PubMed Advanced: Linking PubMed to NCBI Genetics Databases KTL Vaughan Librarian for Bioinformatics & Pharmacy UNC-CH Health Sciences Library

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

Opening PubMed MEDLINE Start at HSL Homepage ( Click on “PubMed (MEDLINE)” link PubMed opens in a new window

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

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 1[substance name]”

1 st Practice Opportunity Find abstracts in PubMed using a gene of your choice (human or animal) 1 st : Keyword search 2 nd : MeSH search 5 minutes to practice Come back to chat about this search

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)

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

2 nd 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

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

3 rd 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 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

For More Information NCBI Tutorials:  PubMed tutorial  Entrez tutorial This class will be available online at Please fill out our online evaluation! -