Introduction to Introduction to PubmedPubmed

Gail P. Taylor, Ph.D.Gail P. Taylor, Ph.D.

UT San AntonioUT San Antonio

MBRS-RISE and MARC-U*STAR MBRS-RISE and MARC-U*STAR Research Training ProgramsResearch Training Programs

3/20063/200602/22/2008

Supplemental Materials:Supplemental Materials:

► Help File from Pubmed:Help File from Pubmed: http://www.ncbi.nlm.nih.gov/entrez/query/static/help/http://www.ncbi.nlm.nih.gov/entrez/query/static/help/

pmhelp.html#Indexpmhelp.html#Index

► Dalhousie Library Pubmed Tutorial:Dalhousie Library Pubmed Tutorial: http://www.library.dal.ca/kellogg/guides/pubmed/INTROFRM.HTMhttp://www.library.dal.ca/kellogg/guides/pubmed/INTROFRM.HTM

What is a Scientific Paper?What is a Scientific Paper? ► Culmination of scientific Culmination of scientific

researchresearch► Report of Report of originaloriginal scientific scientific

findingsfindings► Published in Published in scientific scientific

journaljournal► ReviewedReviewed by peers by peers► Widely availableWidely available► Forms foundation for your Forms foundation for your

research!research!

Each Paper can be Identified as Each Paper can be Identified as a “Reference”a “Reference”

►Taylor, G. P., Anderson, R. A., Reginelli, A . Taylor, G. P., Anderson, R. A., Reginelli, A . D. and Muneoka, K. (1994). FGF-2 induces D. and Muneoka, K. (1994). FGF-2 induces regeneration of the Chick limb bud. Dev. regeneration of the Chick limb bud. Dev.

Biol, 163(1), 282-284 .Biol, 163(1), 282-284 . ►Authors, Date, Title, Journal, Volume(issue), Authors, Date, Title, Journal, Volume(issue),

pages…pages…

CitationsCitations

►Within any scientific paper, other Within any scientific paper, other papers are cited (also can say papers are cited (also can say “referenced”)“referenced”)

►Gives credit for findings, ideasGives credit for findings, ideas►More citations = more impact on fieldMore citations = more impact on field►Listed in references at end of paperListed in references at end of paper

Why Do I want to Find References?Why Do I want to Find References?

►Record of what is current in fieldRecord of what is current in field►Record of important “foundation” papersRecord of important “foundation” papers►Helps you to get overview of fieldHelps you to get overview of field►Tells you what articles to downloadTells you what articles to download►Can save in reference manager and link to Can save in reference manager and link to

actual pdf files of the original article that actual pdf files of the original article that you’ve foundyou’ve found

►Can automatically insert ref into thesisCan automatically insert ref into thesis

Historically: Pre-ComputerHistorically: Pre-Computer

► Biological Abstracts: Monthly publication of Biological Abstracts: Monthly publication of large, Indexed, books of abstracts:large, Indexed, books of abstracts: http://www.biosis.org/products/ba/

► Science Citation Index: Who referenced Science Citation Index: Who referenced what paper, through time…what paper, through time… http://www.isinet.com/products/citation/sci/

► Subscribe to the JournalSubscribe to the Journal► Go to Library that owns journal and xeroxGo to Library that owns journal and xerox► Reprint requestReprint request► Interlibrary loanInterlibrary loan

Medline Medline ► Computerized databaseComputerized database► Over 12 million article referencesOver 12 million article references

4300 biomedical journals and magazines4300 biomedical journals and magazines From over 70 countriesFrom over 70 countries

► Maintained by National Library of Medicine at Maintained by National Library of Medicine at the NIHthe NIH

► Can search for references to journal articles Can search for references to journal articles by using:by using: Text wordsText words Medical Subject Headings (MeSH); Medical Subject Headings (MeSH);

keywords assigned by NLMkeywords assigned by NLM Both…Both…

► Commonly Commonly covers 1966 - the presentcovers 1966 - the present

What is a What is a Medline Medline Record?Record?

