Presentation is loading. Please wait.

Presentation is loading. Please wait.

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

Similar presentations


Presentation on theme: "FORMATION ON :  PubMed Prepared by Diane Sauvé, B. Sc., M. Bibl. April 2014."— Presentation transcript:

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

2 PUBMED 1.Go to: sdis.inrs.ca 2.At the left, click in: Bases de données 3.In the box Titre, write Pubmed and click on Go 4.Click on Pubmed

3 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)

4 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

5 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 :  about 93% are published in english  about 84% have english abstracts written by authors of the articles

6 PUBMED : ADVANCED RESEARCH

7 PUBMED : SEARCH FIELDS

8

9 PUBMED : DISPLAY FIELDS =80

10 PUBMED : DISPLAY FIELDS

11

12

13  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

14

15 Estimation of more than 2880 author names

16 J. Virol. 2012, 86 (8) :

17 3 PUBMED : AUTHOR 1 2

18 Full author name may be searched for references published from 2002 forward if the full author name is available in the article

19 PUBMED : AUTHOR AFFILIATION Author, Corporate Author, and Collaborator Affiliation Display Changes 2013 December 24 Effective 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

20 PUBMED : JOURNAL Enter the journal name or abbreviation

21 J. Virol. 2012, 86 (8) :

22

23 PUBMED : SELECTED TERMS Latent membrane protein 1 LMP 1 Epstein-Barr virus Apoptosis B cells A B C D AND

24 J. Virol. 2012, 86 (8) :

25 PUBMED : ADVANCED RESEARCH Make selection of desired expressions­

26 PUBMED : HISTORY

27 2 1 Clic the left button

28 PUBMED : HISTORY

29 Latent membrane protein 1 Latent membrane proteins 1 Latent membrane protein1 Latent membrane proteins1 No result Latent membrane protein* AND 1

30 PUBMED : ADVANCED RESEARCH Come from: Show index list If you choose this strategy, you will not have the MeSH

31 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:

32 PUBMED : MeSH

33 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

34 PUBMED : MeSH The MeSH types included:  Main Headings  Subheadings  Publication types  Geographics  Supplementary concept records

35 PUBMED : MeSH - MAIN HEADINGS The MeSH 2014 included MeSH Headings in 16 categories:

36 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]

37 PUBMED : MeSH 1 2 3

38

39

40 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

41 PUBMED : HISTORY

42 J. Virol. 2012, 86 (8) :

43 PUBMED : HISTORY #6#7 #9 #8 #4 #5

44 PUBMED : HISTORY Try: Epstein Barr viruses

45 PUBMED : MeSH

46

47 PUBMED : MeSH - SUBHEADINGS

48 =83

49 PUBMED : MeSH - SUBHEADINGS

50 Subheadings Subheadings : are used to help describe more completely a particular aspect of a subject The subheadings logically paired with the main heading 2 letters may be used for subheadings

51 PUBMED : RESEARCH STRATEGY Pathogenicity of Epstein-Barr virus= ( A AND B) OR C A Pathogen* B Epstein-Barr virus EBV … Herpesvirus 4, Human/Pathogenicity C

52 PUBMED : HISTORY

53 PUBMED : MeSH

54 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

55 PUBMED : MeSH

56 Generic terms Specific terms

57 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

58 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

59 J. Virol. 2012, 86 (8) :

60 PUBMED : HISTORY Do we have to add “cell death”?

61 PUBMED : MeSH - ASSOCIATED TERMS

62 J. Virol. 2012, 86 (8) :

63 PUBMED : HISTORY B cell B cells

64 PUBMED : HISTORY The maximum number of searches available in History is 100 History will be lost after 8 hours of inactivity

65 Smallpox virus

66 PUBMED : AUTOMATIC TERM MAPPING  Untagged terms that are entered in the search box are matched (in this order) against :  MeSH translation table MeSH  Journals translation table  Full Author translation table  Author index  Full Investigator (Collaborator) translation table  Investigator (Collaborator) index

67 PUBMED : AUTOMATIC TERM MAPPING  The MeSH Translation Table contains: o MeSH Terms MeSH o See-reference mappings (also known as entry terms) for MeSH terms o MeSH Subheadings o Publication Types o Pharmacologic Actions o Terms derived from the Unified Medical Language System (UMLS) that have equivalent synonyms or lexical variants in English o Supplementary Concepts (chemical, protocol or disease terms) and their synonyms

