novo|seek<br />Unleashing the power of novo|seek<br />New biomedical search engine <br />
Table of Content<br />Presentation of novoseek, thebiomedicalsearchengine<br />Understandthelayout of thesearchengine<br /...
Presentation of novoseek<br />Discover what is novo|seek and why it is different to the other search engines<br />
Presentation of novoseek, thebiomedicalsearchengine<br />1<br />Whatisnovoseek?<br /><ul><li>Itis a searchengineforsearchi...
It retrieves every document where a term is mentioned no matter the synonym used and discards those documents where the te...
You can use the advanced search page.
You can use shortcuts in you search to consult what you need to read faster. For instance by using the square brackets [ ]...
You can use logical operators to specify your search with more details from the main search box.</li></li></ul><li>Underst...
2<br />Understandthelayout of thesearchengine / main page<br />HELP <br />ADVANCED SEARCH & PREF<br />MAIN SEARCH BOX<br /...
2<br />Understandthelayout of thesearchengine / results page<br />POP UP BARS TO GET MORE INFORMATION ON THE RESULTS<br />...
2<br />Understandthelayout of thesearchengine / articledetails<br />POP UP BARS TO GET MORE INFORMATION ON THE RESULTS<br ...
2<br />Understandthelayout of thesearchengine / concept details<br />PRINT <br />NEW SEARCH <br />CONCEPT DETAILS<br />
Discover the different functions<br />Get an in-depth knowledge of the different functions available<br />
3<br />Discoverthedifferentfunctions / Filtersrelatedtosearch<br />Thefiltersrelatedtothesearchare presented in theleftsid...
Pharmacologicalsubstances
Genes & Proteins
Signs & Symptoms
Chemicalsubstances
Organisms
Organs & Bodyparts
Tissues
Cellcomponents
Biologicalfunctions
Procedures / Techniques</li></ul>The bar                    indicatestherelevanceof the concept accordingtothecurrentsearc...
3<br />Discoverthedifferentfunctions / Filtersrelatedtosearch 2<br />Clickonthe “Bibliographics”tabtodisplayalltheAuthorsa...
3<br />Discoverthedifferentfunctions / Filtersrelatedtosearch 3<br />Clickingonthe “i” icondisplaysaninformative pop-up wi...
Addthe concept as a filtertothecurrentsearch Thesearchisrefined and there are lessresults.
Excludethe concept fromthesearchresults.
Gotothe concept details page.</li></li></ul><li>3<br />Discoverthedifferentfunctions / Searchdetails<br />Clickingonthe po...
Thesecond line statestheamount of resultswhenyoursearch has beenmapped.</li></li></ul><li>3<br />Discoverthedifferentfunct...
3<br />Discoverthedifferentfunctions / Choice of database<br />DATABASES<br />By default, thesearchengine looks forresults...
3<br />Discoverthedifferentfunctions / Visualization of results<br />SORT RESULTS<br />DATABASES<br />snippets<br />senten...
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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.

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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Unleashing The Power Of Novoseek

  1. 1. novo|seek<br />Unleashing the power of novo|seek<br />New biomedical search engine <br />
  2. 2. Table of Content<br />Presentation of novoseek, thebiomedicalsearchengine<br />Understandthelayout of thesearchengine<br />Discoverthedifferentfunctions<br />Learnhowtoperformeffectivesearches (case study)<br />
  3. 3. Presentation of novoseek<br />Discover what is novo|seek and why it is different to the other search engines<br />
  4. 4. Presentation of novoseek, thebiomedicalsearchengine<br />1<br />Whatisnovoseek?<br /><ul><li>Itis a searchengineforsearchingthepublishedknowledge in biomedicalliteraturethatidentifies the key biomedical terms taking into account external available data and contextual term information.
  5. 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. </li></ul>Whyisitdifferenttootherbiomedicalsearchengines?<br /><ul><li>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.</li></li></ul><li>1<br />Presentation of novoseek, thebiomedicalsearchengine<br />The conceptual search<br /><ul><li>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.</li></ul>Performmeaningfulsearches<br /><ul><li>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. 6. You can use the advanced search page.
