ExaCT 1.0 User Interface User Guide
Contents
1. The list of articles can be filtered by the status column to reduce the size of the table To filter out articles uncheck one or more of the checkboxes in the top right corner 2 2 Deleting an article An article can be deleted from the server by clicking on the red cross icon next to the article s PMID A confirmation dialog will be shown and if confirmed the article file and the corresponding database record will be deleted 2 3 Changing an article status Status Auto Answers Auto Answers In Progress Complete Processing The status of an article corresponds to a stage in the article curation process and is updated automatically However the status can also be changed manually by selecting the appropriate line in the drop down menu The new status will be stored in the database This feature is needed for example to archive an article and remove it from the current list filtered by Archived status 2 4 Uploading an article Add an article HTML ocat o There are two ways to upload new articles for processing To upload a local file click on the Browse button and select the file The system can currently process only HTML files Single HTML files htm or html or several HTML files in a zip archive zip are accepted For any other file types a dialogue reporting an error will be displayed Once a file is selected hit ok and then press the upload button Alternatively co2. 3 6 Selecting answers Each extracted sentence has a corresponding checkbox If the checkbox is checked the sentence is considered a valid answer for that field if it is not checked the sentence is considered irrelevant By default only the first or none answer is checked To modify the automatic answers check the relevant sentences and uncheck the irrelevant ones 3 7 Adding a new answer If the correct answer is not among the shown automatic answers it can be added to the list by any of the following methods e type anew answer into the textbox next to the Add Item button and click the button e copy and paste a new answer from the article into the textbox and click the Add Item button e select anew answer from the article in the right side panel drag and drop it to the textbox and click the Add Item button e select a new answer from the article in the right side panel right click and select the field name from the menu cnal Health mer ds and wa 2 F Funder 1 Network Set Funding Number d who wa Registration ID Enrollment Interventions Outcomes The checkbox for the added sentence will be automatically checked 3 8 Highlighting snippets d by a grant 04 039 trom Asthma UE Within the suggested sentences snippets for the actual solution are highlighted To overrule the highlighted solution select alternative snippets with the mouse Clicking on a highlighted snippet will r
3. provides further details on the interface features All questions and feedback can be sent via a web form by clicking on the Contact us link on the main page or at the bottom of the menu page 2 Main menu National Research Conseil national Exa CT F l O bed Council Canada de recherches Canada Add an article HTML local Browse Auto Answers In Progress Complete URL Processing Error Cl archived PMID Title Date Y File Status Peace Zoledronic acid prevents bone loss after liver foes PR no ee panana ican ae 2010 02 02 Ile such decile Auto Answers a The efficacy of melatonin for sleep problems in aaa one 19968048 children with autism fragile X 2010 02 02 http www ncbi nim nih gov pme art In Progress ESS _ I 1 1 Help Contact us Log out The menu page lists all articles currently present in the user s directory It shows the corresponding PMID title file name and status The status indicates if the article is being processed by the extraction system Processing has been successfully processed by the system Auto Answers has been processed with errors Error has been worked on by a curator In Progress completely processed by a curator Complete or archived Archived The list of articles can be sorted by any of the columns by clicking on the column name 2 1 Filtering articles Auto Answers In Progress Complete Processing Error L Archived
4. system developed jointly by the National Research Council of Canada and the University of California San Francisco The system is trained to find key information from scientific clinical trial publications namely the descriptions of the trial s interventions population outcome measures funding sources and other critical characteristics Automatically extracted answers are presented to a user through a web browser based interface that assists the users in verifying and changing the extracted information This site allows visitors to test the system s performance on their own data To use the system one has to create an account consisting of a user name and a password After that one will be able to upload and process articles on clinical trials and amend the automatic extractions For each user a separate space is allocated on the server for all uploaded files The files are visible only to the user who uploaded them to the server To get a quick look at the interface click Enter as a guest on the main page The guest account serves as a preview and severely limits the functionality of the interface most buttons are disabled The automatic extractions for two example articles can be viewed but cannot be modified For full functionality please create a user account A good starting point to familiarize oneself with the interface is a short video found on the main page The video demonstrates the main features of ExaCT s UI This guide
