PubMed User's Manual

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A User’s Manual for PubMed
Martin Wall | Eng 518-001 | Spring 2014 |Stan Dicks

A User’s Manual for PubMed 2014
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Table of Contents
SectionI.
Introduction………………………………………………………………………………….p.3
SectionII.
Using the Search Engine………………………………………………………………..p.3
SectionIII.
Using Filters………………………………………………………………………………….p.5
SectionIV.
AdvancedSearchFeatures…………………………………………………………….p.11
SectionV.
Tools and Resources………………………………………………………………………p.32
SectionVI.
Contacting Support………………………………………………………………………..p.40

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SectionI. Introduction
About PubMed
PubMedisa resource thatwas createdbythe National CenterforBiotechnologyInformation(NCBI),itself adivisionof
the National Institutesof Health(NIH). Thisresource wascreatedforthe purpose of providinganeasily-accessible and
comprehensive onlineversionof the National Libraryof Medicine’s(NLM) contents.Over23millionarticlesrelatingto
clinical research,medicalscience andrelatedtopicscanbe searchedthroughthe system.
SectionII. Usingthe Search Engine
Whentypingthe topicof yoursearch intothe navigationbar,be sure to make the descriptionasspecificaspossible,
withoutusinglarge operators,punctuationsorexcessive spaces.Quotationmarks,aswell asusing“and”clarifications,
despite beingnecessarytogettingcorrectsearchresultsincomparable systems,are notneeded.

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For example,the searchbelowfindsanarticle pertainingonlytothe effectivenessof RecombinantHumanGrowth
Hormone (rhGH) in cysticfibrosispatientsbylookingfor“cysticfibrosisrhGH,”ratherthan[cysticfibrosisANDrhGH] or
[“cysticfibrosisrhGH”]
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If you wishtosearch for an article by the Author,putthe lastname followedbythe initialsof the firstinitial orfirstand
middle initial.

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If you wantto create a searchthat includesboththe authorand the subjectof theirarticle,type inthe subjectfirst,
followedbythe authorname.Asmentionedabove,nopunctuationorcapitalizationisnecessaryinyoursearch.
SectionIII: Using Filters
FiltersTab
You can narrow yoursearch criteriadownbyselectinghow youwanttofilterthe results.Forexample,the initial search
for the topicof “Lung Cancer”yieldsover200,000 results:

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But by selectingthe filterof “Clinical Trial”under“Article Types”we candramaticallyreduce thatfigure toonlythe
relevantClinical Trial articleswrittenonthe topic.
By clickingonthe “More” tab, youcan viewthe full range of optionsavailable toFilterby:

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Thiswill allowyoutoscroll throughall of the numerouscriteria under“Article Type”thancan be usedto narrowdowna
clinical trial search.
Under the “PublicationDates”section,inadditiontothe baseline optionsof filteringdown toonlyarticlesthatwere
writteninthe past5 or 10 years,youcan select“CustomRange.”Clickonthisoption.

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Thiswill bringupa seriesof data fieldsinwhichyoucanentera range of datesto searchfor an article withinaspecific
timeframe.

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If you wish to remove all of the filters that you have put into place for a search, click on the “Clear All” button.
Your original searchresultswillnowbe restored.

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Additional Filters
If you wishtonarrow downthe resultsof yoursearch to a smallerlistbylimitingthe criteriathatwill turnup,clickon
the sidebaronthe topleftcornerof the Searchscreen.
Clickon eachof the criteriathatmatch the articlesthatyouwouldlike includedinyoursearchresults.

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SectionIV. Advanced Search Features
Clickon the “Advanced”optionbeneaththe mainSearchnavigationbar.
Thiswill openupthe PubMedAdvcancedSearchBuilder.Youcanuse thisscreento enterincustomizedsearchcriteria.

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You can use the dropdownmenuonthe far right side of the screento modifythe wayinwhichmultiplesearchfields
interactwitheachother.Searching“AND”as selectedbelow will require anysearchitemtoinclude the contentsof both
fields. The example belowwillsearchonlyforarticlesthatinvolve both“lungcancer”and“small cell.”
The final resultof the criteriaandthe relationshipbetweentermswill be displayed

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The final resultof the AdvancedSearchwill alsodisplayonthe SearchResultspage once youhave initiatedyournew
search.
Returningtothe AdvancedSearchpage,youcan also addor subtract search termswiththe “-” and “+” buttonsthatwill
appearto the right of the bottomsearchfield.

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If you wishtoadd your AdvancedSearchresultsto yourHistory, clickthe button“Addto history”to the leftof the
Searchbutton.
The search resultsthatyouhave addedwill nowdisplayatthe bottomof the page underthe “History”header,along
withanypast search resultsthatyouhave savedhere.

