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BIS User`s Manual - TransMed Systems

1. cceccccccssssecceceesseccccaeeeecceseeeeeceeseeueecesssenseeessueeseeessaeaeeeeees 143 ARN SO aurora aar ce nev E ae ee ee ee aces ca epee eee tise ae eee 143 Integration with Reference Entities cccccccssssscccccessecccceessecceseeeseceeseeaeeceesaeesecessueeeeccesaueseceeseeaseeessagaeseeseages 144 Cohort Explorer Integration with Clinical Pattern Matcher ccccccssscccccessececceeseccceceeeseceeseeaeecesseaaeseesseaneeeeees 144 Create Clinical Patteri SOSSIOMN sssrini ieaie E E a EA REA EER 144 Chinical Pattern Matt h r sarrin E EROR 146 Opening Clinical Palerm Matcher grecteire 5 cisctee ga dence ts nenon TEER ETN 146 The Configuration Al CS erisia aaa N 147 Data Explorer in Clinical Pattern ECitor ccccccssscccccsessecccceeesecceeeeeeceeseeaseceessaeseceesseaaeceeesaaaecessseaaseeessagaeeeessages 151 Filtering ini Clinical Pattern EdItOT curneusesatsanceesanesecaasantsnssaanntqesoacatenconesensunoesonnenaeadesinamedasataasbengansaeoadeanedesansandooean 152 Repeat Count of Variable skenen EEEE aE A EA EENEN AEE EEEE 159 T ANNON e a E T E E EE AE A E O E E E 160 Time Adjustments Proximity in Pattern cccccccecceeeseeeeeeeeeeeeeeeceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeceeeeeeeeees 162 COMMON ES SCC TIO M1 e E A E E E E E EE E E E EEE T 163 Calculate Matches crescissi ini nern in s A E A E E E EEE Ra 164 RECE D DAVAT r E EAE E A ee ee ee ee E E E E 164 C hort Reporte rcs nis a TE
2. DateMonth Field Name Deathdate Date Year DateQuarter Group Interval YearAge Month Age DayAge Hour Text Trait Choice Trait e Field Name red arrow Allows the user to edit the name of the field e Group Interval The format of the displayed values o Default Groups combine unique field values o Alphabetical Combines field values into categories according to the character that the values start with Edit Pivot Field Field Name Location of Metastasis Group Interval Default T Group Interval Options Alphabetical Defer Layout Update If checked the pivot table will not apply the changes to the variables and their setup until the Update button is clicked The Update button is inactive if the checkbox is left empty _ Defer Layout Update Fi Defer Layout Update e The RHS of the Pivot Table Editor is where all columns and rows are defined and where data is visualized TransMed Systems Inc 29 BIS USER S MANUAL yy Toolbar E Collapse All g 2ave Pnnt Data Drill Down fiul Show Chart E Show Totals Show Grand Totals e Refresh red Refreshes the calculated data below e Collapse All yellow Collapses all data below into the first variable in the row order e Export Table purple Converts the table as seen to a preview page The user can then choose where and in which forma
3. T a B 06 Chemistry pi All Traits gt Patient Traits gt Patient Fields gt 06 Chemistry Set the Linking Relationship red area below Set the Constraint purple area below Set Group Option black area below Click Group orange area below oS a TransMed Systems Inc mo BIS USER S MANUAL as E Back o Up T Filter 06 Chemistry 06 Chemistry Coe Same Patent Group by all values no values Trait Group Options The user has the option to add Traits to the Filter List in Cohort Explorer by using the Grouping Panel Based on the current Cohort Filter Trait Type and associated Traits the Constraints and Advanced Grouping options may differ Steps to Grouping ona Trait 1 Search for a Trait in the Data Explorer yellow area below 2 Click the Group Icon on the Trait in the search results pink area below Search Results for bun Didn t find what you were looking for eN Search All All Traits gt Patient Traits gt Patient Fields gt 06 Chemistry Set the Linking Relationship red area below Set the Constraint purple area below Set Advanced Grouping if needed black area below oS 2 Click Group orange area below TransMed Systems Inc pe BIS USER S MANUAL as O Up T Filter 06 Chemistry Constraint i All Observations Group b
4. the current filter ends with a Reference Entity Cohort Explorer Integration with Clinical Pattern Matcher Cohort Explorer has the ability to launch the Clinical Pattern Matcher tool without closing the Cohort Explorer tab Clinical Pattern Matcher is a longitudinal data mapping tool that allows the user to view data defined by a certain time sequence Create Clinical Pattern Session The Clinical Pattern button launches a new Clinical Pattern Matcher session with the current Cohort as the starting Cohort With just the click of a button the user can open Clinical Pattern Matcher from Cohort Explorer after defining a Cohort TransMed Systems Inc 144 BIS USER S MANUAL ae The Cohort created in Cohort Explorer will load as a New Cohort unsaved into Clinical Pattern Matcher Note BIS will transition any Cohort Filter to the Highest Entity type before launching the Clinical Pattern Matcher In the Example below the user created a Cohort Filter green area which in turn created a New Cohort yellow area then clicked the Clinical Pattern button red area Cohort Explorer All I Create Cohort Create Report E9 clinical Pattern F Cohort Filter History View HE Icon View Current Cohort Count 650 100 Once the Clinical Pattern Matcher session is open the user will see the New Cohort yellow area below displayed as the starting Cohort J
5. 06 Chemistry e Module gt Trait Linking Relationship o Last breadcrumb in the Cohort Filter is a Module and the user is Transitioning to a Trait gt Same 06 Chemistry Module Linked to 1 FASTING_GLUCOSE 4 Same Patient Is Q gt Is ame atient to 06 Chemistry Patient Sample Experiment Is pat lt lt E B From parent Patient to child Samples to child Experiments to Anisocytosis Y For more Linking Relationship Examples please refer to the Cohort Explorer Section in the BIS User s Example Document Constraint Options in the Filter amp Grouping Panel The Constraint options in Cohort Explorer are not always the same for the Filter Panel and the Grouping Panel The possible Constraint Options that are available in Cohort Explorer are described below Note that based on the current Cohort Filter or the selected Variable the user may get different Constraint Options The user may also get different Constraint Options when using the Filter versus the Grouping Panel Entity Constraint Options A Constraint is an additional filter applied to the Entity to limit the returned results to a certain subset of data In BIS the user has only the following Constraint option for Entities TransMed Systems Inc E BIS USER S MANUAL as All Module Readings Returns ALL Entities based on Cohort Type that have an Entity Module reading v For more Constraint Examples
6. BIS USER S MANUAL Cohort Type Q Patient 23 175 Grouped On ICD9 in Cancer list Change _ Group Count 7 Link Same Patient Constraint 0 All 130 125 120 115 115 E ia l i 1 Plot No Value UINS JO J9DUPD 6 E T WIU UMS G ELT IPUI JIUL JSPBIG 6 bLT awa 7SP9 1q JO 1BDUED G PLT DPU WUT YseaNg 6 S T jew yS0 92g jO 9DUe5 6 S T Group Details View Group Details will display the details of each group as a sortable table Double clicking the row will apply that group to the Cohort Filter This view also displays the Entity count and percent of results relative to that grouping Cohort Type Q Patient 23 175 Grouped On ICD9 in Cancer list Group Count 7 Link Same Patient Constraint All Group Name Patient Count Percent gt Q No Data Values 22 525 97 2 173 9 Cancer of skin 115 0 4962 173 9 Skin cancer 96 0 4142 174 9 Breast cancer female 112 0 4833 174 9 Cancer of breast female 0 5307 175 9 Bresst cancer male 0 5394 175 9 Cancer of breast male 0 466 Entity Details View Entity Details view will display a list of Identifiers for all the Entities in the Current Cohort at the selected Cohort Type in a sortable multi select table While in Details View the user can select an entity to open the Single Entity Viewer Multi Select one or more Entitles from the list and create a Cohort from the selected or Export
7. Module Entity Relationship _E_ Entity Moedule Ownership J Physician T Physician iD PPID W Physician Role r Physician Lic Th Subject ID T Subject ID Tissue Type TU Subject ID yy Breast Histopathology Fay 02 Demographics Alcohol Hormone Smoke Morphology Experimental Histopathology ls Diagnosis P ICDS End Date a Diag Sample Epithelium Selection Quality ls Treatment Fat Patient Physician T Physician First IT Physician Last Physican State TransMed Systems Inc BIS USER S MANUAL as BIS User Overview BIS Log In Screen BIS has a specific log in web page that looks like this Trans 4Med Biolntegration Suite 5 1 Username Password When the user goes to the BIS URL the Log In screen is shown as above The user will enter their Username Password and check the box agreeing to the terms of use Once the box is checked the Log In button will activate The user can then click Log In to launch BIS under their name and securities If a user wishes to view the terms of use before logging in they can click the hyperlink underlined words terms of use to view the terms in an additional browser tab Note Log in should be done using a user name only e g jsmith not a domain qualified user name e g
8. Patient TransMed Systems Inc sig BIS USER S MANUAL a G all 23175 1 Patient 10 v Sample 1D i Patient ID 5 This will add the Diagnosis Module as a Nested level below the Sample level linking through the Diagnosing Sample This is a One to Many link amp all 23175 E Patient 1D v Sample ID e For more Linking Relationship Examples please refer to the Cohort Reporter Section in the BIS User s Example Document Constraints in Cohort Reporter The Constraints in Cohort Reporter limit the returned data The Constraint is considered first in the report query then the Advanced Filters Based on the current Linking Relationships Levels and related Constraints the user may get different Constraint options or have the Constraints change to allowable Constraint combinations by default Constraint options can also be limited by the association of a Timestamp Constraint Defaults By default certain variables will default to certain Constraints e Entity Modules All Module Readings e Modules All Module Readings non limiting e Traits All Observations non limiting e Ifthe combination of Module and Trait constraints conflict each other on the same Level the Constraints may revert back to the default TransMed Systems Inc a92 BIS USER S MANUAL Ss Constraint Rules e f the Module h
9. SB Gene List S i Tools a i Gene list Open Export All Data New Gene List from all f Gene list EEE Name Pnmary Symbol Gene ID Speces 5 Gene List glutamate receptor metak GRM4 2914 Homo sapiens pen NSA2 ribosome biogenesis NSA2 10412 Homo sapiens eneral information insulin like growth factor 2 IGF2R 3482 Homo sapiens ubiquitin related modifier URMI 81605 Homo sapiens sideroflexin 3 SFXN3 81855 Homo sapiens interferon alpha amp IFNAS 3445 Homo sapiens SEC22 vesicle trafficking p SEC226 9554 Homo sapiens Toolbar e View Gene This button will open the Gene List Form or Gene Information E View Gene e Export This will export the selected gene s to a file on the open Workspace and then can be saved to the local drive e New Gene List This will create a new Gene List out of all or the selected genes TransMed Systems Inc 85 BIS USER S MANUAL ae Gene Information Form General Information Panel The General Information Panel displays the basic gene information and the gene alias information Gene Viewer E Dain fyndremma eribical regien gana 4 Eal Export All Down syndrome critical Gene Information region gene 4 Gene Name Oown syndrome critical region gene 4 Species Protein Gene ID Homo sapeens 10261 Entrez Gene DSCRs Gene Authority Primary Symbol Gene Aliases Gene Alias record exists Is Primary Alias Type Gene Alias record exists True
10. and No Data Values e Custom Will group Observations into as many custom groupings as defined and No Data Values 3 Click Group TransMed Systems Inc sa BIS USER S MANUAL as Currency Ce Expenditure Link pal Fy Same Patient Constraint iiil All Observations Quintile Quartile Date Trait When using the Advanced Grouping options for a Date Trait the user must select Group by specific date range Steps to using Advanced Grouping Options 1 Select Group by specific date range green area below 2 Select the method the Observation values should be grouped by using the dropdown red area below e Year Will group Observations into several groupings one per Year and No Data Values e Quarter Will group Observations into several groupings one per Quarter and No Data Values e Month Will group Observations into several groupings one per Month and No Data Values e Date Will group Observations into several groupings one per Date and No Data Values e Custom Will group Observations into as many custom groupings as defined and No Data Values 3 Click Group TransMed Systems Inc ere BIS USER S MANUAL as el Back o Up T Filter Date gn Expenditure Link pa Fy Same Patent Constraint All Observations 3 a sroup J Group by all values no values Year Quarter Month D
11. BIS USER S MANUAL Sy St Di Report Setup hati Molecular Gene Space ied Save amp Close pi Savers E Close TF Data Definition 33 Transforms SP Ad Probe quality Fikers based on probe R Data Ext New Probe gt gene mean 1 absent present ratio and intensity Converts from probe space to Gene space using mean when Probe gt gene multiple probes map to the same Converts from probe gene spece to Gene spece using meant when multiplie probes map to the same gene Required field Using the Transform Editor the user will choose a Transform from the Left Column by highlighting and then clicking on the Plus symbol Probe gt gene mean Converts from probe space to gene space using mean when multiple probes map to the same gene Once the Transform is selected it will display in the middle section yellow area Now the user can edit the name and description of the Transform on the right side green area Also on the right side the user will choose the variable for the Intensity Column using the Single Variable Selector and then choose the Gene Authority from the dropdown option red area TransMed Systems Inc E BIS USER S MANUAL Re E seca E Close T Data Definition Z Transforms dh Add JX Remove Converts from probe space to gene space using mean when multiple probes map to the same gene Intensity Column E Sample Intensity E
12. Diy All Module Readings Ail First Module Reading iiil Last Module Reading No Module Readings a Initial Trait Constraints ill First Observation On First Trait Selected Mii Last Observation On First Trait Selected Ea No Observation On First Trait Selected TransMed Systems Inc a983 BIS USER S MANUAL as e All Module Readings non limiting Show all readings for the module regardless of content This option has the potential to bring back empty null data cells e All Module Readings Show all readings of the module that contain content The results for this option will only bring back results where the module exists e First Module Reading Show all First readings for the Module This option will show all readings associated with the First timestamp of the module This option does not guarantee one reading depending on the module reading timestamps more than one reading can be first e Last Module Reading Show all Last readings for the Module This option will show all readings associated with the Last timestamp of the module This option does not guarantee one reading depending on the module reading timestamps more than one reading can be last e No Module Readings Show all readings that do not have this module This option does not work with Entity Modules o No Traits can be associated with the Module if this Constraint is selected e Set On Initial Trait First Observation Apply no Constr
13. Edit the highlighted Main Level Delete Level Allows the user to Delete the highlighted Main Level TransMed Systems Inc 169 BIS USER S MANUAL ae Edit Trait Filter Allows the user to Edit the highlighted Trait Move to Initial Will move the highlighted Trait to the top of the Trait list for that Module Delete Trait Allows the user to Delete the highlighted Trait f Collapse All E7 Clear Data Definition zy Edit Groups FX Clear Data Definition EA Edit Level Delete Level i ear Data Definition FA Edit Trait Filter Move To Initial A Delete Trait Clear Data Definit EA Levels of the Data Definition The structure of the Data Definition is defined by Levels Some Levels are considered Main Levels and others are Nested Levels As the user adds variables to the definition hierarchy levels and linking options can be defined Group Level The Group Level is comprised of the Cohorts and or Filters the Report Definition should be run against The Default Group is the Project s All Cohort Users can select Patient Cohorts or Patient Filters in the Group area Main Level An Entity or Module can be defined as the Main Level The Main Levels will define the main levels in the generated Data The Main Levels can have their own Traits associated or can host a Nested Level The Main Level is the variable displayed above and around the Traits Nested Level An Entity or Module
14. Trans Med Biolntegration Suite 5 1 BIS User s Manual TransMed Systems Inc 2014 TransMed Systems Inc Revision 5 1 14041 1 BIS USER S MANUAL as The BIS LOGICAL MONE erreien inen N E 5 Part ofthe Logical VO Ce liar tenecen sso race seetacensatannecesesaasceus anes aetouseusenescuncte AEREE AEE 5 WA e dates tae E E T sam O A A E AE A E E E E A E E E E EE E T T 6 Sg E AE OE A E A AA A A E E A E A O A A AT 8 EELT E aE E ance E E EE E AEE EN T E A sen tence se E E EE E E T E 8 Reference ENTES esisin r r E E E E E EE 8 ENUY TRO EI OV SIDS ate geet tncrierectenen saad ee eA NEEE A EEE E EAEE EERE SAAE 9 Module TYD e a E T E E a E 12 E EES A a S eee ee ee A A E E E A E E E E E 12 BE EL ONET a E E E E A 12 EA E Y e ler ser E EE EE E E AE E E E aiatigaaaarede 12 Moale FM aeiae E E e E EE EET I E EN 13 Modde SIV OG UNG erreen E E EE E E areitaban eres tupeneneaversiuaeneriieanens 13 TAGS VEN Ta ea ers ene E psc esse ene 13 BIS Logical MOJE scsnsssaeassusindseesavopseadiundnsousiazesocuenaniae a 15 BIS User OV TVIEW 7 sctsscciscciscnsanaierecacsiscasbecsscciaccuncedncdsarasusdisvaseucenseiessisaasnesisrasseainraancinanuiendiscesneeuncaseesassaanrananeienaes 16 B GOE T a A E E O E A 16 LOT I aa E E E E E E E EE 16 BS OOS ME Men E E EE AE ET E EE EE A E EO E NT 17 Window Navigation TabS cccccssscccccssssecceceesseccceseeeeeeesseaseeeesseeseeeeeseaseceeeseeaeseeesaeseceeesaauseeessanaseeeseuaaseeessagaseeeesaees 17 Conte
15. a Pabent Traas Repeat 1 Adenocarcinoma Medication with data True ia C ae oe K Data Explorer in Clinical Pattern Editor The Data explorer navigation in Clinical Pattern Editor CPE works the same as with any other feature in BIS In CPE however the user has the option to drag and drop the Entities Modules and Traits into the Clinical Pattern Display and then has the option to apply an additional Filter on the Event TransMed Systems Inc aso BIS USER S MANUAL ae The user can add Events to the Clinical Pattern by selecting and dragging the Event into the Clinical Pattern display area Pending where in the Clinical Pattern display the user drags the Event will define the order of Events j Tex i OGlinical Pattern Cdagor 99 FP ancien ane Sisih Pater Matcher Chadi Patlen Eate Emi p d FA Ed laio Bat Nates d a All ora Olinical Pabbe Hamer Hew Clheece Pattern i Sarch Aotaki for bimp ki Dadat hnd what yia wire betters for a Ziar All PAH Simpe Type me jag Sample Ji Ai Tremtis Sample Trags gt Sample Fiii a Simpe Dhi yp E Sempe Dhigrii Tyme T amp ID T Simp D E Carges Miny E sample Irdensty Filtering in Clinical Pattern Editor The user has different filter options for each Event type added to the Clinical Pattern All Events require the user to set a constraint of All Module Readings but certain Trait types allow for Advanced Filtering Each Event is
16. domain jsmith The checkbox will be cleared as the part of the browser cache clear The check does not hold per user but per browser Log Out BIS manages the log in process itself instead of delegating this to the web browser so BIS can also log off the current user This is an added security feature to allow users who access sensitive protected data to log out of the application when not in use For a user to log out of the application they simply need to click the BIS Tools button in the upper left hand corner and select the Log Out button The user will be logged out of BIS and taken back to the Log In page shown above TransMed Systems Inc 16 BIS USER S MANUAL as BIS Tools Menu The BIS logo area in the upper left is the BIS Tools menu This button is always in the upper left and does not move making it easy for the user to find quickly Clicking anywhere inside the logo area will show a dropdown menu giving the user the ability to launch BIS Tools see Properties and Information or Log Out of the application All of the commands on this menu are fixed relative to each other however the first six are Workspace specific and are only shown when the user has a Workspace open The last six menu items are displayed at all times The Workspace Specific Commands are Workspace Explorer Opens the Workspace Explorer tab Workspace Explorer Cohort Explorer Opens a new Cohort Explorer ta
17. e Equal to Y e Before Inclusive lt Y e Before Exclusive un checked lt Y e Between Inclusive Y and Exclusive X Between Y and X e Between Inclusive X and Exclusive Y Between Y and X e Between Inclusive Both Between Y and X e Between Exclusive Both un checked Between Y and X Date with Time Trait When using the Advanced Filter options for a Date with Time Trait the user must first click the button next to Filter on Specific Dates This enables the Filter options so the user can add Filter values and apply the Trait to the Cohort Filter Sometimes a Date with Time Trait is also the Timestamp for a Module so these Icons may differ on the Filter Panel Steps for using Advanced Filter Options 1 Choose Filter on Specific Dates green area below 2 Adda Low Value a High Value both values in the filter boxes red area below TransMed Systems Inc p BIS USER S MANUAL Sy E e Note by clicking the button next to the range the user will get a calendar with times 3 Set the relational operator and inclusive check 4 Click Apply Filter Link Constraint iiil All Observations r O Filter on all dates Filter on specific dates Date of Last Follow up gt Timestamp CCOP VARIOO 2 Myeloma pathology 5 A Same Patient r Link pal A Same Patent Constraint ny All Observations A T Apply Filter A T Apply Filter O Filter on all dates e Fil
18. OCA 253 OCA 250 OCA 250 OCA 250 OC4 250 OC4 008 Count Distinct 06 Chemistry 1 1 Mean ALKALINE PHO Sample ID SPHATASE 407 OCA 269 3 tumor 407 OCA 269 2B 11 26 07 407 OC4 269 3 tumor 407 OCA 269 2A 11 26 07 407 OCA 269 3 tumor 407 OCA 269 1 11 26 07 291 5 OCA 253 core left 2 291 5 OCA 253 core right 4 291 5 OCA 253 core right 3 291 5 OCA 253 core left 1 166 5 OCA 250 normal 3 166 5 OCA 250 normal 2 166 5 OCA 250 normal 4 166 5 Report Data 159 On the toolbar the user can change the Level of the Data red area Create a Cohort purple area Open the Single Entity Viewer yellow area Export the Data green arrow or choose Display Options for the Data blue area g Group S amp S Patient Wii Sample Experimental Histopathology Experiment E Experiment Diagnosis ee from all Patient Q Open Choose Columns e from all Sample ik Open S as SAS Xport a Rotate Level as R Data file Hide Level Header as SPSS sav as XML as XLSX Level Allows the user to change the report data by level this summarizes and collapses the data upon itself TransMed Systems Inc 201 BIS USER S MANUAL Ss e When reviewing the results the user can choose to collapse the results by switching the Level To switch a level click on the Level Dropdown in the toolbar e A Level helps define what data you are looking at The default level is always the lowest last Module
19. Rats w Cytokines Male Patients Rats w Cytokines Brown Rat Male Patients Rats w Cytokines Female Patients Male Patients Rats w Cytokines Brown Rat Female Patients Male Patients Rats w Cytokines Diagram Intersections Entity Item Identifiers The Entity Item identifiers will display in a table This table is sortable selectable and exportable The user can also open the Single Entity Viewer by selecting and either right clicking to View Patient or by clicking the Open button in the toolbar MSURatTraumaQl 0 Hour i MSURatTraumaQ 0 Hour MSURatTraumaQs 0 Hour MSURatTraumaQ4 1 Hour Using the Venn diagram Example The user selects four Patient Cohorts from the Workspace and then clicks the Venn button in the Workspace toolbar or context menu TransMed Systems Inc 93 BIS USER S MANUAL ys Brown Rat Male Patients Patient Cohort 6 701 Patients Rats w Cytokines Patient Cohe 5 Patient Cohort 5 963 Patients 71 Patients Once the Venn diagram tab is open the user can compare the Cohorts by interpreting the diagram e Yellow Arrow All Patients that are in the Brown Rat Cohort Female Patients and the Rats w Cytokines Cohort o Brown Rat Rats w Cytokines e Orange Arrow All Patients that are in the Brown Rat Cohort and the Male Patients Cohort o Brown Rat Male Patients Sets In Ve
20. please refer to the Cohort Explorer Section in the BIS User s Example Document Module Constraint Options A Constraint is an additional filter applied to the Module to limit the returned results to a certain subset of data The user has the following Constraint options for Modules ATH All Module Readings Till First Module Reading iy Last Module Reading All Module Readings Returns ALL Entities based on Cohort Type that have a Module reading First Module Reading Returns ALL Entities based on Cohort Type that have a First Module reading First Module Reading will not be an option if the Module does not have a Timestamp association e Last Module Reading Returns ALL Entities based on Cohort Type that have a Last Module reading Last Module Reading will not be an option if the Module does not have a Timestamp association v For more Constraint Examples please refer to the Cohort Explorer Section in the BIS User s Example Document Trait Constraint Options A Constraint is an additional filter applied to the Trait to limit the returned results to a certain subset of data The user has the following Constraint options for Traits iiil All Observations Till First Observation iy Last Observation No Observations All Observations Returns ALL Entities based on Cohort Type that have an Observation for the Trait with Values First Observation Returns ALL Entities based on Cohort Type th
21. the real Identifier and a fake Identifier to be used for De Identified users This fake De Identified Identifier can be whatever the customer wants and is filled in by the ETL process Typically it is a series of numbers characters generated by the system The real Identifier is usually a system wide identifier like an MRN Date Offsetting Because dates are of critical importance in analysis systems like BIS it is not practical to hide most dates from the user even if the user has only De Identified access to the system However some dates can be identifying features of a patient and thus cannot be shown to the user specifically the date of birth and date of death for a patient To allow De Identified users to see dates for a patient yet still protect the patient identity BIS maintains two sets of dates for all Entities and all Modules fields related to that TransMed Systems Inc 350 BIS USER S MANUAL as Entity The first set is the real dates these are the actual dates of birth treatment death etc as recorded by the customer s data entry systems These dates are only available to users with identified access to the data The other set of dates are the De Identified dates BIS maintains a random date offset of 30 days for each Entity hierarchy in BIS and applies that to all dates for all Entities in that hierarchy This date offset is different for each Entity hierarchy but all
22. 00 AM Deathdate 12 10 1999 12 00 00 AM Species Homo sapiens Sample Diagnosis Type Normal Tissue of Origin Colon and Rectum Tissue Type Fresh Tissue Sample ID OdSa_lamroN MMC 3 4851 Primary vs Met Site of Origin Category Site of Origin Tissue Container Number Gender Male First Name Middle Name Last Name Is Cell Line Father Mother Patient ID Ethnicity Race Parent Type Patient Parent Information Child Entities Panel The Child Entities Panel displays all of the children associated with the Entity The user can open a Child Entity by highlighting the Entity Row and then clicking View Entity button red box or by double clicking on the Entity row Subject MiMSH 0003 Record Details Sample Info Y Sample ID Acquisition Date Y Sample Info MMSH 0003 26 3 10 2004 12 00 00 AM Sample Info MMSH 0003 34 3 10 2004 12 00 00 AM Sample Info MMSH 0003 36 Right Click Sample Info MMSH 0003 4 4 or Double Click Sample Info MMSH 0003 1 Sample Info MMSH 0003 24 Sf 10 2004 12 00 00 AM Module Readings The Module Readings panel displays all Traits associated with the Entity Module selected from the Entity Panels LHS The user can use the horizontal scroll to see all Traits and the vertical scroll to view all observations for the Traits TransMed Systems Inc cae BIS USER S MANUAL ae Each Trait of the Module is represented by a column Each row
23. 6 ALT Mean Mean 3 BUN Mean Min 4 CREATININE Mean Max 6 ALT Report Generation Log The Report Generation Log is created after the report has been fully generated It will tell the user information about the report generation itself and display any errors that may have occurred during generation There is a button to access the Generation Log in the Report Information area on the Report Data Panel Report Information Status Generated Overall Size 68 186 values Last Gen 16 Sep 2013 4 12 35 PM Included in Generation Log e Generated By The user that generated the report e Generation Start Date Time the generation process started e Extract Complete The Date Time and calculated Time the Definition Query was complete e Extract Size Total size of the Report this may differ from the columns show in the Report Data Panel e Columns Removed If the user has selected the Remove Empty Columns option when defining the report the remove columns will be listed e Transform Complete The Date Time and calculated Time the Transform Query was complete e Generation Complete The Date Time and calculated Time the Report was complete TransMed Systems Inc 207 BIS USER S MANUAL as Report Generation Log Generation Log Generated by jmutz Generation Start 9 18 2013 4 12 35 PM Extract Complete 9 18 2013 4 12 38 PM Om 2s Extract Size 21 columns by 331
24. Analysis is the process of breaking down data into smaller parts to gain a better understanding of it Analysis tools are used to take generated data from Cohort Reporter and translate the data results into visualizations and calculations These tools ys Analysis Tools reference an R Server for accuracy This is an option in Cohort Explorer under the Cohort Filter dropdown menu It allows the user to add an additional saved Filter to the end of the current breadcrumbs m Append Cohort Filter Apply Filter will apply all of the settings the user has defined in the Filter Panel to the Cohort Filter An audit is an evaluation of a person organization system process enterprise project or product In BIS the audit feature allows for Admin Users to track activity within the system per project The Back button is on the toolbar of the Data Explorer It allows users to go back to the previous panel view they were just on Trans Med Bio Integration Suite Biolntegration Suite 5 1 BIS Desktop is the main viewing tab within BIS When BIS opens the BIS Desktop will already be open and defaulted to the users Favorite Workspaces This tab never closes and will display the Project and its Workspaces that are currently open BIS USER S MANUAL ys BIS Tools Calculate Matches Category Choice List Choice Trait Choose a Variable BIS Tools is the main menu dropdown in BIS From here the user c
25. BIS Tools Implications of this permission e Regardless of Cohort Reporter permission any user will be able to modify Report artifact properties from the main Workspace Explorer This includes the Report s Name Description and Notes e Report artifacts will still be shown in the Workspace Explorer to all users even those without Cohort Reporter access If a user does not have Cohort Reporter access and they attempt to open the Report they will get a pop up message stating that they do not have access to this feature Clinical Pattern Matcher Users with Permission to Cohort Analyzer will have the following privileges e Full Access to Clinical Pattern Matcher e Full Access to Clinical Pattern Editor e Ability to access Clinical Pattern Matcher from other BIS Tools Implications of this permission e Regardless of Clinical Pattern Matcher permission any user will be able to modify Clinical Pattern artifact properties from the main Workspace Explorer This includes the Name Description and Notes Export Data Ability to Export is a general permission either the user can or cannot Export data of any form from BIS Users with Permission to Export will have the following privileges TransMed Systems Inc 330 BIS USER S MANUAL as e Access to copy to local clipboard from any data grid in BIS that currently supports the copy operation e Utilize any Export button in BIS e Ability to download a CSV SAS SPSS R XML or
26. BIS installation and this scheme will apply across all Projects and Workspaces If a Trait is protected then any user opening a Workspace in De ldentified mode will NOT see that Trait even if it is a part of the Project configuration The following table shows how BIS determines Trait visibility for a particular user TransMed Systems Inc 290 BIS USER S MANUAL a Protected Non Protected Non Project User Project Trait Project Trait Trait User w identified data access Yes Yes NO User w o identified data access No Yes No Identified Projects vs De Identified Projects BIS does not make a distinction between Identified and De Identified Projects Any Project in BIS can contain a mixture of protected and non protected Traits What Traits a user sees when they access a Workspace with a Project depends on what identification mode they open that Workspace in If a user opens a Workspace in Identified mode they will have access to all Traits assigned to the Project that contains that Workspace If they open a Workspace in De Identified mode they will only have access to non protected Traits assigned to that Project The identification modes that users can open a Workspace in are an attribute of their permission for that Workspace s parent Project This means that different users can have different levels of data access to the same Project and thus the same Workspaces In BIS there is no difference be
27. Click Apply Filter orange area below TransMed Systems Inc a BIS USER S MANUAL as Back A Up 2 Group Sample wa Sample T Apply Filter Module Filter Options The user has the option to add Modules to the Filter List in Cohort Explorer by using the Filter Panel Steps to Filtering on a Module 1 Search for a Module in the Data Explorer yellow area below 2 Click the Filter Icon on the Module in the search results pink area below al All Items Search Results for chemistry Didn t find what you were looking for gh g 06 Chemistry pr All Traits gt Patient Traits gt Patient Fields gt 06 Chemistry 3 Set the Linking Relationship red area below 4 Set the Constraint purple area below 5 Click Apply Filter orange area below TransMed Systems Inc 105 BIS USER S MANUAL as eo Back o Up Be Group pf 06 Chemistry 06 Chemistry Coe Same Patent Trait Filter Options The user has the option to add Traits to the Filter List in Cohort Explorer by using the Filter Panel Based on the current Cohort Filter Trait Type and associated Traits the Constraints and Advanced Filters may differ Steps to Filtering on a Trait 1 Search for a Trait in the Data Explorer yellow area below 2 Click the Filter Icon on the Trait in the search
28. Cohort result as the base of the Cohort Filter List This is a New Cohort and will not be saved to the Workspace unless saved by the user in Clinical Pattern Matcher e Non Matching Patients in Cohort Explorer This will launch Cohort Explorer with the Non Matching Cohort result as the base of the Cohort Filter List This is a New Cohort and will not be saved to the Workspace unless saved by the user in Clinical Pattern Matcher e Matching Patients in Cohort Reporter This will launch Cohort Reporter with the Matching Cohort result as the starting Cohort This is a New Cohort and will not be saved to the Workspace unless saved by the user in Clinical Pattern Matcher or Cohort Reporter e Non Matching Patients in Cohort Reporter This will launch Cohort Reporter with the Non Matching Cohort result as the starting Cohort This is a New Cohort and will not be saved to the Workspace unless saved by the user in Clinical Pattern Matcher or Cohort Reporter View Once a Clinical Pattern Match has been run the results are displayed in icon view The user has three view options in Clinical Pattern Matcher and can access the different views by clicking the View dropdown button in the Toolbar e Icon View The Icon View displays the Matched and Non Matched Cohorts as two Cohorts just like in Cohort Explorer Each Icon shows the counts and overall percentage TransMed Systems Inc a66 BIS USER S MANUAL as d 2 Clinical Pattern
29. Diagnosis Observations Type All T x T ie R TransMed Systems Inc BIS USER S MANUAL Proximity Pinute Hour Proximity Day a Qualifier Week Honth Proximity Year Repeat 1 N Birthdate All Patient Diagnosis Observations Type All Yo x T x Cohorts Section The Cohorts section shows the Cohorts that have been selected by the user to run Clinical Pattern matches against Cohorts Tel All n 23 173 Patients The user can add or remove Cohorts in the list by clicking on the Search button red area above this will open the Cohort selector e To Add Cohorts Right Arrow Highlight one or more Cohort s on the Left Side and then click the Right Arrow button The Cohort s will move from the Workspace side to the Selected side The Right Arrow button will activate once a Cohort s is selected e To Delete Cohorts Left Arrow Highlight one or more Cohort s on the Right Side and then click the Left Arrow button The Cohort s will move from the Selected side to the Workspace side The Left Arrow button will activate once a Cohort s is selected If the user removes all Cohorts from the Selector BIS will add the ALL project Cohort to the Clinical Pattern Matcher TransMed Systems Inc a63 BIS USER S MANUAL as If the starting Cohort is a New Cohort the user has the option to save the Cohort to the Works