5. 1 2 3 ExaCT 1 0 User Interface User Guide HVE POGUIC TION ee E E A A 2 PVT eA TVA TOS Olio tee EE E EE E ENE A AEE EENE E TS 3 2 EFREN Aa E aucasesene 3 PAAD E E EEEL E es E E A E os E E A E 4 23 Changing an article SCA NG cessione saueteuenantostovanessescanteatssanohevaraetyebit 4 ZO ACN ana CIC E r nec sacnseutetsneesnescosanactanedsaateesentctauenaescesarscuewucunessaucateeun 4 2 5 Selecting an article for review and editing cccccceeeccccseccecesccccsesececeeeececeseseceeseseceesencesseuaesetsunesss 5 EGINE IMO E ee a EEE E ne eecast 6 S LTOS INE PINE ONO a a E E N 6 ECEE I a T E A 7 fo zh 1B ele e N eee ee en ee rere 7 3 4 Showing hiding unchecked ANSWELS cccccccccccccccceecccseeeeeseeeeeceeeccscceeeeeeeuuueeeessseeeeeeeeeeseseeeeeesuaagegs 7 Dio VICW IIE CONTO arra Gretna davaeniontienesveinnessamcnennarennnenss 8 Bi SIO C EIS ASV No ea ceserece acre ute N E E vaensaceeababsaruacnion 8 SF PIONS a RWS WOT acrescida Enen E i e EEEE o Ra N 8 3 8 Highlighting SEND OS vaxtsacaas ann sctcsnuedaneteosedataposiatacosadeecceasdaacsenuededusnenctasinndceeseaucetainaresadivesactaswoudeinecoas 9 SENE FECA Cla NE O Seen E mu ssmeesscecserusvereasuiecaveneecass 9 SO ODEN A One el e E EE 10 SNE MONEO eraa a E E E E E E eae nasenuteioeannate 10 FE SUMO MLS CS e E N es ieneeseatese 10 Sol ROU othe mani MENU gia eee ch ate sa sete atest serach vas aes oe cece eee 11 1 Introduction ExaCT is an Information Extraction
6. all the selected answers for the final approval Clicking Cancel on the summary screen will return to the editing screen Clicking Save amp Submit will save the current answers and return to the main menu The file status will be updated to Complete 3 13 Returning to the main menu Main Menu Save Changes Save amp Submit To return to the main menu click on the Main Menu button in the bottom right corner of the screen If there have been any unsaved changes to the article extractions a dialog box will appear and ask if the changes need to be saved Clicking Yes will save the changes and then return to the main menu Clicking No will return to the main menu without saving the changes Clicking Cancel will close the dialog box and return to the editing screen
7. emove the highlighting If a sentence is accepted with checkbox checked but does not have any highlighted portions the entire sentence is considered the answer 3 9 Ignoring recent changes To undo changes made to a field click on the blue arrow in the top right corner of the field box This will reset the field to the last saved state 3 10 Opening closing fields Close Funder Clicking on the grey close button next to the field title will minimize that field All checked and unchecked sentences will be hidden and only the first selected answer will be shown in green text next to the title of the field This will indicate that the field has been dealt with Closing the field is simply for convenience and gaining the space and has no effect on the answer The system will accept a checked sentence as an answer even if the field is not closed 3 11 Saving changes Save Changes Save amp Submit Recent changes can be saved at any time by clicking on the Save Changes button in the bottom right corner of the screen The following dialog will appear indicating the saving progress Saving 40 6 t O After the first saving action the article status is updated to In Progress 3 12 Submitting changes Main Menu Save Changes save amp Submit When finished editing press on the Save amp Submit button in the bottom right corner of the screen This will bring up the summary screen with
