FORMATION ON : PubMed Prepared by Diane Sauvé, B. Sc., M. Bibl. April 2014

FORMATION ON :

PubMed

Prepared by Diane Sauvé, B. Sc., M. Bibl.

April 2014

PUBMED

1. Go to: sdis.inrs.ca2. At the left, click in: Bases de données3. In the box Titre, write Pubmed and click on Go4. Click on Pubmed

PUBMED

Started 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 : MEDLINE

Primary 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 : MEDLINE

Small 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 english about 84% have english abstracts written by authors of the articles

PUBMED : ADVANCED RESEARCH

PUBMED : SEARCH FIELDS

PUBMED : SEARCH FIELDS

PUBMED : DISPLAY FIELDS=80

PUBMED : DISPLAY FIELDS



Enter the author’s 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 author’s name in double quotes and tag with [au] in brackets

PUBMED : AUTHOR

PUBMED : AUTHOR

PUBMED : AUTHOR

Estimation of more than 2880 author names

http://www.ncbi.nlm.nih.gov/pubmed/24476258

J. Virol. 2012, 86 (8) : 4380-4393

3

PUBMED : AUTHOR

1 2

PUBMED : AUTHOR

Full author name may be searched for references published from 2002 forward if the

full author name is available in the article

PUBMED : AUTHOR AFFILIATION

Author, 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

PUBMED : JOURNAL

Enter the journal name or abbreviation

J. Virol. 2012, 86 (8) : 4380-4393

J. Virol. 2012, 86 (8) : 4380-4393

PUBMED : SELECTED TERMS

Latent membrane protein 1LMP 1

Epstein-Barr virus

Apoptosis

B cells

A

B

C

D

AND

AND

AND

J. Virol. 2012, 86 (8) : 4380-4393


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Make selection of desired expressions

PUBMED : HISTORY

2

PUBMED : HISTORY

1 Clic the left button

PUBMED : HISTORY

PUBMED : HISTORY

Latent membrane protein 1

Latent membrane proteins 1

Latent membrane protein1

Latent membrane proteins1 No result

Latent membrane protein* AND 1


Come from: Show index list

If you choose this strategy, you will not have the MeSH

PUBMED : MeSH - MAIN HEADINGS MeSH : 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

http://mesh.inserm.fr/



PUBMED : MeSH

PUBMED : MeSH HEADINGS

Give 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 don’t find a MeSH or you find a too generic MeSH

PUBMED : MeSH

The MeSH types included:

Main Headings

Subheadings

Publication types

Geographics

Supplementary concept records

PUBMED : MeSH - MAIN HEADINGS

The MeSH 2014 included 27 149 MeSH Headings in 16 categories:

PUBMED : MeSH - MAIN HEADINGS

11 MeSH

MeSH 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#5

PUBMED : HISTORY

Try: Epstein Barr viruses

PUBMED : MeSH

PUBMED : MeSH

PUBMED : MeSH - SUBHEADINGS

PUBMED : MeSH - SUBHEADINGS=83



Subheadings

Subheadings : are used to help describe more completely a particular aspect of a subject

The subheadings logically paired with the main heading2 letters may be used for subheadings

PUBMED : RESEARCH STRATEGYPathogenicity of Epstein-Barr virus= ( A AND B) OR C

A

Pathogen*

B

Epstein-Barr virusEBV

…

Herpesvirus 4, Human/Pathogenicity

C

PUBMED : HISTORY

PUBMED : MeSH

PUBMED : MeSH - MAJOR TOPICS

MAJR

Major 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 , it’s represented by an asterisk

PUBMED : MeSH

PUBMED : MeSH

Generic terms

Specific 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

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

PUBMED : HISTORY

The maximum number of searches available in History is 100

History will be lost after 8 hours of inactivity

Smallpox virus

http://www.flickr.com/photos/sanofi-pasteur/5280407684/in/photostream/

PUBMED : AUTOMATIC TERM MAPPING

Untagged terms that are entered in the search box are matched (in this order) against :