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Saving Search Results
Clickon the “Save search”optionbeneaththe mainSearchnavigationbar.
PubMedwill autopopulate the textbarwithyourlastsearch.If you wishtosave the subjectwithoutanymodifications,
simplyclickthe “Save”button.

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Thiswill take youto the confirmationscreen.Thisscreenispurelytoshow thatyour resultsare saved,itdoesnot
require anyfurtheraction. Youmay viewall of yoursavedsearchesfromthisscreenbyclickingonthe “manage saved
Searches”buttonat the bottomright cornerof thispage.
On the “SavedSearches”screen,youmayre-searchforany previousentrybyclickingonthe searchwordunderthe
“Name”column.

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If you wishtoedityour listof SavedSearches,youmayselectone orall of the rowsand clickthe “Delete”buttonto
remove termsthatare no longerneededfromthe list.
UsingMeSH
MeSH isa specializedseriesof vocabularytermsdesignedtomake searchingforarticlesinPubMedmore convenient.
Whenyouenteran article (the article belowisthe entryfor“gastritis”),the bottomof the page demonstratesthe
hierarchyof topicsthat leadfromthe mainsectiondownto the individual topic.

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Clickon one of the stagesof the hierarchyto view whatMeSHtermscomprise itssubcategories.Inthiscase,clickon
“stomach diseases.”
Thisscreenillustratesall of the relatedMeSHtermsthatyoucan search by.Clickon the termsthat youwishto include
inyour searchand thenclickon “Addto Search Builder”toaddthe MeSH termsto the box onthe topright of the
screen.

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You will thenclickon“SearchPubMed”to initate asearch that includesthe new MeSHterms.
The newresultswill display,alongwiththe drawn-outversionof the searchcriteriathatyouhave entered.
Whenyousearch usingMeSH,PubMedwill use thishierarchytonarrow downyour searchto articlesthatare relevant
to the specificsectionthatyoudescribe,allowingyoutoavoidthe legworkof sortingthroughirrelevantarticlesthat
have onlya tangential relationshiptothe topicthatyou are searchingfor.

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Sharing Your Search Results
Clickon the “Sendto:” dropdownmenuatthe top of the SearchResultsscreen todisplaythe differentDestination
options.
Selectthe “File”option,Pubmedtobegindownloadingyoursearchresults.The defaultsettingwillattempttodownload
all of the searchresultsthathave beenturnedup,whichisnot recommendedforlargerresultsdue tolimitedcomputer
storage space.

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The secondoption (whichalsoexistsacrossall of the subsequentDestinationcategories) istoselectthe filesthatyou
wouldlike todownloadbyclickingonthe boxesonthe leftside of the searchresultsscreen.
Selectingthe “Collections”optionwill allowyoutoaddarticlesto“My Collections”(see SectionV.formore information
on using“My Collections.”) The firstoptionistodownloadall of the searchresults.

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You will have tosignintoyourNCBI account,if you have notdone so already,to access My Collections.
Thiswill bringtoa screenthatwill askyouto choose whetheryouwishto“Create a new collection”or“Appendtoan
existingcollection.”The “MyCollections”feature isexploredinmore depthlateron.

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The numberresultsthathave beenpostedtoMy Collectionswill appearatthe topof the searchscreennowthat you
have completedthisaction.
The “Order Article”tabwill sendyoutoPubMed’sLoansome Docservice,whichwill allow youtosigninandpurchase
individualarticlesfrompublicationsthatyoudonot have the subscriptionfor.

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Once you have createda profile andsetupyour paymentinformationonLoansome Doc,youwill signinwithyour
Username andPasswordat thisscreen.
The “CitationManager” option will allow youtoselecthow manyarticlesyouwishtoaddto a file thatwill listall of the
articlesina citationformat.Thistool isuseful increatinga Bibliographybecause itputsall of the articles’relevant
informationregardingtheirauthor, yearpublished,etc.inone place.Thisfile will,however,require outside softwareto
operate.ContactHelpif youdo not knowwhattypesof programs youwill needtoinstall inordertodisplaythe
citations.

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The “Clipboard”optionwill allowyoutodownloaditemstothe PubMedclipboard(which,itshouldbe noted,isdistinct
fromyour computer’sCopy/Cut/Paste clipboard). Byclickingon“AddtoClipboard”youwill addeitherthe articlesthat
youselectbycheckingthe boxesorthe first500 itemsin yoursearch to the Clipboard.
The numberof itemssavedtoClipboardwillnow displayonthe SearchResults.

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Clickon the numberof itemstothe right of the “Clipboard”button atthe top rightof the screento accessthe itemsthat
youhave saved usingthisfeature.
Thiswill take youto the screenthat containsall of yourClipboardsavedresults.These resultswill onlyremainin
Clipboardfor8 hours before beingautomaticallydeletedbyPubMedtoconserve datastorage space.

