ReVis: User Manual - CCSL/ICMC
Contents
1. Double click studies to read full text PDFs on Edge Bundles or Table View Right click the studies on Table View to display the selection menu e Include or exclude studies by setting the inclusion or exclusion criteria used If you have any commentary about a study worth keeping for future stages or other reviewers use the commentary feature e If you are not sure whether to include or exclude a study set it to conflict state Use the Finish Current Stage button when you re finished selecting your studies Make sure that by the end of this stage all studies were either included or excluded even the ones in conflict state These will be reviewed in the 4 stage Stage 3 Quality Evaluation Using the quality criteria you set on the quality properties evaluate each of the selected studies based on the full text you read on the previous stage This is an important part of the systematic review as it puts all different studies from different sources in one same evaluation platform allowing comparison between them Main actions e Double click studies to read full text PDFs on Edge Bundles or Table View e Right click the studies on Table View to display the quality menu e Choose the score for each of the studies by clicking on the appropriate menu item e If you have any commentary about a study worth keeping for the next stage use the commentary feature Use the Finish Current Sta2. 7 for inclusion criteria or e for exclusion criteria Also the value part is actually the description of the criterion User s Manual PEx RS gt selection properties 38 I m 8 Q e s mc 1 Description of inclusion criterion i criterion2 Description of inclusion criterion nin i criterion3 Description of inclusion criterion e criterioni Description of exclusion criterion e criterion2 Description of exclusion criterion Oy U N ke WwW e criterion3 Description of exclusion criterion Figure 7 selection properties file quality properties Quality criteria for the third step of the selection quality evaluation entries are in the format name score for each possible quality score An example the default is show in Figure 8 quality properties m uw 5 0 0 2 quality2 2 5 3 quality3 5 0 4 quality4 7 5 5 quality5 10 0 Figure 8 quality properties review properties This file is used internally by the tool unless something s wrong with the review the user won t have to edit it input folder Stores the BibTeX input file for each of the review s steps and optionally the full text PDF s of the entries in the subfolder detailed below folder To open the full texts of the primary studies during the
3. amp b Scalar Quality m Figure 14 Finish Current Stage and Stop Review buttons Remember that no matter which stage you re in all visual exploration features are available use them as you need Stage 1 Pre selection When you first start your review this is the stage you re in The task is to pre select your studies by applying the inclusion exclusion criteria after reading each of the abstracts Main actions e Double click studies to read abstract on Edge Bundles or Table View e Right click the studies on Table View to display the selection menu Include or exclude studies by setting the inclusion or exclusion criteria used e If you have any commentary about a study worth keeping for future stages or other reviewers use the commentary feature e f you not sure whether to include or exclude a study set it to conflict state Use the Finish Current Stage button when you re finished pre selecting your studies Stage 2 Selection This stage is similar to the first only now the task is to select your studies by applying the inclusion exclusion criteria after reading the full text of each pre selected study Studies that were excluded on the first stage will appear in light red and included ones in light green Remember that in order to be able to read the full text inside ReVis you must have prepared the pdf folder as described earlier Main actions 14 User s Manual PEx RS
4. double clicking will show the abstract or the full text The color scale is also the same showing instances which were not analyzed excluded or included second stage also changes like in the Edge Bundles view E Projection s X Network Viewer se 5 ise 6 a 62 3 uo mmm nee Figure 11 Projection The action buttons however are quite different than the other views There a few more options to be explored in this view as explained below User s Manual PEx RS Scalar this is located on the main toolbar above the mappings and works for all views When there are different attributes to be viewed as colors this changes which one 15 active The two most common are Sys Review which shows the included excluded status and Quality which shows the instances scores Save Image saves a PNG image of the current state of the visualization in a user selected folder Search textual search on the studies abstracts A new color scale will be created and instances will be colored according to the frequency of the query in their abstracts Enable Disable Edges initially there are no edges on the projection you can however enable them with this button The undirected edges will then link nearest neighbors in the projection When edges are enabled selecting an instance will also highlight the connected instances Instance Selection default sel
5. USP UNIVERSITY OF SAO PAULO ICME ICMC INSTITUTE OF MATHEMATICS AND COMPUTER SCIENCE ae d DEPARTAMENT OF COMPUTER SCIENCE P O Box 668 13560 970 S o Carlos SP Brazil ReVis User Manual v0 3 Systematic Review Supported by Visual Analytics Rev Hn 7 1 September 2010 Summary Introduction and OVerview eb ii ein egre 3 orbem Emm 3 SEARS ae acad i Dai et eaa 2 Creatine the Input Filed oda 2 Creating qc Poles roe means Imo Ue Mo E 3 Th ReVis Project SUUCIUEE ia 5 Starting the Selection os vest ite acean 7 Vis alizationS PET 7 octo pide td iiec inert dtu pte te ADM D DE 7 PEOISCUON cac oe M eiae lu Lc 9 VIeWEE mt t dme SE Pret met 11 Fabl NCW mr ITE 12 Performing the Selection Four Stages 5 etta tente eise eh oet 13 Stage Ic Pre SSlECU OM csser ne 14 Stage 2 Selection gasses nu bebida RON OUI a E e E eens Qus 14 Stage 3 Quality By alu ae On sssini Aesch sous ui eal unde ides 15 Stage 42 Review Dy Expert isnt eigenen 16 Contact oi e eto Set a ee Me 16 IBID HORT apy Em 17 User Manua