30. Experiment TransMed Systems Inc 189 BIS USER S MANUAL a Example of Linking Relationships I Add Level Diagnosis Patient Module Link ix g gt g Sample Patient from Sample Sample Patient from Sample From child Samples to parent Patient to Diagnosis Diagnosing Sample from Sample 2 From the Sample to the Diagnoses for this Sample to Diagnosis Diagnosis from Patient From Patient to Diagnosis Sample Patient from Sample From child Samples to parent Patient to Diagnosis Diagnosing Sample from Sample 5 6 Items From the Sample to the Diagnoses for this Sample to Diagnosis i 1 1 This will add the Diagnosis Module as a Main level below the Sample level linking through the Patient TransMed Systems Inc 190 BIS USER S MANUAL ae G all 23175 T Patient 10 v Sample ID y Patient ID 2 This will add the Diagnosis Module as a Main level below the Sample level linking through the Diagnosis Sample This is a One to Many link 3 Group Q au 23175 v O Patient i Patient 1D jij Sample a Sample ID 3 This will add the Diagnosis Module as a Nested level under the Patient level linking through the Patient all 23175 ae Patient ID Sample ID 4 This will add the Diagnosis Module as a Nested level under the Sample level linking through the
31. MANUAL Patient Sample Is p Q lt J lai From parent Patient to child Samples to Grade Sample Patient m gt Q Io From child Samples to parent Patient to 1 HEMOGLOBIN e Trait gt Entity Linking Relationship o Last breadcrumb in the Cohort Filter is a Trait and the user is Transitioning to an Entity Is F Q lt Ja Patient Sample From parent Patient to child Samples Patient Sample Experiment Is Q lt lt From parent Patient to child Samples to child Experiments S lt 6 From a Patient Father to the Patient s Children e Entity gt Trait Linking Relationship o Last breadcrumb in the Cohort Filter is an Entity and the user is Transitioning to a Trait Patient Sample Q lt j m From parent Patient to child Samples to Degree of Yascularization Experiment Sample Patient fi From child Experiments to parent Jj gt E la Sample to parent Patient to 1 FASTING GLUCOSE e Trait gt Module Linking Relationship o Last breadcrumb in the Cohort Filter is a Trait and the user is Transitioning to a Module Same 06 Chemistry Module Linked to 1 FASTING_GLUCOSE TransMed Systems Inc a32 o BIS USER S MANUAL Is Q Is Same Patient to 06 Chemistry Patient Sample Io Q lt i lay From parent Patient to child Samples to Degree of Vascularization gt Sample Patient lay de gt Q Io From child Samples to parent Patient to
32. Matcher View Icon View x h Create Cohort P5 Open Cohort Venn Matched Not Matched Count 1 527 6 589 Count 21 648 93 41 e Patient Details Matching View The Patient Details Matching View displays details for the patients that matched the Clinical Pattern A total count is displayed in the lower right corner J Y Clinical Pattern Matcher View Patient Details Matching h Create Cohort Name 1189220 1377363 1788166789 1837197336 3374 e Match View Match View displays the Pattern Time details for pattern matches found red area below and time window settings green area below o The nested table for each row displays each Event s details blue area below clinical Pattern Matcher B iz Match View ilCreate Cohort F Open Cohort Venn Start End FieldName 11 10 1966 12 00 00 AM Birthdate 11 10 1966 12 00 00 AM 2 12 2003 12 00 00 AM Patient Diagnosis Type Colorectal Cancer 2 12 2003 12 00 00 AM Medication Geneng fluorouracil 50 mg mL soln m 50 mg mL 3 2 16 2005 12 00 00 AM Deathdate 2 16 2005 12 00 00 AM 4 11 10 1966 12 00 00 AM 2 12 2003 12 00 00 AM Birthdate to Diagnosis Match 2 12 2003 12 00 00 AM 2 12 2003 12 00 00 AM Ox to Meds Match 99 Matches TransMed Systems Inc 167 BIS USER S MANUAL as Cohort Reporter Cohort Report is a full featured report generator that allows the user to easily create complex report
33. Navigation Toolbar The navigation buttons allow the user to move Back to the previous panel or Up to the parent category e The Back button works similarly to the standard web browser Back button and moves the user back to the previous panel e The Up button moves the user to the parent category for the currently open category folder TransMed Systems Inc C BIS USER S MANUAL ys Category Mapping At the top of Data Explorer is the Category Mapping of the Entity Module or Trait that is currently displayed in the Data Panel A Category is denoted as a folder These folders are active allowing the user to navigate back to a previous folder by clicking on it ies All Items L Subject Traits Subject Fields 02 Demographics Search and Sort Toolbar There is a Search Field and four buttons in the Data Explorer toolbar This toolbar allows the user to re organize the information in the Data Panel Below e Search The Search field green arrow above allows the user to enter two or more characters to search on The search results will display all matches that contain those characters The characters can be part of the Entity Module Trait name part of the Category name or part of a choice name e Dictionary The external data dictionary will when properly integrated with the customer s existing dictionary display dictionary information in the Data Explorer
34. New Time Window Applies a Time Window to the Pattern e Rename Window Opens an edit pop up to change the Time Window name e Delete Deletes the highlighted Event or Time Window selected in the Clinical Pattern below General Information The General Information about the Clinical Pattern can be expanded by clicking the arrow button red arrow below next to the name of the Pattern Clinical Pattern Name New Clinical Pattern Description Created By jmutz Last Updated Notes TransMed Systems Inc a50 BIS USER S MANUAL as Clinical Pattern Display This area displays the Clinical Pattern in a longitudinal format allowing the users to drag drop delete and move Events into the correct order Each Event can be filtered upon have set repeat counts and have associated time windows When the user finds the Event they want to apply to the Clinical Pattern they Click and Drag or click the symbol or double click the variable from the Data Explorer LHS to the Clinical Pattern Display area RHS As the user has the left click held down the Event can be dragged to hover over the black arrows until the arrow turns red A RED arrow indicates that the variable will be set after the arrow when the Event is dropped as shown below The user will repeat this action until the Clinical Pattern is complete Cock gour fi seve ard Clos Ed iiie i ikhas F hem Time Window bd Eensame Tma Window J Delete lah An tres
35. Not Generated 3 Nested Report Generated 4 3 Report Generated 7 22 Wide Data Report Generated B gt DX gt M gt D 2 Clinical Pattern 2 Tine Windows Because users with Identified and De Identified permissions can access the same Workspace BIS implements the concept of protection on most Workspace items to prevent De Identified users from accessing protected data in items created by Identified users De Identified users have limited access to Workspace items that are designated as protected These protected items can be identified by the shield in the lower right corner of their icon Users working in Identified mode can see protected items in the Workspace and can continue to interact with them as usual with no change in behavior Users working in De Identified mode however will have the following limited ability to interact with protected Workspace items e De ldentified users CANNOT open any tool or property information tab for any Workspace item that is marked as protected If a De Identified user attempts to open a protected item they will get the following error message in a pop up window telling them that this operation is invalid TransMed Systems Inc 65 BIS USER S MANUAL as n Access Denied The item selected is protected and cannot be opened when the workspace is in de identified mode To access this item please open this workspace in identified mode If you do not have identif
36. P Enable Auditing i Disable Auditing TransMed Systems Inc sz BIS USER S MANUAL as Cohort Importer The Cohort Importer is a tool used to create a Cohort by identifying entities based on identifiers imported from a text file The text file should contain one identifier per line For example a user could create a large file 10 000 of MRNs and use that to create a Cohort in a workspace This is done by finding all patients associated with those MRNs and putting them into one cohort The Cohort Importer works at the Workspace level and does NOT import new data into BIS like the Data Importer does Cohort Importer allows the user to create a Cohort of any available analyzable entity If duplicate identifiers are in the text file BIS will only add the Entity once If by chance there is more than one Entity with the same identifier in BIS the Cohort Importer will add both Entities to the Cohort Cohort Importer Step 1 The Cohort Importer UI is presented to the user in a wizard paradigm with two main steps Step 1 the user selects the input file the Cohort Type and the Identifier Trait to use Cohort Importer a Welcome to Cohort Importer Cohort Importer allows you to create Cohorts in Ay your Workspace using identifier values contained in a text file that you supply gt Step 1 Select Input Text File Cohort Type and Identifier Trait The input file you supply should contain a list of identifiers that Cohort Importer
37. PDF export file from the Workspace to local computer Implications of this permission e Regardless of Export permission any user will be able to modify Export artifact properties from the main Workspace Explorer This includes the Name Description and Notes e For users without Export permission BIS will hide the Export button therefore the export command will not be available at all to the user e For the Export artifacts users without Export access will still be able to see the Export files in the Workspace but they will not be allowed to download them If a non export user attempts to download a file they will get an error message pop up similar to what a De Identified user gets when they try to open a protected item Access Denied The item selected cannot be opened by users without export permission in this project To access this item please contact your BIS or Project Administrator and request export permission to this project OK Workspace Permission Access If a user has identified access to a Project and thus all Workspaces in the project they implicitly also have De ldentified access to that same Project In these cases the user will have the ability to open Workspaces within that Project in either identified or De Ildentified mode as desired For example a user with Identified access to a Workspace may choose to open that Workspace in De Identified mode to help support another user who is not
38. Project specific Project or all Projects Audit Event Type specific event type or all events Date Range leave blank for all dates Once the appropriate filter criteria are entered click View to display the audit events in a grid in the browser window or Export to CSV to download a filtered version of the audit logs If displaying the data in the browser window the user can click on the column names in the grid to sort the audit data for that column TransMed Systems Inc 260 BIS USER S MANUAL as Security A big part of the Project Entitlement features of BIS is security integration This integration includes the ability to define and manage users and groups within the customer s LDAP compliant enterprise security management application e g Microsoft Active Directory BIS Administrators must first create the appropriate security groups in their own security infrastructure BIS does NOT provide capability for creating and managing security information like user accounts and security groups Administrators then configure BIS to use the LDAP security infrastructure by telling BIS which groups it should look for to provide authorization and authentication information LDAP Integration LDAP provides integration with customer s security management system BIS uses an LDAP interface to get security information users groups group membership from the customer s system and this system is the final authority
39. Properties Workspace Properties is where the Admin user can define and edit information and securities for the Workspace The Non Admin user is able to view the Workspace Properties but is unable to define or edit securities The Workspace Properties tab can be launched from the creation of a new Workspace as shown above from BIS Desktop or from the BIS Tools Menu e From BIS Desktop Select a Workspace in the main display area of BIS Desktop and then click the Properties button either in the toolbar or on the context menu TransMed Systems Inc 400 BIS USER S MANUAL ae i Tools BIS Desktop ig New Workspace Open q Favorite Properties _ Notes jj Project Properties Colon Cancer Study l Study 10 A 7 Trail 001 l Trail 002 o Colon Cancer Study Colon Cancer Study Colon Cancer Study 6 17 2013 2 28 17 PM 6 17 2013 2 06 34 PM 6 17 2013 2 16 44 PM e From BIS Tools Menu If the user has a Workspace open they can open the Workspace Properties tab from the BIS Tools menu directly without going back to the BIS Desktop They do this simply by clicking the BIS Tools button and then selecting Workspace Properties from the drop down menu BIS 5 0 ii Tools GF Workspace Explorer a Cohort Explorer es Cohort Reporter se Clinical Pattern Matcher ek Workspace Properties Close Workspace General Information The General Information panel is displayed by default when the W
40. Properties aig Con Deer Shay Ed Ed Permessions The felleaing wiers pnd groupe can poceti bhi prodi m the B95 Project Explorer and cregte Werksegces wathin it Colon Cancer Study Project Identified Cohort Cohort Cohort Clinical Data Project Grow or User Hame ra Admin pcosa Explorer Reporter Analyrer Palterne Export Aa BesAdmeristraters Gereral Information Ha Project Administrators Aa AT estGrcup Ja faeSens l Fa Patient Cohart amp Filter To change the security and permissions settings the user clicks the Edit Permissions button and makes changes via the Edit Project Permissions window BIS Admins can choose to Edit Permissions on the Security amp Permissions Panel of Project Properties Within the Edit Permissions window there are three permission tabs Groups Users and Effective Permissions The Groups tab allows for all users in the Group to be assigned the same privileges at once e When checkbox is checked next to Group Name checkboxes to the right become active BIS Admin sets privileges per Group TransMed Systems Inc a7 BIS USER S MANUAL as Edit Project Permissions Groups Users Effective Permissions All groups shown below are part of the master group defined in your enterprise security management tool If there is a group missing from this list please make sure it is configured correctly in your security setup Project Identified Cohort Cohor
41. S MANUAL ETI r Expand All Colon Cancer Study b Patient Traits Project jj Sample Traits b 4 Experiment Traits oO General Information E Secunty amp Permissions ed Patient Cohort amp Filter To update the Traits assigned to a Project one by one or by category the user clicks the Add Traits button The system will then display the Edit Project Traits window Edit Project Traits ase ee F Show All Traits L ir All Imported Ee Patient Traits C Birthdate L p Deathdate Fel Patient Fields L Eil Medication L Patient Diagnosis Type L Patient Procedure Type Sample Traits E Expenment Traits In this window all Traits in the system are displayed Checking one level of the tree selects all Traits underneath TransMed Systems Inc 55 BIS USER S MANUAL Sy Note that Traits that have already been added to the Project CANNOT be removed to do so could invalidate user items Filter Lists Clinical Patterns etc that have been built on them As a result any Trait that has already been added to the Project appears in this window as disabled and the user cannot uncheck it The Find input works as a sequential search through the tree not a filter The blue up and down arrows next to the input function as Find Next down and Find Previous up commands The Show button w
42. Select mode of any Table in BIS This will Copy the selected information to the local clipboard If the user clicks the Create Cohort button the user will be prompted to save the current Cohort as a Workspace artifact es Cohort Reporter if Collapse All Constraint All Observations Create Cohort 0 Mg from all Patients from all Samples from all Experiments BIS USER S MANUAL ys If the user clicks the Create New Project from Cohort button the user will be Create New Project from prompted to Name and Save a new Project Cohort This button is found in the Patient Cohort tab A Project can only be created from a Patient Cohort i Create New Project From Cohort When a user clicks the Create Report button from within Cohort Explorer the current Cohort will be launched into a new Cohort Report Create Report Currency Traits are used to record numeric Currency Trait y data in Currency format Data in BIS is generated from information the user defines Data is often represented by a combination of results organized in rows and columns Data is typically the results of measurements and can be visualized using graphs or images The Data Definition is the user defined data to be seen in the Report Using the Data Definition Editor the user can define very complex reports with Entities Modules Traits and Relationships of their Logical E Data Delinition Model Data Definition Tran
43. User s Example Document TransMed Systems Inc 5o BIS USER S MANUAL as Single Entity Viewer The Single Entity Viewer allows the user to see all details about a single Entity This will display all Modules Traits and Observations associated with the individual Entity There are several different ways to open the Single Entity Viewer The user is able to open the Viewer from anywhere in BIS that an Entity detail list is displayed e Cohort Information On the Cohort Members Panel o Highlight Entity in the list and click the Open button in the toolbar double click on the Entity or right click on the Entity to Open e Cohort Explorer Entity Details view o Highlight Entity in the list and click the Open dropdown button in the toolbar double click on the Entity or right click on the Entity to Open e Cohort Explorer Observation Details view o Highlight Entity in the list and click the Open dropdown button in the toolbar double click on the Entity or right click on the Entity to Open e Venn Diagram Members List o Highlight Entity in the list and click the Open button in the toolbar double click on the Entity or right click on the Entity to Open e Clinical Pattern Matcher Matching and Non Matching view o Highlight Entity in the list and right click to View Entity or click the View Entity button in the toolbar e Cohort Reporter Report Data Panel o Highlight
44. Workspace and open them in the Cohort Viewer The user will still have full functionality minus opening Cohort Explorer in the Cohort Viewer pending other privileges allotted Cohort Reporter Users with Permission to Cohort Reporter will have the following privileges TransMed Systems Inc 320 BIS USER S MANUAL as e Full Access to Cohort Reporter e Full Access to Report Tools Panel e Ability to Access Cohort Reporter from other BIS Tools and from the Workspace Implications of this permission e Regardless of Cohort Reporter permission any user will be able to modify Report artifact properties from the main Workspace Explorer This includes the Report name Description and Notes e Report artifacts will still be shown in the Workspace Explorer to all users even those without Cohort Reporter access If a user does not have Cohort Reporter access and they attempt to open the Report they will get a pop up message stating that they do not have access to this feature Cohort Analyzer If user does not have permission to Cohort Reporter the user cannot be given permission to access Cohort Analysis Tools When the user is given Cohort Analyzer access Cohort Reporter will be selected by default Users with Permission to Cohort Analyzer will have the following privileges e Full Access to Cohort Reporter e Full Access to Report Tools Panel e Full Access to Analysis Tools Panel e Ability to Access Cohort Reporter from other
45. X Between Exclusive Both un checked Between Y and X Date with Time Trait When using the Advanced Filter options for a Date with Time Trait the user must first click the button next to Filter on Specific Dates This enables the Filter options allowing the user to add Filter values and apply the Trait to the Cohort Filter Sometimes a Date with Time Trait is also the Timestamp for a Module so these Icons may differ on the Filter Panel Steps for using Advanced Filter Options 1 2 3 4 Click the Filter icon on the Event Tile red area below Choose Filter on Specific Dates green area below Add a Low Value High Value or both to filter boxes black area below E e Note The user will get a calendar by clicking the button next to the range Set relational operator and inclusive check purple area below Click OK yellow area below Date Range 16 BIRTHDT Constraint All Observations _ Filter on all dates Filter on specific dates Repeat 1 Equal to BIRTHDT all After Observations mT e x Before Between Relational Operators After Inclusive 2Y After Exclusive un checked gt Y Equal to Y Before Inclusive lt Y Before Exclusive un checked lt Y Between Inclusive Y and Exclusive X Between Y and X Between Inclusive X and Exclusive Y Between Y and X Between Inclusive Both Between Y and X Trans
46. and a specific Module Links were discussed in further detail above TransMed Systems Inc 137 BIS USER S MANUAL ee j ICDS gt ICDS B a Diagnosis Diagnosis 0 List Breast Dx 0 List Skin The Breadcrumb above is showing that the user started with All Patients in the Project then filtered on the Trait ICD9 for all Patients that have been diagnosed with a breast condition then filtered again on the Trait ICD9 Link to Same Module on all Patients that also had a diagnosis for a skin condition The end result of this Filter is all Patients that have both a breast and skin condition diagnosis Results Toolbar This toolbar displays the current Cohort count and the current viewing option of the Cohort Explorer results Cohort Type Entity Type The Cohort Type changes by default to the Entity Type at the end of the Cohort Filter To display a different Cohort Type for the results the user can select that type in the dropdown menu A user can also pin the Cohort Type so it does not change when the filter Entity Type changes v For more Cohort Type Examples please refer to the Cohort Explorer Section in the BIS User s Example Document Count The Count is the count of Entity members in the selected Cohort Type View The View dropdown gives the user several options on how to view the displayed data Results Viewing Area This are
47. are adding a variable to the Data Definition The linking options will differ based on the existing Levels in the Data Definition and the variables selected TransMed Systems Inc EEE BIS USER S MANUAL as Linking options listed under the Main Level Links section of the dropdown will add the new variable s as a Main Level to the Data Definition The Linking options listed under the Nested Level Links section of the dropdown will add the new variable s as a Nested Level to the Data Definition Linking Options display the Linking relationship in bold then the Linking description below The arrows displayed in the Linking options also show the Relationship between variables One to Many Many to One Direct of the Same The Entities and Modules are displayed as Icons e Entities The Link options dropdown shows the user the entire Linking relationship using the Icons and Arrows Example Patient Sample Experiment From parent Patient to child Samples to child Entity This Linking relationship is showing that the Data Definition level ended in an Entity green box from there the user added another Entity red box To get to the newly added Entity the Data Definition had to transition through 1 Entity yellow box Steps of Linking Relationship 1 Patient Entity Transition One to Many to Child Entity Type Sample 2 Sample Entity Transition One to Many to the Child Entity Type
48. as o Refer to the Clinical Pattern Matcher section below for more on the above options TransMed Systems Inc ECE BIS USER S MANUAL as Cohort Explorer Cohort Explorer is one of the powerful features in the core filtering and grouping engine that BIS is built on This feature will give users control over their logical data model queries enabling them to get precise answers when building Cohorts for reporting and analysis There are two main areas to the Cohort Explorer Tab Data Explorer and Filter amp Cohort Display Data Explorer in Cohort Explorer Data Explorer is the Left Side panel of the Cohort Explorer Tab The user can search for Entities Modules and Traits to apply to the Cohort Filter Once the user has found the variable they were looking for and selects it they will get different options for applying the variable to the Cohort Filter e Filter e Group e Transition Link Relationships and Constraint rules are the same for both the Filter Panel and the Grouping Panel Filter Panel The Filter Panel is displayed in the Data Explorer area of the Cohort Explorer tab The Filter Panel allows the user to quickly add a variable to the Cohort Filter with the BIS standard settings or edit the settings to suit their needs The additional filter options displayed in the Filter Panel will vary based on the type of variable selected Entities and Modules have similar Filter Panels whi
49. authorized to see protected data in De Identified mode For these users opening the Workspace in Identified mode will be the default and opening in De Identified mode will be a menu option See the Opening a Workspace section above for more details Identified vs De Identified Mode in BIS Many places in BIS reflect the user s data access permissions or the protectedness of specific items that they can interact with In these cases BIS provides several visual indicators so that the user can determine the context of the Projects Workspaces and Workspace Artifacts that they are working with Identification in BIS Desktop In the BIS Desktop tab the user can browse through all of the Projects and Workspaces that they can access Both Projects and Workspaces display ID overlays in the lower right corner of their respective TransMed Systems Inc 34 BIS USER S MANUAL Ss icons to indicate the data access level that the user has to them These icons are shown below From left to right De Identified Project Identified Project De ldentified Workspace and Identified Workspace iy Data Access Levels in BIS One of the most important security features of BIS is the Data Access Levels As one of the core features of BIS Data Access Levels give BIS Administrators the ability to restrict the data access of particular users in accordance with PHI and HIPAA standards BIS is designed with two lev
50. below 6 Optional Select Traits owned by the Module to be in the Data Definition black area below e Traits Selected will show nested within the Module Level e The First Trait selected will become bold The First Trait is important for certain Constraint options 7 Optional Check Uncheck Remove Empty Columns yellow area below e This will not display a column with all nulls in the generated Report 8 Click OK orange area below TransMed Systems Inc a73 BIS USER S MANUAL Ss Add Level a 06 Chemistry Fatient Module pal g 06 Chemistry from Patient Constraint ii All Module Readings A eee a Remove ET 4 CREATININE T ALKALINE PHOSPHATASE 23 Items 3 Selected Add Trait Options Traits in Cohort Reporter are owned by a Module In the Data Definition Traits appear on the Module Level The Module Level is highlighted below in blue the Traits are highlighted red F m 06 Chemistry 4 CREATININE The variables nested within the Module are the Traits that the user selected and are owned by the Module Based on the current Data Definition Trait Type and associated Traits the Linking Relationship Options Constraints and Advanced Filters may differ Users can Add Traits one by one or many at a time if they use the Module to Add Traits Steps to Add a Trait 1 Search for a Trait in the Data Explo
51. comma separated list of all unique values returned for each row when the report data is Summarized to a Main level Duplicate values will only be included in the list once Comma Separated Values Group Summary Option e Create a comma separated list of all unique values returned for each Group when the report data is summarized to the Group level Duplicate values will only be included in the list once Count Non Null Level Summary Option e Counts the total number of values returned for this Trait when the report data is summarized to a Main level Duplicate values will be counted each time they appear Count Non Null Group Summary Option e Counts the total number of values returned for this Trait when the report data is summarized to the Group level Duplicate values will be counted each time they appear Min Level Summary Option e Returns the minimum value for all values associated with this trait per level when the report data is summarized to a Main level Min Group Summary Option e Returns the minimum value for all values associated with this trait per Group when the report data is summarized to the Group level Max Level Summary Option e Returns the maximum value for all values associated with this trait per level when the report data is summarized to a Main level Max Group Summary Option TransMed Systems Inc a97 BIS USER S MANUAL as e Returns the maximum value for all values assoc
52. dates within that hierarchy are offset by the exact Same amount This is done so that relative times between events for an Entity remain consistent For De Identified users BIS will return the actual date PLUS the relative offset for all dates related to an Entity Protected Traits The final part of the data access design is the concept of marking specific Traits in the system as protected Protected Traits will NOT be shown to users with De Identified access to the system they will only be available to users with identified access Traits that are protected are identified and marked as such during the initial BIS system configuration when the Trait hierarchy itself is mapped out Note that the Project Entitlement features do NOT provide a way to change the protected status of a Trait this is an enterprise level setting that can only be set when a BIS instance is installed Changing the protected status of an existing Trait can be accomplished through back end system administration tasks but BIS does not provide a user interface for making this change Data Access Example For purposes of De Identifying patient information it is important to understand the potentially confusing difference between protected Traits and date offsetting Making a Trait protected hides that Trait entirely from the user In cases of date Traits it is often the case where the user needs to have access to the Trait but they cannot see the actual value for that Tr
53. determined in the Project Properties tab described below Like the Project permissions there are no deny permissions so any user or user that is a member of an assigned group that is added to the Workspace security settings will have access to that Workspace ie Workspace Properties a Trail 001 E Workspace Explorer EA Edit Permissions Trail 001 The following users and groups can access this project in the BIS Project Explorer and F di create Workspaces within it Workspace Group or User Name General Information A BisAdministrators a Froject Administrators E Security amp Permissions To change Security amp Permissions settings the user clicks the Edit Permissions button and makes changes via the Edit Workspace Permissions pop up window This window has two tabs One to allow the user to assign modify permissions for groups and one to do the same for individual users The groups tab is selected by default The list of groups and users that are displayed in the Edit Workspace Properties are those groups and users that have been granted access to the Project that contains the Workspace in question not the complete list of groups and users that can access BIS The view of the Edit Workspace Permissions window below shows the Groups tab and shows that the groups available to assign to the Workspace are only those groups that have been given access to the Project containing this Workspace TransMed Syst
54. e Trait gt Entity Linking Relationship Patient Sample i From parent Patient to child Samples Is J Diagnosing Sample From the Diagnosis to Sample for this Diagnosis Y For more Linking Relationship Examples please refer to Cohort Explorer Section in the BIS User s Example Document Module Linking Options When adding a Module to the Cohort Filter the user may have multiple Linking options based on the current Cohort Filter Linking Options display the Linking relationship in bold then the Linking description below The arrows displayed in the Linking options also show the Relationship between variables One to Many Many to One Direct of the Same The Entity and Modules are displayed as Icons e Entities e Modules Traits TransMed Systems Inc Em BIS USER S MANUAL eee The Link options dropdown shows the user the entire Linking relationship using the Icons and Arrows Example Sample Patient Entity _ From child Samples to This Linking relationship is showing that the Cohort Filter ended in a Module green box from there the user added another Entity red box To get to the newly added Entity the Cohort Filter had to transition through 1 Entity yellow box Steps of Linking Relationship 1 Sample Module Transition to Owner Entity Type Sample 2 Sample Entity Transition Many One to the Parent Entity Type Patient Some potentia
55. following will be logged when auditing is enabled at the Project level e Workspace Access logs the user ID Project name Workspace name date and time of day every time a user opens a Workspace e Filter Request logs the user ID requesting filter list date and time of day every time a user applies a filter in Cohort Explorer e Grouping Request logs the user ID current filter list grouping options Trait etc date and time of day any time a user groups data in Cohort Explorer e Entity Group Creation logs the user ID Entity Group name date and time of day any time a user creates an Entity Group This could be from Cohort Explorer Venn diagram or any other tool that allows the user to create Entity Groups e Venn diagram logs the user ID Venn inputs date and time of day any time a user creates a Venn diagram e Export File Creation logs the user ID export file name Workspace name date and time of day any time a user creates an export file e Export File Download logs the user ID export file service URL date and time of day any time a user downloads an export file All of these options are either enabled or disabled together there is no ability to enable certain items individually If Project auditing is enabled the user can disable auditing by clicking the Disable Auditing toolbar button If Project auditing is disabled the user can disable it by clicking the Enable Auditing button shown below
56. for they will get different options for how to apply the variable based on which BIS tool they are using In all BIS tools the user can open a folder by clicking the blue down arrow next to the folder name or by using the folder hyperlink below the variable TY 3 BUN i 06 Chemistry LL All Traits gt Patient Traits gt Patient Fields gt 06 Chemist The hyperlink displays the Category that the variable belongs to In the example above 3 BUN is a Trait that is owned by the 06 Chemistry Module the 06 Chemistry Module is then organized in the Patient Fields Category The Patient Fields Category is organized in the Patient Traits Category and the Patient Traits Category is located in the All Traits Category e In Cohort Explorer the user is given the option to Filter green area below Group red area below or Transition yellow area below selected Traits only on any Trait Module Entity or Choice to the Cohort Filter o Refer to the Cohort Explorer section below for more on the above options e In Cohort Reporter the user is given the option to Add any Trait Module Entity or Choice to the definition o Refer to the Cohort Reporter section below for more on the above options e In Clinical Pattern Matcher the user is given the option to Add any Trait Module Entity or Choice to the Pattern TransMed Systems Inc 100 BIS USER S MANUAL
57. from the Workspace e Once Cohort Reporter is open the user can click the Edit Groups button on the Data Definition toolbar to choose from all saved Patient Cohorts and Patient Filter Lists o This will open the Group Selector and the user can choose additional Groups to add to the Report The report will need to be re generated for the change to apply to the results Venn Cohorts in the Data Definition The user has the Option to Venn the Cohorts already selected for the report by utilizing the Venn button on the Data Definition toolbar This function is only an option if the Groups consist of Patient Cohorts only TransMed Systems Inc aB o BIS USER S MANUAL ee T p Patent Report Setup New Report amp all Monkeys 69 D Baboon 24 i Patient ID Data Explorer in Cohort Reporter Data Explorer is the Left Side panel of the Report Setup tab in Cohort Reporter The user can search for Entities Modules and Traits to apply to the Data Definition Once the user has found the variable they were looking for they will be able to add the variable to the Data Definition The Add function will populate an Add Level window Within this window the user can further define the Linking Relationship Constraint options and Advanced Filters for the variable Add Level Window The Add Level window is displayed over the Data Definition area of the Report Setup tab The additional
58. in your enterprise security management tool If there is a group missing from this list please make sure it is configured correctly in your security setup Project Identified Cohort Cohort Cohort Clinical Data Admin Access Explorer Reporter Analyzer Patterns Export BisAdministrators lt Project Administrators BisTestProjectGroup1 OATestGroup1 DANE lt H a BisPowerUsers Cancel The Users tab allows for users to be individually assigned privileges regardless of Group access e When the checkbox next to User Name is checked checkboxes to the right become active BIS Admin sets privileges per User Edit Project Permissions eee Mate Groups Users Effective Permissions All users shown below are part of the master group defined in your enterpnse security management tool If there is a user missing from this list please make sure they are configured correctly in your security setup Project Identified Cohort Cohort Cohort Clinical Data User Name Admin Access Explorer Reporter Analyzer Patterns Export E gaadmin an E gasuperuser gauserl L amp qauseri0 gauser2 qausers gauser4 aoa a F gausers Cancel TransMed Systems Inc 31 BIS USER S MANUAL ys The Effective Permissions tab allows for administrators to view the overall privilege assigned per user regardless of Group access edit Project Permissions Groups Users Effective Permission
