Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University School of Medicine Genomics, Bioinformatics & Medicine

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Doug Brutlag 2011 PubMed Medical literature (Medline) since 1950 Abstracts since 1975 Molecular biology since ,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

Doug Brutlag 2011 PubMed/Entrez Databases

Doug Brutlag 2011 Medline Sample Record UI 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

Doug Brutlag 2011 Medline Fields 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]

Doug Brutlag 2011 PubMed Text Search

Doug Brutlag 2011 PubMed Author Search

Doug Brutlag 2011 MeSH Contains 26,142 Thesaurus Terms & 177,000 Entry Terms Average 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

Doug Brutlag 2011 MeSH Search for Next-Generation DNA Sequencing

Doug Brutlag 2011 MeSH Search for Next-Generation DNA Sequencing

Doug Brutlag 2011 MeSH Search for Next-Generation DNA Sequencing

Doug Brutlag 2011 MeSH Search for Next-Generation DNA Sequencing

Doug Brutlag 2011 MeSH Search for Next-Generation DNA Sequencing

Doug Brutlag 2011 MeSH Search for Next-Generation DNA Sequencing

Doug Brutlag 2011 MeSH Search for Next-Generation DNA Sequencing

Doug Brutlag 2011 Advantages of using MeSH Terms 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

Doug Brutlag 2011 Disadvantages of MeSH Thesaurus terms may not cover all concepts, especially new concepts and jargon Not every concept in abstract or article can get thesaurus terms

Doug Brutlag 2011 Current Awareness HighWire Press Table of Contents & Notification Current Awareness with MyNCBI MyNCBI: PubMed Saved Searches

Doug Brutlag 2011 MyNCBI

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

Doug Brutlag 2011 HighWire Press

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Doug Brutlag 2011 Stanford University Libraries SearchWorks / Databases E-Journals HighWire Press Access from off-campus via proxy server

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Doug Brutlag 2011 Lane Library Services PubMed Lane Ovid Lane Catalog Su-Catalog E-journals PubMed MDConsult Skolar E-Journals

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Doug Brutlag 2011 EndNote 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