formation on : pubmed prepared by diane sauvé, b. sc., m. bibl. april 2014
TRANSCRIPT
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
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
Estimation of more than 2880 author names
http://www.ncbi.nlm.nih.gov/pubmed/24476258
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 : SELECTED TERMS
Latent membrane protein 1LMP 1
Epstein-Barr virus
Apoptosis
B cells
A
B
C
D
AND
AND
AND
PUBMED : HISTORY
Latent membrane protein 1
Latent membrane proteins 1
Latent membrane protein1
Latent membrane proteins1 No result
Latent membrane protein* AND 1
PUBMED : ADVANCED RESEARCH
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
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
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 - 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 : MeSH - SUBHEADINGS
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 : 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 - 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
PUBMED : HISTORY
The maximum number of searches available in History is 100
History will be lost after 8 hours of inactivity
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
PUBMED : AUTOMATIC TERM MAPPING
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
PUBMED : AUTOMATIC TERM MAPPING
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 : AUTOMATIC TERM MAPPING
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]
PUBMED : AUTOMATIC TERM MAPPING
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
Herpesvirus*
PUBMED : AUTOMATIC TERM MAPPING
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
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 : 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
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
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 : 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 : PASSWORD
Most common passwords of 2013
http://splashdata.com/press/worstpasswords2013.htm
PASSWORD
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
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
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 119-121
PUBMED : SEND TO FILE (ENDNOTE)
With Internet Explorer (test version: 11)With Chrome (test version: 34.0.1847.116 m)
PUBMED : SEND TO FILE (ENDNOTE)
With Internet Explorer (test version: 11)With Chrome (test version: 34.0.1847.116 m)
PUBMED : SEND TO FILE (ENDNOTE)
With Internet Explorer (test version: 11)With Chrome (test version: 34.0.1847.116 m)
PUBMED : SEND TO FILE (ENDNOTE)
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With Internet Explorer (test version: 11)With Chrome (test version: 34.0.1847.116 m)
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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 131-133
PUBMED : SEND TO CITATION MANAGER (ENDNOTE)
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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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PUBMED : MY NCBI - RECENT ACTIVITY
Recent Activity is tracking your searches and records viewed for the last 6 months
PUBMED : MY NCBI - COLLECTIONS - FAVORITES
The Favorites collection which helps you keep a list of your preferred NCBI database records.
PUBMED : MY NCBI - FILTERS
The "Popular" category lists the most commonly requested filters according
to each NCBI database.
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 databases
PUBMED : MY NCBI - FILTRES
The "Properties" category groups records according to specific
criteria for each database
PUBMED : MY NCBI - FILTERS
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)
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 : SINGLE CITATION MATCHER
The Single Citation Matcher searchs for a citation when you have some bibliographic information
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 :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