Looking Closer…Looking Closer…

► UI - Unique identifier - Medline numberUI - Unique identifier - Medline number► TI - TitleTI - Title► PG - PagesPG - Pages► AB - AbstractAB - Abstract

Can search any of these fields….

Another Close Look…Another Close Look…

► AU, FAU - AuthorAU, FAU - Author► PT - Journal ArticlePT - Journal Article► CY - CountryCY - Country► TA - JournalTA - Journal► CIN - Complete ref.CIN - Complete ref.► MH - Mesh MH - Mesh

HeadingsHeadings► For Organizing…For Organizing…

MeSH Headings (MH)MeSH Headings (MH)

► Sorting by contentSorting by content► Like the “keywords” Like the “keywords”

associated with an associated with an articlearticle

► Large “filing cabinet”Large “filing cabinet” Choose correct Choose correct

heading, get whole heading, get whole folder dumped into folder dumped into your search…your search…

Topic: Fibroblast Growth Factors

How to Access Medline and Get How to Access Medline and Get Records?Records?

Devise smart computer programs to Devise smart computer programs to search the different fields and mine the search the different fields and mine the Medline database for information…Medline database for information…

How to Access Medline?How to Access Medline?► Privately licensed search programs:Privately licensed search programs:

OvidOvid► UT System buysUT System buys► Access through library ResourcesAccess through library Resources

► For free, over the Internet:For free, over the Internet: PubMed - http://pubmed.govPubMed - http://pubmed.gov

PubmedPubmed

PubmedPubmed

NLM GatewayNLM Gateway

PubmedPubmed

PubmedPubmed

General SearchGeneral Search

Linking PossibilitiesLinking Possibilities

Linking PossibilitiesLinking Possibilities

► Not even an abstractNot even an abstract

► Abstract and sometimes more Abstract and sometimes more (Texas might have subscription)(Texas might have subscription)

► Online AccessOnline Access

► Online + Free on Pubmed CentralOnline + Free on Pubmed Central

Up close…Up close…

► The link is to Blackwell-Synergy OnlineThe link is to Blackwell-Synergy Online► We do not have a subscription…but they We do not have a subscription…but they

DO give more details on the article.DO give more details on the article.

This Article is Available!This Article is Available!

Adding in Boolean LogicAdding in Boolean Logic

► AND – Need to AND – Need to have both wordshave both words

► OR – Need either OR – Need either wordword

► NOT – Cannot NOT – Cannot contain following contain following wordword

Author Search….Author Search….

►http://www.nlm.nih.gov/bsd/viewlet/search/author/author.html

►http://www.nlm.nih.gov/bsd/viewlet/search/autsub/author_and_subject.html

►Can write whole nameCan write whole name►Can go with last name, followed by initialCan go with last name, followed by initial

Taylor g (will get all)Taylor g (will get all) Taylor GP (will get all GP Taylors….Taylor GP (will get all GP Taylors….

PubmedPubmed

Mesh SearchMesh Search

http://www.nlm.nih.gov/bsd/viewlet/mesh/searching/mesh1.html

Looking at the Tabs…Looking at the Tabs…

Check out the new Limit Tab…Check out the new Limit Tab…

Field Limits…look familiar?Field Limits…look familiar?

Choose between text or MESH searching…or Keep both!

Limited SearchLimited Search

The Preview/Index TabThe Preview/Index Tab

► Small summary of ResultsSmall summary of Results► Shows the total number of references Shows the total number of references

that you’ve gotten…that you’ve gotten…► Here, can also add conditions to your Here, can also add conditions to your

search…search…

How to Further Limit…How to Further Limit…

History - What have we done?History - What have we done?

