doug brutlag 2011 bibliographic search doug brutlag professor emeritus of biochemistry
TRANSCRIPT
![Page 1: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/1.jpg)
Doug Brutlag 2011
Bibliographic Searchhttp://biochem158.stanford.edu/
Doug BrutlagProfessor Emeritus of Biochemistry & Medicine
Stanford University School of Medicine
Genomics, Bioinformatics & Medicinehttp://biochem158.stanford.edu/
![Page 2: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/2.jpg)
Doug Brutlag 2011
• Google Scholarhttp://scholar.google.com/
• NLM Medlinehttp://www.nlm.nih.gov/pubs/factsheets/medline.html
• PubMedhttp://pubmed.gov/
• PubMed Centralhttp://www.ncbi.nlm.nih.gov/pmc/
• Stanford University Libraryhttp://searchworks.stanford.edu/
• HighWire Presshttp://highwire.stanford.edu/
• Lane Library - Ovid -Biosis - E Journals - SciSearchhttp://lane.stanford.edu/
• EndNotehttp://www.endnote.com/
Access to Biological Literature
![Page 3: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/3.jpg)
Doug Brutlag 2011
Google Scholarhttp://scholar.google.com/
![Page 4: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/4.jpg)
Doug Brutlag 2011
About Google Scholarhttp://scholar.google.com/intl/en/scholar/about.html
![Page 5: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/5.jpg)
Doug Brutlag 2011
Google Scholar Search http://scholar.google.com/
![Page 6: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/6.jpg)
Doug Brutlag 2011
Google Scholar Preferenceshttp://scholar.google.com/
![Page 7: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/7.jpg)
Doug Brutlag 2011
Advanced Scholar Search http://scholar.google.com/
![Page 8: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/8.jpg)
Doug Brutlag 2011
PubMedhttp://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 Pro
viders– APC Proxy access to Stanford Publicatio
ns• ENTREZ: Abstract Neighboring• MyNCBI: Query Storage and Current Aware
ness
![Page 9: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/9.jpg)
Doug Brutlag 2011
PubMed/Entrez Databaseshttp://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi
![Page 10: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/10.jpg)
Doug Brutlag 2011
Medline Sample Record http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
UI 98408838AU Tao X, Dafu DTI Relationship between synonymous codon
usage and protein structure.MH Codon*MH Protein Folding* MH Protein Structure, Secondary*MH Proteins/genetics …...AB The hypothesis that synonymous codon usage
is related to protein three-dimensional structure is examined by …
PT Journal articleSO FEBS Lett 1998 Aug 28: 434 (1-2) : 93-6
![Page 11: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/11.jpg)
Doug Brutlag 2011
Medline Fieldshttp://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]
![Page 12: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/12.jpg)
Doug Brutlag 2011
PubMed Text Search
![Page 13: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/13.jpg)
Doug Brutlag 2011
PubMed Author Search
![Page 14: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/14.jpg)
Doug Brutlag 2011
MeSH Contains26,142 Thesaurus Terms & 177,000 Entry Terms
Average 10-15 per article3-4 as major points of article = * in PubMedMost specific MeSH assigned for each concept199,000 Supplementary Concept Terms
Subheadings88 Qualifiers used with the ~25,600 MeSH
termsSubheadings focus on sub-aspects of MeSH
term (e.g., Hemoglobins - chemistry, Disease -
diagnosis, Disease - Therapy, etc.)
MeSH Databasehttp://www.nlm.nih.gov/pubs/factsheets/mesh.html
![Page 15: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/15.jpg)
Doug Brutlag 2011
MeSH Search forNext-Generation DNA Sequencing
![Page 16: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/16.jpg)
Doug Brutlag 2011
MeSH Search forNext-Generation DNA Sequencing
![Page 17: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/17.jpg)
Doug Brutlag 2011
MeSH Search forNext-Generation DNA Sequencing
![Page 18: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/18.jpg)
Doug Brutlag 2011
MeSH Search forNext-Generation DNA Sequencing
![Page 19: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/19.jpg)
Doug Brutlag 2011
MeSH Search forNext-Generation DNA Sequencing
![Page 20: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/20.jpg)
Doug Brutlag 2011
MeSH Search forNext-Generation DNA Sequencing
![Page 21: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/21.jpg)
Doug Brutlag 2011
MeSH Search forNext-Generation DNA Sequencing
![Page 22: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/22.jpg)
Doug Brutlag 2011
Advantages of using MeSH Terms 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
![Page 23: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/23.jpg)
Doug Brutlag 2011
Disadvantages of MeSHhttp://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
![Page 24: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/24.jpg)
Doug Brutlag 2011
Current Awareness
• HighWire Press Table of Contents & Notificationhttp://highwire.stanford.edu/
• Current Awareness with MyNCBIhttp://www.cdlib.org/guides/pubmed/currentawareness.rtf
• MyNCBI: PubMed Saved Searches http://www.ncbi.nlm.nih.gov/sites/myncbi/
![Page 25: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/25.jpg)
Doug Brutlag 2011
MyNCBI
![Page 26: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/26.jpg)
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
![Page 27: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/27.jpg)
Doug Brutlag 2011
HighWire Presshttp://highwire.stanford.edu/
![Page 28: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/28.jpg)
Doug Brutlag 2011
Advanced Searchhttp://highwire.stanford.edu/cgi/search?
![Page 29: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/29.jpg)
Doug Brutlag 2011
Advanced Searchhttp://highwire.stanford.edu/cgi/search?
![Page 30: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/30.jpg)
Doug Brutlag 2011
Citation Maphttp://highwire.stanford.edu/cgi/search?
![Page 31: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/31.jpg)
Doug Brutlag 2011
Stanford University Librarieshttp://library.stanford.edu/
• SearchWorkshttp://searchworks.stanford.edu/
• Databaseshttp://library.stanford.edu/catdb/alldata.html
• E-Journalshttp://www.tdnet.com/stanford/
• HighWire Presshttp://highwire.stanford.edu/
• Access from off-campus via proxy serverhttp://library.stanford.edu/apcproxy/
![Page 32: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/32.jpg)
Doug Brutlag 2011
Searchworkshttp://searchworks.stanford.edu/
![Page 33: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/33.jpg)
Doug Brutlag 2011
Searchworkshttp://searchworks.stanford.edu/
![Page 34: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/34.jpg)
Doug Brutlag 2011
Lane Library Serviceshttp://lane.stanford.edu/
• PubMedhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
• Lanehttp://lane.stanford.edu/OvidLane CatalogSu-CatalogE-journalsPubMedMDConsultSkolar
• E-Journalshttp://lane.stanford.edu/reference/indexej.html
![Page 35: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/35.jpg)
Doug Brutlag 2011
Lane Library
![Page 36: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/36.jpg)
Doug Brutlag 2011
BioResearch Portal
![Page 37: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/37.jpg)
Doug Brutlag 2011
Brutlag BioPortal Search
![Page 38: Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry](https://reader035.vdocuments.mx/reader035/viewer/2022062321/56649ebf5503460f94bc983c/html5/thumbnails/38.jpg)
Doug Brutlag 2011
EndNote 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