6. compress the file The content will be di bin duster etc ide12 11 platform11 di revis http infoserver lcad icmc usp br infovis2 PEx User s Manual PEx RS Next open the folder bin and run the file W revis exe Getting Started In order to use ReVis to support the primary studies selection in your systematic review it is first necessary to prepare an input file according to a few rules This input file will include all the primary studies that returned from your search thus the search is not made from within the tool After you prepared your input file you can create a new project within ReVis to generate the visualizations and perform the selection Detailed descriptions of the input file and the tool s user interface are provided in the next sections Creating the Input File The BibTeX file format bib is currently the only format accepted by ReVis It is used to describe and process lists of references mostly in conjunction with LaTeX documents For details about the general structure of a BibTeX file please refer to the site We recommend using the JabRef tool for the input file creation it is free and open source and it is available online for download ReVis treats a BibTeX input file as a collection of entries where each entry represents one primary study returned by your search From all possible fields available for BibTeX entries the following are the most important when us
7. dial Layout le We Min NNNM sax Figure 10 Edge Bundles There are three action buttons available on the toolbar of the Edge Bundles view to see the names hover the mouse over them e Scalar this is located on the main toolbar above the mappings and works for all views When there are different attributes to be viewed as colors this changes which one is active The two most common are Sys Review which shows the included excluded status and Quality which shows the instances scores e Save Image saves a PNG image of the current state of the visualization in a user selected folder User s Manual PEx RS Instance Selection default selection mode for instances currently cannot be changed e Identity Coordination default coordination mode currently cannot be changed Projection The visualization on the right before the table is called a Projection It is a 2D document map that distributes instances along the screen by bringing closer the most similar ones and separating the most different ones based on the textual content in this case the abstract of the studies Again as in the Edge Bundles view the small circles represent studies Direct user interaction on the Projection view is similar to Edge Bundles you can select a single instance or a group by single clicking or dragging the mouse buttons which will highlight them in all other views and
8. ection mode for instances with this enabled selecting will only highlight them in all views Topic Selection alternate selection mode for instances with this enabled selecting will also generate and display the most important topics for the selected group Create Topic Clusters this action will ask for a number N of clusters with a reasonable default and divide the document set into N groups of nearest neighbors It will also generate and display the most important topics for each cluster automatically enabling Topic Selection Show Hide Labels when Topic Selection is enabled this will show or hide the labels that display the generated topics Highlight Label Clusters when Topic Selection and this button are enabled topic clusters will be highlighted when you hover the mouse over them Identity Coordination default coordination mode currently cannot be changed 10 User s Manual PEx RS Network Viewer In the same slot as the Projection visualization but behind it check the tabs is the Network Viewer This visualization is created from the references information on the BibTeX input file and shows all the primary studies with their respective referenced papers It uses a force based layout meaning that studies attract each other depending on how strong is their connection references to each other Thus studies that are far from the center are less cited and studies grouped near the center are more c
9. ge button when you re finished evaluating your studies Make sure that by the end of this stage all selected studies were evaluated 15 User s Manual PEx RS Stage 4 Review by Expert This stage offers both selection and evaluation features to the reviewer it s meant to be used by an expert to evaluate and possibly change all the decisions that were made during the review Main actions Double click studies to read full text PDFs on Edge Bundles or Table View Right click the studies on Table View to display the quality selection menu e Review decisions of studies on conflict state Include or exclude studies by setting the inclusion or exclusion criteria used e Change the score of the studies by clicking on the appropriate menu item If you have any commentary about a study worth keeping for the next stage use the commentary feature Contact For questions suggestions or problems in the use of the tool contact Rafael Messias Martins rafaelmm Q icmc usp br Katia Romero Felizardo katiarf icmc usp br 16 User s Manual PEx RS Bibliography 1 Danny Holten Hierarchical Edge Bundles Visualization of Adjacency Relations in Hierarchical Data IEEE Transactions on Visualization and Computer Graphics TVCG Proceedings of Vis InfoVis 2006 Vol 12 No 5 Pages 741 748 2006 17