► Shows searches you have done…Shows searches you have done…► Can also type at top of page and do come refining to Can also type at top of page and do come refining to

most recent search…most recent search…

Details - Search StrategyDetails - Search Strategy

Can see Can see that some that some words were words were from the from the MeSH, MeSH, some were some were text words, text words, the Lang the Lang limitation, limitation, publish publish date, etc….date, etc….

Getting what you ask for…Getting what you ask for…

► Why is this happening?Why is this happening?► Shouldn’t you get the same number for bubonic Shouldn’t you get the same number for bubonic

and bubonic plague???and bubonic plague???

Plague Solutions…Plague Solutions…► No…remember the MeSH, as well as the fact No…remember the MeSH, as well as the fact

that some references don’t have abstracts…that some references don’t have abstracts…► To look, bring the search to the top.To look, bring the search to the top.► Go to “Details” to figure things out…Go to “Details” to figure things out…

What do I do with Them?What do I do with Them?

► Save your refs as a text file from your browserSave your refs as a text file from your browser► Save your refs as a file directly on your computerSave your refs as a file directly on your computer

Good when you have a whole list of themGood when you have a whole list of them Display them as Medline, then saveDisplay them as Medline, then save Import them into Endnote…Import them into Endnote…

► Save up to 100, making a personal compilation of Save up to 100, making a personal compilation of desired files, for later download/text/ordering..desired files, for later download/text/ordering..

► Order: Loansome doc allows you to buy a copy of Order: Loansome doc allows you to buy a copy of the reference…the reference…

Indirect way of Accessing Indirect way of Accessing Journals:Journals:

► Science Direct: Science Direct: http://www.sciencedirect.com/science/journals - - HUGE HUGE assortment of 1700 scientific journals. Began with Elsevier assortment of 1700 scientific journals. Began with Elsevier (huge publisher) and has expanded. Try here first.(huge publisher) and has expanded. Try here first.

► Wiley Interscience: Wiley Interscience: http://www3.interscience.wiley.com/cgi-bin/browsepj

► Springer Link: Springer Link: http://link.springer-ny.com/forum.htm► Nature Online: http://www.nature.com/nature/ - Nature Online: http://www.nature.com/nature/ - The entire The entire

Nature family of journals.Nature family of journals.► American Chemical Society Web Editions (Online American Chemical Society Web Editions (Online

Journals): http://pubs.acs.org/about.html - Journals): http://pubs.acs.org/about.html - Journals Journals published by the American Chemical Societypublished by the American Chemical Society   

Other Other DatabasesDatabases

► Many are accessible through UTSA’s Library http://www.lib.utsa.edu/Databases/List/OnALPHA.html

► Bioengineering and Biotechnology Database: Illumina (library owns) http://oh1.csa.com/ids70/advanced_search.php?

SID=f6ce4d7ae9d1e2ba64a18f571a5bca61► American Institute of Physics Journals:

http://www.aip.org/ojs/service.html► Applied Science and Technology: Wilsonweb

http://vnweb.hwwilsonweb.com/hww/shared/shared_main.jhtml;jsessionid=HMKMJJJVBM5JVQA3DIMCFGOADUNGIIV0?_requestid=40909

► Engineering Village II (contains Compendex) http://www.engineeringvillage2.org/controller/servlet/Controller?

CID=quickSearch&database=1► Wiley Interscience:

http://www3.interscience.wiley.com/cgi-bin/browsepj

Other Interesting ResourcesOther Interesting Resources

► Annual Reviews Online: Annual Reviews Online: http://www.annualreviews.org/search/search.asp - http://www.annualreviews.org/search/search.asp - Large, general Large, general review articles on particular topics. Look and see if there is one that interests review articles on particular topics. Look and see if there is one that interests you!you!

► Lexis/Nexis: http://web.lexis-nexis.com/universe Popular Press, Lexis/Nexis: http://web.lexis-nexis.com/universe Popular Press, Newspapers, government publications, biographies, transcripts Newspapers, government publications, biographies, transcripts of shows….of shows….