Unleashing The Power Of Novoseek
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www.novoseek.com novo|seek Unleashing the power of novo|seek New biomedical search engine
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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.
Transcript of Unleashing The Power Of Novoseek
www.novoseek.com
novo|seek
Unleashing the power of novo|seek
New biomedical search engine
www.novoseek.com
1. Presentation of novoseek, the biomedical search engine
2. Understand the layout of the search engine
3. Discover the different functions
4. Learn how to perform effective searches (case study)
Table of Content
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Discover what is novo|seek and why it is different to the other search engines
Presentation of novoseek
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Presentation of novoseek, the biomedical search engine
What is novoseek?
It is a search engine for searching the published knowledge in biomedical literature that identifies 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.
Why is it different to other biomedical search engines?
novo|seek indexes biomedical literature using text mining technology that combines information extraction, name entity recognition and knowledge discovery technologies to provide the most relevant and meaningful biomedical search results.
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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.
Perform meaningful searches
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.
1 Presentation of novoseek, the biomedical search engine
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Understand the layout of the search engine
Understand the layout
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MAIN SEARCH BOX
HELP
NEWS & TOOLS BOX
INFORMATION
ADVANCED SEARCH & PREF
2 Understand the layout of the search engine / main page
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CHOICE OF DATABASEOPTIONS TO CHOSE VISUALIZATION OF RESULTS
RESULTS
FILTERS RELATED TO SEARCH POP UP BARS TO GET MORE INFORMATION ON THE RESULTS
2 Understand the layout of the search engine / results page
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ARTICLE DETAILS
POP UP BARS TO GET MORE INFORMATION ON THE RESULTS
LINK TO JOURNAL PRINT
2 Understand the layout of the search engine / article details
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CONCEPT DETAILS PRINT NEW SEARCH
2 Understand the layout of the search engine / concept details
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Get an in-depth knowledge of the different functions available
Discover the different functions
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The filters related to the search are presented in the left sidebar. They are organized in 11 different concepts and identifiable by colors:
Diseases or syndromes Pharmacological substances Genes & Proteins Signs & Symptoms Chemical substances Organisms Organs & Body parts Tissues Cell components Biological functions Procedures / Techniques
The bar indicates the relevance of the concept according to the current search.
The “i” icon allows to add the concept to the current search or see more information on this concept.
3 Discover the different functions / Filters related to search
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3 Discover the different functions / Filters related to search 2
Click on the “Bibliographics” tab to display all the Authors and Journals related to your search.
Click on the “more” link to display all the related concepts as shown below.
Click again on “less” to display again 3 of them as shown in the image above..
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Clicking on the “i” icon displays an informative pop-up window allowing several actions:
Perform a new search for the selected concept (here “brca1 mutation”).
Add the concept as a filter to the current search The search is refined and there are less results.
Exclude the concept from the search results.
Go to the concept details page.
3 Discover the different functions / Filters related to search 3
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Clicking on the pop-up bar “Show search details”, you will be able to consult what is your current search and the corresponding results:
The first line states the amount of results from the text analysis.
The second line states the amount of results when your search has been mapped.
3 Discover the different functions / Search details
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Clicking on the pop-up bar “Show highlight panel”, you will be able to highlight one, several or all of the concepts identified in the results.
For instance, if you check “Diseases or Syndromes”, they are immediately highlighted in the results with the corresponding color as explained before .
√
3 Discover the different functions / Highlight concepts
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By default, the search engine looks for results in MEDLINE database.
Simply by clicking “Full Text” of “Grants”, the results will be looked into these databases accordingly.
The number between brackets simply indicates the amount of results in those databases.
3 Discover the different functions / Choice of database
DATABASES
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By default, the results details are shown with snippets, but you can click the windows to view only “title”, or “sentences” or “complete description”.
By default, the results are sorted by date (newest first) but you can click the list and chose to sort them by date (oldest first) or by relevance.
The print icon opens a new window where the results to your search are ready for printing.
snippets sentences complete
3 Discover the different functions / Visualization of results
DATABASESSORT RESULTS
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By default, there are 10 results by page, but you can easily change your preferences (see page 24) and set it to 20, 30, 40 or 50.
The results shown above are in Medline, when the full text version is available, a direct link to it is shown so you can consult it directly .
3 Discover the different functions / Results page
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LINK TO JOURNAL PRINT
Articles Details: Date / PMID / Authors / Journals
TITLE
3 Discover the different functions / Article details
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CONCEPT
3 Discover the different functions / Concept details
The concept page summarizes all the information related to the very concept. Namely:
Element info with name and alternative names
Links to other databasesRecent documents
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Select the option that best matches your need or combine several of them to make your search even more precise.
You just have to type in what you are looking for. The auto complete function will help you. You can add as many boxes as you need.
The dates help you specify a period, a starting or ending date to match your needs.
3 Discover the different functions / Advanced search page
Select corpus (database) from Medline, Full Text or Grants.
Select fields. This option allows you to select the fields you want your search to be performed in:
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Using tags in your queries:
Make your search be quicker by using the tag corresponding to the concept you want to look for.
[disease], [dis]: Diseases or Syndromes [chemical], [chem], [chm]: Chemical substances [gene], [gen], [protein]: Genes and Proteins [organism], [species]: Organisms [symptom], [sym]: Signs and Symptoms [drug]: Pharmacological substances [tissue]: Tissues [organ]: Organs and Body parts [author], [author name], [auth], [au]: Author names [journal], [jour], [jo]: Journal titles [mesh]: MeSH terms
3 Discover the different functions / Using advanced query shortcuts
Check example
Check example
Check example
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3 Discover the different functions / Using advanced query shortcuts
Using logical operators in your queries:
Make your search be quicker by using logical operators to specify with more details
“ “ specify the exact words to look for . If not specified, the system looks for publications where any of the word appears.
check example with and
AND specify two or more words to look for. The results will include both search terms.
check example
OR specify to look whether for one term or the other into the search results.
check example
NOT exclude one or more search terms from the results. check example
breast cancer
“breast cancer”
Breast AND cancer
Breast OR cancer
Breast NOT cancer
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3 Discover the different functions / Set up preferences
Set the number of related elements to show to 20 (by default), 50 or 100.
Set the number of documents to show on each page to 10 (by default), 20, 30, 40 or 50.
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Case study: Asperger Syndrome and Bipolar disorder in autism
Learn to perform effective searches
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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.
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)
4 Learn how to perform effective searches / Case study
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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.
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.
4 Learn how to perform effective searches / Case study
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4 Learn how to perform effective searches / Case study
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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.
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.
4 Learn how to perform effective searches / Case study
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