User Guide for KITE Availability Tool
Contents
1. National Institute for Health and link Welfare Helsinki Birth 2500 DNA Serum National Institute for Health and link Cohort Study Welfare University of Helsinki Helsinki Sudden 693 DNA pathological slides paraffin embedded tissue National Institute for Health and link Death Study Welfare and University of Tampere University of Helsinki 2014 PT zem FIMM Picture 2 1 The KITE front page view and paths to other pages presented 3 Browse page User Guide for KITE 05 2015 Browse page is for browsing through lists of variables available in each sample collection These variables are divided into categories topics The user can see all the projects and the data categories on a list Click the arrow to open a collection tree and you will see different categories below By selecting a category you will see related variables You can add variables to query cart by clicking the green plus figure It is also possible to select all the variables in a category by selecting Eegen Language selection button is found above the list currently variable data available in Finnish and English See more information about a variable by placing the mouse cursor on a variable row An information box will show up KITE Q Search RG Ouery cart Login Select language EN Browse Variable Metadata gt DILGOM 2007 gt FINRISK 1992 Y FINRISK 1997 Ability to work and function Alcohol consumption Background P Basic informatio2. to one collection for example FINRISK 2002 write the whole collection name FINRISK 2002 to the search field and add all variables to the car KITE e Search RG Ouerycart Login Select language EN FI Search for variables Basic Search Options Search for University of Helsinki 2014 TT somes FIMM Picture 4 1 KITE Basic Search view User Guide for KITE 05 2015 Definitions for Basic search results Table of search results Collection name of the collection Category Topic of the variable for example Health status includes variables that are related to health status topic Label variable specific original code in a given collection Name a short description of the variable Protocol measurement protocol Select by clicking from the right side of the table you can add variables to the query cart You can also add all Information box Description detailed information about a variable such as original question in the questionnaire form or detailed information about laboratory measurement Question nro original question number in questionnaire Protocol measurement protocol Enums enumerations of class variables Min minimum possible value for variable Max maximum possible value for variable Datatype type of data such as integer date free text etc UMLS Unified Medical Language System UMLS Metathesaurus reference library code and description for the variable https uts nim n
3. variable https uts nlm nih gov metathesaurus html Select by clicking from the right side of the table you can add variables to the query cart You can also add all Information box Description detailed information about a variable such as original question in the questionnaire form or detailed information about laboratory measurement Question nro original question number in questionnaire Protocol measurement protocol Enums enumerations of class variables Min minimum possible value for variable Max maximum possible value for variable 10 User Guide for KITE 05 2015 Datatype type of data such as integer date free text etc UMLS Unified Medical Language System UMLS Metathesaurus reference library code and description for the variable https uts nim nih gov metathesaurus html Keywords search words related to the topic of the variables 5 Query cart Query cart lists all the variables selected from the search and browse results Using the query cart you can also export variable metadata from KITE as csv file If the query cart does not have any variables selected the Query cart is empty text is visible If the query cart contains selected variables you can view variables and remove variables that are not needed The Clear button clears all the variables from your query cart Export the variable list by clicking the Export variable list csv button 6 Login Login is not ap
4. User Guide for KITE Availability Tool National INSTITUTE TOF HEAITN anqa VVelTare 05 2015 U 5 2 U 1 D User Guide for KITE 05 2015 Contents Te MATFOCUGCTION MR AA ERA AA EE RE N EE EN 3 GE Gel ee EE 4 3 e Ee Let E 5 4 aeach e LEE 6 Ai BASC SCAG DEE 7 4 2 COUONS SeA ona a a Sd ets esas 8 5 QUEM CaN acetic eee a ee er ee ee ee 11 Os OE DEE 11 EENEG 11 User Guide for KITE 05 2015 1 Introduction KITE is an open web based availability service for researchers to find metadata about existing Finnish sample collections and sample collection variables KITE is a catalog and a query tool developed by the Institute for Molecular Medicine Finland FIMM and the National Institute for Health and Welfare THL and funded by the BBMRI fi KITE gives internationally standardized and summarized information about available sample collections and offers browse and search functionalities for targeted variable search The user can either browse variables straight from the collection trees or use the search tool with several options to find and select specific variables The selected variables are collected to a query cart from where they can be easily downloaded httos kite timm fi F D NATIONAL INSTITUTE BBMRI fi FMM FOR HEALTH AND WELFARE User Guide for KITE 05 2015 2 Front page Available Collections The front page has a table of sample collections showing the collection name number of participants sample type
5. ih gov metathesaurus html Keywords search words related to the topic of the variables 4 2 Options search Options search gives wider options to find variables from specific collections or by using specific variable information fields such as category description variable keywords and reference terms UMLS etc With these options it is possible to limit and control the search results and to target the search as needed User Guide for KITE 05 2015 KITE e Search RG Ouery cart Login Select language EN FI Search for variables BasicSearch Options Select collections for variable search DILGOM 2007 FINRISK 1992 FINRISK 1997 FINRISK 2002 FINRISK 2007 FINRISK 2012 FSZ FBP HBCS Health 2000 2011 HSDS HUB Kuusamo Health Examination METSIM YFS Select variable information fields for search Label UMLS Search for University of Helsinki 2014 PT et FIMM Picture 4 2 KITE Options search view In Select collections for variable search section you can choose collection s which you want to include in the search It is possible to select or deselect all the collections In Select variable information field for search section you can choose from different information fields you want to include in the search It is possible to select or deselect all the information fields Enter the search word s to Search for field Search results See more information about a variable by placing the mouse cursor on a