  7. 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. 8. You can use logical operators to specify your search with more details from the main search box.</li></li></ul><li>Understand the layout<br />Understand the layout of the search engine<br />
  9. 9. 2<br />Understandthelayout of thesearchengine / main page<br />HELP <br />ADVANCED SEARCH & PREF<br />MAIN SEARCH BOX<br />INFORMATION<br />NEWS & TOOLS BOX<br />
  10. 10. 2<br />Understandthelayout of thesearchengine / results page<br />POP UP BARS TO GET MORE INFORMATION ON THE RESULTS<br />FILTERS RELATED TO SEARCH<br />OPTIONS TO CHOSE VISUALIZATION OF RESULTS<br />CHOICE OF DATABASE<br />RESULTS<br />
  11. 11. 2<br />Understandthelayout of thesearchengine / articledetails<br />POP UP BARS TO GET MORE INFORMATION ON THE RESULTS<br />LINK TO JOURNAL<br />PRINT <br />ARTICLE DETAILS<br />
  12. 12. 2<br />Understandthelayout of thesearchengine / concept details<br />PRINT <br />NEW SEARCH <br />CONCEPT DETAILS<br />
  13. 13. Discover the different functions<br />Get an in-depth knowledge of the different functions available<br />
  14. 14. 3<br />Discoverthedifferentfunctions / Filtersrelatedtosearch<br />Thefiltersrelatedtothesearchare presented in theleftsidebar. They are organized in 11 differentconceptsandidentifiablebycolors:<br /><ul><li>Diseasesorsyndromes
  15. 15. Pharmacologicalsubstances
  16. 16. Genes & Proteins
  17. 17. Signs & Symptoms
  18. 18. Chemicalsubstances
  19. 19. Organisms
  20. 20. Organs & Bodyparts
  21. 21. Tissues
  22. 22. Cellcomponents
  23. 23. Biologicalfunctions
  24. 24. Procedures / Techniques</li></ul>The bar indicatestherelevanceof the concept accordingtothecurrentsearch.<br />The “i” iconallowstoaddthe concept tothecurrentsearchorsee more informationonthis concept.<br />
  25. 25. 3<br />Discoverthedifferentfunctions / Filtersrelatedtosearch 2<br />Clickonthe “Bibliographics”tabtodisplayalltheAuthorsandJournalsrelatedtoyoursearch.<br />Clickonthe “more” link todisplayalltherelatedconcepts as shownbelow.<br />Clickagainon “less” todisplayagain 3 of them as shown in theimageabove..<br />
  26. 26. 3<br />Discoverthedifferentfunctions / Filtersrelatedtosearch 3<br />Clickingonthe “i” icondisplaysaninformative pop-up windowallowingseveralactions:<br /><ul><li>Perform a new searchfortheselected concept (here “brca1 mutation”).
  27. 27. Addthe concept as a filtertothecurrentsearch Thesearchisrefined and there are lessresults.
  28. 28. Excludethe concept fromthesearchresults.
  29. 29. Gotothe concept details page.</li></li></ul><li>3<br />Discoverthedifferentfunctions / Searchdetails<br />Clickingonthe pop-up bar “Show searchdetails”, youwillbeabletoconsultwhatisyourcurrentsearch and thecorrespondingresults:<br /><ul><li>Thefirst line statestheamount of resultsfromthetextanalysis.
  30. 30. Thesecond line statestheamount of resultswhenyoursearch has beenmapped.</li></li></ul><li>3<br />Discoverthedifferentfunctions / Highlight concepts<br />√<br />Clickingonthe pop-up bar “Show highlight panel”, youwillbeabletohighlightone, severalorall of theconceptsidentified in theresults.<br />Forinstance, ifyoucheck “DiseasesorSyndromes”, they are immediatelyhighlighted in theresultswiththecorresponding color as explainedbefore .<br />
  31. 31. 3<br />Discoverthedifferentfunctions / Choice of database<br />DATABASES<br />By default, thesearchengine looks forresults in MEDLINE database.<br />Simplybyclicking “Full Text” of “Grants”, theresultswillbelookedintothesedatabasesaccordingly.<br />Thenumberbetweenbracketssimplyindicatestheamount of resultsin thosedatabases.<br />
  32. 32. 3<br />Discoverthedifferentfunctions / Visualization of results<br />SORT RESULTS<br />DATABASES<br />snippets<br />sentences<br />complete<br />By default, theresultsdetails are shownwithsnippets, butyou can clickthewindowstoviewonly “title”, or “sentences” or “complete description”.<br />By default, theresults are sortedby date (newestfirst) butyou can clickthelist and chosetosortthembydate (oldestfirst) orbyrelevance.<br />Theprinticon opens a new windowwheretheresultstoyoursearch are readyforprinting.<br />
  33. 33. 3<br />Discoverthedifferentfunctions / Results page<br />By default, there are 10 resultsby page, butyou can easilychangeyourpreferences (see page 24) and set itto 20, 30, 40 or 50.<br />Theresultsshownabove are in Medline, whenthefull textversionisavailable, a direct link toitisshown so you can consultitdirectly .<br />
  34. 34. 3<br />Discoverthedifferentfunctions / Articledetails<br />TITLE<br />LINK TO JOURNAL<br />PRINT <br />ArticlesDetails: Date / PMID / Authors / Journals<br />
  35. 35. 3<br />Discoverthedifferentfunctions / Concept details<br />CONCEPT<br />The concept page summarizesalltheinformationrelatedtothevery concept. Namely:<br /><ul><li>Elementinfowithname and alternativenames
  36. 36. Links tootherdatabases
  37. 37. Recentdocuments</li></li></ul><li>3<br />Discoverthedifferentfunctions / Advancedsearch page<br /><ul><li>Select corpus (database) fromMedline, Full TextorGrants.
