Doug Brutlag 2011 Bibliographic Search Doug Brutlag Professor Emeritus of Biochemistry.

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/

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

Doug Brutlag 2011

Google Scholarhttp://scholar.google.com/

Doug Brutlag 2011

About Google Scholarhttp://scholar.google.com/intl/en/scholar/about.html

Doug Brutlag 2011

Google Scholar Search http://scholar.google.com/

Doug Brutlag 2011

Google Scholar Preferenceshttp://scholar.google.com/

Doug Brutlag 2011

Advanced Scholar Search http://scholar.google.com/

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

Doug Brutlag 2011

PubMed/Entrez Databaseshttp://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi

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

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]

Doug Brutlag 2011

PubMed Text Search

Doug Brutlag 2011

PubMed Author Search

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

Doug Brutlag 2011

MeSH Search forNext-Generation DNA Sequencing

Doug Brutlag 2011

MeSH Search forNext-Generation DNA Sequencing

Doug Brutlag 2011

MeSH Search forNext-Generation DNA Sequencing

Doug Brutlag 2011

MeSH Search forNext-Generation DNA Sequencing

Doug Brutlag 2011

MeSH Search forNext-Generation DNA Sequencing

Doug Brutlag 2011

MeSH Search forNext-Generation DNA Sequencing

Doug Brutlag 2011

MeSH Search forNext-Generation DNA Sequencing

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

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

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/

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 Presshttp://highwire.stanford.edu/

Doug Brutlag 2011

Advanced Searchhttp://highwire.stanford.edu/cgi/search?

Doug Brutlag 2011

Advanced Searchhttp://highwire.stanford.edu/cgi/search?

Doug Brutlag 2011

Citation Maphttp://highwire.stanford.edu/cgi/search?

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/

Doug Brutlag 2011

Searchworkshttp://searchworks.stanford.edu/

Doug Brutlag 2011

Searchworkshttp://searchworks.stanford.edu/

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

Doug Brutlag 2011

Lane Library

Doug Brutlag 2011

BioResearch Portal

Doug Brutlag 2011

Brutlag BioPortal Search

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