8. g interface gee National Research Conseil national University of California Council Canada de recherches Canada San Francisca gt OF 1 0 Original Article ay P amp m Funding Support Funding for this study was provided by Wageningen Effect of Fish oil on Ventricular antre for Food Sciences pron Deore alliance of major Dutch food f Death in Patients With Implant id t TNO Nutrition Fao d Research M stricht Unive ran i TETA AT pea Research Centre Ra j je hi are lands with Defibrillators financial support by the Dutch government Funder The Study on Omega 3 Fatty Acids and Ven oo Randomized Trial Ingeborg A Brouwer PhD Peter L Zock PhD Funding Number Dirk B cker MD PhD Richard N W Hauer MD F An additional grant was received from the European Union SEAFOODplus Pe PERT EE PET E ee integrated project No 506359 Study Group C cate JAMA 2006 295 2613 2619 Registration ID ABSTRACT Trial Registration clinicaltrials gov Identifier NCT00110838 Context Very long chain n 3 polyunsaturated E are thought to reduce risk of sudden death po cardiac arrhythmia Objective To aa the effect of supplemental jili gt sve ibn The editing screen consists of two panels next to each other The right panel shows the original article and the left panel shows the system s suggestions The extracted information is sorted into five semantic groups and displayed in separate tabs p
9. he article information can be typed manually Then this information can be associated with the article by clicking on the Use This Info button The information will appear at the top of the tab The Clear button will clear the PMID Lookup form The Undo Changes button will restore the publication information recorded in the database at the last save action 3 4 Showing hiding unchecked answers For each information element the automatic extraction method outputs up to five solutions If no sufficiently good solution is found in the text the message shows not found Otherwise the solution with the highest confidence score is displayed To expand the list of system s suggestions to all five choices click on the corresponding button Clicking on the button will suppress the list to show only accepted with checked checkbox answers 3 5 Viewing context The to be To judge the relevance of a sentence it is often helpful to see the sentence in context That is why the suggestions in the left pane are linked with the full text in the right pane through the View Context icon Clicking on the small green icon next to an answer will highlight the corresponding text in the right hand panel and scroll down to the location of the text If the answer s View Context button is grayed out then the answer has been added manually and the system will not be able to highlight the corresponding text
10. py and paste a URL in the textbox labeled URL and click Upload If the upload was successful the file appears in the article table with a status of Processing The processing takes approximately 3 5 minutes per article or longer if the server is busy While the article is being processed the corresponding row of the table is disabled The work with the web site can be continued e g other files can be uploaded reviewed or edited while the processing is performed in the background The menu page is set to automatically refresh every minute When the processing is finished a dialogue notifying the user is shown and the article status is updated to Auto Answers on success or Error on failure If the status is not updated automatically refresh the page manually Now the corresponding table row is clickable to access review and amend the automatic extractions 2 5 Selecting an article for review and editing PMID Title Date File Zoledronic acid prevents bone loss after liver transplantation a randomized do 2010 02 02 Annals 144 16490909 8 19968048 2010 02 02 http www The efficacy of melati W r sleep problems in children with autism 1X To review and edit the automatic extractions for an article click on the corresponding row in the table If the article s status is Processing please wait until the processing is finished and the status is updated 3 Editin
11. ublication information meta information including funding sources and trial registration enrolment including eligibility criteria sample size start and end dates of enrolment and early stopping interventions including the names of experimental and control treatments and their dosage frequency route and duration and finally the primary and secondary outcomes with their corresponding time points 3 1 Toggling panels on off nii a Each panel can be minimized to gain additional space To minimize the left panel click on the lt lt button at the top of the interface To restore the panel click on the gt gt button Similarly to minimize the right panel click on the gt gt button To restore the panel click on the lt lt button 3 2 Changing tabs Publication Info Meta Information Enrollment Interventions Outcomes To view a different information group click on one of the tabs at the top of the left side panel 3 3 PMID lookup PNUD Lookup PROD 19164186 Title ee If the automatically extracted information in the Publication Info tab is incorrect it can be replaced by the information for another PMID using the form at the bottom of the tab Type a valid PMID into the corresponding textbox and click on the Get Info button The system will get the information for the new PMID from the PubMed database and automatically fill in the rest of the fields Alternatively t
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