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FORMATION ON :
PubMed Prepared by Diane Sauv, B. Sc., M. Bibl.April 20141
PUBMED Go to: sdis.inrs.caAt the left, click in: Bases de donnesIn the box Titre, write Pubmed and click on GoClick on Pubmed2
PUBMEDStarted in 1996 is covering over 23.6 million citations
Oldest citations in PubMed date in 1809
5 citations sources: free access to Medline, Pubmed, PubMed-in process, PubMed-as supplied by publisher and PubMed-OldMedline
Database of literature citations, primarily for articles from journals in the life sciences, but also for books and technical reports that are included in the NCBI bookshelf
Made 2.5 billion of searches for 2013 in Medline/Pubmed
Developed and maintained by the National Center for Biotechnology Information (NCBI), at the U.S. National Library of Medicine (NLM)
PUBMED : MEDLINEPrimary component of PubMed with more than 21 million citations
Subject scope of MEDLINE is medicine, nursing, dentistry, veterinary medicine, health care systems, and preclinical sciences
Since 2005, between 2,000-4,000 completed references with Medical Subject Headings are added each day Tuesday to Saturday
+735,000 citations indexed in 2013
Citations from 1946
PUBMED : MEDLINESmall number of newspapers, magazines, newsletters and 5,652 worldwide journal titles (November 2013)
Journals in 39 languages (60 languages for older journals)
Citations added from 2010-2012: about 93% are published in englishabout 84% have english abstracts written by authors of the articles
PUBMED : ADVANCED RESEARCH
PUBMED : SEARCH FIELDS
PUBMED : SEARCH FIELDS
PUBMED : DISPLAY FIELDS
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PUBMED : DISPLAY FIELDS
PUBMED : DISPLAY FIELDS
PUBMED : DISPLAY FIELDS
Enter the authors last name followed by a space, plus the first 2 initials of the given name without punctuation followed by a space and all suffixes at the end (e.g. Vollmer Charles Jr)
PubMed automatically truncates a search for an author's name, e.g., o'brien [au] = o'brien ma, o'brien kr, o'brien d o'brien j [au] = o'brien ja, o'brien jb, o'brien jc jr, o'brien j
To turn off this automatic truncation : enclose the authors name in double quotes and tag with [au] in brackets
PUBMED : AUTHOR
PUBMED : AUTHOR
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PUBMED : AUTHOR
Estimation of more than 2880 author nameshttp://www.ncbi.nlm.nih.gov/pubmed/2447625815
J. Virol. 2012, 86 (8) : 4380-43933
PUBMED : AUTHOR
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PUBMED : AUTHORFull author name may be searched for references published from 2002 forward if the full author name is available in the article
PUBMED : AUTHOR AFFILIATIONAuthor, Corporate Author, and Collaborator Affiliation Display Changes 2013 December 24Effective December 16, NLM now includes Author Affiliations for all Authors, Corporate Authors and Collaborators in PubMed if the data are supplied by publishers in their XML submissions for MEDLINE indexed journals
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PUBMED : JOURNAL
Enter the journal name or abbreviation
J. Virol. 2012, 86 (8) : 4380-4393
J. Virol. 2012, 86 (8) : 4380-4393
PUBMED : SELECTED TERMSLatent membrane protein 1LMP 1
Epstein-Barr virus
Apoptosis
B cellsABCDANDANDAND
J. Virol. 2012, 86 (8) : 4380-4393
PUBMED : ADVANCED RESEARCH
1234Make selection of desired expressions
PUBMED : HISTORY
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PUBMED : HISTORY
1 Clic the left button
PUBMED : HISTORY
PUBMED : HISTORYLatent membrane protein 1