59. is established the user can alter the positions of the start green area above and stop red area above of the window As the user has the left click mouse button held down on the start or stop symbol in the Time Window the symbol can be dragged to hover over an Event box until the box turns red A RED box indicates that the time symbol will be set on that variable when the symbol is dropped The user will repeat this action until the Time Window definition is complete T Be Eee FE een ee ee nets eee es er pl eee Tr wo pia Patter am Refit eM of 2 TransMed Systems Inc 161 BIS USER S MANUAL g Os a ix fs fo oid oh GH Ei phie D ph f a T a Enia Pr hemm Bo Ge leis 7 The user also has the option to expand on the Time Window parameters by setting an Offset to the Start or Stop symbol orange circle above by double clicking on the symbol This action will bring up a time pop up for the user to define the Time Offset Using the dropdown options the user can choose the qualifier Offset Qualifier Time Adjustments Proximity in Pattern The user can define a time frame between two Events by double clicking on the black arrow yellow box below between the Events This action will open a Proximity window for the user to define the Proximity between Events Using the dropdown options the user can choose the qualifier Repeat 1 N Repeat 1 Birthdate All 7 al Patient
60. menu options will open the Workspace in the appropriate mode F5 Open X Ww Favorite fed Propert es g Notes its Project Properties Open Workspace Identified GF Open Workspace De identified Study 10 A Trail 001 Trail 002 Colon Cancer Study Colon Cancer Study Colon Cancer Study SN 6 17 2013 2 28 17 PM 6 17 2013 2 06 34 PM a 6 17 2013 2 16 44 PM Once the Workspace is open the user can see which mode they opened it in by looking at the Context Information Area in the upper right hand corner of the screen If the user opened the Workspace in Identified mode the text ID will be displayed after the name of the Workspace If they opened the Workspace in De Identified mode no text will be displayed after the Workspace name TransMed Systems Inc 230 BIS USER S MANUAL Workspace Trail 001 ID Project Colon Cancer Study User jmutz Identified Workspace Trail 001 Project Colon Cancer Study User jmutz De Identified TransMed Systems Inc BIS USER S MANUAL as Auditing Auditing is implemented at two different levels System level and Project level All auditing in BIS is done in standard CSV format to text file output on the application servers Administrators can view and search these log files using any commercially available log file viewer or using the BIS Audit Reporting Tool supplied with the application System Level Auditing System level auditing logs the foll
61. name and password from the URL allowing another user to log in with their preferences Log Out can be accessed on the BIS Tools dropdown menu Match View is one of the result viewing options in Clinical Pattern Matcher This view displays the Patients that matched the pattern and the pattern specifics A Module is a Trait container associated with an Entity Move Right or Move Left allows the user to select or remove items from the Selector tools This is an option in the Data Definition and allows the user to move the selected Trait to the top of the Module list Move To Initial New Folder allows the user to create a container for artifacts within the Workspace BIS USER S MANUAL Sy New Gene List from All New Gene List from Selected New Item List from All New Item List from Selected New Project New Time Window TransMed Systems Inc 244 This is an option in the Gene List Viewer It allows the user to create a new list to be saved on the Workspace This is an option in the Gene List Viewer It allows the user to select one or more using Multi Select Mode Genes and create a new list to be saved on the Workspace This is an option in the List Viewer It allows the user to create a new list to be saved on the Workspace This is an option in the List Viewer It allows the user to select one or more using Multi Select Mode Items and create a new list to be saved on the Work
62. only for fields that store date time values Field values are grouped by the year Examples of such groups 2003 2004 2005 YearAge This option is in effect only for fields that store date time values Field values are grouped by the number of full years that have elapsed until the current date The lengths of groups are determined by the Numeric Range property MonthAge This option is in effect only for fields that store date time values Field values are grouped by the number of full months that have elapsed until the current date The lengths of groups are determined by the Numeric Range property WeekAge This option is in effect only for fields that store date time values Field values are grouped by the number of full weeks that have elapsed until the current date The lengths of groups are determined by the Numeric Range property DayAge This option is in effect only for fields that store date time values Field values are grouped by the number of full days that have elapsed until the current date The lengths of groups are determined by the Numeric Range property Hour This option is in effect only for fields that store date time values Field values are grouped by the hour regardless of the date to which the current date time value belongs BIS USER S MANUAL ae Default Date DateDay DateDayOfWeek DateDayOrYear Group Interval Options DateWeekOfMonth Edit Pivot Field DateWeekOfYear
63. open Cohort e Cohort Name The name of the Source Entity Cohort that was used as the root of the Cohort Explorer session that created this Cohort If the Entity Cohort that the viewer is being displayed for was NOT created from a Cohort Explorer session it will not have a Source Cohort And None will be displayed e Cohort Type The Entity type of the Source Cohort This may be different than the Entity type of the Cohort being displayed in the Information tab e Cohort Filter Graphical representation of the filter list from Cohort Explorer While this looks similar to the breadcrumb display in Cohort Explorer this Filter List is non functional clicking on the breadcrumbs will not un apply filters or change the Entity Group in any way Filter Lists that Contain Protected Traits As discussed in the Data De Identification section Filter Lists like most items in BIS can be protected items if they contain protected Traits This applies both to Filter Lists that are saved directly to the user s Workspace and to Filter Lists that are saved as a part of an Entity Cohort In both cases users that do not have the Workspace open in Identified mode are not allowed to open and see the protected Filter List For the Cohort Viewer this means that if a user working in De Identified mode opens an Entity Cohort that was created with a protected Filter List BIS hides all details about that Filter List The Source Cohort amp Cohor
64. results pink area below g Back e Up lla All Items bun Search Results for bun Didn t find what you were looking for 3 Set the Linking Relationship red area below 4 Set the Constraint purple area below 5 Set Advanced Filter if needed black area below 6 Click Apply Filter orange area below TransMed Systems Inc 106 BIS USER S MANUAL as E Back g Up a Group aie 3 BUN EL 06 Chemistry 11681 Coe Same Patent Constraint iiil All Observations T Apply Filter e Filter on all values C Filter on specific values Low Unknown Unknown Trait Advanced Filter Options Each Trait type has its own Advanced Filter options This filter once again limits the data Entities returned For each Trait the user has the options of selecting All Values No Filter or Specific Filter e All Values No Filter This Filter does not limit the returned data based on the Observation value e Specific Filter This Filter limits the returned data based on the Observation value The Advanced Filter options are different from the Constraint options which limit the data on the presence of an Observation not the value of the Observation Text Trait When using the Advanced Filter options for a Text Trait the user must first click the button next to Filter on Specific Values This enables the Filter options so the user can add Filter valu
65. rows Columns Removed 2 general lab gt poc urine pregnancy general lab gt preg serum Transform Complete 9 18 2013 4 12 38 PM 0m 0s Generation Completed Successfully 9 18 2013 4 12 38 PM Om 25 The user also has the option to Copy the log to the local clipboard if needed Gene List Selecting Gene List Filter for the Report The Gene List Selector is used in the Report Setup Tab of Cohort Reporter This allows the user to select one or more Gene Lists to be referenced in the Report The Gene List Selector is an option for users if the Data Definition has variables that allow for Gene data When this scenario is presented a Gene Lists button will display in the Data Definition toolbar and will launch the Gene List Selector window Report Setup D Molecular Close f Collapse All Tr Clear Data Definition Gene Lists 1 The Gene List Selector window populates with all Gene Lists in the current Workspace 2 There are two main sides to the window The Workspace Gene Lists and the Selected Gene Lists In the middle of the two sides the user has move options 3 The Workspace Gene Lists side will display as the Gene List Name only Once the List is selected and moved to the Selected Gene Lists side the Name Type of List and Gene count will display 4 The Gene List will then be displayed at the bottom of the Data Definition TransMed Systems Inc 208 BIS US
66. several empty cells e Level Headers This will display and hide the Level Headers row in the report data The Level Headers show the user which Level of the Data Definition the column below belongs to Results Display Area The Results Display Area is where the generated Report Data is displayed in page table The user can alter the viewable data in the table by using the toolbar functions Based on the Data Definition one column of data is generated for each Entity Module or Trait in the Definition Multi Select mode The table also has a Multi Select mode that allows the user to select one or more rows Entities in the Report Data This feature allows the user to create a Cohort or Export some of the Report Data without Exporting the entire grid TransMed Systems Inc aa BIS USER S MANUAL ys Cohort Reporter DDI Level G DDI MODULE fg Create Cohort gt Open gjExport All Data if Display Options G DDI MODULE Time to Recurrence DDI Males g False 73 2 73 i Group Name N stage Local Recurrence Survival Time T stage hes Cohort Reporter A DDI Level DDI MODULE Create Cohort Open AlExport Selected Data QE Display Options E DDI MODULE Time to Group Name N stage Local Recurrence Survival Time T stage l Recurrence DDI Males False 73 73 DBI Males False 63 i 63 DDI Females False B8 BE Open Close MultiSelect Mode Select All Un Select All I
67. shows the user the filter association from one Entity Module or Trait to another The Up button is on the toolbar of the Data Explorer It allows users to go Up to the variable category folder BIS USER S MANUAL Sy Venn diagrams are diagrams that show all possible logical relations between Cohorts Venn can be accessed from the Workspace Cohort Explorer History and Clinical Pattern Matcher The View Gene button is on the Gene List Viewer and allows the user to highlight a gene in the list and view details about that gene View Gene The Workspace is the main container for saved artifacts The user must have a Workspace open to perform any action within BIS The Workspace has security options relative to the Project security The icons display a shield on the Workspace depending on the user s access to the workspace Workspace Explorer Workspace Properties displays the General Workspace Properties Information and Security and Permissions for the active Workspace TransMed Systems Inc 255
68. sss cesses aatas tens vss E gatos canes Rpm ea LACUNA a RE aR RADI eG RL an M SR Senge RUaIEE 201 Res lts Display Ai Cd ca saeinvcnivadetacen veut aaea decee dan tees ae oteacenued aaraa EEEE EAEE 202 Gene List Selecting Gene List Filter for the Report ccccccsssssccccceeseececceessececeseseccecseeueeeessaaseeeeesuanseeessaansses 208 Data Transforms Selecting a Transform for the REpOrt ccccsssssccccssssecceceeseecceceeeeececseeseecesseuaseeessuaueeeesseees 209 REPOR TOI AIG cance zsctesne waa E N A E E E eaaneutiasnaad taeoancouesooes 211 Marno ne R PON TOO oa E E E tues NE OE E E EE 211 POETOE ee AE E EE E EA EE E A E EE A 212 Anane WOO PANE asa E EEEE E i 225 Managing ADalySiS TOO Sneinen EE EE T ET ee oe 225 BIS Terms and Action DICtiONary sssapiisianenatacennnateioensadececwcsieesuseatueessnadshmtanatecceniaicesueed ecneseadeiananatcamuinladeneitereesea de 226 TransMed Systems Inc 4a BIS USER S MANUAL as The BIS Logical Model To understand BIS it is important to understand the BIS Logical Model first All discussion of the features in the Cohort Explorer filter engine and the functionality of Cohort Reporter rely on a firm understanding of the BIS Logical Model Put simply the Logical Model is a data model designed specifically for an organization by TransMed engineers This data model captures as closely as possible the data elements and relationships already present in the customer s organization In
69. tabs For N Log out security purposes the user will be asked to enter their log in credentials again this time WITH the domain name Once authenticated they will be taken to the Audit Log Viewer FP About BIS TransMed Systems Inc 25 BIS USER S MANUAL ae BIS Au DIT LOG Welcome XBTMS cmazzanti Show user AllUsers for project All Projects with event type All Event Types between dates DateTime User Project Workspace ten o Mesage i 2012 05 16 a 09 37 13 jsintz Auditing Auditing Workspace Open Workspace named Auditing wi Lo 2012 05 03 Ga 7 f m jsintz Auditing Auditing Create Subject Group Create Subject Group named TestGroup1 2012 05 03 Do a ny 16 17 30 jsintz Auditing Auditing Create File Create File named Grid export for GroupDetails on 03 May 2012 2012 05 03 pe jsintz Auditing Auditing Export File Export Grid export for GroupDetails on 03 May 2012 2012 05 03 a ia ee s z _ rg jsintz Auditing Auditing Filter Group By Grouped By Subject Diagnosis Type Individual Choices 2012 05 03 n 7 jsintz Auditing Auditing Workspace Open Workspace named Auditing 2012 05 02 n ao jsintz Auditing Auditing Create Subject Group Create Subject Group named jms 5212 The Audit Log Viewer is a simple application At the top of the window the user can enter the following filter criteria User specific user or all users
70. the Clinical Pattern Matcher and does not affect the results just displays Time Window information Traits are the simplest items in the logical model they represent an individual piece of data called an observation to be Recorded in the system lec oC a i 11001 TransMed Systems Inc 253 BIS USER S MANUAL ys Transform Transition Transition Traits Transitions in Cohort Filter TransMed Systems Inc 254 Data transformation refers to the application of a deterministic mathematical function to each point in a data set Transforms are usually applied so that the data appears to more closely meet the assumptions of a statistical inference procedure that is to be applied or to improve the interpretability or appearance of graphs Transition allows the user to jump to the Transition Trait in Cohort Explorer Transition Traits are a special type of Trait that appear in the Data Explorer for Cohort Explorer only Transition Traits represent a relationship that exists between a Module and another type of Data Container either a Module or Entity Unlike relationships that show up in the Relationship section of the Group or Filter panels Transition Traits do not allow the user to make a transition and follow a relationship from one Module Entity to another Instead Transition Traits allow them to filter group on whether the relationship exists or not A Transition in the Cohort Filter
71. the real DOB Dec 7 1941 and DelD value that is offset randomly from the real date Dec 21 1941 in this case plus 14 days Finally note the protected column this indicates which Traits a De Identified user can and cannot see Anything marked as yes protected will be unavailable to a De Identified user The Treatment Module shown in the table next to the patient table represents a single treatment for the patient This table contains one protected field Admin Date It also contains two date fields each containing both the real date and a De Identified date offset the exact same amount as the DOB in the patient table i e 14 days Note that because the Admin Date is marked as protected it is NOT shown to the user in De Identified mode even though it has an offset value So applying our data access rules to these two tables an identified user would see the following Patient Treatment Trait Value Protected Trait Value Protected ID MRN 012334 Yes Date May6 2005 No Dec 7 1941 Name Avastin No Yes rr a Identified User View of the Raw Data shown above A De ldentified user would see the following Patient Treatment VEIE Protected VEIE Protected TransMed Systems Inc 37o BIS USER S MANUAL ae Height 7ainches no Jooo De Identified User View of the Raw Data shown above TransMed Systems Inc 38 BIS USER S MANUAL Ss Project Entitlement Project Entitlement in BIS al
72. to match the filter criteria It is important to understand that no Patients will be removed from the Project as a result of running this update to do so might invalidate Patient Cohorts already created in Workspaces in the Project and thus invalidate any research that is based on those Cohorts Project ETL Refresh The idea behind Project ETL Refresh is that the ETL can call one single non changing function after an incremental load and update any project that chooses to participate in the ETL Auto Refresh function Implementing this will require the following BIS Administrators and BIS Project Administrators will be able to define which Projects will have ETL Refresh with each ETL update by clicking on the Enable ETL Refresh button on the Patient Cohort amp Filter Panel in Project Properties i r q Project Properties hy Tools Colon Cancer Study Refresh From Filter P Enable ETL Refresh Cohort Information Colon Cancer Study Project Cohort Name All PRNO E ee ae Patient Count 11 142 Last Refresh 03 Jun 2015 10 09 25 AM E Security amp Permissions ETL Refresh Disabled Patient Cohort amp Filter Cohort Filter If the Project is refreshed though the ETL Refresh then the Cohort Refresh History will display as Filter refresh started from ETL web service Cohort Refresh History Date User Note 31 Jan 2013 13 54 ETL Filter refresh complete added 12 new Subjects 31 Jan
73. user does not want to use the All Cohort they can click the Edit Groups button in the toolbar to open the Groups Selector and choose from all Patient Cohorts and Filters saved to the Workspace Option Two Cohort Explorer Result Cohort e Create a Cohort in Cohort Explorer and choose Create Report button in the toolbar o This will open Cohort Reporter with the Cohort the user just created in Cohort Explorer This Cohort is a New Cohort and will only be saved within the Report if the user chooses to save the Cohort using the Save Cohort button in the toolbar Option Three Venn diagram Result Cohort e The user can create a Venn diagram from two or more existing Cohorts in Workspace Explorer Highlight a grouping to use in Reporter then click Open Cohort dropdown button on the toolbar and choose Open in Cohort Reporter TransMed Systems Inc pa BIS USER S MANUAL as o This will open Cohort Reporter with the Cohort the user just created from the Venn diagram This Cohort is a New Cohort and will only be saved within the Report unless the user chooses to save the Cohort using the Save Cohort button in the toolbar Option Four Cohort Viewer e The user can open Cohort Reporter from the Patient Cohort Viewer e The user can open the Cohort Viewer from the Workspace e Click on Open Cohort on the toolbar and choose Open in Cohort Reporter o This will open Cohort Reporter with t
74. users to move artifacts from one Workspace to another within the same Project or to the BIS Global Project The scratchpad is located at the bottom of the Workspace Explorer tab To utilize it the user needs to click the up arrow 4 or drag and drop an artifact to the closed scratchpad bar Once the scratchpad is expanded the user can drag and drop artifacts from the open Workspace which makes a copy then drag the artifacts into a new Workspace within the same Project or to the BIS Global Project The user also has the option to remove the item from the scratchpad by highlighting the artifact and clicking the remove button on the side toolbar or right clicking to open a context menu that contains a Remove Items button Generic Patients w Samples DM Drug Product List i Patient Cohort Report Mutz Mutz Mutz Test Project Test Project Test Project Xx Remove Items TransMed Systems Inc CE BIS USER S MANUAL ae Cohort Viewer The Cohort Viewer is designed to be a simple stand alone tab that allows a BIS User to view the contents of an Entity Cohort and take actions on all or part of that Cohort Entity Cohorts in BIS are any Cohorts that have been created from BIS Tools From Workspace Explorer the user may select an Entity Cohort and click the Open button on the toolbar to Open Patient Cohort double click on the Entity Cohort or right click on the Cohort to Open Any one of these options
75. when clicked red arrow above PTINTL Patient Initials ALCOHOL Average number of drinks per week Close TransMed Systems Inc 7 BIS USER S MANUAL as e Sort Order The Sort function toggles the display of Traits between the BIS user defined sorting and alphabetical sorting blue arrow above o Alphabetic Sorts the returned search results alohanumerically red arrow below o Auto Sorts the returned search results by the user defined sort order This is the default Sort order display purple arrow below rue gt S lt e View The view option switches the displayed results from icons to details or vice versa purple arrow above o Detail View Displays the results in List view blue arrow below o Auto View Displays the results in Icon or Detail view based on the amount of results returned yellow arrow below o Icon View Displays the results in Icon thumbnails green arrow below Lee mh To slit A Data Panel The Data Panel is where all search results are displayed The display can show Categories folders Entities Modules Traits or Choices Users in De Identified mode will not see Traits that have been marked as protected during the BIS system configuration Users in Identified mode CAN see protected Traits in the Data Explorer and can add them to any item they create and save to their Workspace Protected Traits can be identified in the display by a small Shield d
76. will open the currently selected Cohort in the Cohort Viewer A Patient Cohort Male Patients v Experiments Toolbar Cohort Name Male Patents w Expenments Description Al male patients that have an expenment in the trial date rang Cohort Type Patent Cohort Member Count 3 305 Created By jmutz Last Updated 10 Sep 2013 12 48 11 PM Source Cohort amp Cohort Filter Notes Trial Date Range 010181 12319 m Display Panel Cohort Display Panels LHS Once open the left panel of the tab is the Cohort area and displays information and commands that relate to the Entity Cohort as a whole It also displays a list of display information panels that when selected can be viewed on the right hand side of the tab Under the toolbar the name of the Entity Cohort bold text Entity Cohort type regular text and an icon showing the type of Cohort in question Patient Cohort Sample Cohort etc is displayed Toolbar The left side toolbar contains one button Open Cohort this will give the user three options on how they would like to open the Cohort when selected Based on Cohort type the user may only be able to Open the Cohort in Cohort Explorer B Open Cohort ye Open in Cohort Explorer es Open in Cohort Reporter EA open in Chrutal Pattern Matcher ha Open in Clinical Pattern Matcher e Open in Cohort Explorer Launches Cohort Explorer wit
77. will use to find the appropnate entities in BIS and add them to the Cohort that it is creating The input file should contain one identifier per line Input Text File Cohort Type Q Patient Identifier Trait TO Patient ID Cancel e The Input Text File should open a Browse window that allows the user to select a text TXT file from their local machine Once a selection is made the name of the file is displayed in input box e The Cohort Type is a dropdown that contains all of the Entity types for analyzable Entities in the BIS installation The Cohort Importer can create Cohorts for any type of analyzable Entity in BIS e The Identifier Trait is the trait for the Entity type chosen above to use when matching values in the text file Items that users can choose from in this dropdown are constrained to being only Text type traits that are associated with the Entity Info Module for the Entity type chosen above TransMed Systems Inc SB BIS USER S MANUAL as o If the user has the Workspace opened De id mode the values in this dropdown are further restricted to non protected traits e The Next button is disabled until the user has selected a Text file Entity type and Identifier trait Cohort Importer Step 2 In Step 2 of the Cohort Importer the user gives the new Cohort a name and selects the location within the Workspace for it to be saved The Import button is disabled until the user has entered
78. window TransMed Systems Inc 390 BIS USER S MANUAL as New Workspace Workspace Name He Project BIS Global Project a Description amp This pop up window will prompt the user for the Workspace name this is required the Project that the Workspace should belong to and an optional Workspace description Workspace Name The name entered in this field will become and be displayed as the Workspace Name Project dropdown This dropdown list allows the user to select which Project they want to create the Workspace in This list will contain the name of every Project that the user has access to If the user has a specific Project selected in the Workspace Display Dropdown Menu on the BIS Desktop that Project will be selected by default If they did not have a specific Project selected i e they have something like Favorite Workspaces selected this dropdown list will simply select the first Project in the list Description Allows the user to create a description about the Workspace This Description can be viewed by any user with access to the Workspace The users can view and edit this description on the Workspace Properties tab and the BIS Desktop Once the required values are entered and the user clicks OK BIS will create the new Workspace and open the Workspace Properties tab for the new Workspace allowing the user to change any additional settings for the Workspace Workspace
79. 006 Row 6 A10011007 Row 7 A10011008 H Save Report The user also has the option to save the message green button above to the local computer TransMed Systems Inc Ca BIS USER S MANUAL ae Workspace Explorer The Workspace Explorer is the main working platform A Workspace must be open to perform any tool functions within BIS Tx gt TDx gt Dx Patent Filter 3 Levels Linked CR Report tist Genersted 3 Nested 1 Main Raport Not Generated 4 3 2 Report Generated Append Patient Cohort 11 442 Patents Folder Display p gt gt s gt gt e gt P y SE Experiment Fiter lt p 3 Main Levels 3 Report Generated pp 4 Main Levels 3 Generated i 6 20 P Report Not Generated d B gt DX gt M gt D Chinics Pettern a 2 Time Windows 4 pon Toolbars 7 22 Wide Data Recort Generated B gt DX gt M gt D 2 Cijnical Pattern 2 Time Windows Breast Dx Scratchpad The user s folders are displayed on the left hand side of the Workspace Explorer tab The user can move artifacts into these folders to keep the Workspace organized This area can be expanded collapsed as the user chooses The right hand side of the Workspace Explorer tab is the Artifact Display area This area is further defined below Toolbars The Left hand Side Toolbar has two functions New Folder and Cohort Importer e New Folder New Folder allows the user to create a c
80. 1D Gene Alias record exists oScR4 True Symbol Gene Alias record exists Dosan syndrome critical rex True Synonym Symbol Symbeol Gene Alias record exists OCRE False Gene Alias record exists O5 CR6 False Gene Information The Gene Information area displays the basic Gene Information This information cannot be changed or edited by the user e Name Full Name of Gene e Species Species Associated with Gene e Chromosome Which Chromosome the Gene Resides on e Gene ID The Gene ID based on authority e Gene Authority The Gene Authority e Primary Symbol The Primary Gene Symbol Gene Aliases This section displays multiple Aliases and for each Alias a Primary Definition Alias Type and Authority is listed Gene Aliases Gene Alias record exists Alias Is Primary Alias Type Authority Gene Alias record exists 102781 True ID Entrez Gene Gene Alias record exists DSCR4 True Symbol Entrez Gene Gene Alias record exists Down syndrome critical rer True Synonym Entrez Gene Gene Alias record exists DCRB False Symbol Entrez Gene Gene Alias record exists DSCRB False Entrez Gene TransMed Systems Inc E Symbol BIS USER S MANUAL ys Interactions Panel The Interaction Panel displays the Type of Interaction the Effect Name Drug Module Name and Authority relative to the interactions and association with the Gene Gennes Wwe E EPH receptor Ad fa Expert Data EPH receptor A Type Effect
81. 2013 13 54 ETL Filter refresh started from ETL web service To turn off the ETL Refresh click the Disable ETL Refresh button TransMed Systems Inc 520 BIS USER S MANUAL ae fq Project Properties Colon Cancer Study gt Refresh From Filter amp Disable ETL Refresh Cohort Information Colon Cancer Study Project Cohort Name All Patient Count 11 142 Last Refresh 03 Jun 2013 10 09 25 AM E Security amp Permissions ETL Refresh Enabled Patient Cohort amp Filter Cohort Filter General Information b k mi If the Project is Refreshed manually through the Refresh From Filter button then the Cohort Refresh History will display as Filter refresh started from Ul Cohort Refresh History Date Note 04 Feb 2013 12 49 j Filter refresh complete added 0 new Subjects 04 Feb 7013 12 49 jn Filter refresh started from UI 04 Feb 2013 12 41 jn Filter refresh complete added 2 new Subjects 04 Feb 2013 12 41 jn Filter refresh started from UI 31 Jan 2013 15 54 Filter refresh complete added 1 new Subjects Project Traits Panel The Project Traits panel displays all of the Traits that have been associated with the Project in a tree control This tree does NOT display all Traits in BIS only those that have been assigned to this Project Traits that are protected in the De Identification scheme will display in bold with Prote
82. A E 33 Workspace Permission ACCESS cece rssat coe seaaterseedasrenouanoavateonsaasiestupedsantanbalicnasaesausatebeoeeianeaccadont ousaisanoeseantateotearseccaunss 34 Identified vs De Identified Mode in BIS ccccssssseccccecceeesseeeccccesaeesseeeceeesseeesseececessseeeuseeceeesssuaeaseceeessaaaaeeeeeeeenas 34 DIGA Cos LEVE Iii BD rora a rE osc ead vada ileum sald doanudipetd oanads nanonastianuncesN danse iosaataenbnoiayioumes Meonawiateanes 35 POJECE Elite ie WC sectseeccentcuneaecteueucestencucaceaecctussareccecccaucaesseucsanubececeantauesnestausesectenceanesosesauubeceqcnceansesestauaveeceenceaneee 39 Workspaces SF OC errs eter set vce eget asa oot oa ease tetova o aE EEEN E EAEE a AEE 39 BS GOO al OSC apigia or sa tsecceqeinranacesshasonasvaneassovadiecaeesagarennvasvanvovaceranisaesessaiamesteiiiat esau E 39 NEWN OrKS DICE eana EE EEEE A E 39 WO eS Ps i E E E anneal coaeeaicebadedebeoaenetemeses 40 NEWPORT AE E EE TE E E E E E E EE eer rer Tt 45 PO ELROD eS aE E TE AE ET N E E A ES 46 General NTOFMALION PANE enner E EEEE EE TE E EE E 46 Secun y amp Permis Sons Pane en E E TE TEET 47 Patient Cohort amp Filter Panel eesssssenssssssseresssssssrerrsssssssrressssssereresssssereressssserereresssseeeresssssererresssseereresssseeeeee 50 POE Tia PaE ore E R E E E a E E 53 AUGE PIG borro e e A E E E E 56 CODON IMPON E os E A sass cstanans tau aatnntannanen eiessared enacts 58 Workspace Explor G orisni E 61 Cohort VIEWEr sisiiescct
83. A E EEE en seca eee sans OON 168 WCE SN ENON WIR SOI EI aeneo a a E 168 Report Functionality OvervieW sssseessessseresssrerosserersssreresssreressererosserressseeresssrerossererossreeesssreressererosserreesseerees 168 LHS Toolbar of Cohort Reporter siissseisssenoitereinniieni inei an E AE EE E a 168 REDOC EUD T a E E E E E E ee nee reer 169 Data Definition Defining the Report cccccsssssccccsessecccceeseeccesaeeseceesaeaeeccesseaeeceeseaeeceesaeaseeeeseaaseeessaaaeeeeeages 169 Data Exolorer in Cohort Reportel ssasisvconsencusnanseatancduvandactansamesieonvansadeatsontanssidvaiemdeapsaoanseundesiemaisantiacsssareantawssieabees 174 Pad VSN VVC OW eorn E E E EA A A 174 Linking Options in Cohort Reporter ssssssssesesssssreesssrrresssrerosserrrossrreesssreresssrerossereesssrrressreressereresseereesseerees 188 TransMed Systems Inc 3 BIS USER S MANUAL as Constraints in Cohort REPOFter ccccsssscccccsssscccccseseccccceesecceesauseececsaeseeceeseeeccesseeeecesseeaeceessaaueeeessuaneseeseaansses 192 WSCOTIRETEN ENCOEMEIEES wetsicsaninsansnarustatnnens ensue ecneqainss tines E A AEA E A 198 CCI US Da oN aescstee wens ccs cnececen E E E E EA E OAA cuceaaiiaeadan 198 General Information Panel cccccsssssscccccccseesseeeccceesaeesseeeceeeesaeeseeeeeeeesaeeeeeeeeeeesaeeesseeeeeessaeaesseseeeesueaaaeeeeeeenanaaes 199 REPO Data AS fa setts r E E E aiden ac E seasance tasndan igoadesieioess 200 THO WO AN
84. Authority Maree Gene antagonist Inhabition Databank dasatinib EPHA2 General Information Ontologies Panel The Ontologies Panel displays the Name Type and Authority of the Ontology relative to the Gene Gene Viewer EPH receptor Az Cal Export Data Name Authonty Type skeletal system developme GenBank Bidlogical Process protein phosphorylation Affymetrix Proprietary Dat Biological Process neural tube development GenBank Biological Process integral to plasma membn Affymetnx Proprietary Dat Cell Component axial mesoderm formation GenBank Biological Process kinase activity Affymetnix Proprietary Dat Molecular Function wil morphogenesis GenBank Binlogical Process transmembrane receptor Affymetrix Proprietary Dat Molecular Function Pathways Panel The Pathways Panel displays the Name and Authority of the Pathways relative to the Gene TransMed Systems Inc ca BIS USER S MANUAL ys EPH receptor A Gene T General Information oa Interactions E Ontologies Gene Viewer EPH receptor Az Export Data Name Authority Stabilization and expansion of the E cadherin PID 4xon guidance Homo sapiens human KEGG EGFR1 NetPath Direct p53 effectors PID TransMed Systems Inc sts BIS USER S MANUAL as Venn diagram Venn diagrams are diagrams that show all possible logical relations between Cohorts Choice Lists and Gene Lists Venn can be accessed from the Wor
85. Date with Time Trait the user must first click the button next to Filter on Specific Dates This will enable the Filter options allowing the user to enter Filter values and add Traits to the Data Definition Sometimes a Date with Time Trait is also the Timestamp for a Module so these Icons may differ Steps for using Advanced Filter Options 1 Bring up the Add or Edit Trait window 2 Choose Filter on Specific Dates green area below TransMed Systems Inc a86 BIS USER S MANUAL as 3 Adda Low Value High Value or both to filter boxes red area below m e Note The user will get a calendar by clicking the button next to the range 4 Set the relational operator and inclusive check yellow area below 5 Click OK Add Trait 1 Date of Last Follow up CHA CCOP VARIOO2 Link pal g Date of Last Follow up from Patient Constraint iiil All Observations Summary pal Max ae Max Equal to After Before Between Relational Operators e After Inclusive 2Y e After Exclusive un checked gt Y e Equal to Y e Before Inclusive lt Y e Before Exclusive un checked lt Y e Between Inclusive Y and Exclusive X Between Y and X e Between Inclusive X and Exclusive Y Between Y and X e Between Inclusive Both Between Y and X e Between Exclusive Both un checked Between Y and X Choice Trait When using the Advanced Filter options for a Choice Trait th
86. Display area When the Trait is in the Clinical Pattern Display the user can set the filter parameters by clicking on the filter icon attached to the Trait Box Trait filter options will vary based on Trait Type Date Trait When using the Advanced Filter options for a Date Trait the user must first click the button next to Filter on Specific Dates This enables the Filter options allowing the user to add Filter values and apply the Trait to the Cohort Filter Steps for using Advanced Filter Options 1 Click the Filter icon on the Event Tile red area below 2 Choose Filter on Specific Dates green area below 3 Adda Low Value High Value or both to filter boxes black area below E e Note The user will get a calendar by clicking the button next to the range 4 Set relational operator and inclusive check purple area below 5 Click OK yellow area below Date Range Date Constraint I All Observations Equal to Date All oy After Observations Before X Between i Cancel Relational Operators e After Inclusive 2Y e After Exclusive un checked gt Y e Equal to Y e Before Inclusive lt Y e Before Exclusive un checked lt Y e Between Inclusive Y and Exclusive X Between Y and X e Between Inclusive X and Exclusive Y Between Y and X TransMed Systems Inc s154 BIS USER S MANUAL as Between Inclusive Both Between Y and
87. Drill Down button in the toolbar The Report Data associated with those cell s will be displayed TransMed Systems Inc pa BIS USER S MANUAL ys e Create Cohort Allows the user to save the current Cohort as an artifact on the Workspace e Open Opens the highlighted row in the Single Entity Viewer e Close Closes the Drill Down view e Export Exports the view as seen to the Workspace as a CSV file Analysis Tools Panel Analysis tools are the set of visualizations and tools provided for analytical research in BIS These work similarly to the Report Tools except these are more specialized in nature Analysis tools are also custom built by the client Managing Analysis Tools The Analysis Tools panel is where all of the saved Analysis Tools visualizations are stored Each saved tool is an artifact and can be edited just like the artifacts saved in Workspace Explorer Toolbar a Refresh Open EA Edit Info Notes Duplicate X Delete Hay Execute iy Execute All e Refresh Refreshes the Analysis Tools Panel e Open Opens the highlighted tool into editor view mode e Edit Info Edits information name and description of the tool highlighted below e Notes Applies Notes to the tool highlighted below These notes are only visible when the note button is clicked and can be viewed and edited by all users with access to the report e Duplicate Duplicates the tool highlighted below for quick variable ch