10. h file in order to customize them for your own review The detailed description of each file is presented in the next section The ReVis Project s Structure The folder file structure of a ReVis project is shown in Figure 6 Each file has an important role on the generation of the visualizations and the performing of the primary study selection Properties files can be edited inside the tool by double clicking them BibTeX files can also be edited but in text mode only as stated earlier we recommend a tool such as JabRef Each folder and file is explained below in details After you understand the structure edit the selection and quality files according to your review then check the next section on how to start the selection Projects 4 3 5 12 ReVis Projecti 3 D config quality properties sS review properties selection properties Qi input pdf 3 papers bib e review pip e Figure 6 A ReVis project s structure e config folder This folder stores configuration files for the review as properties files The general format for the entries is name value specific details are explained below e selection properties Inclusion and exclusion criteria for the first and second steps of the selection An example the default is show in Figure 7 although it follows the same rule as all properties files name value the name part must begin with
11. ing ReVis In this entry the first line a contains the entry key There is no special formatting for this field but if you re using JabRef we recommend using the tool s automatic key generation feature The b item includes the names of the authors of the entry They can be written as the last name followed by the initials separated by comma Each author is separated from the others with an and statement Items c and d are respectively the title and the year of the entry The abstract d is not often included in BibTeX files but in this case it is absolutely necessary without it the visualizations can t be generated The remaining lines e are the references of the http www bibtex org http www latex project org http jabref sourceforge net User s Manual PEx RS entry each reference represented by its title one per line It is very important that titles are written in the exact same way throughout the whole file or else the tool will not be able to correlate entries ARTICLE Martins2010 author Martins R and Felizardo K title ReVis User Manual year 2010 abstract ReVis is a tool for ot references titlel title2 Figure 1 Example of a ReVis entry on a BibTeX file Creating Project With the input file ready start ReVis and you will see the tool s main menu Figure 2 File Team Tools Window Help D mE Figure 2 ReVis mai
12. ited Figure 12 Again the direct user interaction and the colors are similar to the views already described please check the two previous sections A simple selecting in this view however will also highlight referenced items that are not on the review themselves on a lighter gray Selecting a study that is not on the review one that is only referenced will also highlight its main study the study that is on the review and references the first Since this view has edges automatically enabled selecting an instance will also select all the connected instances The action buttons available in this view are the following Scalar this is located on the main toolbar above the mappings and works for all views When there are different attributes to be viewed as colors this changes which one is active The two most common are Sys Review which shows the included excluded status and Quality which shows the instances scores Save Image saves a PNG image of the current state of the visualization in a user selected folder e Enable Disable Edges initially the edges are automatically enabled you can however disable them with this button This affects the Force button and the propagation of instance selection e Start Stop Force as said earlier the Network Viewer distribution of instances on the 2D area of the screen is made with a force based layout You can control this process by starting stopping the f
13. l Introduction Overview Projection Explorer PEx is a flexible visualization tool that has several text handling facilities which allows for a VTM Visual Text Mining exploration of a collection of documents It is an open source tool that has been developed at the University of Sao Paulo ReVis Systematic Review Supported by Visual Analytics is an extension of PEx created to support selection and quality evaluation of primary studies in systematic reviews It offers visual mappings of the set of primary studies to be reviewed in order to help the user explore the data ReVis the selection and quality evaluation are performed in four consecutive stages 1 the pre selection when the user includes or excludes studies based on their abstracts 2 the selection when the user includes or excludes studies based on their full texts 3 quality evaluation when the user applies a score to the selected papers based on the quality of their content and 4 review when an expert has the chance to change the selection or quality evaluation if needed It s important to note that ReVis acts only on the selection and quality evaluation of the studies not on the initial search To use the tool the user must first create the queries and obtain the full set of primary studies to be analyzed Installation First you must download the program ReVis in e http ccsl icmc usp br redmine projects revis files After you must de