Latent membrane proteins 1Latent membrane protein1Latent membrane proteins1No result
Latent membrane protein* AND 1
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PUBMED : ADVANCED RESEARCH
Come from: Show index listIf you choose this strategy, you will not have the MeSH
PUBMED : MeSH - MAIN HEADINGSMeSH : Medical Subject Headings
MeSH is the controlled vocabulary used for indexing articles for the MEDLINE subset of PubMed
Published since 1954
MeSH terms are arranged hierarchically (tree structure) by subject categories with more specific terms arranged beneath broader terms
It is updated weekly and reviewed annually
MeSH in english-french, english-swedish and english-spanish-portuguese: HTTP://mesh.inserm.fr
PUBMED : MeSH
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PUBMED : MeSH HEADINGSGive more complete results because you have no more problem of spelling variations, synonyms and near-synonyms
Give greater accuracy using the major descriptor ( MeSH major topic)
Permit to specify particular aspects of a descriptor in using subheadings
However, the references bearing the PubMed-in process and PubMed- as supplied by publisher or Pubmed status are not found because they have not yet or they will not received descriptors
However, if the research focuses on a new topic or subject very sharp, it could be that you dont find a MeSH or you find a too generic MeSH
PUBMED : MeSHThe MeSH types included:
Main Headings
Subheadings
Publication types
Geographics
Supplementary concept records34
PUBMED : MeSH - MAIN HEADINGSThe MeSH 2014 included 27 149 MeSH Headings in 16 categories:
PUBMED : MeSH - MAIN HEADINGS
11 MeSHMeSH Heading : Subject analysts examine each article and assign the most specific MeSH terms applicable, with a related subheading; typically 10 to 12 headings per citation[mh] or [MeSH]
PUBMED : MeSH
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PUBMED : MeSH
PUBMED : MeSH
PUBMED : MeSH - SUPPLEMENTARY CONCEPTS Formely called Supplementary chemical records
219,266 headings
Used to index chemicals, drugs and other concepts such rare diseases for Medline
Searched by Substance name [NM]
No tree numbers
Updated weekly
PUBMED : HISTORY
J. Virol. 2012, 86 (8) : 4380-4393
PUBMED : HISTORY
#6#7#9#8#4#543
PUBMED : HISTORY
Try: Epstein Barr viruses
PUBMED : MeSH
PUBMED : MeSH
PUBMED : MeSH - SUBHEADINGS
PUBMED : MeSH - SUBHEADINGS
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PUBMED : MeSH - SUBHEADINGS
PUBMED : MeSH - SUBHEADINGS
SubheadingsSubheadings : are used to help describe more completely a particular aspect of a subjectThe subheadings logically paired with the main heading2 letters may be used for subheadings
PUBMED : RESEARCH STRATEGY
Pathogenicity of Epstein-Barr virus= ( A AND B) OR CAPathogen*BEpstein-Barr virusEBVHerpesvirus 4, Human/PathogenicityC51
PUBMED : HISTORY
PUBMED : MeSH
PUBMED : MeSH - MAJOR TOPICS
MAJRMajor Topics : used [majr] to restrict a search to citations where the term is the major topic or focus of the article, in the display reference , its represented by an asterisk
PUBMED : MeSH
PUBMED : MeSH
Generic termsSpecific terms
PUBMED : MeSH - EXPLOSION
What you cannot see in Search details:The terms that are more specific under Herpesviridae in the MeSH they are also searched 57
PUBMED : MeSH - ENTRY TERMS
Many synonyms, near-synonyms, and closely related concepts are included as entry terms to help users find the most relevant MeSH descriptor for the concept they are seeking
J. Virol. 2012, 86 (8) : 4380-4393
PUBMED : HISTORY
Do we have to add cell death?
