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Unleashing The Power Of Novoseek

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This presentation aims to explain to you how novoseek works in an in-depth way. Feel free to use it, distribute, embed on your blog or website or use part of it for class purposes. …

This presentation aims to explain to you how novoseek works in an in-depth way. Feel free to use it, distribute, embed on your blog or website or use part of it for class purposes.

Any questions you may have regarding it, you can reach us at http://twitter.com/novoseek or directly on http://www.novoseek.com through the contact form.


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  • 1. novo|seek
    Unleashing the power of novo|seek
    New biomedical search engine
  • 2. Table of Content
    Presentation of novoseek, thebiomedicalsearchengine
    Understandthelayout of thesearchengine
    Discoverthedifferentfunctions
    Learnhowtoperformeffectivesearches (case study)
  • 3. Presentation of novoseek
    Discover what is novo|seek and why it is different to the other search engines
  • 4. Presentation of novoseek, thebiomedicalsearchengine
    1
    Whatisnovoseek?
    • Itis a searchengineforsearchingthepublishedknowledge in biomedicalliteraturethatidentifies the key biomedical terms taking into account external available data and contextual term information.
    • 5. It retrieves every document where a term is mentioned no matter the synonym used and discards those documents where the term is used with an unwanted meaning.
    Whyisitdifferenttootherbiomedicalsearchengines?
    • novo|seek indexes biomedical literature using text mining technology that combines information extraction, name entity recognitionand knowledge discovery technologies to provide the most relevant and meaningful biomedical search results.
  • 1
    Presentation of novoseek, thebiomedicalsearchengine
    The conceptual search
    • As a result of this indexing technology, novo|seek retrieves every document where a term is mentioned no matter the synonym used and discards those documents where the term is used with an unwanted meaning.
    Performmeaningfulsearches
    • Novoseek allows you to look for publications in an easy, intuitive and quick way. There are several ways to find what you need to read quickly.
    • 6. You can use the advanced search page.
    • 7. You can use shortcuts in you search to consult what you need to read faster. For instance by using the square brackets [ ] and specifying what you want to consult.
    • 8. You can use logical operators to specify your search with more details from the main search box.
  • Understand the layout
    Understand the layout of the search engine
  • 9. 2
    Understandthelayout of thesearchengine / main page
    HELP
    ADVANCED SEARCH & PREF
    MAIN SEARCH BOX
    INFORMATION
    NEWS & TOOLS BOX
  • 10. 2
    Understandthelayout of thesearchengine / results page
    POP UP BARS TO GET MORE INFORMATION ON THE RESULTS
    FILTERS RELATED TO SEARCH
    OPTIONS TO CHOSE VISUALIZATION OF RESULTS
    CHOICE OF DATABASE
    RESULTS
  • 11. 2
    Understandthelayout of thesearchengine / articledetails
    POP UP BARS TO GET MORE INFORMATION ON THE RESULTS
    LINK TO JOURNAL
    PRINT
    ARTICLE DETAILS
  • 12. 2
    Understandthelayout of thesearchengine / concept details
    PRINT
    NEW SEARCH
    CONCEPT DETAILS
  • 13. Discover the different functions
    Get an in-depth knowledge of the different functions available
  • 14. 3
    Discoverthedifferentfunctions / Filtersrelatedtosearch
    Thefiltersrelatedtothesearchare presented in theleftsidebar. They are organized in 11 differentconceptsandidentifiablebycolors:
    The bar indicatestherelevanceof the concept accordingtothecurrentsearch.
    The “i” iconallowstoaddthe concept tothecurrentsearchorsee more informationonthis concept.
  • 25. 3
    Discoverthedifferentfunctions / Filtersrelatedtosearch 2
    Clickonthe “Bibliographics”tabtodisplayalltheAuthorsandJournalsrelatedtoyoursearch.
    Clickonthe “more” link todisplayalltherelatedconcepts as shownbelow.
    Clickagainon “less” todisplayagain 3 of them as shown in theimageabove..
  • 26. 3
    Discoverthedifferentfunctions / Filtersrelatedtosearch 3
    Clickingonthe “i” icondisplaysaninformative pop-up windowallowingseveralactions:
    • Perform a new searchfortheselected concept (here “brca1 mutation”).
    • 27. Addthe concept as a filtertothecurrentsearch Thesearchisrefined and there are lessresults.
    • 28. Excludethe concept fromthesearchresults.
    • 29. Gotothe concept details page.
  • 3
    Discoverthedifferentfunctions / Searchdetails
    Clickingonthe pop-up bar “Show searchdetails”, youwillbeabletoconsultwhatisyourcurrentsearch and thecorrespondingresults:
    • Thefirst line statestheamount of resultsfromthetextanalysis.
    • 30. Thesecond line statestheamount of resultswhenyoursearch has beenmapped.
  • 3
    Discoverthedifferentfunctions / Highlight concepts