MeSH translation table Journals translation table Full Author translation table Author index Full Investigator (Collaborator) translation table Investigator (Collaborator) index

http://www.nlm.nih.gov/pubs/factsheets/mesh.html


The MeSH Translation Table contains:

o MeSH Termso See-reference mappings (also known as entry terms) for MeSH terms o MeSH Subheadingso Publication Typeso Pharmacologic Actionso Terms derived from the Unified Medical Language System (UMLS) that have

equivalent synonyms or lexical variants in Englisho Supplementary Concepts (chemical, protocol or disease terms) and their synonyms

http://www.nlm.nih.gov/pubs/factsheets/mesh.html

PUBMED : PUBLICATION TYPES: 73

PUBMED : PUBLICATION TYPES


When 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



Terms 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]


Truncation, 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

http://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.How_PubMed_works_aut

Herpesvirus*


Truncation 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

Herpesviruses

http://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.How_PubMed_works_aut

PUBMED : RECIPE FOR AN OPTIMAL RESEARCH

1. Put a word or phrase without quotes

2. Make a second search with the plural of the word or the phrase without quotes

3. Don’t forget to also search with abbreviations

4. Use the “Show search details” for points 1-3 to correct the terms or expressions displayed within the “Show search details”

5. See if you can find a descriptor and if so, look in the MeSH database for additional information to modify the search

6. Put the phrase in double quotes or use the truncation

PUBMED :

Pseudomonas aeruginosa

http://phil.cdc.gov/phil/home.asp

PUBMED : TERM SUGGESTED

PUBMED : AUTHOR KEYWORDS

Author 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

http://www.ncbi.nlm.nih.gov/pubmed/

PUBMED : DISPLAY SETTINGS

PUBMED : DISPLAY SETTINGS - SUMMARY

PUBMED : DISPLAY SETTINGS - SUMMARY

PUBMED : DISPLAY SETTINGS - SUMMARY - TEXT

PUBMED : DISPLAY SETTINGS - SUMMARY - TEXT

PUBMED : DISPLAY SETTINGS - ABSTRACT


PUBMED : DISPLAY SETTINGS - ABSTRACTStructured abstract

PUBMED : DISPLAY SETTINGS - STRUCTURED ABSTRACT

Formats 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 guidelines


PUBMED : DISPLAY SETTINGS - ABSTRACT - TEXT



Date created

Organization that supplied citation dataModification date

Issue

PUBMED : DISPLAY SETTINGS - MEDLINEPubmed unique identifier

Status tagCompletion date

ISSNVolume

Publication date

Abstract

Full author name

Affiliation

Language

Pagination TitlePii or doi that serves the role of pagination

Author

Grant number

Date created

PUBMED : DISPLAY SETTINGS - MEDLINEPublication type

Place of publicationFull journal title

Enzyme Commission or Registry number of CAS

MeSH terms

Other identification numbersMeSH date

Publication history status date

Publication status

Date of electronic publicationJournal title abbreviation

NLM unique ID

Subset

Date the citation was added to PubMed

Create date

Article identifierSource

PUBMED : DISPLAY SETTINGS - XML

Xml (ExTENSIBLE Markup Language) is generally used for displaying and manipulating data in software applications

PUBMED :

Bacillus anthracis


PUBMED : STATUS TAGS

PUBMED : STATUS TAG - PUBMED - AS SUPPLIED BY PUBLISHER

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, etc Bibliographic data has been reviewed

PUBMED : STATUS TAG - PUBMED - OLDMEDLINE

Over 2 million OLDMEDLINE citations, most without abstracts Citations originally printed in hardcopy indexes published from 1946 throught 1965 that

have not yet had all of their original subject terms mapped to current MeSH Partially MeSH indexed Bibliographic data has been reviewed Bibliographic data has been reviewed

PUBMED : STATUS TAG - PUBMED

PUBMED : STATUS TAG - PUBMED-BOOKS & DOCUMENTS

PUBMED : STATUS TAG - PUBMED

PUBMED : SAVE SEARCH




PUBMED :

