1. Doug Brutlag 2011 Bibliographic Search http://biochem158.stanford.edu/ http://biochem158.stanford.edu/ Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University School of Medicine Genomics, Bioinformatics & Medicine http://biochem158.stanford.edu/

2. Doug Brutlag 2011 Google Scholar http://scholar.google.com/ NLM Medline http://www.nlm.nih.gov/pubs/factsheets/medline.html PubMed http://pubmed.gov/ PubMed Central http://www.ncbi.nlm.nih.gov/pmc/ Stanford University Library http://searchworks.stanford.edu/ HighWire Press http://highwire.stanford.edu/ Lane Library - Ovid -Biosis - E Journals - SciSearch http://lane.stanford.edu/ EndNote http://www.endnote.com/ Access to Biological Literature

3. Doug Brutlag 2011 Google Scholar http://scholar.google.com/ http://scholar.google.com/

4. Doug Brutlag 2011 About Google Scholar http://scholar.google.com/intl/en/scholar/about.html http://scholar.google.com/intl/en/scholar/about.html

5. Doug Brutlag 2011 Google Scholar Search http://scholar.google.com/ http://scholar.google.com/

6. Doug Brutlag 2011 Google Scholar Preferences http://scholar.google.com/ http://scholar.google.com/

7. Doug Brutlag 2011 Advanced Scholar Search http://scholar.google.com/ http://scholar.google.com/

8. Doug Brutlag 2011 PubMed http://www.nlm.nih.gov/pubs/factsheets/medline.html http://www.nlm.nih.gov/pubs/factsheets/medline.html Medical literature (Medline) since 1950 Abstracts since 1975 Molecular biology since 1985 5,400 journals worldwide 18 million abstracts, 700,000/ last year, 2,000- 4,000 / day MeSH Medical Subject Heading Thesaurus –Controlled vocabulary –Indexing terms –Search concepts Unified Medical Language System (UMLS) Journal Database LinkOut to journal publishers and other Providers –APC Proxy access to Stanford PublicationsAPC Proxy access to Stanford Publications ENTREZ: Abstract Neighboring MyNCBI: Query Storage and Current Awareness

9. Doug Brutlag 2011 PubMed/Entrez Databases http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi

10. Doug Brutlag 2011 Medline Sample Record http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed UI98408838 AUTao X, Dafu D TIRelationship between synonymous codon usage and protein structure. MHCodon* MHProtein Folding* MHProtein Structure, Secondary* MHProteins/genetics …... ABThe hypothesis that synonymous codon usage is related to protein three-dimensional structure is examined by … PTJournal article SOFEBS Lett 1998 Aug 28: 434 (1-2) : 93-6

11. Doug Brutlag 2011 Medline Fields http://www.ncbi.nlm.nih.gov/entrez/meshbrowser.cgi http://www.ncbi.nlm.nih.gov/entrez/meshbrowser.cgi All Fields[ALL] Affiliation [AD] Author[AU] EC/RN Number[RN] Entrez Date[EDAT] Issue [IP] Journal Title [TA] Language [LA] MeSH Date[MHDA] MeSH Major [MAJR] MeSH Subheads[SH] MeSH Terms[MESH] Publication Date[DP] Publication Type [PT] Subset [SB] Substance Name [NM] Text Words [TW] Title [TI] Title/Abstract[TIAB] Unique Identifiers[UID] Volume[VI]

12. Doug Brutlag 2011 PubMed Text Search

13. Doug Brutlag 2011 PubMed Author Search

14. Doug Brutlag 2011 MeSH Contains 26,142 Thesaurus Terms & 177,000 Entry Terms Average 10-15 per article 3-4 as major points of article = * in PubMed Most specific MeSH assigned for each concept 199,000 Supplementary Concept Terms Subheadings 88 Qualifiers used with the ~25,600 MeSH terms Subheadings focus on sub-aspects of MeSH term (e.g., Hemoglobins - chemistry, Disease - diagnosis, Disease - Therapy, etc.) MeSH Database http://www.nlm.nih.gov/pubs/factsheets/mesh.html http://www.nlm.nih.gov/pubs/factsheets/mesh.html