PUBMED : MeSH - ASSOCIATED TERMS
J. Virol. 2012, 86 (8) : 4380-4393
PUBMED : HISTORY
B cell
B cells
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PUBMED : HISTORY
The maximum number of searches available in History is 100History will be lost after 8 hours of inactivity64
Smallpox virushttp://www.flickr.com/photos/sanofi-pasteur/5280407684/in/photostream/
PUBMED : AUTOMATIC TERM MAPPINGUntagged terms that are entered in the search box are matched (in this order) against :MeSH translation tableJournals translation tableFull Author translation tableAuthor indexFull Investigator (Collaborator)translation tableInvestigator (Collaborator) index
PUBMED : AUTOMATIC TERM MAPPINGThe MeSH Translation Table contains:
MeSH TermsSee-reference mappings (also known as entry terms) for MeSH terms MeSH SubheadingsPublication TypesPharmacologic ActionsTerms derived from the Unified Medical Language System (UMLS) that have equivalent synonyms or lexical variants in EnglishSupplementary Concepts (chemical, protocol or disease terms) and their synonyms67
PUBMED : PUBLICATION TYPES
: 7368
PUBMED : PUBLICATION TYPES
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PUBMED : AUTOMATIC TERM MAPPINGWhen a match is found for a term or phrase in a translation table the mapping process is complete and does not continue on to the next translation table
When you enter your search terms as a phrase, PubMed will not perform automatic term mapping that includes the MeSH term and any specific terms indented under that term in the MeSH hierarchy
If no match is found, PubMed breaks apart the phrase and repeats the above automatic process untill a match is found. Pubmed ignores stopwords in searches
If there is no match, the individual terms will be combined with AND together and searched in all fields
PUBMED : STOPWORDS
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PUBMED : AUTOMATIC TERM MAPPING
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PUBMED : AUTOMATIC TERM MAPPINGTerms enclosed in double quotes will be searched in all fields and not processed using automatic term mapping"Herpesvirus 4, human"
Herpesvirus 4, human
Herpesvirus 4, human[MeSH Terms]
PUBMED : AUTOMATIC TERM MAPPINGTruncation, quotes, search tags turn off automatic term mapping and the process that includes the MeSH term and any specific terms indented under that term in the MeSH hierarchy
N.B. If a truncated term (e.g., tox* for toxic, toxicologic, toxicology, toxicological, toxicologist, toxicologists ) produces more than 600 variations, a warning message displays to lengthen the root word to search for all endings
Herpesvirus*
PUBMED : AUTOMATIC TERM MAPPINGTruncation turns off automatic term mapping and the process that includes the MeSH term and any specific terms indented under that term in the MeSH hierarchy
Herpesvirus
Herpesviruses75
PUBMED : RECIPE FOR AN OPTIMAL RESEARCHPut a word or phrase without quotes
Make a second search with the plural of the word or the phrase without quotes
Dont forget to also search with abbreviations
Use the Show search details for points 1-3 to correct the terms or expressions displayed within the Show search details
See if you can find a descriptor and if so, look in the MeSH database for additional information to modify the search
Put the phrase in double quotes or use the truncationPUBMED :
Pseudomonas aeruginosahttp://phil.cdc.gov/phil/home.asp77
PUBMED : TERM SUGGESTED
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PUBMED : AUTHOR KEYWORDSAuthor Keywords in PubMed (2013 February 07)PubMed now displays author keywords when supplied by publishers. NLM will not review author keywords for accuracy or add them to non-publisher supplied citations. Author keywords can be searched untagged or using the Other Term [OT] or Text Words [TW] tags
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PUBMED : DISPLAY SETTINGS
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PUBMED : DISPLAY SETTINGS - SUMMARY
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PUBMED : DISPLAY SETTINGS - SUMMARY
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PUBMED : DISPLAY SETTINGS - SUMMARY - TEXT
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PUBMED : DISPLAY SETTINGS - SUMMARY - TEXT
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PUBMED : DISPLAY SETTINGS - ABSTRACT