68 PUBMED : PUBLICATION TYPES : 73

69 PUBMED : PUBLICATION TYPES

70 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

71 PUBMED : STOPWORDS

72 PUBMED : AUTOMATIC TERM MAPPING

73 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]

74 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 hierarchyautomatic term mapping 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

75 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 hierarchyautomatic term mapping Herpesvirus Herpesviruses

76 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

77 PUBMED : Pseudomonas aeruginosa

78 PUBMED : TERM SUGGESTED

79 PUBMED : AUTHOR KEYWORDS Author Keywords in PubMed (2013 February 07) PubMedPubMed 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

80 PUBMED : DISPLAY SETTINGS

81 PUBMED : DISPLAY SETTINGS - SUMMARY

82

83 PUBMED : DISPLAY SETTINGS - SUMMARY - TEXT

84

85 PUBMED : DISPLAY SETTINGS - ABSTRACT

86

87 Structured abstract

88 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

89 PUBMED : DISPLAY SETTINGS - ABSTRACT

90 PUBMED : DISPLAY SETTINGS - ABSTRACT - TEXT

91

92

93 Date created Organization that supplied citation data Modification date Issue PUBMED : DISPLAY SETTINGS - MEDLINE Pubmed unique identifier Status tag Completion date ISSN Volume Publication date Abstract Full author name Affiliation Language Pagination Title Pii or doi that serves the role of pagination Author Grant number Date created

94 PUBMED : DISPLAY SETTINGS - MEDLINE Publication type Place of publication Full journal title Enzyme Commission or Registry number of CAS MeSH terms Other identification numbers MeSH date Publication history status date Publication status Date of electronic publication Journal title abbreviation NLM unique ID Subset Date the citation was added to PubMed Create date Article identifier Source

95 PUBMED : DISPLAY SETTINGS - XML Xml (ExTENSIBLE Markup Language) is generally used for displaying and manipulating data in software applications

96 PUBMED : Bacillus anthracis

97 PUBMED : STATUS TAGS

98 PUBMED : STATUS TAG - PUBMED - AS SUPPLIED BY PUBLISHER

99 PUBMED : STATUS TAG - PUBMED - IN PROCESS Citations bibliographic data will be reviewed and indexed

100 PUBMED : STATUS TAG - PUBMED - INDEXED FOR MEDLINE  Citations have been indexed with MeSH terms, Publication Type, Substance Names, etc  Bibliographic data has been reviewed

101 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

102 PUBMED : STATUS TAG - PUBMED

103 PUBMED : STATUS TAG - PUBMED-BOOKS & DOCUMENTS

104 PUBMED : STATUS TAG - PUBMED

105 PUBMED : SAVE SEARCH

106

107

108

109 PUBMED : Influenza virus /

110 PUBMED : SIGN IN TO NCBI

111 If you have an account If you need an account

112 PUBMED : PASSWORD Most common passwords of PASSWORD

113 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 :

114 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 : * Translation of : 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/ PASSWORD

115 PUBMED : NEW ACCOUNT TO NCBI

116 PUBMED : SEND TO FILE (ENDNOTE)

117 With Internet Explorer (test version: 11): see the slides 113, , 121 With Chrome (test version: m): see the slides , 121 With Firefox (test version 19.0): see slides

118 PUBMED : SEND TO FILE (ENDNOTE) With Internet Explorer (test version: 11)

119 PUBMED : SEND TO FILE (ENDNOTE ) With Chrome (test version: m)

120 PUBMED : SEND TO FILE (ENDNOTE) With Internet Explorer (test version: 11) With Chrome (test version: m)

121 PUBMED : SEND TO FILE (ENDNOTE) With Internet Explorer (test version: 11) With Chrome (test version: m)

122 PUBMED : SEND TO FILE (ENDNOTE) With Internet Explorer (test version: 11) With Chrome (test version: m)

123 PUBMED : SEND TO FILE (ENDNOTE) 1 2 With Internet Explorer (test version: 11) With Chrome (test version: m) 3

124 PUBMED : SEND TO FILE (ENDNOTE) 1 2 With Firefox (test version : 19.0)

125 PUBMED : SEND TO FILE (ENDNOTE) 1 2 With Firefox (test version : 19.0)

126 PUBMED : SEND TO FILE (ENDNOTE)

127 PUBMED : SEND TO CITATION MANAGER (ENDNOTE)

128 With Internet Explorer (test version: 11): see the slides 129, With Chrome (test version: m): see the slides 130, With Firefox (test version 19.0): see slides

