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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!. K.T. Vaughan, instructor Nani Vaidhyanathan, assistant Topics: Searching PubMed for genes (keyword and MeSH)

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PubMed Advanced: Linking PubMed to NCBI Genetics Databases

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  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 1[substance 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.libproxy.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/evaluationform.cfm

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