88. E E E EE 98 CODO EXDION CD ecte stan vutnsatanntsaustsatuincesetesssssadnoadanateaniiwadueadsetecedssesnssdesutnaubisatnaadicaincsbecesssddesstuinbinsiniidanainennaunesteds 102 TransMed Systems Inc aoo BIS USER S MANUAL as Data Explorer in Cohort EXPlONGl scsssisciencddvecawsasvinssncdssdavia innnan EE AINEA EENEN ADNANE dualawad svucsnaodesamsbeddesnsndoansasededes 102 Fe PANE eag A ers ene niet tinnet a tepasne eased esa vases tate vag apittep nicest EA E ns thaamnanteanmennitaeae 102 SOUS TE FP IVC E EEEE NEEE E E NIEA EA E A NERE A E E E E E 113 Constraint Options in the Filter amp Grouping Panel cccccccsssssccccceesececcceeseececsaeaeeceseaeueecessauaeceesseeneeeeseeansees 133 IS Or RETTEN EAE e E ra r E Er E E E r A 135 Cohort Explorer TOOID AN vicssccsevccesiaceancessnsnnwstsaictucosuaucachec sauebeadsancasuasesiccamsuswabsatouusteicueussianedibdedsuudansaawantueseusavwcteasvanene 136 CONO PIET SUNS cerca asa ties cnincdu tenon E E E E R AE E A E 137 Cohort Filter Breadcrumb S a a cinssaavsaertanvnivarsanancutedadi iE ea E r E NEES EEEE EEE EE S 137 PROS UIES TOO E a E A E EE E EE EEE E AEE E E E E EE 138 REUE VIENE A a A E E E O 138 g E A E ATA E T ETE E E E A E areata AE E E E A E E A E E E E T E T E 141 Export in Workspace x OIOL ED sacsacsesoneeaasacccudazecusaeasmoecceneecacsaesaenaessuntoeeoassaeoioansaamnneagidennanmateaasantousaineievasennsoesenandecea 142 Cohort Explorer Integration with Cohort Reporter
89. ER S MANUAL as ind Report Setup fai fae a Molecular a Close f Data Definition 2 Transforms Expand All E7 Clear Data Definition eN Gene Lists a Group amp All 23175 b gt Jj Sample ii Traits 4 Traits 2 gt E Expenment Tihs Traits 5 gt 5 Molecular Observation ry Traits 2 Gene 15 Gene List 14 Items Data Transforms Selecting a Transform for the Report Data Transforms can be added to each report Before the user can add Transforms to the Report the Report must be generated at least one time Once there is Data displayed in the Report Data Panel the user can add a Transform re generate and Run Analysis Tools on the new Data Transform Algorithms can be added and customized by the customer For the BIS manual a Molecular Transform will be referenced Probe to Gene mean Transform the data from probe space to gene space This transform maps the probes to genes and applies a mean function to summarize up to the gene level For example multiple probes can map to gene ABC The transform first translates the probes to the corresponding genes then gathers all of the values for each gene and returns the mean value of the intensity The result is the ability to do analysis directly against gene expressions rather than the relative intensity of probes Transforms can be added to the Report on the Transforms tab inside the Report Setup tab TransMed Systems Inc 209
90. Entity in the list and click the Open dropdown button in the toolbar double click on the Entity or right click on the Entity to Open Overview The Single Entity Viewer has 3 main areas e Entity Module Panels purple area below e Module Readings red area below e Observation Details yellow area below TransMed Systems Inc 7 BIS USER S MANUAL ae o 10011005 Entity Panels The Entity Panels display the General Information Child Entities and Modules associated with the open Entity The user navigates this column by highlighting the Entity Module to be viewed and the results will display in the Details Areas RHS 10011005 Patent oO General Information Entity Information Jdi Sample Children cil Entities A 02 Demographics A 04 and 12 Physical Examination Associated B 05 Lead Electrocardiogram Modules 06 Chemistry io 07 Hematology General Information Panel The General Information Panel displays Entity Information Traits and Details If the Entity has a parent Entity then the user can use the hyper link green box to open the related Entity TransMed Systems Inc o BIS USER S MANUAL as Sample 1584 3 CMM Normal Patient 1584 Patient Information Sample Sample Sample ID 1584 3 CMM Normal Acquisition Date 10 7 1997 12 00 00 PM Anatomical Location Unknown Sample Information Patient Patient Birthdate 2 18 1912 12 00
91. Filter Open Source Cohort TransMed Systems Inc 2460 Workspace The Open button allows the user to Open the selected artifacts from the Workspace When a Cohort is selected the user is given additional options to launch BIS Tools BIS Desktop The Open button allows the user to open the selected Workspace in Identified or De Identified mode Entity Lists The Open dropdown allows the user to open the selected Entity in the Single Entity Viewer The Open Cohort button allows the user to open the current Cohort launching different BIS Tools from within the Cohort Information tab P Open Cohortas The Open Cohort Filter button allows the user to import an existing Filter List from the Workspace into Cohort Explorer This list will replace the current Cohort Filter In the Cohort Information tab the user can select the Open Cohort Filter button to launch Cohort Explorer with the current Cohort Filter Open Source Cohort button allows the user to open the Source Cohort Information Tab from within the current Cohort Information tab Open Source Cohort BIS USER S MANUAL ys The Pathways is one of the information panels inside of the Gene Viewer This will give the user information about that gene s Pathways Pathways A Patient Cohort is a Cohort that is comprised of all Patients If the Cohort filter is viewed the user will see that the filter ends in Patient Entity or a Patient Trait Patient Cohor
92. From this table the user can access the Single Entity Viewer by selecting a row and clicking the Open dropdown in the toolbar If this button is disabled no row has been selected Open dropdown will change appearance based on Entity type amp Open Expenment SJ dud Open Sample G Open Patient The user also has the option to select one multiple or all Entities in the list for e Export if permissions apply e Copy if permissions apply e Cohort Creation Source Cohort amp Cohort Filter The Source Cohort amp Cohort Filter Panel displays information about how the Entity Cohort was created If an Entity Cohort is created from Cohort Explorer in addition to the members of the Cohort BIS will also save the Source Cohort i e the Entity Cohort that was used as the root of the Cohort Explorer session and the Filter List that was used to create the Cohort TransMed Systems Inc Bo BIS USER S MANUAL ae k AI Experiment Cohort GF e a Toolbar FA Open Cohort Open Source Cohort f Save Cohort Filter 4 Open Cohort Filter Ta Male Experiments Source Cohort Information Cohort Info H Experiment Cohort Cohort Name All Cohort Type Patient Cohort Oo General Information Cohort Filter Cohort Filter k Cohort Experiments JNE ETIN Ean b Patient i S b gt Source Cohort amp Cohort Filter This area displays information about the Source Cohort and the Cohort Filter of the
93. K Clinical Pattern Matcher Clinical Pattern w New Clinical Pattern ae d 0 Time Windows TransMed Systems Inc 145 BIS USER S MANUAL ae Clinical Pattern Matcher Clinical Pattern Matcher is one of the major Tools in BIS While it is tightly integrated with both Cohort Explorer and Cohort Reporter the Clinical Pattern Matcher tool gives the user more information about the longitudinal aspect of the data they are matching on Longitudinal filtering is the application of a Clinical Pattern comparative to Patient Cohorts relative to a longitudinal timeline The design of the Clinical Pattern Matcher tool is very consistent with that of other tools in BIS There is the configuration area the LHS which displays the options that the user needs to configure to run the pattern match process These configuration options include the Clinical Pattern to match and the Entity Cohorts to analyze for matches The results display area the RHS of the screen displays the calculated results A View dropdown changes the view of the output results just like in Cohort Explorer i Tools DAR Clin tcal Pattern Matcher O R Results Toolbar View G88 pon View G create Cohort F Open Cohort Vern Clinical Pattern f Quix Matched Not Matched J B gt DXA gt M gt D oF Count 480 5 179 Daunt 0 7096 3E a i 2 Tien Windies Cohorts Hosa iQ Male Patients w Experiments LADJ Fates bf Female Patients
94. L a Report Setup Tab The Report Setup is where the user defines the parameters and variables for the report By default saved reports will open to the General Information panel and new reports will open to the Report Setup tab m a E Z Cohort Reporter ij Tools m amp Cohort Reporter TEN Generate Data o Level Fy 06 Chemistry F Cohort Reporter amp Patient WH Report h Patient Patient ID ii Tools ef fay iza hes i Peri n Transforms Tab Back d up Collapse All Clear Data Definition Spee Ae eiat ola Cale et L B Alem Data Explorer Patient Traits Data Definition Data Definition Defining the Report The Data Definition is the logical linking model for the report The Data Definition Editor is where the user defines the data wanted in the report itself Using the Data Definition Editor the user can define very complex reports using the Entities Modules Traits Constraints and Linking Relationships The user can access the Data Definition by clicking the Report Setup button on the toolbar The report Definition is displayed on the right side and the Data Explorer is displayed on the left side of the Data Definition sub tab Data Definition Toolbar Based on which variable is highlighted in the Data Definition the toolbar will change Edit Groups Allows the user to Edit the Report Groups Edit Level Allows the user to
95. Med Systems Inc 155 BIS USER S MANUAL Ss e Between Exclusive Both un checked Between Y and X Choice Trait When using the Advanced Filter options for a Choice Trait the user must first click the button next to Filter on Specific Choices This will enable the Filter options allowing the user to add Filter values and apply Traits to the Cohort Filter Steps for using Advanced Filter Options 1 Click the Filter icon on the Event Tile red area below 2 Choose Filter on Specific Choices green area below 3 Optional Add a saved Choice List from the Workspace blue area below which will then only show the Choices on that list in the Filter Area 4 Check the Choices to be filtered on black area below 5 IT a e The user can re sort the checked items by clicking on the checked Choices move to the top of the list for easy viewing e The user can save the currently checked Choices as a new Choice List by clicking the F button e The count at the bottom of the choice area will update as Choices are checked and un checked 5 Click OK yellow area below button This will make all Constraint I All Observations wm 4 Filter on all choices in the list above E Fiter on specie choices 2 Search Choices J Name _ American indian Aleutian or Eskimo Asian J 7 _ Black African American Race AII of 9 choices selected Observations ral 5 Can
96. OCA 00S e 15 67 6 886 360 Male Pabents 39 OCA 001 17 61 1 246 214 OCA we 6 19 2009 Blood The highlighted rows are referencing one Group Patient One row is displayed per Group All data from the lower levels is not summarized into one row Viewing Nested Levels If the Data Definition has Nested Levels each Nested Level can be viewed in the generated Report Data The Nested Level will display the Nested Traits non summarized and show the columns for the levels above the Nested Level Gl Cohort Reporter Cohort Reporter Level g 06 Chemistry Nested Level ipen Ha Expe G Patient li 06 Chemistry 4 CREATININE Patient OCA 296 06 Chemistry 0 8 Patient Patient ID 06 Chemistry Patient OCA 198 06 Chemistry Patient 10011006 06 Chemistry 71 85 The highlighted rows are referencing one row per observation The Traits associated with the Nested Table are non summarized Viewing Summary Options If a Trait is connected to a Nested Module or Entity then the summary rules will apply on the Main merge table lowest level If the Trait is connected to a Main level Entity or Module then the summary rules for that Trait will not apply until the level is changed The Header of the column in the generated Report will change if a summary rule has been applied to that column TransMed Systems Inc 2060 BIS USER S MANUAL ys 3 BUN 4 CREATININE 6 ALT Mean 3 BUN Min 4 CREATININE Max
97. Project because he has explicitly been given De ldentified access to the Project on the Users tab Even though this user is a member of a group that has Identified access to the Project he specifically gets De Identified access because of the settings in the Users tab e The user rmcumber will have no access to the Project and will not see it appear in his BIS Desktop This user is not a member of any group that has access to the Project nor has access been assigned explicitly Project Identified Cohort Cohort Cohort Clinical Data Group or User Name i Admin Access Explorer Reporter Analyzer Patterns Export a BisAdministrators a Project Administrators beargill cmazzant kjunker dbarnhill 9 amp 2 Myeloma Researchers Group and User Display In a large organization there could be thousands or tens of thousands of users in the customer s enterprise security tool To eliminate showing all users and groups in the pop up above BIS installations will require the following 1 A Group or an Organizational Unit must be defined in the customer s security infrastructure that will be the root of all BIS Groups displayed in the pop up window above When this window is opened BIS will query the root groups and list all groups contained within it in the Groups tab of this window The location in the customer s LDAP structure of this root group will be a configurable option in the BIS application setting
98. The user has the option to open the Artifact from within the Search window Workspace Explorer x Trail 002 Workspace Search FP Open Bactions 7 Fas Delete z Refresh Icon View Search Results for study close search oe erent B Study 776 Control Ei Trail 002 Context Menu Search Results Context Menu Most of the toolbar functions are also available in the right click context menu The user can highlight and then right click on an Artifact to see menu options The context menu is also available while in search mode Artifact Display The Artifact Display Panel is where all artifacts saved in the current Workspace are contained As artifacts are added to the Workspace they will display in Icon View default and in alphabetic order TransMed Systems Inc CE BIS USER S MANUAL as Workspace Explorer 7 Mutz FAopen Pactions J Delete P gt gt S gt gt E Experiment Filter 3 Levels Linked CR Report Not Generated 3 Nested 1 Main Report Not Generated 4 3 2 Report Generated Append Patient Cohort 41 442 Patents Protected Workspace Items S Refresh Dx gt TDx gt tTx Patent Filter z a Si 3 Main Levels 3 Report Generated 4 Main Levels 3 Report Generated 6 20 Report Not Generated B gt DX gt M gt D Chica Pattern 2 Time Windows GE Icon View Q 3 Levels Linked Report
99. Times 2 N variable value appears Two or More times in the history Three or More Times 3 N variable value appears Three or More times in the history Four or More Times 4 N variable value appears Four or More times in the history TransMed Systems Inc 159 BIS USER S MANUAL as Repeat Count Select repeat type Once 1 Once 1 Zero or More Times 0 N One or More Times 1 N Two or More Times 2 N Three or More Times 3 N Four or More Times 4 N Time Windows A Time Window is an additional time frame to be compared parallel to the pattern The Time Window does not change the returned results it gives additional information about the results to the user A Time Window can be associated with each Event in the Pattern The user can add a Time Window by clicking the New Time Window button in the toolbar and a yellow window will populate above the Clinical Pattern More than one window can be created by repeating the above fee New Time Window Cheka Patera Heme Ge Oe Offset Start Time Window z2 C stop Time Time Window 1 The user can edit the name of the window by clicking the Rename Time Window button in the toolbar This button will populate an edit pop up to alter the name TransMed Systems Inc 160 BIS USER S MANUAL as Window Name New window name Time Adjustments in Time Windows Once a Time Window
100. a is where all of the data collected from the above Cohort Filter is viewed The user can change the view to suit their needs Virtualized Grids and View Options There are many different views within Cohort Explorer Icon Histogram Group Details Entity Details and Observation Details Some of the options may change based on the selected Cohort Type Doe gga Icon View Icon View FE Icon View alte Histogram View alte Histogram View Histogram View ai tai Group Details a Group Details a Group Details p pa Patient Details Jii Sample Details M Experiment Details Observation Details Observation Details Observation Details TransMed Systems Inc EN BIS USER S MANUAL ae Icon View Icon View is the default view of BIS and shows all results in Icon form The icon will reference the current Cohort Type selected Cohort Explorer E All iy Create Cohort P Create Report 22 Clinical Pattern FP Cohort Filter amp History ge tco9 a gt B Diagnosis M List Cancer 650 View HE Icon View All hi Create Cohort Create Report 3 Clinical Pattern F Cohort Filter History gt J Diagnosis 1 List Cancer 3 895 View Icon View Histogram View Histogram View is a Bar Chart View This will show each result group as a bar on the X axis The user can select the bar to apply that grouping to the Cohort Filter TransMed Systems Inc 139
101. a name for the Cohort When the user clicks the Finish button Cohort Importer will create the Cohort and search for Entities in the system whose Identifier given in step 1 match the values from input file Each Patient that is added to the cohort MUST be a member of the Project in which the user is working If a valid Identifier is supplied for an Entity outside the scope of the current Project that Entity will NOT be added to the Cohort Cohort Importer Step 2 Enter Cohort Name and Choose Workspace Location Patient Cohort Name Workspace Location 4 Lf Mutz d mi Export gt Deleted Items 1st fel All Patients Ke anova results Baboon h BDXMD Brown Rat TO BuN TO Chemistry Tl an When complete Cohort Importer will give the user a report of the success failure of the import including e Import Status TransMed Systems Inc 59 BIS USER S MANUAL as e Number of Entities imported e Values in the input file which were NOT imported because they could not be matched to an Entity in the Project Cohort Importer Success Cohort Created Patients Added to Cohort Test 100 Patients 19 Patients not found in Project Test Project 0 Cohort Test 200 Patients was not created No valid Patients were provided Patientss not added Row 1 A10011002 Row 2 A10011003 Row 3 A10011004 Row 4 A10011005 Row 5 A10011
102. a result The summarization rules for data moving up in level are defined in the Data Definition as the user is adding Variables as explained in the Summary and Group Summary Options per Trait Type section Patient Main Level sort All Gate M Display Options G Patient E Chemistry Jii Sample Cmt Mean 3 Mean 4 rarer rene Patent ID BUN CREATININE Dne Cov Sample ID HiAce Date CoV Tiasue of Origin iwiza 2008 5 00 40 pm ood Eresit 1DfTh 2008 1 45 00 A Bood Lymph L 1S 2009 12250200 Fi Lures NS 2008 12 25 52 p Breast a TL 2008 3 00 00 PH ney a 21 2008 4 05 08 PH Dond Debit 4 24 2008 4 33 54 PH Colon and Rectum The highlighted rows are referencing one Patient One row is displayed per Patient All data from the lower levels is not summarized into one row Group Highest Level The group level will collapse the previous levels on themselves to give overall group counts using summarized values The summarization rules for data moving up in level are defined in the Data Definition as the user is adding Variables TransMed Systems Inc 205 BIS USER S MANUAL ys gt Cohort Reporter Level gt Group ip Ma n gt Epor All Data M Display Options D Patient 06 Chemistry Jdi Sample 8 Count Mean Sum CSV CSV s Max Max CSV CSV Mean M Mean 4 Group Name Distinct CSV Patient ID enn area AREN Sample Acquisitio Tissue of Patent NE Sample ID n Date Ongen
103. a user is in two different groups that are assigned to a Project and one of those groups has identified access to the Project the user will have Identified access to the Project regardless of the access level they are granted in the other group For example consider the following users from the screenshot below and their group membership The Myeloma Researchers group contains the users cmazzanti bcargill and kjunker The BIS Admins group contains kjunker and dbarnhill The user rmcumber is in neither group These five users will have the following access e The user bcargill will have De Identified access to the Project because he is in the Myeloma Researchers group which has been granted De Identified access to the Project TransMed Systems Inc 490 BIS USER S MANUAL as e The user cmazzanti will have Identified access to the Project because he has explicitly been given Identified access to the Project on the Users tab The permissions he has been given as a member of the Myeloma Researchers group are overridden in this case e The user kjunker will have Identified access to the Project because he is in the BIS Admins group While kjunker is also a member of the Myeloma Researchers the permissions for the BIS Admins group are more permissive so he is given those e The user dbarnhill will have De Identified access to this
104. aint on Module and allow the Initial Trait of the Module within the Data Definition to define the Constraint This option will show all FIRST Observations for the Trait o Note The First Observation is not always associated with the First Module Reading e Set On Initial Trait Last Observation Apply no Constraint on Module and allow the Initial Trait of the Module within the Data Definition to define the Constraint This option will show all LAST Observations for the Trait o Note The Last Observation is not always associated with the Last Module Reading e Set On Initial Trait No Observation Apply no Constraint on Module and allow the Initial Trait of the Module within the Data Definition to define the Constraint This option will show Entities without Observations for the Trait Constraint Options for Traits All Trait types have the same constraint options Based on the Module and other Trait constraints the Trait constraint options may differ li All Observations non limiting io All Observations Till First Observation Mii Last Observation No Observations li All Observations non limiting iiil All Observations No Observations TransMed Systems Inc a BIS USER S MANUAL as e All Observations non limiting Show ALL observations for the trait regardless of content This option has the potential to bring back empty null data cells e All Observations Show ALL Observ
105. ait as that could potentially identify the patient In these cases the Date Trait should NOT be protected since that would hide the date from the user Rather it should be left unprotected and the date offsetting function of the BIS De Identification design will display the De Identified value for that date Consider the following data that is in the BIS database for a patient These tables represent part of one Module for that patient showing their personal information and the information for one specific treatment These tables represent the raw data that is in BIS not data that would be shown to a user 2 See Entity Hierarchies in the above for more information TransMed Systems Inc 360 BIS USER S MANUAL a Patient Treatment Do MRN 012334 Protected Trait Value Protected ID May 6 2005 Date DelD_ ID A999812278 Noo DelD May 20 2005 pom eet et _ Name Avastin NO o Admin ID May7 2005 Date Height 72inches no Looking at this data you can see that the patient which is an Entity has two different Identifier values ID and DelD_ID The first is their real identifier in the system most likely an MRN from a customer s EMR system The second is a fake identifier generated by the system to give the user a way to reference the patient but does not identify the patient in any other system For the date of birth DOB there are two values for the same Trait an identified value that corresponds to
106. ait it is assumed that all observations made for that Trait are done for that UoM Date Traits Date traits are used to record a date without an associated time This is important for observations like date of birth admission date diagnosis date etc Date Traits are typically used to record when other observations like those defined by Numeric Traits are made They are not typically used directly in statistical analysis but are important in querying and reporting BIS can also determine time periods numeric value for number of days for example for Entities in the system by calculating the time between two observations for Date Traits TransMed Systems Inc C BIS USER S MANUAL as Date Time Traits Date Time traits are used to record date and time information This is important for observations like medication administration time procedure date etc The time part of the observation is optional if not supplied BIS assumes midnight on the date value for the observation note that for traits where time is not important the Date trait type should be used Date Time Traits are typically used to record when other observations like those defined by Numeric Traits are made They are not typically used directly in statistical analysis but are important in querying and reporting BIS can also determine time periods numeric value for number of days for example for Entities in the system by calculating the time between t
107. ait name e Link Options o Link options allow the user to define the relationship of the Trait to the previous item breadcrumb in the Cohort Filter e Constraint Options o Constraint options allow the user to define the set of results returned More on Constraint options below e Apply Filter Button e Advanced Filter o Filter Options change based on Trait Type More on Advanced Filter options below TransMed Systems Inc 103 BIS USER S MANUAL Navigation Buttons Back Up 2 Group i aio 3 BUN Eun 202 Entity Icon foo 06 Chemistn Owner Module Wiss Q B Sample Patient Link Options Constraint Options Constraint iiil All Observations Apply Button Filter on all values O Filter on specific values Advanced Filter Low Unknown High Unknown Entity Filter Options The user has the option to add Entities to the Filter List in Cohort Explorer by using the Filter Panel Entities in Cohort Explorer are expressed as an Exist Trait and that Exist Trait is owned by an Entity Module Steps to Filtering on an Entity 1 Search for an Entity in the Data Explorer yellow area below 2 Click the Filter Icon on the Entity in the search results pink area below eC Back lb Allttems __ Search Results for sample Didn t find what you were looking for 3 Set the Linking Relationship red area below 4 Set the Constraint purple area below 5
108. an access Workspace Explorer Cohort Explorer Cohort Reporter Clinical Pattern Matcher Workspace Properties Close Workspace BIS Desktop ii Tools Y Data Importer Audit Logs About BIS and Log Out These menu options may change depending on the area within BIS that the user utilizes the menu Calculated Matches is how the user will generate a Clinical Pattern against the selected Cohort The Category in the Column Selector Multi Variable Selector and Single Variable Selector is the Parent Node within the Data Definition A Choice List is a saved artifact of selected Choice Trait observations that can be used again in Cohort Explorer and Cohort Reporter when referencing the same Trait Choice Traits in BIS Module observations from a defined list of choices All values for Choice Trait observation must be one of the choices defined for that Trait Choice Traits are useful for recording observations from multiple choice lists like ICD 9 codes ethnicity or cancer stages Choose a Variable will populate the Single Variable Selector to choose a variable in the Choose a variable Report and Analysis tools TransMed Systems Inc pe BIS USER S MANUAL yy This is found in the Display Options dropdown menu of Cohort Reporter Choose Columns Choose Columns lets the user select which columns are displayed in the generated Report Data Choose Variables will populate the Multi Choose Variables Variable Se
109. and X Date Trait When using the Advanced Filter options for a Date Trait the user must first click the button next to Filter on Specific Dates This will enable the Filter options allowing the user to enter Filter values and add Traits to the Data Definition Steps for using Advanced Filter Options 1 Bring up the Add or Edit Trait window 2 Choose Filter on Specific Dates green area below 3 Adda Low Value High Value or both to filter boxes red area below E e Note The user will get a calendar by clicking the button next to the range 4 Set the relational operator and inclusive check yellow area below TransMed Systems Inc a85 BIS USER S MANUAL as 5 Click OK Add Trait 1 gt Date Expenditure Link gsi Date from Patient Constraint iliil All Observations Summary pal Max a Max 0 Filter on all dates Filter on specific dates After Enter date Equalto M indusve After Before Between Cancel Relational Operators e After Inclusive 2Y e After Exclusive un checked gt Y e Equal to Y e Before Inclusive lt Y e Before Exclusive un checked lt Y e Between Inclusive Y and Exclusive X Between Y and X e Between Inclusive X and Exclusive Y Between Y and X e Between Inclusive Both Between Y and X e Between Exclusive Both un checked Between Y and X Date with Time Trait When using the Advanced Filter options for a
110. and manage users Groups in most systems are hierarchical they can contain other groups as well as containing users When setting up BIS it is important to understand this hierarchical nature and how to correctly configure the groups that BIS will reference Because these groups live in the customer s enterprise security system e g Active Directory they must be managed by the customer and not by BIS As mentioned in the previous sections BISAdministrators and BISGroups do not of themselves give the user access to the BIS application Only membership in the BISUsers group does this For example consider the following security hierarchy groups are shown in green users in blue Root Level Security Group BiSUsers BISAdministrators Group Group Brian Avery David user user user In this security design Brian and Avery are members of the BISUsers group Avery and David are both members of the BISAdministrators group Avery is member of both groups which is allowed In this case the users will have the following access e Brian will have standard user access to BIS e Avery will have administrator access to BIS e David will have no access to BIS because he is not in the BISUsers group Because of the group of groups approach a common security design for BIS would be like this TransMed Systems Inc BIS USER S MANUAL Root Level Security Group BISUsers Group Brian BISAdminis
111. anges e Delete Permanently deletes the tool highlighted below e Execute Re Executes the tool highlighted below e Execute All Re Executes all saved Analysis Tools Workspace All saved Analysis Tools are listed in the Panel in Icon View with Name Description and tool type Icons displayed with the exclamation symbol denote that the tool needs to be edited and re executed Icons displayed with the gear symbol denote that the tool is still generating TransMed Systems Inc 2235 BIS USER S MANUAL Sy BIS Terms and Action Dictionary Item About BIS Actions Dropdown Menu Add All Traits Add Traits All Workspaces TransMed Systems Inc 226 Description About BIS gives the user information about the current version of BIS This menu holds Workspace actions Once an Artifact s are selected the user can choose an Action from this menu This allows the user to Add a Transform to the Report in the Report Setup Transforms tab Add ALL Traits is in Project Properties This allows users to Add ALL Traits in the BIS repository to the project Add Traits is in Project Properties This allows users to add Traits to the project All Workspaces will display all Workspaces bed the user has access to the on BIS Desktop tab iw All Workspaces BIS USER S MANUAL yy Analysis Tools Append Cohort Filter Apply Filter Audit Logs BIS Desktop TransMed Systems Inc a
112. ap problem To create a Project the user must open a Workspace and run Cohort Explorer To open a Workspace the user must select a Project To solve this all BIS installations will come with a default Project called BIS Global Project that cannot be modified or deleted A default install of BIS will grant access to this Project only to members of the BIS Admins user group The BIS Global Project is special in that it has access to the entire universe of data available to the BIS installation all Entities Modules and Traits This configuration along with the name and the description of the Project cannot be changed BIS Admins can grant other BIS Users access to the BIS Global Project but this practice is highly discouraged Instead it is recommended that BIS Admins create a default All Data Project for the standard non admin users to use and keep the BIS Global Project secure for admin use only New Workspace In the BIS Desktop one of the primary operations a BIS Administrator or Project Administrator can perform is creating a new Workspace The Admin user can also assign other users to this Workspace so they can perform data exploration and analysis operations To create a new Workspace the Admin user clicks the New Workspace button at the far left hand side of the toolbar This button is enabled provided that the user is a BIS Administrator or Project Administrator When clicked the user will see the following pop up
113. apsed once all variables have been selected When the column is collapsed the user can still edit the field settings without having to expand the column The top section purple area is locked and will always display the toolbar Name Description and Level options e Save and Close Button Saves and closes the chart in the current state The chart will be saved as an artifact on the Report Tools panel in Cohort Reporter o Ifno name is defined by the user the chart will save with the BIS default name e Close Closes the Pivot table without saving changes o User will be prompted with a message of confirmation if changes have been made e Name field Allows the user to name the Chart This name will display in BIS Report Tools panel and will not export with the Chart e Description field Allows the user to enter a brief description about the Chart that can be viewed in the Report Tools panel e Level dropdown By changing the level the Pivot Table variables will change TransMed Systems Inc ae BIS USER S MANUAL as o The level dropdown defaults to the lowest level the lowest level will give true numbers while the higher level tables will change numbers by summarization rules The Variable section is the expandable collapsible section The user can expand the section by clicking on the Add Variables button and Collapse the section by clicking on the Done button Add Variables Expanded View Based on whic
114. are any users that you would like to have access to this workspace that are NOT in this list please contact a BIS Administrator for assistance User Name rphillips cmazzanti fdupont mohnson joillespie Pe a a F a F a8 jmiller TransMed Systems Inc 44 BIS USER S MANUAL as New Project Creating a BIS Project cannot be done directly from the BIS Desktop as the BIS Admin is required to specify a Patient Cohort that the Project will be based upon To do this the BIS Admin must first define the Patient Cohort themselves or use a Patient Cohort created by another user in the system The following assumes that the BIS Admin will create the Patient Cohort upon which to base the Project Log into BIS as a user with BIS Admin privileges In the BIS Desktop select the BIS Global Project from the Workspace Display Dropdown Menu a J Open a Workspace in the BIS Global Project if there is not a Workspace available create a new Workspace in the BIS Global Project first Open Cohort Explorer within the Workspace Create the Patient Cohort that will define the Entities available to the new Project Save the Patient Cohort from Cohort Explorer to the Workspace a oe Select the Patient Cohort in the Workspace Explorer and click the New Project button on the toolbar 8 Inthe pop up window that is displayed enter a name and description for the new Project then click OK New P
115. as a Limited Constraint All Module Readings First Module Reading Last Module Reading the Traits associated with the Module can be Limited or Non Limited e f the Module has a Limited Constraint No Module Readings NO Traits can be associated with the Module e If the Module has a Non Limited Constraint All Module Readings non limiting ALL Traits associated with the Module have to be Non Limited e f ANY Trait associated within a Module is Limited All Observations First Observation Last Observation No Observation the Module has to be Limited default All Module Readings e If the Initial Trait is set to No Observations the Module will be set to Set on Initial No Observations e If ANY Trait is set to No Observations Excluding when Set on Initial No Observations those Traits will be moved to the end of the Trait list Constraint Options for Entities rm All Module Readings li All Module Readings non limiting e All Module Readings Show all readings of the module that contain content The results for this option will only bring back results where the module exists e All Module Readings non limiting Show all readings for the module regardless of content This option has the potential to bring back empty null data cells Constraint Options for Modules B Module Constraints I All Module Readings non limiting
116. at have a First Observation for the Trait Last Observation Returns ALL Entities based on Cohort Type that have a Last Observation for the Trait TransMed Systems Inc aa o BIS USER S MANUAL as e No Observations Returns ALL Entities based on Cohort Type that DO NOT have an Observation for the Trait Null values Based on the Link option selected or the current Cohort Filter the Trait Constraint options may be limited to All Observations and No Observations iliil All Observations No Observations Y For more Constraint Examples please refer to the Cohort Explorer Section in the BIS User s Example Document Use of Reference Entities When filtering on a Reference Entity in Cohort Explorer there is a chance that the Filter List breadcrumbs will lock after the Entity is added to the filter This lock is to prevent the user from getting unwanted results by filtering back to another Entity type If the filter is going to lock the user will be prompted with a warning before they apply the filter Screen Shot of warning Once the user has applied the Filter on the Reference Entity or any Traits associated the Cohort Type dropdown will change from the list of Entities to the Reference Entity that was just added to the filter Cohort Explorer SF all re Create Cohort Create Report na Clinical Pattern Fl Cohort Filter History a PatientPhysician Record 9 a Ei h Physicia