129 PUBMED : SEND TO CITATION MANAGER (ENDNOTE) With Internet Explorer (test version: 11)

130 PUBMED : SEND TO CITATION MANAGER (ENDNOTE) With Chrome (test version: m)

131 PUBMED : SEND TO CITATION MANAGER (ENDNOTE) 1 2 With Firefox (test version : 19.0)

132 PUBMED : SEND TO CITATION MANAGER (ENDNOTE) 1 2 With Internet Explorer (test version: 11 With Chrome (test version: m) With Firefox (test version 19.0)

133 PUBMED : SEND TO CITATION MANAGER (ENDNOTE)

134 PUBMED : SEND TO COLLECTIONS

135 1 2

136 1 2 3 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.

137 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

138 PUBMED : SEND TO CLIPBOARD The maximum number of 500 references

139 PUBMED : SEND TO CLIPBOARD References in the clipboard are representes by the search number #0

140 PUBMED : SEND TO CLIPBOARD 1 2 To remove all references To remove selected references

141 PUBMED : SEND BY

142

143

144

145 PUBMED : SEND TO MY BIBLIOGRAPHY

146 You need to identify yourself

147 PUBMED : SEND TO MY BIBLIOGRAPHY Limite: 500 références téléchargées par bloc

148 PUBMED : SEND TO MY BIBLIOGRAPHY

149 1 2

150

151

152

153

154

155

156

157

158 PUBMED : Rabies virus

159 PUBMED : NCBI ACCOUNT SETTINGS

160

161 PUBMED : MY NCBI - CUSTOMIZE HOMEPAGE 1 2

162

163 PUBMED : MY NCBI - SITE PREFERENCES

164

165

166 PUBMED : MY NCBI - SAVE SEARCH Send to references Edit the strategy

167 PUBMED : MY NCBI - MY BIBLIOGRAPHY

168 PUBMED : MY NCBI - RECENT ACTIVITY Recent Activity is tracking your searches and records viewed for the last 6 months

169 PUBMED : MY NCBI - COLLECTIONS

170 PUBMED : MY NCBI - COLLECTIONS - FAVORITES The Favorites collection which helps you keep a list of your preferred NCBI database records.

171 PUBMED : MY NCBI - COLLECTIONS - FAVORITES

172

173 PUBMED : MY NCBI - COLLECTIONS

174

175 1 2 3

176

177 1 2 3

178

179 PUBMED : MY NCBI - FILTERS You can have up to 15 active filters using My NCBI

180 PUBMED : MY NCBI - FILTERS

181

182 The "Popular" category lists the most commonly requested filters according to each NCBI database.

183 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

184 PUBMED : MY NCBI - FILTRES The "Properties" category groups records according to specific criteria for each database

185 PUBMED : MY NCBI - FILTERS The "Links" category groups records that have links to other NCBI databases

186 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)

187 PUBMED : FILTERS

188 P 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

189 PUBMED : Mycobacterium tuberculosis

190 OR PUBMED : FIND RELATED DATA

191

192 PUBMED : SINGLE CITATION MATCHER The Single Citation Matcher searchs for a citation when you have some bibliographic information

193 PUBMED : SINGLE CITATION MATCHER To find a specific reference

194 PUBMED : SINGLE CITATION MATCHER

195 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

196 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

197

198 2 Drag and drop the XML icon onto the feed reader interface 1 Click

199 PUBMED : RSS

200 PUBMED :SIGN OUT Most of the information in coming from the sites :

201 Web address to see again this presentation : Under the heading : Formations/Autoformations/Pubmed/Formation PowerPoint IAF : Anglais

202 EndNote formation Michel Courcelles # 4275

203 For comments: Diane Sauvé # 4340


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

Similar presentations


Ads by Google