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PUBMED : DISPLAY SETTINGS - ABSTRACT
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PUBMED : DISPLAY SETTINGS - ABSTRACT
Structured abstract87
PUBMED : DISPLAY SETTINGS - STRUCTURED ABSTRACTFormats were developed in the late 1980s and early 1990s
To assist health professionals in selecting clinically relevant and methodologically valid journal articles
To guide authors in summarizing the content of their article
To facilitate the peer-review process
To enhance computerized literature searching
Standardized formats for structured abstracts have been defined for original research studies, review articles and clinical practice guidelines88
PUBMED : DISPLAY SETTINGS - ABSTRACT
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PUBMED : DISPLAY SETTINGS - ABSTRACT - TEXT
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PUBMED : DISPLAY SETTINGS - ABSTRACT - TEXT
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PUBMED : DISPLAY SETTINGS - ABSTRACT - TEXT
92Date createdOrganization that supplied citation dataModification dateIssue
PUBMED : DISPLAY SETTINGS - MEDLINE
Pubmed unique identifierStatus tagCompletion dateISSNVolumePublication dateAbstractFull author nameAffiliationLanguagePaginationTitlePii or doi that serves the role of paginationAuthorGrant numberDate created93
PUBMED : DISPLAY SETTINGS - MEDLINEPublication typePlace of publicationFull journal titleEnzyme Commission or Registry number of CASMeSH termsOther identification numbersMeSH datePublication history status datePublication statusDate of electronic publicationJournal title abbreviationNLM unique IDSubsetDate the citation was added to PubMedCreate dateArticle identifierSource94
PUBMED : DISPLAY SETTINGS - XML
Xml (ExTENSIBLE Markup Language) is generally used for displaying and manipulating data in software applications95PUBMED :
Bacillus anthracishttp://phil.cdc.gov/phil/home.asp96
PUBMED : STATUS TAGS
PUBMED : STATUS TAG - PUBMED - AS SUPPLIED BY PUBLISHER
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PUBMED : STATUS TAG - PUBMED - IN PROCESS
Citations bibliographic data will be reviewed and indexed
PUBMED : STATUS TAG - PUBMED - INDEXED FOR MEDLINE
Citations have been indexed with MeSH terms, Publication Type, Substance Names, etcBibliographic data has been reviewed
PUBMED : STATUS TAG - PUBMED - OLDMEDLINEOver 2 million OLDMEDLINE citations, most without abstractsCitations originally printed in hardcopy indexes published from 1946 throught 1965 that have not yet had all of their original subject terms mapped to current MeSHPartially MeSH indexed Bibliographic data has been reviewedBibliographic data has been reviewed
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PUBMED : STATUS TAG - PUBMED
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PUBMED : STATUS TAG - PUBMED-BOOKS & DOCUMENTS
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PUBMED : STATUS TAG - PUBMED
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PUBMED : SAVE SEARCH
PUBMED : SAVE SEARCH
PUBMED : SAVE SEARCH
PUBMED : SAVE SEARCH
PUBMED :
Influenza virushttp://www.flickr.com/photos/sanofi-pasteur/5280410308/in/photostream/109
PUBMED : SIGN IN TO NCBI
PUBMED : SIGN IN TO NCBI
If you have an accountIf you need an accountPUBMED : PASSWORD
Most common passwords of 2013
http://splashdata.com/press/worstpasswords2013.htmPASSWORD112
How to select your password? by Burin Gerek
Take care of the lenght A good password must have at least 8 characters
Choose well your words Avoid words that can be found in a dictionary, the names of dogs, cats of fish or dates birth, to use the same code for your login or password
No note on your keyboard Avoid putting your password on a post-it and attach it to the keyboard or on the screen, or worse to store it in a computer filePASSWORDTranslation of : http://www.symantec.com/region/fr/resources/mots_passe.html113PUBMED : PASSWORD
How to select your password? by Burin Gerek
Use exotic characters It must be composed of at least 3 differents types of characters among the 4 existing types of characters (uppercase, lowercase, numbers and special characters) *
Choose a sentence, a poem or the title of a movie that you know and take the first letters to form the password, for example:: Gone with the Wind" = GwtW26#?
