1,
• 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

10
Linking Entrez Gene to PubMed

• All NCBI databases use PubMed articles as
  foundation
• 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.
• All is backed up with PubMed article links
• Either use the Display pull-down menu or the
  PubMed link on the right

11
3rd 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

12
Key Points from Today

• PubMed has lots of articles on genetic topics
  not just human or medically relevant
• Searching for literature on a gene can take many
  routes
• 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

13
For More Information

• NCBI Tutorials
• PubMed tutorial - http//www.nlm.nih.gov.libproxy.
  lib.unc.edu/bsd/pubmed_tutorial/m1001.html
• Entrez tutorial - http//www.ncbi.nlm.nih.gov.libp
  roxy.lib.unc.edu/Entrez/tutor.html
• This class will be available online at
  http//www.hsl.unc.edu/Bioinformatics
• Please fill out our online evaluation! -
  http//www.hsl.unc.edu/services/classes/evaluation
  form.cfm