6. n P Biology P Biomarkers DNA gt Follow up General health status Health and wellbeing P Health status Health status last year Height and weight questions Indexes P Laboratory results Medication Nutrition Other questions University of Helsinki 2014 Label AMM AMM_K9 KI K14A K14B K16 K5 K5VUOSI KOULV KUNT_K14 Display name Occupation Occupation code Number of persons in household Number of persons in household under the age of 7 Number of persons in household aged between 7 and 16 Domicile under the age of 7 Spouse Number of spouse s years of education Number of years of education Mother s birth municipality Od un Picture 3 1 KITE Browse page view The collection trees on left and the variable table on right Add all KA Ka Fi EA EA ii E1 ii EMA User Guide for KITE 05 2015 Definitions for Browse page Variable table Label variable specific original code in a given collection Display name a short description of the variable Select by clicking EJ from the right side of the table you can add variables to the query cart You can also add all Information box Description detailed information about a variable such as original question in the questionnaire form or detailed information about laboratory measurement Question nro original question number in questionnaire Protocol measurement protocol Enums enumerations of class variables Min minimum
7. plicable yet Contact information Email biopankki thl fi National Institute for Health and Welfare THL THL Biobank 11
8. possible value for variable Max maximum possible value for variable Datatype type of data such as integer date free text etc UMLS Unified Medical Language System UMLS Metathesaurus reference library code and description for the variable https uts nim nih gov metathesaurus html Keywords search words related to the topic of the variables 4 Search page The Search page offers two options for collection variable search Basic search is a quick search with one simple field for search word s Options search has more options to limit and control the search results User Guide for KITE 05 2015 4 1 Basic search Basic search is a quick search for finding variables The user can enter search word s and find variables matching the specific subject This search will find variables from all the collections that match the search word s Enter the search word to Search for field Search results See more information about a variable by placing the mouse cursor on a variable row An information box will show up Search summary shows terms found per each collection Language selection is above the search field currently variable data available in Finnish and English TIP Use basic search if you want to search in which collection there is data about specific topic For example to find in which sample collection information on Smoking is available TIP If you want to view and download all the variables belonging
9. s owner institute and link to collection web page By clicking link under the web page heading it will open to a new window to collection s web page By clicking you will find summarized details about the collection The collections are described using MIABIS attributes hitp obmri wiki wikidot com en dataset collection Browse collection variables by categories button will lead to browse page read more in page 5 Search menu button leads to search page read more in page 6 Query cart menu button leads to query cart read more in page 11 and also shows the number of variables in the query cart To search page To query cart KITE Q search RG Query cart Login Se KITE is an open web based database that contains information on available sample collections In KITE you can find metadata about existing Finnish sample collections and you can browse through lists of variables available in each sample collection KITE has also a query tool that allows searching for specific variables Variables of interest can be selected into a query cart and downloaded Variables Search To browse page Browse collection variables by categories Available Collections Collection Participants Sample types Owner institute web Info ES To collection page DILGOM 2007 2014 5024 DNA EDTA plasma serum PBMC cells PAXgene RNA National Institute for Health and 8 un To see details Health 2000 2011 8680 DNA plasma serum
10. variable row An information box will show up Search summary shows variables found per each collection that answer the specific search criteria Language selection is above the search field currently variable data available in Finnish and English TIP If you want to find information about a specific variable for which you have the original variable code select only Label in the Select variable information fields for search box TIP If you want to find similar variables from different collection select the Display name and UMLS in the Select variable information fields for search box User Guide for KITE 05 2015 Definitions for Options search Variable information fields Category search by topic Description use detailed variable description for search Display name search using short descriptions Keywords search includes related keywords and returns more variables Label search by variable code UMLS search by reference term Definitions for Options search results Table of search results Collection name of the collection Category combining topic for variables for example Health status includes variables that are related to health status topic Label variable specific original code in a given collection Name a short description of the variable Protocol measurement protocol UMLS Unified Medical Language System UMLS reference library code and description for the
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