Change your passwords regularly
Translation of : http://www.symantec.com/region/fr/resources/mots_passe.html
* Translation of : http://www.cnil.fr/linstitution/actualite/article/article/securite-comment-construire-un-mot-de-passe-sur-et-gerer-la-liste-de-ses-codes-dacces/
PASSWORD114
PUBMED : NEW ACCOUNT TO NCBI
PUBMED : SEND TO FILE (ENDNOTE)
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PUBMED : SEND TO FILE (ENDNOTE)With Internet Explorer (test version: 11): see the slides 113, 115-118, 121
With Chrome (test version: 34.0.1847.116 m): see the slides 114-118, 121
With Firefox (test version 19.0): see slides 119-121117
PUBMED : SEND TO FILE (ENDNOTE)
With Internet Explorer (test version: 11)118
PUBMED : SEND TO FILE (ENDNOTE)
With Chrome (test version: 34.0.1847.116 m)119
PUBMED : SEND TO FILE (ENDNOTE)
With Internet Explorer (test version: 11)With Chrome (test version: 34.0.1847.116 m)120
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With Internet Explorer (test version: 11)With Chrome (test version: 34.0.1847.116 m)121
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With Internet Explorer (test version: 11)With Chrome (test version: 34.0.1847.116 m)122
PUBMED : SEND TO FILE (ENDNOTE)
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PUBMED : SEND TO CITATION MANAGER (ENDNOTE)
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PUBMED : SEND TO CITATION MANAGER (ENDNOTE)With Internet Explorer (test version: 11): see the slides 129, 132-133
With Chrome (test version: 34.0.1847.116 m): see the slides 130, 132-133
With Firefox (test version 19.0): see slides 131-133128
PUBMED : SEND TO CITATION MANAGER (ENDNOTE)With Internet Explorer (test version: 11)
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PUBMED : SEND TO CITATION MANAGER (ENDNOTE)With Chrome (test version: 34.0.1847.116 m)
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PUBMED : SEND TO CITATION MANAGER (ENDNOTE)
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PUBMED : SEND TO CITATION MANAGER (ENDNOTE)
12With Internet Explorer (test version: 11With Chrome (test version: 34.0.1847.116 m)With Firefox (test version 19.0)132
PUBMED : SEND TO CITATION MANAGER (ENDNOTE)
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PUBMED : SEND TO COLLECTIONS
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PUBMED : SEND TO COLLECTIONS
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PUBMED : SEND TO COLLECTIONS12
3Limit of 1,000 referencesLimit of 100 alphanumeric charactersNote that accounts that do not register any activity in 2 years will be deleted.136
PUBMED : SEND TO CLIPBOARD
To save references temporarily to selected citations from one or several searches. It will be lost after 8 hours of inactivity on PubMed or other NCBI databases. 231137
PUBMED : SEND TO CLIPBOARD
The maximum number of 500 references138
PUBMED : SEND TO CLIPBOARDReferences in the clipboard are representes by the search number #0
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PUBMED : SEND TO CLIPBOARD
12To remove all referencesTo remove selected references140
PUBMED : SEND BY E-MAIL
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PUBMED : SEND BY E-MAIL
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PUBMED : SEND BY E-MAIL
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PUBMED : SEND BY E-MAIL
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PUBMED : SEND TO MY BIBLIOGRAPHY
PUBMED : SEND TO MY BIBLIOGRAPHY1234You need to identify yourself
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PUBMED : SEND TO MY BIBLIOGRAPHY
Limite: 500 rfrences tlcharges par bloc
PUBMED : SEND TO MY BIBLIOGRAPHY
PUBMED : SEND TO MY BIBLIOGRAPHY
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PUBMED : SEND TO MY BIBLIOGRAPHY
PUBMED : SEND TO MY BIBLIOGRAPHY
PUBMED : SEND TO MY BIBLIOGRAPHY
PUBMED : SEND TO MY BIBLIOGRAPHY
PUBMED : SEND TO MY BIBLIOGRAPHY
PUBMED : SEND TO MY BIBLIOGRAPHY
PUBMED : SEND TO MY BIBLIOGRAPHY
PUBMED : SEND TO MY BIBLIOGRAPHY
PUBMED :