Influenza virus


PUBMED : SIGN IN TO NCBI

PUBMED : SIGN IN TO NCBI

If you have an account

If you need an account

PUBMED : PASSWORD

Most common passwords of 2013

http://splashdata.com/press/worstpasswords2013.htm

PASSWORD

http://splashdata.com/press/worstpasswords2013.htm

How to select your password? by Burçin Gerçek

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 file

PASSWORD

Translation of : http://www.symantec.com/region/fr/resources/mots_passe.html

http://www.symantec.com/region/fr/resources/mots_passe.html



PUBMED : PASSWORD

How to select your password? by Burçin Gerçek

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/

PASSWORD




http://www.cnil.fr/linstitution/actualite/article/article/securite-comment-construire-un-mot-de-passe-sur-et-gerer-la-liste-de-ses-codes-dacces/

http://www.cnil.fr/linstitution/actualite/article/article/securite-comment-construire-un-mot-de-passe-sur-et-gerer-la-liste-de-ses-codes-dacces/

PUBMED : NEW ACCOUNT TO NCBI

PUBMED : SEND TO FILE (ENDNOTE)

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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 119-121


With Internet Explorer (test version: 11)


With Chrome (test version: 34.0.1847.116 m)


With Internet Explorer (test version: 11)With Chrome (test version: 34.0.1847.116 m)






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With Firefox (test version : 19.0)


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PUBMED : SEND TO CITATION MANAGER (ENDNOTE)

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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 131-133


With Internet Explorer (test version: 11)


With Chrome (test version: 34.0.1847.116 m)


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With Internet Explorer (test version: 11With Chrome (test version: 34.0.1847.116 m)With Firefox (test version 19.0)


PUBMED : SEND TO COLLECTIONS


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Limit of 1,000 references

Limit of 100 alphanumeric characters

Note that accounts that do not register any activity in 2 years

will be deleted.

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.

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The maximum number of 500 references


References in the clipboard are representes by the search number #0


1

2

To remove all references

To remove selected

references

PUBMED : SEND BY E-MAIL

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45

6




PUBMED : SEND TO MY BIBLIOGRAPHY

PUBMED : SEND TO MY BIBLIOGRAPHY1

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You need to identify

yourself


Limite: 500 références téléchargées

par bloc



12









PUBMED :

Rabies virus


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 - SAVE SEARCH

Send to references

Edit the strategy

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.





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PUBMED : MY NCBI - FILTERS

You can have up to 15 active filters using My NCBI


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The "Popular" category lists the most commonly requested filters according

to each NCBI database.


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 databases

PUBMED : MY NCBI - FILTRES

The "Properties" category groups records according to specific

criteria for each database


The "Links" category groups records that have links to other NCBI databases

PUBMED : FILTERS

Links to Web accessible full text articles (all available free of charge)

Links to Web accessible full text articles (some may require subscription)

PUBMED : FILTERS

P

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 process

PUBMED :

Mycobacterium tuberculosis


OR

PUBMED : FIND RELATED DATA

PUBMED : FIND RELATED DATA

PUBMED : SINGLE CITATION MATCHER

The Single Citation Matcher searchs for a citation when you have some bibliographic information


To find a specific reference


PUBMED : RELATED CITATIONS

The Related citations See all…link 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

PUBMED : RRS

RSS (Really Simple Syndication) is an XML-based format used to send new items or information to recipients who use RSS feed readers

PUBMED: RSS

PUBMED : RSS

2

PUBMED : RSS

Drag and drop the XML icon onto the feed reader interface

1

Click

PUBMED : RSS

PUBMED :SIGN OUT

Most of the information in coming from the sites :

http://www.ncbi.nlm.nih.gov/pubmed

http://www.ncbi.nlm.nih.gov/books/NBK3827/





Web address to see again this presentation:

HTTP://SDIS.INRS.CA/

Under the heading :

Formations/Autoformations/Pubmed/Formation PowerPoint IAF : Anglais

http://sdis.inrs.ca/AUTOFORMATIONS

EndNote formation

Michel Courcelles

# 4275

michel.courcelles @iaf.inrs.ca

For comments:

Diane Sauvé

# 4340

[email protected]

Documents

FORMATION ON : PubMed Prepared by Diane Sauvé, B. Sc., M. Bibl. April 2014