117. ate Custom Date with Time Trait When using the Advanced Grouping options for a Date with Time Trait the user must select Group by specific date range Steps to using Advanced Grouping Options 1 Select Group by specific date range green area below 2 Select the method the Observation values should be grouped by using the dropdown red area below e Year Will group Observations into several groupings one per Year and No Data Values e Quarter Will group Observations into 2 groupings one per Quarter and No Data Values e Month Will group Observations into 2 groupings one per Month and No Data Values e Date Will group Observations into 2 groupings one per Date and No Data Values e Custom Will group Observations into as many custom groupings as defined and No Data Values Time can also be applied to the custom grouping 3 Click Group TransMed Systems Inc e BIS USER S MANUAL as e Back o Up T Filter G Date of Last Follow up CCOP VARIOO2 Link pal Same Patent Constraint iiil All Observations 3 Be Group O Group by all values no values Choice Trait When using the Advanced Grouping options for a Choice Trait the user must select Group by individual choices Steps to using Advanced Grouping Options 1 Select Group by individual choices green area below 2 Select a saved Choice List optional
118. ated to This is part of the power of this relationship it allows us to create links between Entities and Modules at different Entity levels These relationships are considered secondary type relationships in BIS as they are not required unlike the Entity Ownership and Entity Entity relationships Module Module The last type of relationship in BIS is the Module Module relationship blue arrow in the diagram above This relationship is almost exactly like the Module Entity relationship we just discussed except that it exists between two Modules instead of a Module and an Entity Transition Traits As mentioned in the Traits section above Transition Traits are a special type of Trait Transition Traits represent a relationship that exists between a Module and another type of Data Container either a Module or Entity Unlike relationships that show up in the Relationship section of the Group or Filter panels Transition Traits do not allow the user to make a transition and follow a relationship from one Module Entity to another Instead Transition Traits allow them to filter group on whether the relationship exists or not This is a subtle but important distinction This gives the user the ability to filter on the presence of a relationship without being forced to make a transition For example consider a BIS installation that has an Entity called Sample that is linked to a Module called Diagnosis Using a Transition Trait the u
119. atient Entity and Patient ID are the default start to the definition If a De Identified user is creating the report the default definition will be the De Identified Patient ID F l Report Setup New Report 1 f Collapse All Tf Clear Data Definition SS Eee 14 Patient ID Cohorts Selecting Groups for a Report Reporter requires a Patient Cohort or a Patient Filter to generate the Data Definition All Cohorts Filters to be used in Cohort Reporter must be of the Highest Entity type The Groups are used to give the report a base of Patients to start with that base of Patients can then be limited and filtered on as defined in the definition If there is more than one Cohort Filter in the report each will become a Group within the report The Cohort Filter used to create the Cohort will not be referenced in the report just the Cohort Entities If the user selects a Filter List as one or more of the Report Groups the Filter will be run at the time of Report generation This means that if the Report is re generated the results could differ based on the Entities that meet the Filter The user has several options to choose starting Group s Option One BIS Tools Menu e Open BIS Tools dropdown and choose Cohort Reporter o This will open Cohort Reporter with an All Patients Cohort AIl is defined as the starting Project Cohort the group of Patients used to create the Project o Ifthe
120. ations for the Trait that contain content e First Observation Show ALL First Observations for the Trait This option will show all observations associated with the First timestamp of the Trait when there is a value present This option does not guarantee one observation depending on the Trait observation timestamp more than one observation can be first e Last Observation Show ALL Last Observations for the Trait This option will show all observations associated with the Last timestamp of the Trait when there is a value present This option does not guarantee one observation depending on the Trait observation timestamp more than one observation can be last e No Observations Show all observations with null values for this Trait Y For more Constraint Examples please refer to the Cohort Reporter Section in the BIS User s Example Document Summary and Group Summary Options per Trait Type By applying a Summary option the user is defining how they would like the data displayed in the generated report If a Trait is associated with the lowest Main Level the Summary rules will not apply until the data viewing level is moved to a higher Main Level If a Trait is associated with a Nested Level the summary rules will apply at all levels of data excluding Nested views By applying a Group Summary filter the user is defining how they would like the data displayed when the level of the data is changed to the Group Level Summary Optio
121. aying information or recounting certain events in a widely presentable form The icon with the exclamation icon overlay notes that the report did not fully generate The gear overlay notes that the Report is still generating and the shield overlay notes that the report was created by an ID user or has protected information TransMed Systems Inc 249 BIS USER S MANUAL Sy The Report Data panel within Cohort Report Data Reporter is where generated data is displayed in a table format The Report Setup Tab is where the user will navigate through and set up the Report parameters Cohorts Data Definition Gene List and Transforms Report Setup Report Tools are used to take generated Report Tools data from Cohort Reporter and translate the data results into visualizations This is found in the Display Options dropdown menu of Cohort Reporter Rotate Rotate Level Level allows the user to Rotate the last level of the report to display the data in vertical format Rotate Level A Sample Cohort is a Cohort that is comprised of all samples If the Cohort filter is viewed the user will see that the filter ends in sample Entity or sample Trait Sample Cohort TransMed Systems Inc 250 BIS USER S MANUAL ay Save and Close Save Cohort Filter Scratch Pad Search Security amp Permissions TransMed Systems Inc 251 The Save and Close option allows the user to save the cur
122. b Cohort Explorer Cohort Reporter Opens a new Cohort Reporter tab Cohort Reporter Clinical Pattern Matcher Opens the Clinical Pattern Matcher tab Clinical Pattern Matcher Workspace Properties Open the Workspace Properties tab for Workspace Properties the Workspace that is currently open Close Workspace Close Workspace Closes the Workspace that is currently open _ andall associated tabs The BIS Tool Commands that are Shown at All Times are BIS Desktop Opens the BIS Desktop tab BIS Desktop Audit Logs Opens the BIS Audit Log viewer This option is only shown Audit Logs to users with access to the Audit Log Help Opens the current BIS User Manual as a PDF on the local Help computer About BIS About BIS Opens the BIS Version Information window Log Out Log Out Logs the user out of the system Window Navigation Tabs Immediately to the right of the BIS Tools menu button are the main application window tabs These tabs are fixed in position and do not move relative to each other when different windows are opened and closed Tie Patient Cohort F a pc venn plus O02 dem zero hi ni TransMed Systems Inc ao BIS USER S MANUAL as To save space horizontally only the currently active window has its tab information displayed in full All other tabs are collapsed down to just their icon All tabs display tooltips when the mouse is moved over them the toolt
123. c 79 BIS USER S MANUAL as the list below As the user selects a different Reading row from the Module Readings section below the values above will reflect the change When the Observation Details are expanded the user will see two columns Trait and Value The Trait column is a list of all Traits associated with the Module excluding Multi choice Traits and the Values column contains the Value that correlates with the Trait Reminder This view is only showing the user one Reading at a time The Reading is represented as its own row red box The user can also filter in this section using the Search Observations field or Hide empty Values button Search Trait Description 1 FASTING_GLUCOSE 3 BUN i 4 CREATININE Traits 7 ALKALINE PHOSPHATASE 8 TOTAL_BILIRUBIN gt AST Observation Values TransMed Systems Inc 800 BIS USER S MANUAL as Choice List Viewer The Choice List Viewer is a tool that allows the user to open a saved Choice List from the Workspace and view the choices in the list From the Workspace the user can double click right click or use the open button on the Workspace toolbar to open the List Viewer Workspace Explorer Mutz Breast Dx ICD List 36 Choices Duplicate Cell Subject Diagnosis Type Lis 11 Choices Edit Info Notes Delete 3 Level Linked Once open the Choice List viewer has two panels General Information and Li
124. calculated and turned into a table of results ee ee ee Generate Data The Global Project is the default project in BIS Each Project must be created from a Workspace but a Workspace has to be created within a project Global Project is the starting project for users to define Workspaces and additional projects Global Project Go to Category is an option in the Selector Go To Category tools This will collapse variables into the Parent Nodes Group is a function in Cohort Explorer The Group function allows the user to preview the results before they are applied to the Cohort Filter TransMed Systems Inc 2400 BIS USER S MANUAL ys Group Details View Hide Level Header Histogram View History Icon Details TransMed Systems Inc p Alters view of data results in Cohort Explorer to show the user the group results into table format and allows the user to export the data Help is found on the BIS Tools menu This will take the user to the BIS user documentation This is found in the Display Options dropdown menu of Cohort Reporter Hide Level Headers allows the user to Hide Show the Level Headers in the Report Data above the column headers im Hide Level Header Alters view of data results in Cohort Explorer a to show the user the data results in Bar Dk Chart format alte Histogram View The history can be viewed at the bottom of the Cohort Explorer data results this will show the his
125. ce Go to the Data Results tab and select the gene s to be saved onto the list blue box Click the Create Gene List button in the toolbar yellow box oS A Save Gene List window will populate Name the Gene List and click OK Two Sample t test Molecular Variable Statistic P Value Mean of X Mean of Sample Intensity Probe 1 Sample Intensity Probe 1 0 6786 Sample Intensity Probe 1 Sample Intensity Probe 3 2 471 0 06648 Sa mple Intensity Probe 3 0 005352 0 9959 Sa mple Intensity Probe 3 27 626 0 03377 Sample Intensity Probe 3 0 3106 0 7712 gt Sample Intensity Probe 3 The Gene List will save to the current Workspace for future use Gene 15 Gene List 14 Items How to View a Gene List From the Workspace a user can open the Gene List Viewer by double clicking on the Icon right clicking to open or by highlighting and clicking the Open button on the Workspace toolbar TransMed Systems Inc ee BIS USER S MANUAL ys Workspace Explorer x Fed FA Edit Info F Notes _ Duplicate Study Colon Active Venn w Demo Patient Cohort Patient Cohort 6 735 Patients 0 Patients Gene 15 Gene list Gene List Gene List 14 Items Duplicate 404 Items ED Edit Info Other Platforms 4 Top 4 Genes Molecular Platform List E Notes Gene List 8 items 3 Items General Information Panel A Delete Z Refresh Venn w Demo Patient C
126. cel Repeat 1 Text Trait When using the Advanced Filter options for a Text Trait the user must first click the button next to Filter on Specific Values This will enable the Filter options allowing the user to add Filter values and apply Traits to the Cohort Filter TransMed Systems Inc a56 BIS USER S MANUAL as Steps for using Advanced Filter Options Click the Filter icon on the Event Tile red area below Choose Filter on Specific Vales green area below Add values to filter box black area below e Note that each value should be on a separate line Limit 500 lines Select method the values should be filtered by in dropdown blue area below e Starts With Will search for Observations that Start With the value entered e Ends With Will search for Observations that End With the value entered e Contains Will search for Observations that Contain the value entered e Exact Match Will search for Observations that are an Exact Match to the values entered default e Click OK yellow area below Text Pattern Match uu Last Name Constraint hal All Observations o Filter on all values Filter on specific values 2 3 Repeat 1 ai Last Name Me x Numeric Trait When using the Advanced Filter options for a Numeric Trait the user must first click the button next to Filter on Specific Values This will enable the Filter options al
127. ch include e Back Up and Group navigation buttons o Back allows the user to move Back to the previous panel displayed o Up allows user to move up to Owner Module o Group allows the user to switch to the Grouping Panel e Entity Module Icon e Entity Module Name displayed in bold e Owner Module displayed below the Entity Module name e Link Options o Link options allow the user to define the relationship of the Entity to the previous item breadcrumb in the Cohort Filter e Constraint Options o Constraint options allow the user to define the set of results returned More on Constraint options in the Constraint Options in the Filter amp Grouping Panel section e Apply Filter Button TransMed Systems Inc ET BIS USER S MANUAL a Navigation Buttons Entity Name Entity Icon Link Options Constraint Options Constraint iiil All Module Readings T Apply Filter Apply Button r Traits have a different set of Filter Panels A Trait Filter Panel is defined by the Trait type which includes e Back Up and Group navigation buttons o Back allows the user to move Back to the previous panel displayed o Up allows user to move up to Owner Module o Group allows the user to switch to the Grouping Panel e Trait Icon o Note the page color behind the Trait icon denotes the Owner Entity type e Trait Name displayed in bold e Owner Module displayed below the Tr
128. cher Generated Results o When working in Clinical Pattern Matcher the user can launch the Venn diagram tab by clicking on the Venn button in the toolbar The original Cohorts and the Matched Cohort will be compared in Venn Venn diagram Overview There are 4 main sections to the Venn diagram tab e Toolbar purple area below e Venn Sets green area below e Result diagram and Intersections yellow amp red area below e Entity Item Identifiers blue area below TransMed Systems Inc C BIS USER S MANUAL Venn Diagram Patient Items List Name Set Count Name Brown Rat 67 SP1 Rat_5 Female Patients 5963 SP1 Rat_6 SESDE TVO L SP1 Rat_7 Rats w Cytokines SP1 Rat _ amp SP1 Rat_9 SP1 Rat_10 SP1 R t_11 SP1 Rat_12 SP1 Rat_13 SP1 Rat_i4 SP1 Rat_15 SP1 Rat_16 SP1 Rat_17 SP1 Rat_i SP1 Rat_2 SP1 Rat_3 SP1 Rat_4 TransMed Systems Inc BIS USER S MANUAL ae Toolbar The toolbar contains 4 buttons Open Cohort Open Export Data and Create Cohort open Cohort Open Eel Export All Data hia Create Cohort Venn Cohort toolbar Popen ki Gal Export All Data New Gene List from all Venn Gene List toolbar Open Cohort The Open Cohort button gives the user 3 options on how they want to proceed with the currently selected Cohort s Open in Cohort Explorer Open in Clinical Pattern Matcher and Open in Cohort Reporter Open Cohort Open HA Expo Open in Cohor
129. cs Auditing Patient Sample Li Exists Sample Meme 2 Refresh History Cohort Refresh bate User Hote 26 Aug 2013 15 58 jmutz Filter refresh complete added 0 new Patents 26 Aug 2013 15 58 jmutz Filter refresh started from Ul 26 Aug 2013 15 57 jmutz Filter refresh complete added 300 new Patients 26 Aug 2013 15 57 jmutz Filter refresh started from U Refreshing a Project Patient Cohort If the Entity Group that is used to create a Project is associated with a Filter List then the user will have the option to refresh the Cohort from that filter When the user clicks the Refresh from Filter button they will get the following message Refresh Project Patient Cohort Refreshing the Project Patient Cohort will re run the Cohort Filter that the Patient Cohort was originally created from Any new Patients found will be added to the existing cohort no Patient will be removed for consistency purposes This operation cannot be undone Continue Cancel If the user clicks OK then the system will refresh the Patient Cohort for the Project from its filter This refresh will do the following e Update the Cohort Refresh Filter status log shown at the bottom of the window TransMed Systems Inc st BIS USER S MANUAL as e Query the database for all Entities that match the filter criteria e Update the Project Entity Cohort to be the UNION of the existing Cohort plus any new Patients found
130. cted next to them Each Entity identifier will be auto selected by default anytime a new Project is created These identifiers are needed for most BIS tools to work properly Users are unable to unselect these identifiers TransMed Systems Inc Ea BIS USER S MANUAL a Toots E im fj Project Properties i Tools ig Colon Cancer Study Colon Cancer Study gt 6G Patient Traits sis ini b Sample Traits ce gt 4 Experiment Traits General Information E Secunty amp Permissions Patient Cohort amp Filter Users can view all Traits currently assigned to the project by clicking the Expand All button in the toolbar Accordingly the user can click the Collapse All button to reduce the traits being viewed 7 Project Properties x 7 Add Traits Eg Add All Traits Colon Cancer Study 4 Patient Traits shal 4 Patient Fields 4 m DDI MODULE Enrollment E Security amp Permissions T Text DX Proc Path Calcium Cation Electrolytes Value Lowe Eg Patient Cohort amp Filter eee E General Information Date of Last Follow up E Is your mother or father of Ashkenazi J Auditing a MultiChoiceTrait d Patient Patient ID Protected T Patient 10 P Sample Traits e a m i ll TOJect I rats To add traits to the Project the user can click the Add Traits or Add All Traits button in the toolbar TransMed Systems Inc sa BIS USER
131. directly associated to the Main Level The Nested Level will define the Nested Levels in the generated Data and assume summary rules on the Main viewing Levels The Nested Level is displayed as indented attached to the Main Level Traits Traits are directly related to a Module or Entity Traits are displayed under the Main Level A Trait can be attached to a Main or Nested Level TransMed Systems Inc amw BIS USER S MANUAL ae Female Patients 5963 Group Level G Report Cohorts Main Level 4 CREATININE Acquisition Date Main Level Tissue of Origin Editing Existing Variables Each Main Level Nested Level and Trait can be edited or deleted by highlighting the variable then double clicking right clicking or using the toolbar functions Edit or Delete Main Levels can only be deleted when all Main Levels below it are removed f Collapse All F Clear Data Definition amp Female Patients 5963 amp Male Patients 6701 i Patient ID E 3 BUN E 4 CREATININE i Sample ID La Acquisition Date Tissue of Origin Building a Report If the report is new the user will see the default Data Definition Group Cohorts Project s All Cohort unless the Report is opened using another BIS Tool or a Saved Cohort TransMed Systems Inc ano BIS USER S MANUAL ys Highest Level Entity P
132. e displayed below the Trait name e Link Options o Link options allow the user to define the relationship of the Trait to the previous item breadcrumb in the Cohort Filter e Constraint Options o Constraint options allow the user to define the set of results returned More on Constraint options below e Summary Options e Advanced Filter o Filter Options change based on Trait Type More on Advanced Filter options below e OK amp Cancel Buttons TransMed Systems Inc aso o BIS USER S MANUAL as Add Trait Trait loon 3 BUN Trat Name gui Owner Module Q E 3 BUN from Patient Link Options Constraint Options Constraint PT All m Summary summary Options Filter on all values D Filter on specific values Low Unknown High Unknown Advanced Filter OK Cancel OK amp Cancel Buttons Add Entity Options Entities in Cohort Reporter are expressed as an Exist Trait and that Exist Trait is owned by an Entity Module In the Data Definition Entities appear as Module Level The Entity Module Level is highlighted below in blue E Sample ID Ke Acquisition Date Tissue of Ongin The variables nested within the Entity Module are the Traits that the user selected and are owned by the Module Steps to Adding an Entity 1 Search for an Entity in the Data Explorer yellow area below 2 Click the Plus Icon on the E
133. e SEE Favorite Open Workspace De identified Notes Properties Project Properties Workspace Display The Workspace Display area shows all Workspaces associated with the project selected from the Workspace Display Dropdown TransMed Systems Inc a BIS USER S MANUAL ae ij Colon Cancer Study Study 10 A a Trail 001 j Trail 002 TG Colon Cancer Study Ma Colon Cancer Study i Colon Cancer Study 6 17 2013 2 28 17 PM 6 17 2013 2 06 34 PM a 6 17 2013 2 16 44 PM Each Workspace will display the Name of the Workspace the Project the Workspace is located in and the Date and Time the Workspace was created The Workspace Icon may change based on the user s security settings Opening a Workspace To open a Workspace the user can select the Workspace then e Double click on the highlighted Workspace e Click the Open button in the toolbar e Right click to the context menu to Open If a user has identified access to a Workspace they are then given the option to open the Workspace in either Identified or De Identified mode Identified mode is the default and this is how the Workspace will be opened if the user opens from the context menu or by double clicking the Workspace in the BIS Desktop However if the user clicks the Open button on the toolbar instead they will get a menu with two options Open Workspace Identified Open Workspace De Identified Selecting one of these
134. e current Entity Count of the Cohort e Notes Any Notes the user has created to correspond with the Cohort Patient Cohort Male Patients wl Experiments EA Edit Info T Edit Notes i Create New Project From Cohort Cohort Name Male Patients w Experiments Description All male patients that have an experiment in the trial date range Cohort Type Patient Cohort Member Count 3 305 Created By jmutz Last Updated 10 Sep 2015 12 48 11 PM Trial Date Range 010181 123191 e Edit Information Displays the Edit Cohort Information window to allow the user to edit the name and description of the Cohort e Edit Notes Displays the Edit Notes window to allow the user to add edit notes Notes can be viewed and edited by all users with access to the Workspace e Create New Project From Cohort Creates a new BIS Project from this Entity Cohort This function is only available to BIS Admins and only when the Cohort is a Patient Cohort Cohort Members Panel The Cohort Members display panel shows a table containing all of the Entities that are members of the current Entity Cohort TransMed Systems Inc a BIS USER S MANUAL as i Tools TE Cohort ral Male Patients w Experiments Toolbar FA Open Cohort Male Patients w 5 Patient 1D Ka Experiments 1262945053 Patient Cohort Des Re eae 1377363 E 1584 oO General Information 1608963064 Cohort Patients 1788166789 Member List
135. e pattern Clinical Pattern Editor takes each event Entity Module or Trait filtered as needed defined by the user and searches for results based on the order of the events in the pattern relative to time e Example All patients that had Symptom A then were started on Drug B and were then diagnosed with Disease K e Example All patients that were admitted to the Hospital then had an Appendectomy then were discharged from the Hospital and were then re admitted to the Hospital within 30 days of discharge The user will access the Clinical Pattern Editor when they create or edit a Clinical Pattern The user can access the Clinical Pattern Editor from inside the Clinical Pattern Matcher tool The appearance of the Clinical Pattern Editor mimics several other areas within BIS The editor is made up of toolbars the Data Explorer on the LHS and the Pattern display on the RHS TransMed Systems Inc 149 BIS USER S MANUAL ae FA tdt info Cdi Hotes ew Te Wij ere Tima Widow Det e Save and Close Saves the current Clinical Pattern on the Workspace and in the currently open Clinical Pattern Matcher session e Edit Info Allows the user to edit name and description of the Clinical Pattern If this is a new Pattern the user is asked to name and save e Edit Notes Allows the user to add notes about the Clinical Pattern All notes will be displayed as the user requests them All users are able to view and edit notes e
136. e to group the results o Grouping Options change based on Trait Type More on Advanced Grouping options in the Trait Advanced Grouping Options section Navigation Buttons Entity Name Entity Icon 06 Chemistry Owner Module 5 oy B Same Patient Link Options Constraint Options Constraint All Observations Group Button Advanced Grouping Group by all values no values O Group by specific numeric range Quartile After the Group Button is clicked The Grouping display toolbar shows the user that a Grouping operation has been performed and the details of the grouping function 1 Grouped On Displays the name of the Entity Module or Trait that the grouping results reference 2 Group Count Number of result groupings 3 Link Option Selected The Link selected before applying the Grouping 4 Constraint Option Selected The Constraint selected before applying the Grouping Grouped On Birthdate by Year 2 l Group Count 102 Link Same Patient C nstraint Q au The toolbar also contains user actions TransMed Systems Inc aso o BIS USER S MANUAL as e Change Click the Change button to change the current Grouping settings The Group Panel will open up in the Data Explorer and allow the user to change the parameters of the Grouping and reapply e Clear Click the Clear button to clear the current Grouping this will hide the Grouping Info Pa
137. e user has several export formats to choose from The export will be saved to the open Workspace then can be opened and saved to the local drive al Export Selected Data The shield on the icon indicates the user that created the report was Identified or De Identified Export Selected Data The Export Graph button is inside most Report and Analysis tools and allows the user to export the chart populated from the executed tool FEl Export Graph Export Graph Export All Data allows the user to export the full tables in BIS The user has several export formats to choose from The export will be saved to the Export All Data open Workspace then can be opened and saved to the local drive Export All Data The shield on the icon indicates the user that created the report was Identified or De Identified Favorite option allows the user to choose which Workspace s is their favorite The items marked favorite will show by default when BIS is opened The plus icon will make the highlighted Workspace a Favorite item and the minus icon will remove the highlighted Workspace from the Favorite list Favorite TransMed Systems Inc 238 BIS USER S MANUAL ys Favorite Workspace is the default view as the user logs into BIS This will display all of the users Favorite Workspace s on the BIS Desktop Tab Favorite Workspace A Filter is a tool to refine the Entity Module Filter or Trait being applied to o
138. e user must first click the button next to Filter on Specific Choices This will enable the Filter options allowing the user to enter Filter values and add Traits to the Data Definition Steps for using Advanced Filter Options 1 Bring up the Add or Edit Trait window TransMed Systems Inc 187 o BIS USER S MANUAL as 2 Choose Filter on Specific Choices green area below 3 Optional Add a saved Choice List from the Workspace yellow area below which will then only show the Choices on that list in the generated results 4 Check the Choices to be filtered on red area below e The user can re sort the checked items by clicking on the a button This will make all checked Choices move to the top of the list for easy viewing e The user can save the currently checked Choices as a new Choice List by clicking the Fe button e The count at the bottom of the choice area will update as Choices are checked and un checked 5 Click OK Edit Filter 1 a Species B Patient Constraint iiil All Observations Summary pal None 2 Comma Separated Values Search Choices Name Mus musculus Papio hamadryas Rattus norvegicus Cancel Y For more Data Definition Examples please refer to the Cohort Reporter Section in the BIS User s Example Document Linking Options in Cohort Reporter The Linking Relationship is the first setting the user should select when they
139. ecoration in the lower right corner of their icon in the Data Explorer Compare the following Search results in the Data Explorer using the same search word radiation between Identified and De Identified users TransMed Systems Inc 8 BIS USER S MANUAL Identified User Search 2 First_Radiation 2 Radiation i Radiation Ig Radiation ie Radiation E Radiation E STM_End kD STM_Start Radiation date Radiation ef Prior Radiation and Chemotherapy Td radiation Ti Radiation f Radiation Dose Exposure EAN De Identified User Search Stop Radiation date E Radiation Exposure Ji Radiation Exposure Exposure ef Prior Radiation and Chemotherapy f radiation ef Radiation yf Radiation qf RADIATION Search Results Toolbar When searching in BIS the user has the option to see the results with or without additional information The additional information displays is configured with the ETL process Ti 173 9 Cancer of skin 124 results for cancer Trait ICD9 m Code 173 9 x Additional Info Search All Close Search results with additional information displayed PEF 124 results for cancer f 173 9 Cancer of skin P _ Additional Info Q Search All Close TransMed Systems Inc 99 Search results without additional information displayed BIS USER S MANUAL as Selecting from Data Explorer Once the user has found the variable they were looking
140. ect Properties is where all the General Information Security amp Permissions Patient Cohort amp Filter Project Traits and Auditing are defined for a Project Project Properties A protected Trait is a Trait that has been identified as protected during initial installation This means that only Identified Protected Traits Users will have access to view the true value of these Traits These Traits will have a shield icon overlay to denote that it is protected Recent Workspaces will display the users 5 Recent Workspace most recently viewed Workspaces on the BIS Desktop Tab TransMed Systems Inc 248 BIS USER S MANUAL ys Anywhere in BIS the Refresh button will h Refres simply refresh the current tab This is an option in the Project Properties Refresh from Filter and allows user to manually Refresh the Project Cohort Refresh From Filter This allows the user to Remove a Transform Remove from the Report in the Report Setup Transforms tab The Rename Time Window button allows Re Name Time Window the user to edit the name of the time window within Clinical Pattern Editor H Rename Time Window The Repeat Count is a filter tool inside Clinical Pattern Editor All Entities Modules and Traits can have a repeat associated The Repeat Count will look in the Patient history for the number of times a variable met the match Repeat Count A report of data is made with the specific intention of rel
141. ecting All Values No Filter or Specific Filter e All Values No Filter This Filter does not limit the returned data based on the Observation value e Specific Filter This Filter limits the returned data based on the Observation value The Advanced Filter options are different from the Constraint options which limit the data on the presence of an Observation not the value of the Observation Text Trait When using the Advanced Filter options for a Text Trait the user must first click the button next to Filter on Specific Values This will enable the Filter options allowing the user to enter Filter values and add Traits to the Data Definition Steps for using Advanced Filter Options 1 Bring up the Add or Edit Trait window 2 Choose Filter on Specific Vales green area below 3 Add values to filter box red area below e Note that each value should be on a separate line Limit 500 lines 4 Select the method the values should be filtered by from the dropdown yellow area below TransMed Systems Inc a82 o BIS USER S MANUAL as e Starts With Will search for Observations that Start With the value entered e Ends With Will search for Observations that End With the value entered e Contains Will search for Observations that Contain the value entered e Exact Match Will search for Observations that are an Exact Match to the values entered default 5 Clic
142. ed to each customer s specific data model so the icons and colors shown above are only examples The specific Entity icons and colors used in your BIS installation will be documented and explained by your TransMed customer representative TransMed Systems Inc a BIS USER S MANUAL as Module Types Module Types in BIS are used to organize the Traits that are defined to contain observable data for an Entity Like Traits all Module Types defined in BIS belong to a specific Entity type Module Types defined for a Patient Entity for example cannot be used to contain data for a Sample Entity Because Module Types are organizations of Traits and Traits also belong to specific Entity types it follows then that all Traits in BIS must be assigned to Module Types that belong to the same Entity type as the Trait Module Types like Entities are considered data containers in BIS This means that they can define a set of Traits and belong to relationships with other data containers The main difference between Entities and Module Types with respect to data storage is that Module Types are designed to contain multiple and repeated data observations while Entities are designed to contain only a single data observation Relationships Relationships are shown by the arrows in the BIS Logical Model diagram above Unlike the other meta data definition items in the Logical Model Entities Modules and Traits they do not define how BIS w
143. elete X button above the Clinical Pattern section Clicking Delete will remove the existing Clinical Pattern and replace it with a New Clinical Pattern yet to be defined i Clinical Pattern 7 Q B gt DX gt M gt D TO t a Tene Heg TransMed Systems Inc 148 BIS USER S MANUAL as Editing a Clinical Pattern Clinical Pattern Editor From inside Clinical Pattern Matcher the user can click on the pencil button red arrow below above the Clinical Pattern section to launch the Editor If this isa new CPM session the user will create the Clinical Pattern by opening the Editor applying a pattern and then saving the Clinical Pattern to match against Clinical Pattern q X 2 Tema WA ieee 2 r B gt DX gt M gt D Within the Clinical Pattern Editor the user can define the Clinical Pattern to be matched against Clinical Pattern Editor is used to create a longitudinal pattern of events relative to Patients highest level Entity A Clinical Pattern is a user defined set of events in specified time order e The time ordered events are defined by a sequence of Entities Modules and Traits e Event timestamps are used to determine the sequence matching between events e Proximity specifications can be set to define relative time between events e Events can be refined by filter options in the Clinical Pattern Editor A Time Window is an additional time frame to be compared parallel to th
144. els of data access that users can be granted 1 Identified D users with identified data access can see all protected and identifying information for patients in the system This includes the name date of birth and other identifying Traits for the patient Access to this data is typically restricted by an IRB within the customer s organization 2 De ldentified De ID users with De Identified access can see most of the data that the identified user can with the exception of Traits that are deemed protected Protected Traits are those that would allow the user to potentially identify a patient BIS does not by default specify that any fields in particular are protected This is a configuration option that is customer specific How Data Access in BIS Works Data De Identification in BIS works on three different aspects of the data the Identification ID Trait for Entities date obfuscation and hiding protected fields Entity Identifier Trait Remapping The first thing that BIS does in De Identifying data in the system is maintain two different Traits for the Identifier of an Entity Entities in the system are things like patients samples etc Every Entity refers to a Trait that contains the Identifier of the Entity Since the Identifier of an Entity is its primary identifying value this value must be altered for De Identified users Every Entity in BIS is actually mapped to two different Trait values for the name
145. ems Inc 430 BIS USER S MANUAL as Edit Workspace Permissions Groups Users The list of groups shown below are all groups that have been granted access to the Project that this workspace is part of If there are any other groups that you would like to have access to this workspace please contact a BIS Administrator for assistance Filter Groups _ Group Name Ea of BisAdministrators This is done because confusion may result if a user is allowed to grant access to a Workspace to a particular group that does not have access to the Project containing the Workspace In this case even though the user in that group would technically have access to the Workspace they would never be able to see the Workspace because the Project that it is in is not available to them As with the Groups tab the Users tab shown below in the Edit Workspace Permissions window does not show all users that have access to BIS but only those users that have access to the Project containing the Workspace This list will include all of the users that have been granted access to this Workspace s containing Project explicitly assigned on the Users tab on the Project Permissions window or implicitly via group membership assigned on the Groups tab on the Project Properties Edit Workspace Permissions Groups Users The list of users shown below are all users who have been granted access to the Project that this workspace is part of If there