15. Doug Brutlag 2011 MeSH Search for Next-Generation DNA Sequencing

16. Doug Brutlag 2011 MeSH Search for Next-Generation DNA Sequencing

17. Doug Brutlag 2011 MeSH Search for Next-Generation DNA Sequencing

18. Doug Brutlag 2011 MeSH Search for Next-Generation DNA Sequencing

19. Doug Brutlag 2011 MeSH Search for Next-Generation DNA Sequencing

20. Doug Brutlag 2011 MeSH Search for Next-Generation DNA Sequencing

21. Doug Brutlag 2011 MeSH Search for Next-Generation DNA Sequencing

22. Doug Brutlag 2011 Advantages of using MeSH Terms http://www.nlm.nih.gov/mesh/introduction2007.html http://www.nlm.nih.gov/mesh/introduction2007.html Represent a subject concept & no synonyms needed Find relevant articles on a search topic that may not be explicitly mentioned in a title or abstract Focus search specifically eliminate irrelevant records Increase search efficiency Get complete & reliable results

23. Doug Brutlag 2011 Disadvantages of MeSH http://www.nlm.nih.gov/mesh/introduction2007.html http://www.nlm.nih.gov/mesh/introduction2007.html Thesaurus terms may not cover all concepts, especially new concepts and jargon Not every concept in abstract or article can get thesaurus terms

24. Doug Brutlag 2011 Current Awareness HighWire Press Table of Contents & Notification http://highwire.stanford.edu/ Current Awareness with MyNCBI http://www.cdlib.org/guides/pubmed/currentawareness.rtf MyNCBI: PubMed Saved Searches http://www.ncbi.nlm.nih.gov/sites/myncbi/

25. Doug Brutlag 2011 MyNCBI

26. Doug Brutlag 2011 HighWire Press, An Introduction 1995 launch of Journal of Biological Chemistry Online Self-funding after first 18 months 1,000+ journals in Science & Medicine, Humanities & Social Sciences Many of the world’s most cited, highest impact Science & Medical journals Not-for-profit publishers and societies Perception: premium service at a premium price

27. Doug Brutlag 2011 HighWire Press http://highwire.stanford.edu/ http://highwire.stanford.edu/

28. Doug Brutlag 2011 Advanced Search http://highwire.stanford.edu/cgi/search? http://highwire.stanford.edu/cgi/search?

29. Doug Brutlag 2011 Advanced Search http://highwire.stanford.edu/cgi/search? http://highwire.stanford.edu/cgi/search?

30. Doug Brutlag 2011 Citation Map http://highwire.stanford.edu/cgi/search? http://highwire.stanford.edu/cgi/search?

31. Doug Brutlag 2011 Stanford University Libraries http://library.stanford.edu/ http://library.stanford.edu/ SearchWorks http://searchworks.stanford.edu / Databases http://library.stanford.edu/catdb/alldata.html E-Journals http://www.tdnet.com/stanford/ HighWire Press http://highwire.stanford.edu/ Access from off-campus via proxy server http://library.stanford.edu/apcproxy/

32. Doug Brutlag 2011 Searchworks http://searchworks.stanford.edu/ http://searchworks.stanford.edu/

33. Doug Brutlag 2011 Searchworks http://searchworks.stanford.edu/ http://searchworks.stanford.edu/

34. Doug Brutlag 2011 Lane Library Services http://lane.stanford.edu/ http://lane.stanford.edu/ PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed Lane http://lane.stanford.edu/ http://lane.stanford.edu/ Ovid Lane Catalog Su-Catalog E-journals PubMed MDConsult Skolar E-Journals http://lane.stanford.edu/reference/indexej.html

35. Doug Brutlag 2011 Lane Library

36. Doug Brutlag 2011 BioResearch Portal

37. Doug Brutlag 2011 Brutlag BioPortal Search

38. Doug Brutlag 2011 EndNote http://www.endnote.com/ http://www.endnote.com/ Personal Bibliographic Database Imports from hundreds of reference formats Saves MeSH Terms and URLs of References Powerful Search and Sort Methods Connects directly to PubMed, Biosis and other sources Integrates directly with Word Automatically formats bibliographies and footnotes Formats citations & references for hundreds of journals Complete user control of formatting