    Clickingonthe pop-up bar “Show highlight panel”, youwillbeabletohighlightone, severalorall of theconceptsidentified in theresults.
    Forinstance, ifyoucheck “DiseasesorSyndromes”, they are immediatelyhighlighted in theresultswiththecorresponding color as explainedbefore .
  • 31. 3
    Discoverthedifferentfunctions / Choice of database
    DATABASES
    By default, thesearchengine looks forresults in MEDLINE database.
    Simplybyclicking “Full Text” of “Grants”, theresultswillbelookedintothesedatabasesaccordingly.
    Thenumberbetweenbracketssimplyindicatestheamount of resultsin thosedatabases.
  • 32. 3
    Discoverthedifferentfunctions / Visualization of results
    SORT RESULTS
    DATABASES
    snippets
    sentences
    complete
    By default, theresultsdetails are shownwithsnippets, butyou can clickthewindowstoviewonly “title”, or “sentences” or “complete description”.
    By default, theresults are sortedby date (newestfirst) butyou can clickthelist and chosetosortthembydate (oldestfirst) orbyrelevance.
    Theprinticon opens a new windowwheretheresultstoyoursearch are readyforprinting.
  • 33. 3
    Discoverthedifferentfunctions / Results page
    By default, there are 10 resultsby page, butyou can easilychangeyourpreferences (see page 24) and set itto 20, 30, 40 or 50.
    Theresultsshownabove are in Medline, whenthefull textversionisavailable, a direct link toitisshown so you can consultitdirectly .
  • 34. 3
    Discoverthedifferentfunctions / Articledetails
    TITLE
    LINK TO JOURNAL
    PRINT
    ArticlesDetails: Date / PMID / Authors / Journals
  • 35. 3
    Discoverthedifferentfunctions / Concept details
    CONCEPT
    The concept page summarizesalltheinformationrelatedtothevery concept. Namely:
    • Elementinfowithname and alternativenames
    • 36. Links tootherdatabases
    • 37. Recentdocuments
  • 3
    Discoverthedifferentfunctions / Advancedsearch page
    • Select corpus (database) fromMedline, Full TextorGrants.
    • 38. Selectfields. Thisoptionallowsyoutoselectthefieldsyouwantyoursearchtobeperformed in:
    • 39. Select the option thatbestmatchesyourneedorcombine several of them tomakeyoursearcheven more precise.
    • 40. Youjusthavetotype in whatyou are lookingfor. Theauto complete functionwillhelpyou. You can add as many boxes as youneed.
    • 41. Thedateshelpyouspecify a period, a startingorending date to match yourneeds.
  • 3
    Discoverthedifferentfunctions / Usingadvancedqueryshortcuts
    Usingtags in yourqueries:
    • Make your search be quicker by using the tag corresponding to the concept you want to look for.
    • 42. [disease], [dis]: DiseasesorSyndromes
    • 43. [chemical], [chem], [chm]: Chemicalsubstances
    • 44. [gene], [gen], [protein]: Genes and Proteins
    • 45. [organism], [species]: Organisms
    • 46. [symptom], [sym]: Signs and Symptoms
    • 47. [drug]: Pharmacologicalsubstances
    • 48. [tissue]: Tissues
    • 49. [organ]: Organs and Bodyparts
    • 50. [author], [authorname], [auth], [au]: Authornames
    • 51. [journal], [jour], [jo]: Journaltitles
    • 52. [mesh]: MeSHterms
    Checkexample
    Checkexample
    Checkexample
  • 53. 3
    Discoverthedifferentfunctions / Usingadvancedqueryshortcuts
    Usinglogicaloperators in yourqueries:
    • Make your search be quicker by using logical operators to specify with more details
    • 54. “ “specifytheexactwordsto look for . Ifnotspecified, thesystem looks forpublicationswhereany of thewordappears.
    checkexamplewith and
    • AND specifytwoor more wordsto look for. Theresultswillincludebothsearchterms.
    checkexample
    • ORspecifyto look whetherforonetermortheotherintothesearchresults.
    checkexample
    • NOTexcludeoneor more searchtermsfromtheresults.
    checkexample
    breastcancer
    “breastcancer”
    Breast AND cancer
    Breast OR cancer
    Breast NOT cancer
  • 55. 3
    Discoverthedifferentfunctions / Set up preferences
    Set thenumber of relatedelementsto showto 20 (by default), 50 or 100.
    Set thenumber of documentsto show oneach page to 10 (by default), 20, 30, 40 or 50.
  • 56. Learn to perform effective searches
    Case study: Asperger Syndrome and Bipolar disorder in autism
  • 57. 4
    Learnhowtoperformeffectivesearches / Case study
    Case study: Asperger Syndrome and Bipolar disorder in autism
    • We want to know more about effects of Asperger Syndrome and Bipolar disorder in people affected by autism. Let’s describe how to perform this complex search step by step.
    • 58. First we type in ”autism“ in the main search box.
    • 59. The results page for autism displays 10.657 publications in Medline. (on July 3rd 2009)
  • 4
    Learnhowtoperformeffectivesearches / Case study
    Case study: Asperger Syndrome and Bipolar disorder in autism
    • From here, we should use the related concepts in the left sidebar to refine the search. As they are classified by relevance to the current search and by concept, we should be able to identify what we need quickly.
    • 60. We now click on the “more” link next to “Diseases or Syndromes” to display all the related concepts.
    • 61. We can see all the Diseases or Syndromes related to the current search for autism. ”Asperger syndrome” is 7th in the list.
    • 62. We simply have to click the “i” icon and chose “Add filter” (or click directly on the words) to add it to the current search.
    • 63. The filter is added to the search and we now have 684 results in Medline as shown in next slide.
  • 4
    Learnhowtoperformeffectivesearches / Case study
  • 64. 4
    Learnhowtoperformeffectivesearches / Case study
    Case study: Asperger Syndrome and Bipolar disorder in autism
    • We repeat the same process with “bipolar disorder”. This one is almost at the bottom of the list.
    • 65. We now have 11 results in Medline for the search on Asperger syndrome and bipolar disorder in autism.
    • 66. According to the medical librarian interested in these publications, there were satisfying enough.
  • More resources on novoseek
    use novoseek
    Install in firefoxsearch bar
    Installthewidget
    Makesuggestions
    Reachusontwitter
    Writetous
  • 67. Contact Info
    ValentinVivier
    Marketing Department
    vvivier@bioalma.com
    Phone: +34 91 141 71 50