146. ent panel in the right hand side RHS as shown below General Information Panel a _ fq Project Properties w i F ii Tools lis Colon Cancer Study EA Edit Info Edit Notes Colon Cancer Study Project Name Colon Cancer Study Project Description Created By jsintz General Information Last Updated 26 Aug 2015 03 34 06 PM E Security amp Permissions Notes The General Information panel displays the Project name description the user that created the Project the date that the Project was last updated and the Project Notes Edit Info The name and description are editable in a pop up window by clicking the Edit Info button in the toolbar Edit Project Information Project Name Colon Cancer Study Description Edit Notes The Project Notes can be entered and altered by clicking the Edit Notes button in the toolbar TransMed Systems Inc 460 BIS USER S MANUAL as Edit Notes Ys Colon Cancer Study Project Notes Security amp Permissions Panel The Security amp Permissions panel displays the groups and the users that have access to the Project and the data level to which they have access There are no deny permissions so any user or user that is a member of a group that is added to the Project security settings will have access to that Project ij Project
147. eport Panel in table format Cohort Reporter 3 3 Level 5 Experiment Create Cohort Open EA Export All Data Display Options g Patient A 06 Chemistry WW Sample Mean 4 CREATININE All OCA 348 OCA 348 3B snap tumor 12 23 2008 9 45 25 AM Skeletal Muscle Group Name Patient ID Mean 3 BUN Mean 6 ALT Sample ID Acquisition Date Tissue of Origin All OCA 351 OCA 351 3B snap normal 1 9 2009 12 00 00 PM Colon All OCA 351 OCA 351 normal 2 1 9 2009 12 00 00 PM Colon All OCA 351 OCA 351 tumor 2 1 9 2009 12 00 00 PM Colon All OCA 351 OCA 351 3B snap tumor 1 9 2009 12 00 00 PM Colon All OCA 353 OCA 353 3B snap L shoul 1 15 2009 12 50 00 PM Lung All OCA 353 J OCA 353 L shoulder norm 1 15 2009 12 50 00 PM Lung All OCA 353 OCA 353 3B snap nose tu 1 15 2009 12 50 00 PM Lung More information about the generated Results is below in the Report Data Panel section General Information Panel p General Information TransMed Systems Inc s199 BIS USER S MANUAL ys Cohort Reporter Expeerinnaent EA Edit Info Edit Notes General Information Report Name Expenment Description Created By jmutz Last Updated January 17 2014 10 00 10 AM The General Information Panel displays the basic information about the report e Report Name The name of the Report as displayed in Workspace Explorer e Description The description of the Report as defined by the user e Created By The user i
148. er a 2 j 1 Diiia 2 Li Ecsta Patient Sample Semple Experenert Breadcrumbs 42 272 vaw Bi icon View Results Toolbar Results Viewing area Etera 40 gt Pabernt Sample gt So ars gt Sampe Expemment gt Expenment gosts 8 30 2019 TJS AH a Al gt Patent Sample gt Saemple tanb rampi Experimen gt Expenment qausta gt Experiment Sample 8 30 2013 11 35 36 AH 41 2 Potent Sample gt Semple gccts 2 Sample Expermern gt Expenment esists gt Expenment Deagnces B30 2013 TJA 24 Cohort Filter Breadcrumbs Cohort Explorer displays a Cohort Filter or Breadcrumbs of the Entities Modules and Traits that were selected to define the Cohort The user can easily see the path taken to get to the current Cohort and the user can also easily move backwards in the Breadcrumbs to remove part of the filter or go back to the starting All a Gender al Patient Diagnosis Type gt f Patient gt C Diagnosis J0 Male 0 List Lymphoma This Breadcrumb as seen above is showing that the user started with All Patients in the Project then filtered on the Gender Trait to get all Patients that are male The user then filtered on the Trait Patient Diagnosis Type for all Patients that have been diagnosed with Lymphoma The end result is all male Patients that have been diagnosed with Lymphoma The Filter can also contain Links A link is related to the Patient
149. ere it makes sense In BIS we do this by using something we call data containers There are two types of data containers in BIS Entities and Modules each with different rules about how they collect data and how they use Traits Fundamentally however both are simply groupings of Traits used to gather and analyze data Entities In BIS there are two types or Entities Analyzable and Reference Entities shown by the circles in diagram above are the primary component of the logical model and the only one of the four model items mentioned that can exist by themselves The other items Modules Traits and Relationships are all built around Entities Entities are one of two data containers in BIS the other being Module Type Data containers in BIS can contain Traits and belong to relationships with other data containers Most tools in BIS work at either the Entity level exclusively e g Cohort Explorer or at the data container level e g Cohort Reporter However the way Entities work with Traits is significantly different than the way Module Types do Analyzable Entities Analyzable Entities are the primary Entity type used within BIS All analysis and reporting in BIS is based around the various Analyzable Entities that have been configured in the system Typical Analyzable Entities defined in a BIS install include Patients Samples Experiments and Encounters These Entities are directly related to each other in a Parent C
150. es and apply the Trait to the Cohort Filter Steps for using Advanced Filter Options 1 Choose Filter on Specific Vales green area below 2 Add values to filter box red area below e Note that each value should be on a separate line Limit 500 lines 3 Select method in the dropdown that the values should be filtered by yellow area below e Starts With Will search for Observations that Start With the value entered e Ends With Will search for Observations that End With the value entered e Contains Will search for Observations that Contain the value entered TransMed Systems Inc 107 BIS USER S MANUAL as e Exact Match Will search for Observations that are an Exact Match to the values entered default 4 Click Apply Filter E Back g Up ae Group Last Name Patient Link S Same Patient Constraint iiil All Observations T Apply Filter 4 0 Filter on all values Exact Match Exact Match Starts With Ends With Contains 3 Numeric Trait When using the Advanced Filter options for a Numeric Trait the user must first click the button next to Filter on Specific Values This enables the Filter options so the user can add Filter values and apply the Trait to the Cohort Filter Steps for using Advanced Filter Options y Choose Filter on Specific Vales green area below 2 Add a Low Value a High Value or both to filter boxes red area be
151. etail View can be seen in Cohort Explorer and Workspace Explorer so Detail View Disable Auditing is found in Project Disable Auditing Properties It allows Admin users to turn off amp Disable Auditing the Auditing process for the Project Display Options is a dropdown menu on the Report Data toolbar It contains several functions that will alter the Report Data below 5 Display Options Display Options Duplicate will make a copy of whatever artifact is highlighted This copy will be placed in the same Workspace as the Duplicate original The duplicate will have the same name as the original with a number after the title based on how many copies there are of that artifact TransMed Systems Inc 2340 BIS USER S MANUAL ys Edit Cohorts reference in their Report by opening the Cohort Selector edit cohorts The Edit Cohorts button allows users to ZI choose which Cohort s they want to Edit Cohorts The Report Data Definition Editor is where Edit Data Definition the user defines what data will be generated for the Report The Edit Gene List button allows users to choose which Gene List s they want to reference in their Report This will open the Gene List Selector Edit Gene Lists Edit Gene List information on Workspace and report artifacts This area will edit the title and description of the artifact Edit Information Edit Information allows the user to edit _ The Edit Le
152. etween Y and X e Between Inclusive Both Between Y and X e Between Exclusive Both un checked Between Y and X Currency Trait When using the Advanced Filter options for a Currency Trait the user must first click the button next to Filter on Specific Values This will enable the Filter options allowing the user to enter Filter values and add Traits to the Data Definition Steps for using Advanced Filter Options 1 Bring up the Add or Edit Trait window 2 Choose Filter on Specific Vales green area below 3 Adda Low Value High Value or both to filter boxes red area below 4 Set the relational operator and inclusive check yellow area below 5 Click OK TransMed Systems Inc pea BIS USER S MANUAL as Add Trait 1 a Currency lt Expenditure Link pal g Currency from Patient Constraint iiil All Observations Summary pal Mean a Mean O Filter on all values Filter on specific values 2 Greater T Equal to Greater Than Less Than Between Cancel Relational Operators e Greater Than Inclusive 2Y e Greater Than Exclusive un checked gt Y e Equal to Y e Less Than Inclusive lt Y e Less Than Exclusive un checked lt Y e Between Inclusive Y and Exclusive X Between Y and X e Between Inclusive X and Exclusive Y Between Y and X e Between Inclusive Both Between Y and X e Between Exclusive Both un checked Between Y
153. filter options are displayed in the Add Level window based on the selected variable Entities and Modules have similar Add Level windows which include TransMed Systems Inc 174 Entity Module Icon Entity Module Name displayed in bold Owner Module displayed below the Entity Module name Level Name can be edited Link Options o Link options allow the user to define the relationship of the Entity to the previous item breadcrumb in the Cohort Filter Constraint Options o Constraint options allow the user to define the set of results returned More on Constraint options below Owned Traits to be selected for the Data Definition Generation Options Viewing Options OK and Cancel Buttons BIS USER S MANUAL a Add Level Entity Module Icon i Sample Owner Module Level Name Entity Module Name Link Options We ee ee Constraint I1 All Module Readings Generation Options Viewing Options Owned Traits Sample ID L Acquisition Date Date Time L Anatomical Location lena m 1i Items 1 Selected OK amp Cancel Buttons When a user selects a Trait from the Data Explorer they will get an Add Trait window shown below An Add Trait window is defined by the Trait type which includes e Trait Icon o Note that the page color behind the Trait icon denotes the Owner Entity type e Trait Name displayed in bold e Owner Modul
154. ge of the column s grand total value is displayed o PercentOfRow For data cells the percentage of the row s total value is displayed for total cells the percentage of the row s grand total value is displayed PercentOfColumnGrandTotal Percent of the summary in the Column Grand Total value PercentOfRowGrandTotal Percent of the summary in the Row Grand Total value PercentOfGrandTotal Percent of the summary in the Grand Total value O O RankInColumnSmallestToLargest The summary value s rank in its column with the smallest value in the column as 1 and each larger value assigned a higher rank o RanklnRowSmallestToLargest The summary value s rank in its row with the smallest value in the row as 1 and each larger value assigned a higher rank o RanklnColumnLargestToSmallest The summary value s rank in its column with the largest value in the column as 1 and each smaller value assigned a higher rank o RanklnRowLargestToSmallest The summary value s rank in its row with the largest value in the row as 1 and each smaller value assigned a higher rank o Index An index value that reflects the summary value s importance in its row and column context This value is calculated as follows value in cell x Grand Total of Grand Totals Grand Row Total x Grand Column Total TransMed Systems Inc 26 BIS USER S MANUAL a e Group Interval Changes the format for the grouped variables o Default Gr
155. generated the user will have the option to save a Cohort of the Reference Entity when the Report is set to that level Generating Data Once the Data Definition is defined the user can then Save and Close Save As or just Close the Data Definition i Tools 7 ne A Report Setup x New Report ial Save amp Close ial Save As Close TransMed Systems Inc 198 BIS USER S MANUAL as e Save amp Close This will prompt the user to give the report a name if this is a new report and generate data if changes have been made e Save As This will prompt the user to give the report a name will auto assign a duplicate name and generate data if changes have been made e Close This will close the report and prompt the user to save if changes have been made to the Report Setup The report generation process is a synchronous process that once started will run on the server until all of the appropriate report data has been extracted calculated and merged for the report This means that the user can close a report and come back to it later even if the report is closed during the generation process The status of the Report generation can be viewed from the Workspace an in progress gear will appear on the Report Icon The data will generate a status bar to advise the user that generation is in progress Generating Data E Se Se ee ee eS Se Once all of the data is generated it will display in the Data R
156. h Pivot Area yellow area is highlighted to the right the Available Variables purple area will alter as needed Available Variables 9 p All Variables Variable Eh Group Sh Patient OI MODULE Module H H stage Integer Survival Time Real Row Labels iT Gender T i Tl Pathology Grade stage nteger H Time to Recurrence Real Tumor Sie Real Time to Metastatic Relpase Real Calumn Labels ci Tumor Size s Values Pca Patent C Defer Layout Update e Report Filter A Report Filter is a field that has a page orientation in the Pivot Table Only one item or all items can be displayed in a Report Filter at one time e Row Labels Row Labels refer to fields that have a row orientation in the Pivot Table each occupying a row TransMed Systems Inc pa BIS USER S MANUAL as e Nested Row A Nested Row is a row that has data relative to the row above e Column Labels Column Labels refer to fields that have a column orientation in the Pivot Table each occupying a column e Values The Values area refers to an area of the Pivot Table Field list that displays the cells in the Pivot that contain the summary data and the way in which those cells are summarized in the Pivot Table For the user to add variables to the different Pivot areas they first need to highlight the area on the right and then highlight the variable followed by clicking the add button next to the area The add button w
157. h the open Cohort as starting breadcrumb in the Filter List TransMed Systems Inc w BIS USER S MANUAL ae Cohort Explorer Male Patients w Experiments In Create Cohort 2 Create Report Male Patients w e Open in Cohort Reporter Launches Cohort Reporter with the open Cohort as the starting Cohort in the report The Data Definition is not affected by this Cohort s Filter List Report Setup Mew Report X Collapse Al f Clear Data Definition 2 Group S Male Patients w Expenments 3305 i Patient 1D e Open in Clinical Pattern Matcher Launches Clinical Pattern Matcher with the open Cohort as the Cohort to be matched ii Tools E 2 Clinical Pattern Matcher u Clinical Pattern g New Clinical Pattern ka ror 0 Time Windows Male Patients w Experiments diair 3 305 Patients General Information Panel The General Information panel shows the general details about the Entity Cohort including e Cohort Name The name of the Cohort as displayed on the LHS and in Workspace Explorer e Description The description of the Cohort as defined by the user e Cohort Type The Entity type of the Cohort E g Patient Sample Experiment e Created By The user in BIS that created this Cohort TransMed Systems Inc ma BIS USER S MANUAL as e Last Updated The last date and time this Cohort was updated or edited e Member Count Th
158. ha 3 963 Prti Configuration Area Results Area Opening Clinical Pattern Matcher There are several different ways to open the Clinical Patter Matcher Tool CPM e BIS Tools Menu o To start a New CPM session the user can select Clinical Pattern Matcher from the BIS Tools Menu dropdown The new session will open with the project s All Cohort and a blank Clinical Pattern e Workspace Explorer Artifacts o To start a New CPM session the user can select Workspace artifacts The user can select one or more high level Cohorts Patient or one Clinical Pattern to start the CPM session e Cohort Explorer o To start a New CPM session the user can select the Clinical Pattern button in Cohort Explorer after they have created a Cohort Filter This will launch the new session with that Cohort as the starting CPM Cohort e Venn diagram TransMed Systems Inc aa BIS USER S MANUAL as o To start a New CPM session the user can select the Open in Clinical Pattern button in the Venn diagram This will launch the new session with that Cohort as the starting CPM Cohort e Cohort Viewer o To start a New CPM session the user can select the Open in Clinical Pattern button in the Cohort viewer This will launch the new session with that Cohort as the starting CPM Cohort Y For more Clinical Pattern Examples please refer to the Clinical Pattern Matcher Section in the BIS User s Example Document The Conf
159. hat store date time values Field values are grouped by the days of the week Examples of such groups Sunday Monday Tuesday the actual names of the days of the week are determined by the current culture DateDayOfYear This option is in effect only for fields that store date time values Field values are grouped by the number of the day in which they occur in a year The following groups can be created 1 2 3 365 366 in a leap year DateWeekOfMonth This option is in effect only for fields that store date time values Field values are grouped by the number of the week in which they occur in a month The following groups can be created 1 2 3 4 and 5 The first week is the week containing the 1st day of the month DateWeekOfYear This option is in effect only for fields that store date time values Field values are grouped by the number of the week in a year in which they occur The following groups can be created 1 2 3 52 53 DateMonth This option is in effect only for fields that store date time values Field values are grouped by the month Examples of groups January February March the actual names of the months are determined by the current culture DateQuarter This option is in effect only for fields that store date time values Field values are sorted by the quarterly intervals of the year The following groups can be created 1 2 3 and 4 Each quarter includes three months DateYear This option is in effect
160. he Patient Cohort from the Cohort Viewer Option Five Workspace Explorer e The user can choose one or more existing Patient Cohorts from Workspace Explorer e The user can open the Cohort Reporter by first highlighting the Cohort s on the Workspace then clicking Open in Cohort Reporter o This will open Cohort Reporter with all of the Patient Cohorts the user selected on the Workspace Explorer Option Six Clinical Pattern Matcher Result Cohort e The user can use a Cohort that was created in Clinical Pattern Matcher Calculate a Cohort in CPM and click Open Cohort on the toolbar choose Matching Patient in Cohort Reporter or Non Matching Patients in Cohort Reporter o This will open Cohort Reporter with the Cohort the user selected in CPM This Cohort is a New Cohort and will only be saved within the Report if the user choses to save the Cohort using the Save Cohort button in the toolbar Option Seven Add Filter List from the Workspace e The user can choose one or more existing Patient Filter Lists from Workspace Explorer e The user can open the Cohort Reporter by first highlighting the Filter List s on the Workspace then clicking Open in Cohort Reporter o This will open Cohort Reporter with all of the Patient Filter Lists the user selected on the Workspace Explorer Option Eight Add Cohorts Filter Lists to an Existing Report e The user can select additional Groups to add to an existing Report
161. hild relationship Each Entity can own a Child Entity as well as own Entity Traits and Modules Since Analyzable Entities are the most common and most referenced type of Entity this document will refer to them simply as Entities dropping the Analyzable part for brevity Reference Entities below will always be referred to as such Reference Entities Unlike Analyzable Entities Reference Entities do not have a Parent Child relationship with other Entities They can however own Entity Traits and Modules Reference Entities are used to model more complex concepts in the application like Doctor or Facility things where using a simple Choice Trait would be insufficient For example a Facility can have its own set of data stored in modules and traits around it location number of beds staff etc A facility is not something a typical BIS user would want to analyze in terms of patient care but being able to create complex queries using facilities to identify patients is important Reference Entities are defined in two ways within the BIS schema TransMed Systems Inc BIS USER S MANUAL as They exist by themselves and can be linked to just like the Analyzable Entities They can also share a relationship with Modules owned by Analyzable Entities This relationship allows the user to filter on the details of the Reference Entity without leaving the hierarchal schema In this case Analyzable Entities appear very similar to C
162. hoice Traits Entity Relationships Entities are the primary items within BIS that users search for and perform analysis on Entity types are configured based on TransMed s analysis of a customer s needs and are given names that match the items the customer is familiar with in their day to day business process Typical examples are patients samples experiments and drugs In many cases BIS Users will interact with one specific Entity type at a time In Cohort Explorer for example the user will search for patients or samples In other cases however it is important to understand the concept of Entity Hierarchies An Entity Hierarchy is a set of parent child relationships between two or more Entity Types that BIS knows about and can traverse automatically when necessary For example consider the following set of Entities e Patient represents a Patient that has come to the customer s health care facility for treatment e Sample represents a tissue or fluid sample of some type taken from a Patient e Experiment represents an experiment like gene expression or sequencing done on a Sample e Drug represents a medication given to a Patient while they are receiving treatment In this example the first three Entities form a natural parent child grandchild hierarchy with the Patient Entity at the top Looking at the hierarchy from the top down one Patient can have multiple Samples and each of those Samples can have many Ex
163. iated with this trait per Group when the report data is summarized to the Group level Mean Level Summary Option e Calculates the mean of all values returned for this trait per level when the report data is summarized to a Main level Mean Group Summary Option e Calculates the mean of all values returned for this trait per level when the report data is summarized to the Group level Median Level Summary Option e Calculates the median of all values returned for this trait per level when the report data is summarized to a Main level Median Group Summary Option e Calculates the median of all values returned for this trait per level when the report data is summarized to the Group level Sum Level Summary Option e Calculates the sum of all values returned for this trait per level when the report data is summarized to a Main level Sum Group Summary Option e Calculates the sum of all values returned for this trait per level when the report data is Summarized to the Group level Use of Reference Entities In Cohort Reporter there are no limitations on applying Reference Entities to the Data Definition other that the standard tool restrictions After the user has added a Reference Entity to the Definition they can continue to add other Entities Modules and Traits If the Reference Entity is applied as the last main level the user may only have the option to add to the Main levels above When the report is
164. ied access to this workspace please contact your BIS administrator for the appropriate access permissions OK e De lIdentified users CAN move rename and delete protected items in the Workspace This allows users without elevated data access privileges to perform maintenance operations on protected Workspace items BIS uses the following rules to determine if a Workspace item is protected or not Clinical Pattern A Clinical Pattern is protected if it contains one or more Protected Traits Filter List A Filter List is protected if it contains one or more Protected Traits Entity Cohort Entity Cohorts themselves are never protected as they are a simply lists of Entities in the system with no additional identifying information To associate identifying information with an Entity Cohort the user must use a Filter List which is protected Note When an Entity Cohort is saved in Cohort Explorer the Filter List that was used to create the Entity Cohort is saved with it While the Entity Cohort itself will not be protected it is possible that the associated Filter List will be In this case a De Identified user may interact with the Entity Cohort but not the associated Filter List See Filter Lists that Contain Protected Traits for more information Export File An Export File is protected if it was created by a user working in Identified mode It is not protected if it was created in De Identified mode Export files contain data as shown o
165. iguration Area On the LHS of the Clinical Pattern Matcher tool is the main Configuration Area It is here that the user sets the options for running a Clinical Pattern match This area allows the user to select a Clinical Pattern to match on and one or more Entity Groups to look for matches in After the user has selected the appropriate inputs they can click the large Calculate Matches button to run the tool Clinical Pattern ae B gt DX gt M gt D 2 Time Windows d 3 305 Patients Female Patients f 5 963 Patients oO Calculate Matches Ms Male Patients w Experiments fi Clinical Pattern Section The first section at the top of the Configuration Area is the Clinical Pattern section Clinical Pattern 79 B gt DX gt M gt D r n A I 2 Tma Windows This shows the user the current Clinical Pattern that is selected including e Pattern name e Time Window information TransMed Systems Inc 147 BIS USER S MANUAL as The Clinical Pattern Matcher tool can only run matches against a single Clinical Pattern at a time so the user can only ever have one Clinical Pattern selected in this section At the top right of the Clinical Pattern section are three buttons as shown in the image above e Edit The Edit button red arrow launches the Clinical Pattern Editor tool inside the Clinical Pattern Matcher tool to allow the user to quickly make changes to the Clinical Pattern save and continue to calculate ma
166. ill contain data Rather they define how the data that BIS does contain will be related to each other All relationships in BIS are between data containers Entities and Modules There are four types of relationships in BIS Entity Ownership Entity Entity Entity Module and Module Module Relationships in the data are one of the most powerful features of the application and understanding how to use them is the key to utilizing the full power of BIS Entity Ownership The Entity Ownership relationship shown by the black arrows in the diagram above has already been discussed this is the relationship where a Module belongs to an Entity type as an inherent part of its design All Modules in BIS must be specified as belonging to an Entity type and they cannot be used to contain observation data for other Entity types The Entity ownership relationship is a one to many relationship between the Entity Type and the Module a single Entity can be the parent of many Module observations in the system Entity Entity The Entity Entity relationship red arrow in the diagram above is a defined parent child relationship between two different Entity types This is a very powerful relationship that allows BIS to track multiple levels of analyzable Entities for example Patients and Tissue Samples In a system like BIS both Patients and Samples are Entities because users are allowed to perform research on either However there is an inhere
167. ill stay inactive until a variable is highlighted If the user decides to edit the variable chosen they can highlight the variable in the selected area and either Click the Delete button to remove the Variable or click the dropdown arrow on the selected Variable and choose an option from the list Move Up Move Down Move to Beginning Move to End Move to Report Filter Move to Row Labels Move to Column Labels Move to Values Pas Remove Field ra Field Settings Dropdown Options will vary based on where the variable is when selected e Move Up Moves the Variable Up in the list within the Area e Move Down Moves the Variable Down in the list within the Area e Move to Beginning Moves the Variable to the Top of the list within the Area e Move to End Moves the Variable Bottom of the list within the Area e Move to Report Filter Moves the Variable from the current area to the Report Filter area e Move to Row Labels Moves the Variable from the current area to the Row Labels area e Move to Column Labels Moves the Variable from the current area to the Column Labels area e Move to Values Moves the Variable from the current area to the Values area e Remove Field Removes the selected field from the current area e Field Settings Populates an Edit Pivot Field window to edit the field parameters TransMed Systems Inc 25 BIS USER S MANUAL ys Edit Pivot Field The options in this wind
168. in the Workspace Explorer and click the Delete button on the toolbar or hit the Delete key on the keyboard or Right Click to context menu They will be prompted to confirm the delete in a pop up window Delete Selected Items Are you sure you want to move the selected items to the Deleted Items folder If the user confirms the delete the selected items are then moved to the special Deleted Items folder The items are not purged from the system and are still available to the user This way if a dependency exists between the item being deleted and another item in the user s Workspace that dependency is NOT removed or invalidated Because the deleted item still exists in the user s Workspace albeit in the Deleted Items folder that item can still be referenced used and opened just like it was before it was deleted Undeleting Items To undelete an item the user can simply open the Deleted Items folder and move the item in question back into the Workspace in any location that they choose As with the deletion process none of the item s relationships with other BIS items are changed when the item is moved TransMed Systems Inc CE BIS USER S MANUAL ae Artifacts and Icons Each Artifact in Workspace Explorer is given an Icon Some icons will have different status symbols attached to them based on security or generation non Boga gt PRA Scratchpad Scratchpad is the BIS clipboard and allows
169. ince the tool open is relative to the Report that is open the Tool tab is attached to the Cohort Reporter tab To close the Tool the user has to click on the X on the sub tab or the Close button on the toolbar this will prompt the user with a save message if needed The user is then returned to the Cohort Reporter tab Bar Chart B The Report Setup within Cohort Reporter also opens as a sub tab of Cohort Reporter tab Since the Setup open is relative to the Report that is open the Report Setup tab is attached to the Cohort Reporter Tab To close the Report Setup the user can choose to click on the X on the sub tab or the Close button on the toolbar this will prompt the user with a save message if necessary The user is then returned to the Cohort Reporter tab Report Setup New Report TransMed Systems Inc 190 BIS USER S MANUAL as Closing Sub Tabs in Clinical Pattern Matcher In Clinical Pattern Matcher the Editor opens in a sub tab of Clinical Pattern Matcher tab To close the Clinical Pattern Editor the user must click on the X on the sub tab or the Close button on the toolbar this will prompt the user with a save message if necessary The user is then returned to the Clinical Pattern Matcher tab Clinical Pattern Editor New Clinical Pattern Context Information Area The Context Information Area in the upper right hand corner of the window give
170. ip displays all of the information shown on the tab when it is expanded All tab information is displayed in two lines The upper line in larger bold text shows the name of the tool window the tab is for e g Cohort Explorer Venn diagram etc The second line displays some context for that window typically the name of the item that has been opened in that window e g Cohort name Clinical Pattern name etc As the user clicks on different tabs the application will switch to the window associated with the new tab The tab clicked will then fully expand displaying its information as described in the above paragraph The tab that the user just left will be collapsed down to just its icon Close Buttons All tabs except the BIS Desktop window have a close button in their upper right corner allowing the user to close that window The BIS Desktop window can never be closed as it is the starting point for the entire application All Workspaces are opened from the BIS Desktop window and closing a Workspace will return the user back to this window to open another Cohort Explorer Close ta All Closing a Workspace To close a Workspace completely the user needs to either e Click the BIS Tools menu button and select the Close Workspace menu option e Close all open Workspace tabs individually Opening One Workspace When Another Workspace ts Already Open If the user has a Workspace open and would like to open a diffe
171. is displaying a different Module Reading and each cell contains the Observation for the Trait All 06 Chemistry Module Readings Trait Headers 1 3i 8 ALKALINE P Reading Y FASTING_GL Yf 3 BUN T TY Y ToTaL_Beu Y UCOSE CREATININE HATAS PUBIN Module Readings Observation Values If the Module contains over 50 Traits the Module Readings section will only show the Reading column and the first Trait and Timestamp of the Module To view the other Traits within the Module the user can view the Observation Details section above Filter Options The User can filter on any of the Traits within the horizontal list by clicking on the Filter icon red circle below next to each header title This will prompt a filter window where the user can omit select green arrow below certain observation values and filter on values by selecting parameters from the dropdown options purple arrows below Si CREATININ E E l Select All 62 Filter Options in Dropdowns purple arrows ee 8S Show rows with value that Is not equal to Is less than And Is less than or equal to Is greater than Is greater than or equal to Is null Filter Clear Filter Ts not mull Observation Details The Observation Details can expand and collapse to display the Observation values for the Reading selected in the Module Readings section below The displayed values will default to the first Reading in TransMed Systems In
172. it Info Notes Duplicate Venn and New Project e Edit Info Edit Information allows the user to edit the information for the selected artifact in the Workspace This area will edit the title and description of the artifact e Notes Notes allows the user to add a note on Workspace artifacts All artifact notes will be displayed as the user requests them All users are able to view and edit notes e Duplicate Duplicate will make a copy of the highlighted artifact This copy will be placed in the same Workspace as the original The Duplicate will have the same name as the original with a number after the title based on how many copies of that artifact exist o To duplicate any artifact the user must simply highlight the artifact and click Duplicate in the Workspace Toolbar s Actions dropdown menu The duplicate will mimic the name of the original followed by a number All parts of the artifact are duplicated including notes and descriptions o Exported artifacts and Folders do not have the duplicate function Brown Rat 2 Patient Cohort Ac Patients Patient Cohort 67 Patients Original Duplicate e Venn Venn diagrams are diagrams that show all possible logical relations between Cohorts or Choice Lists o BIS allows the user to create a Venn diagram from 2 Cohorts of the same Entity type or 2 Choice Lists of the same type To create a Venn the user should highlight multiple Cohorts Choice Lists and the
173. ivencecieescecediteeusasecvceneantvcasediceaunecstueusesteeauecsaiWeusscicwousaadcuesced deecasseusvauceaieesdeen us saeuecheweuseativeemseaawe 70 SiS ENE VIEW CN iiticaiscatcsecsesicevessssctwiisuiceracaacdeacaticnwecsvantvdsssisirsapsaansasapiguwna seine eiaseieesss saaevisasiaiinastnaiasaauanesst een 76 OVO N ee I eE OES E EEE EE E wecedasedeeeate toeemenedainsesan Wedmoasecioeanaesioaasepadensacaneceantaneteecnans 76 CHOKE LIST VIG W OF P an E 81 Gene List Gene List Viewer cccccsccscccsccsccecccccceccecccsccecceccccccucceccecccecceccesccucceccecccucceccesscucceccesscucceccescouccecconce 83 How to Create a Gene List nssenssesssesssesssessesssesssessscsssessscssrcssscesressresssesssesssesssesssesssesssesssesssosseosseosseosseosseessees 83 POW TO VIEW a GENS E aeea ae E E EEE AEE EE EE E E 83 Gene inioimation FORM isss a a 86 NENA CLASP A airn S A 89 Creating a Venn GiagramM aececi a aa E EN E S E G iaai 89 MSG CU EED E E E E A E E E A N E E E E 89 D EDIO OT arra a A E A A S 96 Design Overview ccccssccssccnscceseceseccseceneceseeseeeeeeeeeseeseeeseeeeeaeesaeeseeeceaeesaeeseeeeeaeesaeseeeeceseesaessaeeceseesaessaeseeaecsaeesasenaees 96 EN AT atian Hele oy aeinn E E ee EE E 96 Category Mapping ssssssessessessressessessresrrsressesseesreeressrosresreoreoseosresreesesseoseesrroreeseeseeoresreoseeseesreoseoseoseesreereeseeseeee 97 Sar CU GING SORE TOOD N r AE AONA EONA EOE ONE E AA EEO OEO 97 DA tal PANE aee A A A
174. k OK Edit Filter 1 gt Last Name _ Patient Constraint iiil All Observations Summary pal None amp Comma Separated Values 0 Filter on all values Filter on specific values 2 Filter Cancel Numeric Trait When using the Advanced Filter options for a Numeric Trait the user must first click the button next to Filter on Specific Values This will enable the Filter options allowing the user to enter Filter values and add Traits to the Data Definition Steps for using Advanced Filter Options 1 Bring up the Add or Edit Trait window 2 Choose Filter on Specific Vales green area below 3 Adda Low Value High Value or both to filter boxes red area below 4 Set the relational operator and inclusive check yellow area below 5 Click OK TransMed Systems Inc 183 BIS USER S MANUAL as Add Trait 1 aO 13 URINE PH me 08 Urinalysis Link Q E 13 URINE_PH from Patient Constraint iiil All Observations Summary S Mean gh Mean Filter on all values Filter on specific values GreaterT Equal to Greater Than Less Than Between Cancel Relational Operators e Greater Than Inclusive 2Y e Greater Than Exclusive un checked gt Y e Equal to Y e Less Than Inclusive lt Y e Less Than Exclusive un checked lt Y e Between Inclusive Y and Exclusive X Between Y and X e Between Inclusive X and Exclusive Y B
