novo|seekUnleashing the power of novo|seekNew biomedical search engine

Table of ContentPresentation of novoseek, thebiomedicalsearchengineUnderstandthelayout of thesearchengineDiscoverthedifferentfunctionsLearnhowtoperformeffectivesearches (case study)

Presentation of novoseekDiscover what is novo|seek and why it is different to the other search engines

Presentation of novoseek, thebiomedicalsearchengine1Whatisnovoseek?Itis a searchengineforsearchingthepublishedknowledge in biomedicalliteraturethatidentifies the key biomedical terms taking into account external available data and contextual term information.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.

Itis a searchengineforsearchingthepublishedknowledge in biomedicalliteraturethatidentifies the key biomedical terms taking into account external available data and contextual term information.

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.

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.

1Presentation of novoseek, thebiomedicalsearchengineThe conceptual searchAs 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.PerformmeaningfulsearchesNovoseek 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.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 [ ] and specifying what you want to consult.You can use logical operators to specify your search with more details from the main search box.

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.

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.

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 [ ] and specifying what you want to consult.

You can use logical operators to specify your search with more details from the main search box.

Understand the layoutUnderstand the layout of the search engine

2Understandthelayout of thesearchengine / main pageHELP ADVANCED SEARCH & PREFMAIN SEARCH BOXINFORMATIONNEWS & TOOLS BOX

2Understandthelayout of thesearchengine / results pagePOP UP BARS TO GET MORE INFORMATION ON THE RESULTSFILTERS RELATED TO SEARCHOPTIONS TO CHOSE VISUALIZATION OF RESULTSCHOICE OF DATABASERESULTS

2Understandthelayout of thesearchengine / articledetailsPOP UP BARS TO GET MORE INFORMATION ON THE RESULTSLINK TO JOURNALPRINT ARTICLE DETAILS

2Understandthelayout of thesearchengine / concept detailsPRINT NEW SEARCH CONCEPT DETAILS

Discover the different functionsGet an in-depth knowledge of the different functions available

3Discoverthedifferentfunctions / FiltersrelatedtosearchThefiltersrelatedtothesearchare presented in theleftsidebar. They are organized in 11 differentconceptsandidentifiablebycolors:DiseasesorsyndromesPharmacologicalsubstancesGenes & ProteinsSigns & SymptomsChemicalsubstancesOrganismsOrgans & BodypartsTissuesCellcomponentsBiologicalfunctionsProcedures / TechniquesThe bar indicatestherelevanceof the concept accordingtothecurrentsearch.The “i” iconallowstoaddthe concept tothecurrentsearchorsee more informationonthis concept.

Diseasesorsyndromes

Pharmacologicalsubstances

Genes & Proteins

Signs & Symptoms

Chemicalsubstances

Organisms

Organs & Bodyparts

Tissues

Cellcomponents

Biologicalfunctions

Procedures / Techniques

3Discoverthedifferentfunctions / Filtersrelatedtosearch 2Clickonthe “Bibliographics”tabtodisplayalltheAuthorsandJournalsrelatedtoyoursearch.Clickonthe “more” link todisplayalltherelatedconcepts as shownbelow.Clickagainon “less” todisplayagain 3 of them as shown in theimageabove..

3Discoverthedifferentfunctions / Filtersrelatedtosearch 3Clickingonthe “i” icondisplaysaninformative pop-up windowallowingseveralactions:Perform a new searchfortheselected concept (here “brca1 mutation”).Addthe concept as a filtertothecurrentsearch Thesearchisrefined and there are lessresults.Excludethe concept fromthesearchresults.Gotothe concept details page.

Perform a new searchfortheselected concept (here “brca1 mutation”).

Addthe concept as a filtertothecurrentsearch Thesearchisrefined and there are lessresults.

Excludethe concept fromthesearchresults.

Gotothe concept details page.

3Discoverthedifferentfunctions / SearchdetailsClickingonthe pop-up bar “Show searchdetails”, youwillbeabletoconsultwhatisyourcurrentsearch and thecorrespondingresults:Thefirst line statestheamount of resultsfromthetextanalysis.Thesecond line statestheamount of resultswhenyoursearch has beenmapped.

Thefirst line statestheamount of resultsfromthetextanalysis.

Thesecond line statestheamount of resultswhenyoursearch has beenmapped.

3Discoverthedifferentfunctions / 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 .

3Discoverthedifferentfunctions / Choice of databaseDATABASESBy default, thesearchengine looks forresults in MEDLINE database.Simplybyclicking “Full Text” of “Grants”, theresultswillbelookedintothesedatabasesaccordingly.Thenumberbetweenbracketssimplyindicatestheamount of resultsin thosedatabases.

3Discoverthedifferentfunctions / Visualization of resultsSORT RESULTSDATABASESsnippetssentencescompleteBy 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.

3Discoverthedifferentfunctions / Results pageBy 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 .