  38. 38. Selectfields. Thisoptionallowsyoutoselectthefieldsyouwantyoursearchtobeperformed in:
  39. 39. Select the option thatbestmatchesyourneedorcombine several of them tomakeyoursearcheven more precise.
  40. 40. Youjusthavetotype in whatyou are lookingfor. Theauto complete functionwillhelpyou. You can add as many boxes as youneed.
  41. 41. Thedateshelpyouspecify a period, a startingorending date to match yourneeds.</li></li></ul><li>3<br />Discoverthedifferentfunctions / Usingadvancedqueryshortcuts<br />Usingtags in yourqueries:<br /><ul><li>Make your search be quicker by using the tag corresponding to the concept you want to look for.
  42. 42. [disease], [dis]: DiseasesorSyndromes
  43. 43. [chemical], [chem], [chm]: Chemicalsubstances
  44. 44. [gene], [gen], [protein]: Genes and Proteins
  45. 45. [organism], [species]: Organisms
  46. 46. [symptom], [sym]: Signs and Symptoms
  47. 47. [drug]: Pharmacologicalsubstances
  48. 48. [tissue]: Tissues
  49. 49. [organ]: Organs and Bodyparts
  50. 50. [author], [authorname], [auth], [au]: Authornames
  51. 51. [journal], [jour], [jo]: Journaltitles
  52. 52. [mesh]: MeSHterms</li></ul>Checkexample<br />Checkexample<br />Checkexample<br />
  53. 53. 3<br />Discoverthedifferentfunctions / Usingadvancedqueryshortcuts<br />Usinglogicaloperators in yourqueries:<br /><ul><li>Make your search be quicker by using logical operators to specify with more details
  54. 54. “ “specifytheexactwordsto look for . Ifnotspecified, thesystem looks forpublicationswhereany of thewordappears.</li></ul>checkexamplewith and<br /><ul><li>AND specifytwoor more wordsto look for. Theresultswillincludebothsearchterms.</li></ul>checkexample<br /><ul><li>ORspecifyto look whetherforonetermortheotherintothesearchresults.</li></ul>checkexample<br /><ul><li>NOTexcludeoneor more searchtermsfromtheresults. </li></ul>checkexample<br />breastcancer<br />“breastcancer”<br />Breast AND cancer<br />Breast OR cancer<br />Breast NOT cancer<br />
  55. 55. 3<br />Discoverthedifferentfunctions / Set up preferences<br />Set thenumber of relatedelementsto showto 20 (by default), 50 or 100.<br />Set thenumber of documentsto show oneach page to 10 (by default), 20, 30, 40 or 50.<br />
  56. 56. Learn to perform effective searches<br />Case study: Asperger Syndrome and Bipolar disorder in autism<br />
  57. 57. 4<br />Learnhowtoperformeffectivesearches / Case study<br />Case study: Asperger Syndrome and Bipolar disorder in autism<br /><ul><li>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. 58. First we type in ”autism“ in the main search box.
  59. 59. The results page for autism displays 10.657 publications in Medline. (on July 3rd 2009)</li></li></ul><li>4<br />Learnhowtoperformeffectivesearches / Case study<br />Case study: Asperger Syndrome and Bipolar disorder in autism<br /><ul><li>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. 60. We now click on the “more” link next to “Diseases or Syndromes” to display all the related concepts.
  61. 61. We can see all the Diseases or Syndromes related to the current search for autism. ”Asperger syndrome” is 7th in the list.
  62. 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. 63. The filter is added to the search and we now have 684 results in Medline as shown in next slide.</li></li></ul><li>4<br />Learnhowtoperformeffectivesearches / Case study<br />
  64. 64. 4<br />Learnhowtoperformeffectivesearches / Case study<br />Case study: Asperger Syndrome and Bipolar disorder in autism<br /><ul><li>We repeat the same process with “bipolar disorder”. This one is almost at the bottom of the list.
  65. 65. We now have 11 results in Medline for the search on Asperger syndrome and bipolar disorder in autism.
  66. 66. According to the medical librarian interested in these publications, there were satisfying enough.</li></li></ul><li>More resources on novoseek<br />use novoseek<br />Install in firefoxsearch bar<br />Installthewidget<br />Makesuggestions<br />Reachusontwitter<br />Writetous<br />
  67. 67. Contact Info<br />ValentinVivier<br />Marketing Department<br />vvivier@bioalma.com <br />Phone: +34 91 141 71 50<br />
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