175. k or Un Check 3 Variables to Add Remove Fi Poorly Differentiated from the Pivot Display M Undifferentiated Ri well Differentiated Pivot Chart BIS has the ability to take the Pivot Table and transform it into a Chart Once all variables have been designated filters and sorted the user can click the Show Chart button in the toolbar By default the chart will open to display the selected variable from the table highlight the rows to be displayed on the chart then click Show Chart Once the Chart panel is expanded the user can pick a chart style Refresh Collapse All lt Show Totals gil Hide Chart es Bar Side By Side Series 20 lt Use Selection Show Points Labels Show Totals Show Grand Totals Invert Axes Wil Export Chart Area Full Stacked Series 20 Area Series 20 i i he d Area Stacked Senes 2D 1 1 1 N 1 1 Bar Full Stacked Senes 20 Bar Sade By Side Senes 20 Bar Stacked Series 20 lung Senes 20 Point Senes 20 E Pie Senes 20 e Use Selection green arrow Will use the selected row columns from the table to calculate the chart e Show Point Labels blue arrow Will show the labels values for each point on the chart e Show Totals orange arrow Will display the row totals on the chart e Show Grand Totals black arrow Will display the grand totals on the chart e Invert Axes brown arrow Will flip the axes Default rows on the X axis Columns value
176. kspace Cohort Explorer History Data Definition and Clinical Pattern Matcher Creating a Venn diagram The user can create a Venn diagram from several areas within BIS Each diagram requires at least 2 items and is limited to four items to generate a diagram If more than four items are applied in Venn the results will display on the Intersections tab of the Venn diagram tab e Opening Venn from the Workspace o When working in the Workspace the user can highlight 2 or more Cohorts of the same Entity type and click the Venn button in the toolbar to launch the Venn diagram tab o When working in the Workspace the user can highlight 2 or more Choice Lists of the Same type and click the Venn button in the toolbar to launch the Venn diagram tab o When working in the Workspace the user can highlight 2 or more Gene Lists of the same type and click the Venn button in the toolbar to launch the Venn diagram tab e Opening Venn from Cohort Explorer History Section o When working in Cohort Explorer the user can highlight 2 or more Filter lines of the same Cohort type from the History section and click the Venn button in the toolbar to launch the Venn diagram tab e Opening Venn from Cohort Reporter Data Definition o When working in Cohort Reporter and more than one Group is present the user can select the Groups Level and then click the Venn button in the toolbar to launch the Venn diagram tab e Opening Venn from Clinical Pattern Mat
177. l Linking Relationships shown below e Module gt Entity Linking Relationship o Last breadcrumb in the Cohort Filter is a Module and the user is Transitioning to an Entity i Io Q Same Patient Is Q lt I Patient Sample E From parent Patient to child Samples Sample Patient de gt Braet P From child Samples to parent Patient Patient Sample Experiment Is Q lt lt From parent Patient to child Samples to child Experiments Experiment Sample Patient From child Experiments to parent Sample to parent Patient e Entity gt Module Linking Relationship TransMed Systems Inc e BIS USER S MANUAL as o Last breadcrumb in the Cohort Filter is an Entity and the user is Transitioning to a Module Q gt Same Patient to 06 Chemistry pie z gt Same Sample o to Tumor Stage sample Sample Experiment Juss 5 From parent Sample to child Experiments to Molecular Observation e Module gt Module Linking Relationship o Last breadcrumb in the Cohort Filter is a Module and the user is Transitioning to a Module gt Same Patient B S B to 07 Hematology l Patient Sample Io F Q lt i m From parent Patient to child Samples to Breast Histopathology Sample Patient Jjj gt Q Is From child Samples to parent Patient to 06 Chemistry Patient Sample Experiment Io Q SmE 8 B From parent Patient to child Sample
178. lected Add Module Options Modules in Cohort Reporter are expressed as an Exist Trait and that Exist Trait is owned by a Module In the Data Definition Modules appear as Module Levels The Module Level is highlighted below in blue T B 06 Chemistry 2 3 BUN 4 CREATININE 6 ALT The variables nested within the Module are the Traits that the user selected and are owned by the Module Steps to Filtering on a Module 1 Search for a Module in the Data Explorer yellow area below 2 Click the Plus Icon on the Module in the search results pink area below TransMed Systems Inc a BIS USER S MANUAL as E Back il All Items ae Search Results for chemistry Didn t find what you were looking for Qo Search All e 06 Chemistry 3 py All Traits gt Patient Traits gt Patient Fields gt 06 Chemistry 3 Optional Edit Level Name green area below e This name will display as the Report Level in the Data Definition as well as the Generated Data 4 Set the Linking Relationship red area below e More on Linking Relationships below 5 Set the Constraint purple area below e The Constraint is considered a Limiting or Non Limiting Factor to the Data Definition e The Constraint is considered in the Report query before the Trait Advanced filter e The default Constraint for a Module is All Module Readings non limiting e More on Constraints
179. lector to choose variable s in the Report and Analysis tools Clear Data Definition is in the Report Setup tab of Cohort Reporter This allows the user Clear Data Definition to clear the Data Definition and return it to BIS default The Groups defined will not change This button is in Cohort Explorer allowing Clinical Pattern the user to start a new Clinical Pattern session with the current Cohort Filter The Clinical Pattern Editor creates new or Clinical Pattern Editor edits existing Clinical Patterns that can be applied in Clinical Pattern Matcher A Clinical Pattern is a grouping of Entities Modules and or Traits connected linearly by Clinical Pattern Matcher time reference In BIS the Clinical Pattern Matcher allows the user to apply Clinical a Patterns to saved Cohorts a ea ater Mater TransMed Systems Inc 2290 BIS USER S MANUAL Sy Close Workspace Cohort Cohort Explorer Cohort Filter Cohort Importer TransMed Systems Inc 230 Close will close the current panel or tab that is open If changes have been made the user will be prompted to save Close Workspace is on the BIS Tools menu This will close the Workspace and all items within the Workspace that are open BIS allows only one Workspace to be open ata time If any item needs to be saved before closing BIS will prompt the user A Cohort is a grouping of like Entities that can be saved and used or referenced again to populate
180. ll Experiments Expenment Cohort 40 395 Expenments 7 9 2013 4 21 55 PM Male Expenments Expenment Cohort 15 911 Expernments 8 9 2013 2 07 20 PM gt Rat w exp Expenment Cohort 63 Expenments 8 12 2013 10 23 56 AM All Monkeys 8 26 2013 11 54 51 AM Open P Open Cohort Delete Open In Clinical Pattern Match PE Open In Cohort Reporter Context Menu i All Patients 5 31 2013 11 19 18 AM anova results 2013 2 47 50 PM Venn 2013 11 19 39 AM Baboon Workspace Item Inter Relations The core of the problem with deleting items in BIS is the fact that Workspace items can be highly inter related For example a user can Create a list of Diagnoses and save that list to their Workspace Used that list in a Cohort Explorer and create a Cohort that they save to their Workspace Used that Cohort to help define a Report in Cohort Reporter They save that Report to their Workspace Now what happens if the user deletes the list of Diagnoses that they created in step 1 Well since the Clinical Pattern created in step 2 was related to that list it is now invalid Since that Clinical Pattern is now invalid the Patient Cohort created from it is also invalid Because BIS is designed as a research platform capable of performing reproducible analytical functions allowing the user to delete items that other items rely on creates a dependency problem that has the potential to invalidate analysis The e
181. low 3 Set the relational operator and inclusive check 4 Click Apply Filter TransMed Systems Inc 108 BIS USER S MANUAL as aia 13 URINE PH eaii 08 Urinalysis 11681 Link pal c g Same Patient Constraint iiil All Observations 4 T Apply Filter i Filter on all values Filter on specific values Unknown Relational Operators e Greater Than Inclusive 2Y e Greater Than Exclusive un checked gt Y e Equal to Y e Less Than Inclusive lt Y e Less Than Exclusive un checked lt Y e Between Inclusive Y and Exclusive X Between Y and X e Between Inclusive X and Exclusive Y Between Y and X e Between Inclusive Both Between Y and X e Between Exclusive Both un checked Between Y and X Currency Trait When using the Advanced Filter options on a Currency Trait the user must first click the button next to Filter on Specific Values This enables the Filter options so the user can add Filter values and apply the Trait to the Cohort Filter Steps for using Advanced Filter Options 1 Choose Filter on Specific Vales green area below 2 Adda Low Value a High Value or both to filter boxes red area below 3 Set the relational operator and inclusive check 4 Click Apply Filter TransMed Systems Inc 109 BIS USER S MANUAL as Currency Expenditure Link Q Same Patient Constraint ny All Observations A T Apply Fi
182. lowing the user to add Filter values and apply Traits to the Cohort Filter Steps for using Advanced Filter Options 1 2 3 4 5 TransMed Systems Inc 157 Click the Filter icon on the Event Tile red area below Choose Filter on Specific Vales green area below Add a Low Value High Value or both to filter boxes black area below Set relational operator and inclusive check purple area below Click OK yellow area below BIS USER S MANUAL as Numeric Range Constraint All Observations __ Filter on all values Repeat 1 gus Biti Equal to Hegi 3 BUN All Observations Less Than Greater T Greater Than Relational Operators Greater Than Inclusive gt Y Greater Than Exclusive un checked gt Y Equal to Y Less Than Inclusive lt Y Less Than Exclusive un checked lt Y Between Inclusive Y and Exclusive X Between Y and X Between Inclusive X and Exclusive Y Between Y and X Between Inclusive Both Between Y and X Between Exclusive Both un checked Between Y and X Currency Trait When using the Advanced Filter options for a Currency Trait the user must first click the button next to Filter on Specific Values This will enable the Filter options allowing the user to add Filter values and apply Traits to the Cohort Filter Steps for using Advanced Filter Options Click the Filter icon on the Even
183. lows designated staff BIS Admins the ability to create and administer different Projects within the BIS system environment Projects within BIS will have the following features Constraint of Entities BIS Admins can constrain the top level Entities typically Patients of the BIS system to a defined subset of all Entities loaded into the system This constraint can be done using either an Entity Group Cohort or Filter Set that then defines the Entity Group Constraint of Traits BIS Admins can constrain the Traits that are available to the BIS Users in the Trait Explorer of the various tools Cohort Explorer Clinical Pattern Editor etc Security Permissions BIS Admins can constrain which users have access to what Projects using enterprise security integration They also determine the level of data security access Identified De Identified for each Project Workspaces and Projects The Project Entitlement features the Project as the top level object within the BIS environment sitting above and containing user created Workspaces All Workspaces created in BIS must be done in the context of a Project that has been defined by the BIS Admins BIS Global Project The process of defining a new Project within BIS requires the user BIS Admin to create a Patient Entity Cohort also called a Patient Cohort first Patient Cohorts can only be created from the tools available within a Workspace which results in a bootstr
184. lter _ Filter on all values Filter on specific values Relational Operators e Greater Than Inclusive 2Y e Greater Than Exclusive un checked gt Y e Equal to Y e Less Than Inclusive lt Y e Less Than Exclusive un checked lt Y e Between Inclusive Y and Exclusive X Between Y and X e Between Inclusive X and Exclusive Y Between Y and X e Between Inclusive Both Between Y and X e Between Exclusive Both un checked Between Y and X Date Trait When using the Advanced Filter options on a Date Trait the user must first click the button next to Filter on Specific Dates This enables the Filter options so the user can add Filter values and apply the Trait to the Cohort Filter Steps for using Advanced Filter Options 1 Choose Filter on Specific Dates green area below 2 Adda Low Value a High Value both values in the filter boxes red area below E e Note by clicking the button next to the range the user will get a calendar 3 Set the relational operator and inclusive check 4 Click Apply Filter TransMed Systems Inc po BIS USER S MANUAL as Date EFH Expenditure Link Q Same Patient Constraint Iiii All Observations A T Apply Filter O Filter on all dates Filter on specific dates Enter date Relational Operators e After Inclusive 2Y e After Exclusive un checked gt Y
185. n BIS that created the Report e Last Updated The last date and time this Report was updated or edited e Notes Any Notes the user has created to correspond with the Report Notes can be viewed and edited by all users with access to the Workspace e Data Definition Summary Displays the summary of the Data Definition General Information Toolbar The toolbar of the General Information Panel is located above the information and has buttons that allow the report information to be edited e Edit Info Allows the user to change the report name and add a description about the report e Notes Allows the user to add notes about the report These notes can be viewed and edited by all users that have access to the Workspace Report Data Panel The Report Data panel in Cohort Reporter displays all of the data generated for the current report The user can view and edit the columns of the data generated as needed in this panel TransMed Systems Inc 20 BIS USER S MANUAL Sy Cohort Reporter 3 Main Levels 3 Nested Levels isroup Name Male Patents Male Patents Male Patients Male Patents Male Patents Male Patients Male Patents Male Patients Male Patients Male Patents Female Patients Female Patients Female Patients Female Patients Female Patients Toolbar Toolbar Uli Sample Patent ID OCA 269 OCA 265 OC4 269 OCA 269 OCA 269 OCA 269 OCA 253 OCA 253 OCA 253
186. n Exists Gi ar i i l f gt gt UD East Physician Ul Exists Cohort Type F Physician View g Icon View I Physician With the Cohort Type now displaying the Reference Entity all view options in Cohort Explorer excluding Observation Details will also display the Reference Entity information TransMed Systems Inc 1350 BIS USER S MANUAL ae Cohort Explorer Toolbar The main toolbar in Cohort Explorer has been designed for both ease of use and to fit on lower resolution displays The buttons in the toolbar apply to the end result Cohort displayed in the Viewing area e Create Cohort Create Cohort allows the user to save the current Cohort as an artifact on the Workspace Based on the current View the user may have the option to Create Cohort from All or Create Cohort from Selected Kel Create Cohort Kel Create Cohort mo from all Patients mo from selected Patients e Create Report When the user clicks this button Cohort Reporter will launch The current Cohort will become the starting Cohort for the Reporter e Clinical Pattern When the user clicks this button Clinical Pattern Matcher will launch The current Cohort will become the starting Cohort for Clinical Pattern Matcher e Cohort Filter The Cohort Filter is a dropdown that allows the user to o Open Cohort Filter Clear current Filter and add saved Filter o Append Cohort Filter Apply an existing Filter to
187. n a BIS install include Patients Tissue Samples Experiments and Facilities Entities are linked to each other by a hierarchy system The ETL Refresh is found in Project Properties It allows users to turn On or Off the ETL process of automatically adding new Patients to the Project based on ETL data Disable ETL Refresh loads P Enable ETL Refresh BIS USER S MANUAL a Execute Execute All Expand All Experiment Cohort TransMed Systems Inc 237 Execute is used in the Report Tools and Analysis Tools of BIS Clicking the Execute button will start the Report Analysis Tool generation and create the visualization or report Execute is used in the Analysis Tools Panel Clicking the Execute All button will re execute the Analysis Tools on the panel Workspace Expand is an option in all Selector windows The Expand button will expand the category highlighted to show the variables in Flat view Expand All is found in several places within BIS It allows users to Expand All data to full Expand All view for easier viewing An Experiment Cohort is a Cohort that is comprised of only experiments If the Cohort filter is viewed the user will see that the filter ends in experiment The Experiment Cohort is an Entity that is the last on the hierarchy chain BIS USER S MANUAL ys Export Selected Data allows the user to export the selected data tables in BIS using Multi Select Mode Th
188. n click the Venn button in the Workspace Explorer Toolbar s Actions dropdown menu or in the context menu o This will launch the Venn diagram feature in BIS allowing the user to compare the artifacts Venn will be discussed in detail below e New Project New Project button allows the user to create a new Project from a Patient Cohort that is saved within the Workspace Delete Delete Using the delete function on any artifact within the Workspace Explorer will move that item into the Deleted Items Folder See below for more about BIS Delete Options e BIS has the ability to delete items in a user s Workspace On the surface this seems like a trivial thing to implement however when you look at the problem more closely there is quite a bit of TransMed Systems Inc C BIS USER S MANUAL as complexity involved It is important for one to have an overall understanding of this complexity so that they can understand the context in which the new Soft Delete functionality has been implemented Refresh Refresh Anywhere in BIS the Refresh button will simply refresh the current tab By clicking Refresh the status of reports in generation will change View Dropdown View Dropdown The View dropdown includes Icon View and Detail View these options allow the user to alter the display of information in the Display Panel Workspace Search Workspace Search Allows the user to search for Artifacts within the Workspace
189. n the user s screen which in Identified mode will contain the actual IDs of Entities and non obfuscated dates To allow De Identified users access to exports containing non obfuscated dates would potentially violate data privacy compliance rules Reports Reports are marked protected if an ID user created it Reports are unprotected if the made by a De Identified DID user or the Identified ID user has removed the Patient ID from the Data Definition All other items Not protected Folders and Choice Lists are never protected Views There are two view options within the Workspace Explorer tab Icon View and Detail View TransMed Systems Inc 66 BIS USER S MANUAL ae Icon View The Icon View is the default view of Workspace Explorer This view shows the user all saved artifacts and folders as Icons The Icons are labeled with the artifact name artifact type and count Shown above Detail View The Detail View switches the panel to display all artifacts and folders in List format This view will display artifact name artifact type artifact information and last modified date time Workspace Explorer yi Mute Popen Bactions JP Delete Refresh lt Detail View gt Q Name Y Type Y Information Y Modified gt Deleted Items Folder Deleted Items Folder 5 14 2013 11 09 49 AM Export Folder Folder 5 31 2013 11 27 53 AM Jj All Samples Sample Cohort 34 314 Samples 7 9 2013 4 22 03 PM gt A
190. nd displays the count when the report data is summarized to a Main level Count Each Distinct Group Summary Option Patient level only e Creates a new column for each choice value that appears in the data for this Trait and displays the count when the report data is summarized to the Group level Flag Each Boolean Level Summary Option TransMed Systems Inc 196 BIS USER S MANUAL as e Creates a new column for each choice value that appears in the data for this Trait when the report data is summarized to a Main level A value of 1 is displayed when a choice value exists and 0 when no choice value exists Flag Each Boolean Group Summary Option Patient level only e Creates a new column for each choice value that appears in the data for this Trait when the report data is summarized to the Group level A value of 1 is displayed when a choice value exists and 0 when no choice value exists Flag Each Name Level Summary Option e Creates a new column for each choice value that appears in the data for this Trait displaying the value of the Trait itself when the report data is summarized to a Main level Flag Each Name Group Summary Option Patient level only e Creates a new column for each choice value that appears in the data for this Trait displaying the value of the Trait itself when the report data is summarized to the Group level Comma Separated Values Level Summary Option e Creates a
191. ne of the BIS features A Filter Choice Trait is one of the observations within a Choice Trait These Observations can be searched for in Data Explorer Filter Choice Trait A Cohort Filter or Filter List is the Filter associated with an existing Cohort When in E i Cohort Explorer the user can choose a saved J p Cohort Filter and apply it to a new Cohort The saved Filter List is an artifact on the Workspace and is Entity specific Filter List A folder is a container within BIS that helps organize Traits Modules and Entities Folders are in the Data Explorer and can be created in Workspace Explorer to help organize artifacts The Gene List is comprised of Genes saved Gene List from an Analysis Tool TransMed Systems Inc 2390 BIS USER S MANUAL Sy The Gene Lists button is found on the Data Definition toolbar The button will only appear to the user when the Definition below is defined as molecular Gene Lists This will allow the user to select a saved Gene list and apply it to the report as an addition filter The general information is a panel that is in the Project Properties Workspace Properties Cohort Details and Cohort Reporter This panel shows the Title Description Created By Last Updated and Notes about the item General Information aJ l When the user clicks Generate Data in the Cohort Reporter the report parameters A defined in the Data Definition are
192. nel e Sort Clicking on the Sort dropdown will give the user sort options for the Grouping results Entity Group Options The user has the option to add Entities to the Filter List in Cohort Explorer by using the Group Panel Entities in Cohort Explorer are expressed as an Exist Trait and that Exist Trait is owned by an Entity Module Steps to Grouping on an Entity 1 Search for an Entity in the Data Explorer yellow area below 2 Click the Group Icon on the Entity in the search results pink area below E Back lah All Items Search Results for sample Didn t find what you were looking for 3 Set the Linking Relationship red area below 4 Set the Constraint purple area below 5 Set Group Option black area below 6 Click Group orange area below TransMed Systems Inc 116 BIS USER S MANUAL as o Up T Filter Sample sample Group by all values no values Module Group Options The user has the option to add Modules to the Filter List in Cohort Explorer by using the Grouping Panel Steps to Grouping on a Module 1 Search for a Module in the Data Explorer yellow area below 2 Click the Group Icon on the Module in the search results pink area below El Back il All Items Search Results for chemistry Didn t find what you were looking for eN Search All
193. ng Options display the Linking relationship in bold then the Linking description below The arrows displayed in the Linking options also show the Relationship between variables TransMed Systems Inc 1300 BIS USER S MANUAL as One to Many gt Many to One Direct of the Same The Entity and Modules are displayed as Icons e Entities The Link options dropdown shows the user the entire Linking relationship using the Icons and Arrows Example Patient Sample Experiment From parent Patient to child Samples to child Experiments to This Linking relationship is showing that the current Cohort Filter ends in a Trait green box from there the user added another Trait red box To get to the newly added Trait the Cohort Filter had to transition through 3 Entities yellow boxes Steps of Linking Relationship 1 Patient Trait Transition to Owner Entity Type Patient 2 Patient Entity Transition One Many to the Child Entity Type Sample 3 Sample Entity Transition One Many to the Child Entity Type Experiment 4 Experiment Entity to selected Experiment Trait Some potential Linking Relationships are shown below e Trait gt Trait Linking Relationship o Last breadcrumb in the Cohort Filter is a Trait and the user is Transitioning to a Trait Same 06 Chemistry Module ae Linked to 1 FASTING _GLUCOSE gt Same Patient to 3 BUN TransMed Systems Inc pa BIS USER S
194. nn Grouping List Name Set Count Brown Rat 67 Female Patients 5963 Male Patients 6701 Rats w Cytokines 21 Diagram Intersections TransMed Systems Inc CE BIS USER S MANUAL ys Once the user identifies the intersection s they want to utilize they can highlight the intersection s and proceed with viewing the Identifiers save the selected intersection s as a Cohort on the Workspace and or launch Cohort Explorer Cohort Reporter or Clinical Pattern Matcher TransMed Systems Inc 95 BIS USER S MANUAL Ss Data Explorer The Data Explorer is used in Cohort Explorer Cohort Reporter and Clinical Pattern Matcher to assist the user in refining the end result data The Data Explorer displays all of Entities Modules and Traits assigned to the Project This allows the users to Filter and or Group on these items to create a Cohort Report Data or a Pattern Match Items that are assigned to the Project but do not have an associated Timestamp Trait will not appear in Clinical Pattern Matcher Design overview The Data Explorer is displayed as the Left hand Column in Cohort Explorer Cohort Reporter and Clinical Pattern Matcher There are four main sections e Navigation Toolbar yellow area below e Category Mapping green area below e Search and Sort Toolbar red area below e Data Panel purple area below El Back o Up ems All Imported Patient Traits i Sample Traits Experiment Traits
195. ns will change based on Trait Type Real Integer Choice Text Currency Data Date w Time The Summary and Group Summary options are interdependent on one another Based on the Summary the user selected the Group Summary options may change and vice versa TransMed Systems Inc a5 BIS USER S MANUAL as S Level Summary Options Omit Calculate the mean of all values returned for this trait for each Min row in the parent level Max Mean Median Sum Cnn Alen Bleoll a Group Summary Options Omit Calculate the mean of all values returned for this trait for each Min group in the group level Max Mean Median Sum Count Marn Ale oll Summary Descriptions Omit Level Summary Option e This Trait will be removed from the report data when summarized to a Main level Omit Group Summary Option e This Trait will be removed from the report data when summarized to the Group level Count All Distinct Level Summary Option e Counts the number of times a value uniquely appears for this Trait when the report data is summarized to a Main level Values will only be counted once Count All Distinct Group Summary Option e Counts the number of times a value uniquely appears for this Trait when the report data is summarized to the Group level Values will only be counted once Count Each Distinct Level Summary Option e Creates a new column for each choice value that appears in the data for this Trait a
196. nt relationship between the two as Samples come from Patients The result is a one to many relationship between the two Entities one Patient can be the parent of multiple Samples The Entity Entity relationship is considered one of the fundamental relationships in BIS TransMed Systems Inc fren BIS USER S MANUAL Q lt J Patient Sample Jue lt ea Sample Experiment From parent Patient to child Samples sh From parent Sample to child Experiments a Patient Sample Experiment Q lt lt a From parent Patent to child Samples to child Expenments A J Experiment Sample J gt Q Sample Patient m F From child Experiments to parent Sample a From child Samples to parent Patient a Experiment Sample Patient A gt Q From child Experiments to parent Sample to parent Patient Module Entity The Module Entity relationship green arrow in the Conceptual Diagram A1 diagram above at first seems exactly like the Entity Ownership relationship discussed previously However there is an important difference between the two Entity Ownership is a fundamental relationship all Modules must be owned by a specific Entity type Module Entity relationships are optional and are used to define secondary relationships between Modules and Entities Note that unlike Entity Ownership the Module Entity relationship does NOT require that the Module belongs to the same Entity type as the Entity that it is rel
197. ntity Module Name ICD 9 Code Trait Trait MRN Diagnosis Date Trait Trait BIS Logical Model for a Patient Diagnosis relationship In this diagram we see one Entity Patient with two contained Traits Name MRN and one Module Diagnosis also with two contained Traits ICD 9 Code Diagnosis Date The Diagnosis Module here is owned by the Patient Entity All of the Traits in question here are also owned by the Patient Entity allowing them to be contained by any data container owned by it either the Patient Entity itself or the Diagnosis Module Continuing this example imagine there was another Entity called Sample Now Sample also needs a Name Trait However the Patient s Name Trait cannot be associated with the Sample because they are different Entities In this case we would have to create two separate Traits Name and Sample Name for the Patient and Sample Entities respectively TransMed Systems Inc o BIS USER S MANUAL as Entities can contain Traits in BIS Traits define what values BIS can store for an Entity and a Trait being a member of an Entity type instead of a Module Type defines how the data will be stored The rules for storing data at the Entity level are fairly restrictive only one observation per Trait can be made for an Entity This is the primary difference with respect to data storage between Entities and Module Types Module Types are not limited to the numbe
198. ntity in the search results pink area below TransMed Systems Inc a BIS USER S MANUAL as e Back A Up l All Items iS Search Results for sample Didn t find what you were looking for eN Search All lji Sample F J pY All Traits gt Sample Traits gt Sample Fields gt Sample 3 Optional Edit Level Name green area below e This name will display as the Report Level in the Data Definition as well as the Generated Data 4 Set the Linking Relationship red area below e More on Linking Relationships below 5 Set the Constraint purple area below e The Constraint is considered a Limiting or Non Limiting Factor to the Data Definition e The Constraint is considered in the Report query before the Trait Advanced filter e The default Constraint for an Entity Module is All Module Readings e More on Constraints below 6 Optional Select Traits owned by the Entity Module to be in the Definition black area below e Traits Selected will show nested within the Entity Module 7 Optional Check Uncheck Remove Empty Columns yellow area below e This will not display a column with all nulls in the generated Report 8 Click OK orange area below TransMed Systems Inc 77 BIS USER S MANUAL Ss Add Level Ja Sample Sample Entity Sample ID Acquisition Date Date Time El Anatomical Location Choice 1i Items 1 Se
199. ntrez Gene Required field BIS can now re generate the data to apply the Transform to the data The user will see the column headers change in the Report Data to reflect the Transforms modifications Probe Sample Intensity Before Transform 3 654 at 90 3 Gene Intensity After Transform 56 2999992370605 Report Tools Panel Report tools are set calculations that produce visualizations and refined results for the Report Data generated The user can create a Pivot Table or add in custom Report Tools Managing Report Tools The Report Tools panel is where all of the saved Report Tools visualizations are stored Each saved tool is an artifact and can be edited duplicated and deleted just like the artifacts saved in Workspace Explorer Toolbar TransMed Systems Inc paa BIS USER S MANUAL ys e Refresh Refreshes the Report Tools Panel e Open Opens the highlighted tool into editor view mode e Edit Info Edit information name and description of the tool highlighted below e Notes Applies Notes to the tool highlighted below These notes are only visible when the note button is clicked and can be viewed and edited by all users with access to the report e Duplicate Duplicates the tool highlighted below for quick variable changes e Delete Permanently deletes the tool highlighted below Workspace All saved Report Tools are listed in Icon view with Name Description and tool type yellow area Coh
200. nvert Selection Copy Selection Levels The Level refers to the Level of the generated Report Data The levels are determined by the Data Definition one level is displayed per Main and Nested Level for different viewing and summary options TransMed Systems Inc 203 BIS USER S MANUAL ae Viewing Main Levels Example amp Female Patients 5963 amp Male Patients 6701 Main Level i Patient 1D v Sample ID a Acquisition Date Main Level Tissue of Origin cohort Reporter Cohort Reporter Level jj Sample 2 Group Patient Main Level tui Sample Main Level Lowest Level This level will show the user multiple rows per Sample based on the definition Counts within the Lowest Level are true counts specific to that Module Entity TransMed Systems Inc 204 BIS USER S MANUAL yy D Patent E 06 Chemistry ii Sample Patient IO Mean 3 BUN amr Sample ID Aquisition Date OCA J350 J6 snap Tumar 12 30 2008 9 05 21 AM OCA J50 E Tumai 12 30 2008 9 05 37 AM OCe 350 E Tumai 12 30 2008 9 05 06 aM OCA 350 B Tumor 3 12 30 2008 9 05 11 AM DCA M9 HW inip Mormal 12 23 2008 00 00 PM OCA 345 Tumor 2 12 23 2008 5 00 03 FM DCA Hp Seana Tume aga 2008 5 00 40 FH a Sample owned by the Patient Patient Level Will collapse the lowest level into one row per Patient The counts at this level may use the summarized values to display
201. ohort 11 Patients Generic Drug Product List 10 352 Items U Platforms Molecular Platform List 13 Items The General Information page shows the general details about the Gene List including List Name The name of the List as displayed on the LHS and in Workspace Explorer Description The description of the List as defined by user List Type The type of List displayed Item Count The number of Genes in the List Created By The user in BIS that created this List Last Updated The last date and time this List was updated or edited Notes Any Notes the user has created to correspond with the List Gene List Dene 15 EA Edit Info Edit Notes Gene 15 List Name Gene List Description List Type Item Count Created By Last Updated Notes Toolbar Gene 15 Using HP Patients and Platform U95A4 Gene List 14 jmutz 08 Aug 2013 04 27 22 PM Edit Information Displays the Edit Gene List Information pop up window to allow the user to edit the name and description of the List TransMed Systems Inc CE BIS USER S MANUAL ae e Edit Notes Displays the Edit Notes pop up window to allow the user to add edit notes Notes can be viewed and edited by all users with access to the Workspace List Members The List Members section displays all of the genes in the list With each Gene Name there is also a correlating Species Protein Gene ID Gene Authority and Primary Symbol x
202. ohorts in the report Clinical Pattern Matcher Will open Clinical Pattern Matcher with the current Cohorts as the starting Cohorts in the Matcher Report When a Report is highlighted and the user clicks the Open button in the toolbar Cohort Reporter will open referencing this report One Clinical Pattern Will launch Clinical Pattern Matcher with that Pattern as the Starting Pattern in the Matcher Multiple Clinical Patterns When more than one clinical pattern is selected in the Workspace the open button will launch one Clinical Pattern Matcher tab for each pattern selected using each Pattern as the starting Pattern in the Matcher Export Item When the user selects an exported item BIS will prompt the user to open the item on the local drive One Filter List When a Filter List is selected Cohort Explorer will open by default with the selected Filter list in the breadcrumbs If the Filter is a Patient Filter then the user will be given the option to open that Filter in Cohort Explorer or Cohort Reporter Multiple Filter Lists When more than one Filter List is selected one Cohort Explorer tab will open per list selected using the Filter Lists in the breadcrumbs TransMed Systems Inc 62 BIS USER S MANUAL ys Folder When a Folder is highlighted the open button will open the Folder to display its contents in the display area of the Workspace Actions Dropdown The Actions Dropdown Menu contains several functions Ed
203. on all security membership BIS does not implement its own user group management interface BIS User Groups BIS requires that four user groups be defined within the user s external LDAP based security infrastructure These groups provide access to different functions within BIS The actual names of these groups are left to the customer s discretion however the group names must be mapped correctly in the BIS configuration settings BISUsers BISUsers is the most important group to define in the application security settings Log in access to BIS is granted exclusively to users that are members of the BISUsers group If a user is not part of this group they will not be allowed to log in to BIS Membership in the BISUsers group does support a hierarchical group membership BISAdministrators BIS Admins are defined as any members of the BISAdministrators group These users have access to special features related to Project Management described in the appropriate sections of this document and to all Projects including the BIS Global Project BIS Admins are the only users that can create Projects and edit their properties BISAdministrators is a secondary group meaning that it is used to define a set of permissions for a user that has already been granted access to BIS by membership in the BISUsers group A user must still be in the BISUsers group either directly or indirectly to log into the application See the Groups of Groups sec