3Discoverthedifferentfunctions / ArticledetailsTITLELINK TO JOURNALPRINT ArticlesDetails: Date / PMID / Authors / Journals

3Discoverthedifferentfunctions / Concept detailsCONCEPTThe concept page summarizesalltheinformationrelatedtothevery concept. Namely:Elementinfowithname and alternativenamesLinks tootherdatabasesRecentdocuments

Elementinfowithname and alternativenames

Links tootherdatabases

Recentdocuments

3Discoverthedifferentfunctions / Advancedsearch pageSelect corpus (database) fromMedline, Full TextorGrants.Selectfields. Thisoptionallowsyoutoselectthefieldsyouwantyoursearchtobeperformed in:Select the option thatbestmatchesyourneedorcombine several of them tomakeyoursearcheven more precise.Youjusthavetotype in whatyou are lookingfor. Theauto complete functionwillhelpyou. You can add as many boxes as youneed.Thedateshelpyouspecify a period, a startingorending date to match yourneeds.

Select corpus (database) fromMedline, Full TextorGrants.

Selectfields. Thisoptionallowsyoutoselectthefieldsyouwantyoursearchtobeperformed in:

Select the option thatbestmatchesyourneedorcombine several of them tomakeyoursearcheven more precise.

Youjusthavetotype in whatyou are lookingfor. Theauto complete functionwillhelpyou. You can add as many boxes as youneed.

Thedateshelpyouspecify a period, a startingorending date to match yourneeds.

3Discoverthedifferentfunctions / UsingadvancedqueryshortcutsUsingtags in yourqueries:Make your search be quicker by using the tag corresponding to the concept you want to look for.[disease], [dis]: DiseasesorSyndromes[chemical], [chem], [chm]: Chemicalsubstances[gene], [gen], [protein]: Genes and Proteins[organism], [species]: Organisms[symptom], [sym]: Signs and Symptoms[drug]: Pharmacologicalsubstances[tissue]: Tissues[organ]: Organs and Bodyparts[author], [authorname], [auth], [au]: Authornames[journal], [jour], [jo]: Journaltitles[mesh]: MeSHtermsCheckexampleCheckexampleCheckexample

Make your search be quicker by using the tag corresponding to the concept you want to look for.

[disease], [dis]: DiseasesorSyndromes

[chemical], [chem], [chm]: Chemicalsubstances

[gene], [gen], [protein]: Genes and Proteins

[organism], [species]: Organisms

[symptom], [sym]: Signs and Symptoms

[drug]: Pharmacologicalsubstances

[tissue]: Tissues

[organ]: Organs and Bodyparts

[author], [authorname], [auth], [au]: Authornames

[journal], [jour], [jo]: Journaltitles

[mesh]: MeSHterms

3Discoverthedifferentfunctions / UsingadvancedqueryshortcutsUsinglogicaloperators in yourqueries:Make your search be quicker by using logical operators to specify with more details“ “specifytheexactwordsto look for . Ifnotspecified, thesystem looks forpublicationswhereany of thewordappears.checkexamplewith andAND specifytwoor more wordsto look for. Theresultswillincludebothsearchterms.checkexampleORspecifyto look whetherforonetermortheotherintothesearchresults.checkexampleNOTexcludeoneor more searchtermsfromtheresults. checkexamplebreastcancer“breastcancer”Breast AND cancerBreast OR cancerBreast NOT cancer

Make your search be quicker by using logical operators to specify with more details

“ “specifytheexactwordsto look for . Ifnotspecified, thesystem looks forpublicationswhereany of thewordappears.

AND specifytwoor more wordsto look for. Theresultswillincludebothsearchterms.

ORspecifyto look whetherforonetermortheotherintothesearchresults.

NOTexcludeoneor more searchtermsfromtheresults.

3Discoverthedifferentfunctions / Set up preferencesSet 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.

Learn to perform effective searchesCase study: Asperger Syndrome and Bipolar disorder in autism

4Learnhowtoperformeffectivesearches / Case studyCase study: Asperger Syndrome and Bipolar disorder in autismWe 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.First we type in ”autism“ in the main search box. The results page for autism displays 10.657 publications in Medline. (on July 3rd 2009)

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.

First we type in ”autism“ in the main search box.

The results page for autism displays 10.657 publications in Medline. (on July 3rd 2009)

4Learnhowtoperformeffectivesearches / Case studyCase study: Asperger Syndrome and Bipolar disorder in autismFrom 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.We now click on the “more” link next to “Diseases or Syndromes” to display all the related concepts.We can see all the Diseases or Syndromes related to the current search for autism. ”Asperger syndrome” is 7th in the list.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.The filter is added to the search and we now have 684 results in Medline as shown in next slide.

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.

We now click on the “more” link next to “Diseases or Syndromes” to display all the related concepts.

We can see all the Diseases or Syndromes related to the current search for autism. ”Asperger syndrome” is 7th in the list.

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.

The filter is added to the search and we now have 684 results in Medline as shown in next slide.

4Learnhowtoperformeffectivesearches / Case study

4Learnhowtoperformeffectivesearches / Case studyCase study: Asperger Syndrome and Bipolar disorder in autismWe repeat the same process with “bipolar disorder”. This one is almost at the bottom of the list. We now have 11 results in Medline for the search on Asperger syndrome and bipolar disorder in autism.According to the medical librarian interested in these publications, there were satisfying enough.

We repeat the same process with “bipolar disorder”. This one is almost at the bottom of the list.

We now have 11 results in Medline for the search on Asperger syndrome and bipolar disorder in autism.

According to the medical librarian interested in these publications, there were satisfying enough.

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Contact InfoValentinVivierMarketing Departmentvvivier@bioalma.com Phone: +34 91 141 71 50