Rabies virushttp://www.flickr.com/photos/sanofi-pasteur/5279807113/in/photostream/158
PUBMED : NCBI ACCOUNT SETTINGS
PUBMED : NCBI ACCOUNT SETTINGS
PUBMED : MY NCBI - CUSTOMIZE HOMEPAGE
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PUBMED : MY NCBI - CUSTOMIZE HOMEPAGE
PUBMED : MY NCBI - SITE PREFERENCES
PUBMED : MY NCBI - SITE PREFERENCES
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PUBMED : MY NCBI - SITE PREFERENCES
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PUBMED : MY NCBI - SAVE SEARCH
Send to referencesEdit the strategy166
PUBMED : MY NCBI - MY BIBLIOGRAPHY
PUBMED : MY NCBI - RECENT ACTIVITY
Recent Activity is tracking your searches and records viewed for the last 6 months
PUBMED : MY NCBI - COLLECTIONS
PUBMED : MY NCBI - COLLECTIONS - FAVORITES
The Favorites collection which helps you keep a list of your preferred NCBI database records.
PUBMED : MY NCBI - COLLECTIONS - FAVORITES
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PUBMED : MY NCBI - FILTERS
You can have up to 15 active filters using My NCBI 179
PUBMED : MY NCBI - FILTERS
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PUBMED : MY NCBI - FILTERS
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PUBMED : MY NCBI - FILTERS
The "Popular" category lists the most commonly requested filters according to each NCBI database.182
PUBMED : MY NCBI - FILTERS
The "LinkOut" category groups records that have links to resources provided by outside organizations, such as full-text publications, biological databases, consumer health information, library holdings and research tools. These links provide supplemental information related to records in NCBI databases183
PUBMED : MY NCBI - FILTRES
The "Properties" category groups records according to specific criteria for each database184
PUBMED : MY NCBI - FILTERS
The "Links" category groups records that have links to other NCBI databases185
PUBMED : FILTERSLinks to Web accessible full text articles (all available free of charge)Links to Web accessible full text articles (some may require subscription)186
PUBMED : FILTERS
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PUBMED : FILTERS
The "in process" and "supplied by publisher" citations may be excluded for some filter selections (article types, species, sex and ages) because they have not yet completed the MEDLINE indexing process188PUBMED :
Mycobacterium tuberculosishttp://phil.cdc.gov/phil/home.asp189OR
PUBMED : FIND RELATED DATA
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PUBMED : FIND RELATED DATA
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PUBMED : SINGLE CITATION MATCHER
The Single Citation Matcher searchs for a citation when you have some bibliographic information192
PUBMED : SINGLE CITATION MATCHER
To find a specific reference193
PUBMED : SINGLE CITATION MATCHER
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PUBMED : RELATED CITATIONS The Related citations See alllink will retrieve a pre-calculated set of PubMed citations that are closely related to the selected article. The related citations will be displayed in ranked order from most to least relevant, with the linked from citation displayed first
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RSS (Really Simple Syndication) is an XML-based format used to send new items or information to recipients who use RSS feed readersPUBMED: RSS196
PUBMED : RSS
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PUBMED : RSS
Drag and drop the XML icon onto the feed reader interface 1Click198
PUBMED : RSS
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PUBMED :SIGN OUTMost of the information in coming from the sites :
http://www.ncbi.nlm.nih.gov/pubmedhttp://www.ncbi.nlm.nih.gov/books/NBK3827/200
Web address to see again this presentation:
HTTP://SDIS.INRS.CA/
Under the heading :
Formations/Autoformations/Pubmed/Formation PowerPoint IAF : Anglais
EndNote formation
Michel Courcelles
# 4275
michel.courcelles @iaf.inrs.ca202
For comments:
Diane Sauv
# 4340
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