14. link primary studies are bundled or grouped together by proximity 1 Instances are hierarchically distributed along the three concentric circles of the radial layout of the visualization The hierarchy is based on the frequency of text topics that are automatically extracted from the studies abstracts by the tool You can check the topics by hovering the mouse over the arcs on the outer circles You can also see the instances keys as defined on the BibTeX input by hovering the mouse over them Initially all instances are grey which means they haven t been analyzed yet According to the color scale on the top left of the view the colors vary from red the study has been excluded to green the study has been included inclusion exclusion is done on the Table view In the second step the scale changes studies included excluded in the first step are colored in weak red and green while studies included excluded in the second step itself are colored in strong red and green User s Manual PEx RS Double clicking an instance will activate a context dependent action on the first step it opens the study s abstract on the second step it opens the full text if available Single clicking an instance will select it and also highlight it on all other visualizations You can also select a group of instances by dragging the left or right mouse button or by single clicking a topic arc Inverted Ra
15. n menu To start a new project select File then New Project Figure 3 UTIVIV File Team Tools Window Help NewProject Ctrl Shift N New F e Open Project Ctrl Shift O Open Recent Project Project Group Exit Figure 3 ReVis File menu ad User s Manual PEx RS You will see the window on Figure 4 choose ReVis Project and press Next Creates a new Systematic Review project with Visual Analysis support You may indicate a bib file as the input or it creates an empty one Figure 4 New Project initial window Fill in your project s name the location where it will be stored and indicate where is your BibTeX input file Figure 5 Name and Location 1 Choose Project 2 Name and Location ProjectName ReVis Projecti Project Location C Users RafaelDocuments WetBeansProjects Browse ProjectFolder c sers RafaellDocuments NetBeansProjects ReVis Projecti BibTeX File Browse Please choose your BibTeX Ee gt a Se Figure 5 New Project second window 4 User s Manual PEx RS Press Finish and the project will be created You can see it in the Projects view usually in the left side of the main window There s a specific folder and file structure for ReVis projects Figure 6 you must understand this structure and the utility of eac
16. orce if you find it necessary Instance Selection default selection mode for instances currently cannot be changed 11 User s Manual PEx RS Identity Coordination default coordination mode currently cannot be changed mn Figura 12 Network Viewer Table View To support the insights obtained with the previously presented visualizations the Table View shows all the studies in a familiar table like layout and provides the user with the selection evaluation functions needed for the review The color scale used follows the same as the Edge Bundles view so that when you eventually change the color scale in one the other is automatically updated One possible user interaction with the table is sorting by clicking on the headers you can sort the table by the studies IDs or by number of citations received The most important actions however are presented in the right click popup menu described below and displayed in Figure 13 12 User s Manual PEx RS Primary Studies gt 36 Primary Studies D E3 Gal ID Cit Cit N isse n Comments Conflict Include criterion3 Exclusion 2 criterion2 0 E Figure 13 The Table view e Comments it s possible to leave review comments on each study by using this feature The tool will show a dialog with a
17. second step of the review you must put the PDF files in this folder The names of the files must match the BibTeX key of the respective entry papers stageN bib These are the input files for each stage of the selection They are used internally and shouldn t be edited by the user review pip The pipeline file for the review used to generate the visualizations It is used internally and shouldn t be edited by the user User s Manual PEx RS Starting the Selection To start the selection press the green play button on the tool s main toolbar Figure 9 while focusing your project Note make sure you edited the selection and files as stated in the previous section Proiects fl 3 Figure 9 Main toolbar Visualizations After a few messages of progress both in dialogs and in the output view four visualizations are created and displayed Of these three are immediately visible the Network Viewer is initially behind Projection Edge Bundles The first visualization on the left is called Edge Bundles Figure 10 Each of the small circles instances represents one primary study and the edges link studies that have cited each other The edge direction is represented by the color the citing study is on the light blue end and the cited study is on the dark blue end of the edge The name of the visualization comes from the fact that the edges that
18. text area filled with the possible current commentaries allowing for inserting and editing This is especially useful if the review is being done by more than one reviewer e Conflict in case there has been a conflict with one or more studies whether to include exclude them or not this feature can be used to mark the study so that it can be decided later Include this submenu shows all the inclusion criteria specified in the selection properties file to include the study in the review just click on the criteria used to decide This will change the study color to green e Exclude this submenu shows all the exclusion criteria specified in the selection properties file to exclude the study from the review just click on the criteria used to decide This will change the study color to red e Quality this submenu is available in stages 3 and 4 it shows the scores specified in quality properties file By selecting a score you evaluate the selected study Performing the Selection Four Stages As stated earlier in the introduction in ReVis the selection and quality evaluation actions are organized in four main stages After finishing one stage you can start the next one by clicking on 213 User s Manual PEx RS the Finish Current Stage button on the main toolbar Figure 14 You can also use the red Stop Review button anytime to save the review s current state and stop it 3 c8 a
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