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If you wouldlike toeditthe contentsof Clipboard,thereare several methodsof makingchangestoit. If youwishto
change the order inwhichyourselectionsappear,clickon“DisplaySetting”atthe top leftof the screen.
You can change the Format of the display,the numberof articlesthatwill displayperpage and whatcriteriawill be used
to determine the orderof the articles.

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Clickon the itemsthatyouwishto delete byclickingonthe boxesandthenclickon“Remove selecteditems.”
You will be askedtoconfirmthe deletionof yourselections.Click“OK.”

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The numberof deletedselectionswill nowappearatthe top of the page.
The “Email” optionwill sendyourselectionstoanemail addressof yourchoice.Once youchoose the option,a number
of fieldswill appearthatwill allowyoutochoose the Format,Order,Number,etc.of the articlesthatyouwishto send
withthismethod.

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The top of the screenwill nowdisplayamessage indicatingthatyouremail hasbeen
The final Destinationoptionistoadd yoursearchresultsto “My Bibliography.”

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Your selectionswill be notedasbeingsavedto“MyBibliography”atthe top of the Search Resultsscreen.
Article Versions
Some articleslistedonPubMeddonotallowyou to accesstheirfull textwithoutasubscriptiontothe journal orother
type of resource whichtheybelongto.If youwishto see if yourorganizationalreadyhasa subscriptionthatyoucanuse,
clickon the article and thengointothe linkbuttonprovidedinthe topleft-handcorner.

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If you onlyneedasingle article andeitherdonothave a subscription(individualororganization-wide) ordonot wishto
pay the resource’ssubscriptionfee,youmaypurchase accessto individual PubMedarticlesthroughLoansomeoc™,
PubMed’s resource forpurchasingsingle articlesfromperiodicals/journalsthatrequire subscriptions
SectionIV. Tools and Resources
UsingMyNCBI
You can use PubMedto access the MyNCBI desktop,aresource available toall NCBIresource services.Clickonthe
“MyNCBI” buttonoff of the PubMedsearchbar.

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From the MyNCBIdesktop,youcan performa numberof tasks.“SearchNCBI databases”will allow youtosearch
PubMedand otherNCBIresources.“RecentActivity”tellsyouwhatyourrecentsearchesandcross-navigationshave
beenandyou mayrevisitanyof those by clickingontheminthe task pane.“SavedSearches”performsthe same
functionasthe above-mentionedsection,allowingyoutorevisitany pastsearchtopic.The sectioncontaining “My
Bibliography,”isexplained atlengthbelow.
My Bibliography
Clickon the “Manage My Bibliography”button.

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Thispage allowsyoutosave articlestoa Bibliographyforlaterreference. Clickonthe “AddCitation”buttontocreate
your firstreference.
Choose PubMedfromthe listof optionsonthe drop-downbarand click“Go to PubMed.”

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Thiswill take youto the PubMedsearchpage.Once youhave searchedforyour selection,clickonthe “Sendto”button.
UsingPubMedCommons
At the openingscreen,youwillsee awindowonthe leftside thatleadstothe PubMedCommonsresource.Clickonitto
enter.

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Thisresource will allowyoutoviewthe CommentsthatotherPubMedusershave made thatcomplement,contradictor
fill inthe gapsto the informationthatisprovidedintheiradjoiningarticle. Thisaspectof PubMedisstill initsPilotphase
as of this publication,withjustover1000 of PubMed’sarticleshavingCommentsadded.However,Commonscan
neverthelessprovidekeyinsightsandimportantsupplementaldatatousers’knowledge.
Start by searchingthe name of the Commentauthorthat youwant to locate.

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Thiswill take youto a listof search resultsthatmatch that Author. Onlythe commentsandthe title of the article will be
visible onthisscreen,however….
...youcan viewthe original article byclickingonsaidtitle.

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You can alsolinkback to the original article byclickingthe “Permalink”buttononthe bottomleftof anindividualsearch
result.

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Thislink,unlike the titlelink,willtake youimmediatelytothe bottomof the original article inordertoallowyoutose e
the commentinthe initial context.
Lastly,if youwouldlike toshare a Commentthatyou have discoveredinCommons,clickonthe “Share”buttonbelow.

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You will nowhave the optionof transmittingyourselectedCommentsviaFacebook,TwitterorGoogle +. You may also
copy andpaste the URL to enterintoyour navigationbaror create a hyperlinkwith.
SectionVI. Contacting Support
Everysectionof PubMedcontainsa linkat the bottomof the screenthatallowsyouto reachthe PubMedHelpDesk.
Clickon thislinktocontact themwithanyquestions/problems.

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Fill outthe subjectfields,describingyourprobleminasmuch detail aspossible.Please ensure thatyouinclude your
email addresstoreceive aresponse.

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