204. ontainer for artifacts within the Workspace e Cohort Importer Cohort Importer allows users to create a Cohort from a text file which will be saved to the open Workspace The Right hand Side Toolbar allows the user to navigate to specific BIS functionality based on the selected artifacts in the Workspace Depending on which artifact s are selected the user will get different toolbar options TransMed Systems Inc CE BIS USER S MANUAL Open Open The Open button allows the user to open the selected artifacts from the Workspace The Open button in Workspace Explorer has different functions based on the artifact s that are highlighted in the Display Panel One Cohort When one Cohort is selected the Open button will give the user 4 options Cohort Information Will open the Cohort Viewer Cohort Explorer Will open Cohort Explorer with the current Cohort as the starting breadcrumb in the Filter List Cohort Reporter Will open Cohort Reporter with the current Cohort as the starting Cohort group in the report Clinical Pattern Matcher Will open Clinical Pattern Matcher with the current Cohort as the starting Cohort in the Matcher Multiple Cohorts When two or more Cohorts of the same Entity type are selected the Open button will give 3 options Cohort Information Will open the Cohort Viewer for each selected Cohort Cohort Reporter Will open Cohort Reporter with the current Cohorts as the starting C
205. or Entity in the Data Definition e Each Level of the Data Definitions is displayed in the Level dropdown as either a Main Level or a Nested Level e More on Levels below Create Cohort Allows the user to Create a Cohort from all or from the selected Entities in the Report Data e f the Report has more than one Entity level the user may have the option to save a Cohort as more than one Entity Type Open Will Open the Single Entity Viewer for the selected Entity in the Report Data e f the Report has more than one Entity level the user may have the option to open the Single Entity Viewer as more than one Entity Type Export Data The user can export the data as displayed which will save a copy on the current Workspace The user can then open and save the export to the local drive e The user can also use the Multi Select table mode and select one or more rows to export e Export and Copy features are protected features not all users will have access to Export Display Options e Choose Columns Opens the Multi Column Selector and allows the user to select which columns to display in the Data The user must redefine the columns with every level change o There isa limit of 500 columns allowed in the display at one time e Rotate Level This will Rotate the Report data allowing the user to see the columns of the last level converted into rows This view helps the user find and identify the data better when there are
206. orks to filter the tree to make it easier for the user to add new Traits Edit Project Traits Show All Traits All Traits gt Um All Imported Traits Currently In Project 4 G Patient Traits Traits Not Currently In Project LJ Birthdate Protected Traits _ Deathdate Fa Patient Fields Options are green area above e All Traits This view shows all Traits in the tree This is the default e Traits Currently in Project This view shows only those Traits currently assigned to the Project e Traits Not Currently In Project This view shows only those Traits NOT currently assigned to the Project e Protected Traits This view shows any Traits that have a status of protected Auditing Panel The Auditing panel in the Project Properties tab controls all of the Project level auditing settings for a Project TransMed Systems Inc 56 BIS USER S MANUAL ys i Tools v ii Project Jon hag Colon Cancer D Enable Auditing ig Colon Cancer Study Project Auditing Osabled Project Project level auditing will log the following actions performed in any workspace contained within this project Workspace Access Genera Information 0 Fiter Requests Group By Requests E Secunty amp Permissions Entity Set Creation cS Patient Cohort amp Filter Venn Diagram Requests Export File Creaton E Project Traits Export File Download In the BIS Auditing implementation the
207. orkspace Properties are opened The Workspace name description the Project that the Workspace belongs to the user that created the Workspace the last updated date and Workspace notes are shown TransMed Systems Inc a BIS USER S MANUAL oF Workspace Explorer Sad Favorite Edit Info El Edit Notes GF Trail 001 Workspace Name Trail 001 Workspace Description Project Colon Cancer Study i General Information J Created By jmutz ate Last Updated 17 Jun 2013 02 06 34 PM E Security amp Permissions pdate un Notes Edit Info The name and description are editable in a pop up window by clicking the Edit Info button in the toolbar Edit Workspace Information Workspace Name Trial Treatment Description Trial treatment 41009 Edit Notes The Workspace notes can be entered and altered by clicking the Edit Notes button in the toolbar The user can also edit the Workspace notes from the BIS Desktop tab TransMed Systems Inc 420 BIS USER S MANUAL as Edit Notes Trial Treatment mo Workspace Trial Treatment A1009 Security amp Permissions The Security amp Permissions page displays the groups and the users that have access to the Workspace Data access permissions cannot be set at the Workspace level like they can at the Project level Users are granted the same data access permissions to all Workspaces within a Project and these permissions are
208. ort Reporter DDIPivot Open Edit Info Notes Duplicate 7s Delete Pivot Table Tumor size vs Gender then Grade MOD Male higher instance than Female Pivot Table Tumor Size vs Grade Pivot Table Tumor Size vs Metastatic Outcome Ref T stage False Outcome in Samller tumor size present Pivot Table Icons displayed with the exclamation symbol denote that the tool needs to be edited and re executed Icons displayed with the gear symbol denote that the tool is still generating Pivot Table The term pivot means to rotate In the case of a Pivot table the user can rotate the data to examine it from a variety of perspectives The Pivot Table is not static it will change as the user pivots the fields A pivot table is a visual data summarization Data within the pivot table can be sorted counted averaged or totaled into a collapsible table In BIS the pivot table will apply the generated Report Data and organize it for the user to create a pivot TransMed Systems Inc aa BIS USER S MANUAL ae Overview The Pivot table is designed the same as the other Report Tools Multiple toolbars a LHS column where the variables are defined and a RHS results display area Tama ppi vi angar Th Cat Eeecraptis pir hia hoghar wvataece thes Piai T Eegeet Piiri hil Lanes H Ger T Pathestoge Grace e The Left hand Side column yellow area can be expanded to add variables and coll
209. other words BIS conforms itself to an organization s data instead of expecting the customer to conform their data and workflow to an unfamiliar pre existing data model This application s ability to conform is why BIS is different from almost all other research and analytic applications In doing this users can learn to use BIS much more quickly than typical analytical applications as all of the data within the application is presented to the user in familiar terms Parts of the Logical Model Every BIS Logical Model is composed of four main items Traits Entities Modules and Relationships These are fundamentally related to each other like so Entity Entity Relationship LI Entity O Module Module Entity Relationship Entity Module Ownership AAR Module Module Relationship Conceptual diagram of the BIS Logical Data Model A1 TransMed Systems Inc So BIS USER S MANUAL as Traits Traits are the simplest items in the logical model they represent an individual piece of data called an observation to be recorded in the system Examples of Traits would be things like Height Weight or White Blood Cell Count All data is loaded into BIS as Observations defined by Traits E g Height Trait 5 7 Observation Trait Types Not all data being loaded into an analytical program is the same Some data is measuring numeric values like height and weight some is measuring dates and times like a birth date I
210. oups combine unique field values o Numeric This option is in effect only for fields that store numeric values Field values are grouped into intervals as defined by the Numeric Range property e Numeric Interval Range green arrow Applies a value range to the variable for display Edit Pivot Field Field Name Tumor Size Numenic Average Summary Type Average Summary Display Type Default Group Interval Numeric Numeric Interval Range Summary Type Summary Display Type Group Interval Default AbsoluteVariation PercentVanation PercentOfColumn PercentOfRow PercentOfColumnGrandTotal PercentOfRowGrandTotal PercentOfGrandTotal RankInColumnSmallestToLargest RankInRowSmallestToLargest RankInColumnLargestToSmallest RankInRowLargestToSmallest Index TransMed Systems Inc 27 BIS USER S MANUAL as Date Trait e Field Name red arrow Allows the user to edit the name of the field e Group Interval The format of the displayed values O O TransMed Systems Inc e Default Groups combine unique field values Date This option is in effect only for fields that store date time values Field values are grouped by the date part The time part of the values is ignored DateDay This option is in effect only for fields that store date time values Field values are grouped by the day part The following groups can be created 1 2 3 31 DateDayOfWeek This option is in effect only for fields t
211. ow will change based on the variable type selected Numeric Trait e Field Name red arrow Allows the user to edit the name of the field e Summary Type This option is defining how the data is to be calculated in the Pivot Table o Count The number of values excluding Null and DBNull values Sum The sum of the values Min The smallest value Max The largest value Average The average of the values StdDev An estimate of the standard deviation of a population where the sample is a subset of the entire population O StdDevp The standard deviation of a population where the population is all of the data to be summarized o Var An estimate of the variance of a population where the sample is a subset of the O O O O O entire population o Varp The variance of a population where the population is all of the data to be summarized e Summary Display Type This option is defining how the data is to be displayed in the Pivot Table o Default The calculated summary values are displayed as is o AbsoluteVariation The absolute variance between the current value and the previously calculated value for the current field is displayed in the cell o PercentVariation The percentage variance between the current value and the previously calculated value for the current field is displayed in the cell o PercentOfColumn For data cells the percentage of the column s total value is displayed for total cells the percenta
212. owing user actions System Log In User ID date and time will be logged Project Level Auditing Project level auditing logs Project and Workspace related events to the BIS Audit Log See the Auditing section of the Project Properties tab for more information Auditing Configuration At the application level there will be two auditing configuration options in the BIS application configuration file System Level Logging on off If this is on the system will log all System Level Auditing items Default Project Logging on off This determines the default state for all newly created Projects in BIS Audit can still be enabled disabled on a Project by Project basis in the Project Properties tab BIS Audit Log Viewer Tool While BIS generates standard CSV audit log files that can be viewed in B S 5 1 any commercial log viewer the easiest way to view the logs from within i the application is to launch the BIS Audit Log viewer The Audit Log viewer is available only to the BIS Admin users and provides a quick and dl BIS Desktop easy interface to view filter and sort and export events in the audit logs 4 Tools i Audit Logs To launch the BIS Audit Log viewer the user clicks on the BIS Tools menu in the main application and selects the Audit Logs menu item Help The BIS Audit Log viewer launches in a separate web browser tab or web browser window if the browser does not support multiple
213. p title Select Arrow Select None is one of the options in Multi Select None Select Mode It un selects all rows in the table Show Chart is a function inside the Pivot Show Chart Table This will allow the user to see the Pivot Table results in Chart view Le Show Total is a function inside of the Pivot F Show Totals Show Totals Table This allows the users to Show or not show the Totals columns and rows Show Grand Totals Show Grand Totals Show Totals v Total The Single Entity Viewer will allow the user to view all the observations listed under an Single Entity Viewer Entity This can be accessed in Cohort Explorer in Patient Details View by double clicking on the Entity ID TransMed Systems Inc 252 BIS USER S MANUAL ys This Sort option sorts the data as defined by ETL relevance Sort 1 9 sorts the numeric data ina melts descending format Sort 9 1 sorts the numeric data in an sci ascending format Sort A Z sorts the text data in a descending A Z port format Sort Z A sorts the text data in an ascending format Text Traits are the last type of Trait the user can define in BIS Observations for these Traits simply hold chunks of free form text entered by the user in some way Text fields can be searched on so they are useful for things like MRN name etc Text Trait A Time Window is a reference tool used in the Clinical Pattern This tool runs parallel Time Window to
214. pace Calculate Matches To Calculate Matches and run the Clinical Pattern shown against the Cohort s that have been selected the user needs to click Calculate Matches Once the Clinical Pattern Matcher has completed the matching process the results will display as two icons Matched and Not Matched d 2 Clinical Pattern Matcher View 108 Icon View Ia Create Cohort E5 Open Cohort Venn Matched Not Matched Count 1 527 6 589 Count 21 648 93 41 Results Display Area The Display area has a default message whenever the Clinical Pattern Matcher is opened This message displays the steps that need to be taken before the user can Calculates Matches In some cases based on how the Clinical Pattern Matcher was opened some of these steps may already be complete TransMed Systems Inc as BIS USER S MANUAL ys No Clinical Pattern Matches have been calculated To calculate matches Choose a valid Clinical Pattern on the left Choose one or more Cohorts Click the Calculate Matches button If you see this message after you have already clicked Calculate Matches it is because one of the inputs to the Clinical Pattern Matcher the Clinical Pattern or the Cohorts has changed Simply click the Calculate Matches button again to recalculate the matches The user should only see this message before they have clicked Calculate Matches or after the c
215. periments that were performed on it From the bottom up each Experiment belongs to exactly one Sample and each Sample belongs to exactly one Patient We say that Patient Sample is a one to many relationship and likewise with Sample Experiment r e Experiment 7 Analyzable Entity Heirarchy i i LH Analyzable Entity Hierarchy and relationship to Reference Entity Drug The final Entity Drug is not a member of this hierarchy because it does not have a one to many relationship with any of the other Entities listed In fact it has a many to many relationship to the TransMed Systems Inc Bo BIS USER S MANUAL as Patient The logic behind this is that one patient in a hospital can and typically will be given many drugs and the same drug is obviously given to many different patients Entity Hierarchies come into play in BIS when dealing with things like date offsetting as a part of the data protection scheme used by BIS to hide sensitive PHI HIPAA information using data access levels Since dates like birthdate are a key piece of identifying information a user seeing unidentified information is not allowed to see a patient s true birth date However the age of the patient is usually important to anal
216. r of observations they can store The Traits typically used at the Entity type level contain unique non changing data for that Entity For example for a Patient Entity Traits would be used to define the Name DOB and primary system identifier typically an MRN for that Patient These are data values that are not prone to repeated observation so it makes sense to store them at the Entity level Other observation data like ICU readings or lab results can be made multiple times for an Entity so they make more sense to store at the Module Type level Entity Colors In each installation of BIS each entity defined in the system will be assigned a specific icon and a color This color will be a major design element in the Entity s icon and will serve to indicate which traits belong to which Entity For example consider the following two icons for the Entities Patient and Sample S Ul Icons for the Patient left and Sample right Entities Looking at these Entity icons we see that green is a main color in the Patient icon and red is a main color in the Sample icon To show how which BIS traits belong to which entity BIS will change the color of the page behind each trait type icon Patient traits will get green backgrounds ALCOHOL HORMONE DAYIDT Example Patient traits and Sample traits will get red backgrounds Percent Tumor Section Quality Timestamp Example Sample traits Every BIS installation is customiz
217. rent information and close the El tab at the same time Ifthe user has not LE previously saved the area BIS will prompt the user to name and save This button is in a oe P T N various areas of Cohort Reporter The Save As option allows the user to save the current information as a new Report Save Cohort Filter allows the user to save the current Filter to an artifact on the Workspace The user can save a filter from within Cohort Explorer or the Cohort Information tab save Cohort Filter Scratch Pad is the BIS clipboard and allows users to move artifacts from one Workspace Eee to another within the same project or to the BIS Global Project The Search is found on the Data Explorer and Selector tools The user can click the Search button to activate the Search of the item typed into the Search Field Project Properties Security and Permissions allows the Admin users to define which users will have access to the project and the type of access the user will have Workspace Properties Security and Permissions allows the Admin users to refine the existing project users to the users that will have access to the Workspace BIS USER S MANUAL a Select All is one of the options in Multi Select All Select Mode It selects all rows in the table Select is seen in Cohort Explorer when the data results are in Group Details View The filter is applied to the Filter List by clicking on the Select arrow next to the grou
218. rent one it is not necessary to close the open one first In this case the user can switch back to the BIS Desktop window and select a different Workspace to open BIS will then prompt the user to confirm they want to close the current workspace and open a new one as seen below TransMed Systems Inc pe BIS USER S MANUAL as Confirm Close Workspace BIS can only open one workspace at a time Opening a new workspace will close the one that is already open If you need to compare two workspaces side by side you can open another web browser and start another BIS session for the other workspace Do you wish to close the existing workspace and open the one selected If the user clicks OK BIS will run through its normal close Workspace actions prompting the user to save artifacts where appropriate If the user clicks Cancel the open new Workspace action will be canceled Comparing Workspaces BIS only allows the user to open one Workspace at a time If a user would like to compare the contents of two Workspaces side by side they can simply launch a new web browser window and log into BIS a second time In the new web browser they can then load the Workspace that they want to compare BIS does not prevent the user from logging into the application more than once Closing Sub tabs in Cohort Reporter In Cohort Reporter the Report Tools and Analysis Tools open in a sub tab of the Cohort Reporter tab S
219. reports In BIS the Cohort Explorer is the core Filtering and Grouping engine This engine can create both simple and complex filters to create Patient Sample or Experiment Cohorts A Cohort Filter is the Filter associated with a Cohort The Filter is the chain of filters applied to create the Cohort The user can save this filter as an artifact on the Workspace When in Cohort Explorer the user can choose a saved Cohort Filter and apply it to a new Cohort The Cohort Importer is a tool used to create a Cohort by identifying entities based on identifiers imported from a text file EN Cohort Importer BIS USER S MANUAL ys Cohort Members Cohort Reporter Collapse All Constraint Create Cohort TransMed Systems Inc p Cohort Members is the list of members in the Cohort currently open This title might change based on Entity Cohort Patients Cohort Experiments and Cohort Samples Cohort Report is a full featured report generator that allows the user to easily create complex reports and perform analysis on the data generated within BIS Cohort Reporter is fully integrated with Clinical Pattern Matcher Cohort Explorer Venn Diagram and other BIS features Collapse All is a button in several places in BIS This will Collapse all data for easier viewing A Constraint is a limit that is applied to a variable before it is added to the Filter Data Definition or Clinical Pattern Copy is found in Multi
220. represented by a tile The Tile shows the user the Name Constraint Filter Repeat and sequence of the Event Event Sequence Event Type icon Event Name Entity Filter Options The user has the option to add Entities to the Clinical Pattern in Clinical Pattern Editor After the user has found the Entity in the Data Explorer they can then apply the Entity by dragging and dropping or double click or click symbol the Entity from the Data Explorer to the Clinical Pattern Display area When the Entity is in the Clinical Pattern Display the user can view the defined constraint TransMed Systems Inc a52 o BIS USER S MANUAL as udu Sample exists m e x Jii Constraint iiil All Module Readings Module Filter Options The user has the option to add Modules to the Clinical Pattern in Clinical Pattern Editor Once the user has found the Module in the Data Explorer they can then click apply it to the Clinical Pattern Display area Once the Module is in the Clinical Pattern Display the user can view the defined constraint 06 Chemistry exists TransMed Systems Inc a53 BIS USER S MANUAL as Trait Filter Options The user has the option to add Traits to the Clinical Pattern in Clinical Pattern Editor After the user has found the Trait in the Data Explorer they can then apply the Trait from the Data Explorer to the Clinical Pattern
221. rer yellow area below 2 Click the Plus Icon on the Trait or double click in the search results pink area below TransMed Systems Inc 180 BIS USER S MANUAL as El Back o Up al All Items LG Patient Traits a Patient Fields fic 06 Chemistry 3 Set the Linking Relationship red area below e More on Linking Relationships below 4 Set the Constraint purple area below e The Constraint is considered a Limiting or Non Limiting Factor to the Data Definition e The Constraint is considered in the Report query before the Trait Advanced filter e The default Constraint for a Trait is All Observations non limiting e More on Constraints below 5 Optional Set Summary Rules e The Summary Rule is how the generated Report Data will summarize as the Levels in the Report are changed e More on Summary Rules below 6 Optional Set Advanced Filter if needed black area below 7 Click Ok orange area below TransMed Systems Inc asno BIS USER S MANUAL as Add Trait a 3 BUN MBI d6 Chemistry Q E 3 BUN from Patient Constraint ll All Observations non limiting Filter on all values i Filter on specific values Low Unknown High Unknown Trait Advanced Filter Options Each Trait type has its own Advanced Filter options This filter once again limits the data returned in the Generated Report For each Trait the user has the options of sel
222. roject Project Name He Description Cancel Project Name The Project Name will be displayed in the Workspace Display Dropdown and in the Context Data across the top of BIS when open Description The Description text box allows the user to create a description about the Project This Description can be viewed by any user with access to the Project The user can view and edit this description on the Project Properties tab At this point BIS will create the new Project in the system with the following attributes The name and description as entered in the New Project pop up window shown above Entities in the Project are constrained to those in the Patient Cohort selected in step 7 above Default security settings Identified access granted to BIS Admins only Default Trait settings Entity Identifiers in ID and De ID versions TransMed Systems Inc 45 BIS USER S MANUAL ae After the Project has been created BIS will open the Project Properties tab for the Project so that the user can complete the Project configuration Project Properties The Project Properties tab is displayed immediately after creating a new Project or if the BIS Admin selects a specific Project in the Workspace Display Menu and clicks the Project Properties button in the toolbar The left hand side LHS displays the name of the Project in bold with a five item menu underneath Each of these menu items displays a differ
223. rt the list of Identifiers generated from the Venn intersection selection Venn Sets The grouping section shows the user which Items are being compared in the Diagram Each Item is displayed with a count If the user checks the boxes next to the Item the diagram will then highlight the intersection of those Items Furthermore if the user highlights an intersection in the diagram the proper boxes will display with a check next to the Items Sets In Venn Grouping List Name Set Count Brown Rat Female Patients Male Patients Rats w Cytokines Diagram Results The diagram is made up of circles where each circle represents one of the Items being compared Whenever an Item has an Entity that resides in more than one of the comparison Items it creates an intersection in the diagram yellow arrow below TransMed Systems Inc 20 BIS USER S MANUAL as Intersection Results The intersections tab is at the bottom of the results area This will display the Items and intersections as text instead of visualizations The user can read the Item comparisons by looking at the Intersections tab table Each Item is displayed on its own and then displayed with each possible intersection The Items being compared are separated by the symbol Intersection Brown Rat Female Patients Male Patients Rats w Cytokines Brown Rat Rats w Cytokines Female Patients Rats w Cytokines Brown Rat Female Patients
224. s 2 A Group that contains all users authorized to access BIS must be defined This is the same group described as the BlISUsers group at the beginning of this document BIS will query this group for its members to display the users in the Users tab of the pop up above Patient Cohort amp Filter Panel This panel displays the information for the Patient Cohort and Filter List if one is related that were used to define the Entity constraints for this Project The RHS contains The Cohort information the Project Cohort Filter associated with the Patient Cohort and the Cohort Refresh History Cohort Information Name Entity Count and Last Refreshed Date are displayed TransMed Systems Inc 50 BIS USER S MANUAL ae Cohort Filter The Cohort Filter is the Filter List or breadcrumbs that were used to create the Project Cohort Cohort Refresh History Displays the following information for each time the Cohort List was refreshed Date performed the user that performed the refresh and any notes about the refresh including whether or not any new patients were added Project Properties Cole Camer Sbudy Refresh From Filter P Enable ETL Aefresh 3 Colon Cancer Study a ee Cohort Information Project Cohort Name All Patient Coumt 11 442 26 4ug 2013 03 58 05 PH i Secunty amp Penmissons i Disabled wi General information Project Cohort Filter 3 Project Traits Ej B lt m p Wdsmme i
225. s Effective Permissions All users shown below are part of the master group defined in your enterprise secunty management tool If there is a user missing from this list please make sure they are configured correctly in your secunty setup PT Project Identified Cohort Cohort Cohort Clinical Data a User Name Admin Access Explorer Reporter Analyzer Patterns Export qaadmin gqasuperuser gauserl gauserl0 is E E E 8 s 4 HE ew g gauser2 gausers gauser4 gausers HERE ee ERE Ae EE HR HAHA A HAHAHA D Project Administrator The BIS Project Administrator will have the following privileges e Full access to Project Properties of the specified project e Full access to ALL Workspaces with the project e Full access to Workspace Permissions Project Admin and BIS Admin will be the only users that can create or edit permissions to a Workspace e No access to view Audit logs for the specific Project This is still restricted to BIS Admins Cohort Explorer Users with Permission to Cohort Explorer will have the following privileges e Full access to the Cohort Explorer tool Implications of this permission e Regardless of Cohort Explorer permission any user will be able to modify Cohort artifact properties from the main Workspace Explorer This includes the Cohort name Description and Notes e fa user does not have access to Cohort Explorer they will still be allowed to view Cohorts from the
226. s and perform analysis on the data in BIS Unlike Cohort Explorer which returns Entity counts Cohort Reporter returns a list of values and observations based on the report Definition Entity counts can be achieved by changing the results viewing level Integration with R Server R Server is the advanced statistic and analytics calculation engine behind Cohort Reporter BIS uses R to generate data and images for the Report and Analysis tools in the application Report Functionality Overview Cohort Reporter allows the user to define the report parameters create visualizations relative to the report and express complexity as needed to display the data as desired The LHS of the Cohort Reporter is where the user can navigate through the different areas of Reporter Each area is a panel each one stores and displays different information about the report Consider the panels as the Report s Workspace The Panels include General Information Report Data Report Tools and Analysis Tools E Report Setup Generate Data E DDI Report LHS Toolbar of Cohort Reporter The LHS toolbar will stay the same when viewing individual panels within the report E Report Setup Generate Data Report Setup Will take the user to the Report Setup tab which includes the Data Definition Editor and Transform Editor Generate Data Will calculate report data based on the Data Definition TransMed Systems Inc a68 BIS USER S MANUA
227. s a user missing from this list please make sure they are configured correctly in your security setup Project Identified Cohort Cohort Cohort Clinical Data Admin Access Explorer Reporter Analyzer Patterns Export gaadmin gauserl User Name gauserid gauser2 qausers gauser4 qausers gauser gauser 3 s s s S s s S S EER HEE ee Ee EERE HEHE A EER EE Ee EER HEE EE A EER HE ee A Apply Resolving Permissions Conflicts Because BIS allows both user and group level access it is possible for a user to be in more than one group that is assigned to a Project In this case it is possible for that user to have more than one set of data access permissions for a particular Project To resolve conflicts BIS determines a user s data access to a Project in the following manner 1 Ifa user is assigned explicitly to a Project i e by selecting that user specifically in the Users tab of the Edit Project Permissions pop up their data access permission is what is assigned to them directly In this case BIS will ignore any other data access permissions granted to any group that the user happens to be a member of 2 Ifa user is assigned implicitly to a Project via membership in a group BIS will give that user data access permission equal to the MOST PERMISSIVE access granted to any group the user is a part of In this case Identified access is more permissive than De Identified access So if
228. s on the Y e Export Chart purple arrow Will convert the table as seen to a preview page The user can then choose where and in which format to save the table e Hide Chart pink arrow Will take the user back to the table view TransMed Systems Inc p BIS USER S MANUAL as Bar Side By Side Series 2D v V Use Selection X Show Points Labels Show Totals Show Grand Totals Invert Axes alll Export Chart 7 666667 Ascending Colon Moderately Differentiated Ascending Colon Undifferentiated Steps to Create Pivot Table Create a report define data and generate data Click on Report Tools tab on the LHS of the Cohort Reporter screen i Click on the Pivot Table icon in the toolbar on the RHS of the Report Tools Panel This will open the Pivot Table Editor Name the table add description if needed and choose table level Define variables into the proper areas Filter variables as needed Click on Show Chart Define chart settings OO NAM Repeat above if changes are needed 10 Export if needed table or chart 11 Save and Close Pivot Table Example This Pivot table is comparing the Tumor Size based on Tumor Size Pathology Grade and Gender Variables Chosen Values Edit Pivot Field Field Name Patient Summary Type Custom Z Summary Display Type Default Cancel TransMed Systems Inc Pere BIS USER S MANUAL as Row Labels Edit Pi
229. s pic Ph Sigal 2 Lists AM TransMed Systems Inc o BIS USER S MANUAL ys Workspace Display Dropdown Menu The main dropdown in the desktop window allows the user to filter down the display to the Workspaces for a certain project This dropdown shows the following Favorite Workspaces Shows all of the Workspaces the user has marked as favorites default at Log in Recent Workspaces Shows a list of the last five Workspaces that the user has opened All Workspaces Shows all Workspaces that the user has access to regardless of Project Individual Projects Shows all of the Projects that the user has access to even if they do not have any Workspaces in that Project This section is separated from the three menu items above by the Project Search filter Ww Favorite Workspaces Gq Recent Workspaces All Workspaces Search Projects lis BIS Global Project ij Lymphoma Study i Melanoma Research ij Squamous Cell Analysis BIS Desktop Toolbar The BIS Desktop Toolbar offers several options to the user based on which Workspace is highlighted below EH New Workspace E5 Open 5 TE Favorite id Properties Notes ie Project Properties Refresh 2 Icon View New Workspace Allows the user to create a new Workspace within the Project Open Allows the user to open the selected Workspace in Identified or De Identified mode Favorite Allows the user to choose which Workspace s is are their favori
230. s the user contextual information about the current Workspace and Project that they have open as well as the username they are logged in with Workspace Stutz ID Project Test Project User cmazzanti Workspace Explorer l Gl New Folder r A Open LP Actions A Delete Refresh Workspace Shows the name of the Workspace that the user currently has open If no Workspace is currently open this is not shown If the Workspace is opened in identified mode there will be an IDY displayed after the name of the Workspace Project Shows the name of the Project that contains the currently open Workspace As with the Workspace information this is not shown if no Workspace is currently open See the Project Entitlement section of this document for more information User Shows the username of the currently logged in user This should be displayed at all times BIS Desktop The BIS Desktop is the defau t window for BIS and will be the first window shown when the user starts the application Since the tabs at the top do not move the BIS Desktop will always be the first tab in the list It is displayed with the Desktop icon The main features of the BIS Desktop are the Desktop Toolbar the Workspace Display Dropdown menu and the main Workspace Display area Cokes Cancer Mudy erat Doi 2 20 17 PH l LADDI rgi PH Taai Project Taal rojet l Sintz Study 10 A Workspace Display Bras
231. s to child Experiments to Expenment Diagnosis Experiment Sample Patient B e gt Jj gt Q Io From child Experiments to parent Sample to parent Patient to 06 Chemistry e Module gt Trait Linking Relationship o Last breadcrumb in the Cohort Filter is a Module and the user is Transitioning to a Trait TransMed Systems Inc a23 BIS USER S MANUAL as Same 06 Chemistry Module Linked to 06 Chemistry Same Experiment Diagnosis Module Linked to Experiment Diagnosis K gt Same Patient B S m to 1 FASTING_GLUCOSE N Patient Sample Io Q lt i From parent Patient to child Samples to Percent Tumor Patient Sample y Experiment iB p Q lt ie F D From parent Patient to child Samples to child Experiments to Anisocytosis e Trait gt Module Linking Relationship o Last breadcrumb in the Cohort Filter is a Trait and the user is Transitioning to a Module gt Same 06 Chemistry Module Linked to 3 BUN gt Same Patient B S B to 06 Chemistry 1 _ Patient Sample Io Q lt i law From parent Patient to child Samples to Breast Histopathology Y For more Linking Relationship Examples please refer to the Cohort Explorer Section in the BIS User s Example Document Trait Linking Options When adding a Trait to the Cohort Filter the user may have multiple Linking options based on the current Cohort Filter Linki
232. sMed Systems Inc 232 BIS USER S MANUAL Ty The Data Explorer is the search tool used to add Traits Modules and Entities to Cohort Explorer Cohort Reporter Data Definition and Clinical Patterns Data Explorer The BIS Data Importer is a feature for users to import Patient data from a CSV file into the BIS database The user can apply this data to specific Projects within BIS allowing for the Data to be viewed by Identified users with access to the Project Data Importer Date Traits are used to record date Date Trait information Date with Time Traits are used to record Date with Time Trait date and time information A De ldentified User is not authorized to see De Identified User protected data De Identified users can be defined in project and Workspace security Delete on any artifact within the Workspace Delete Explorer will move that item into the Deleted Items Folder TransMed Systems Inc 233 BIS USER S MANUAL ay The History shows a list of filters used during the current Cohort Explorer session Delete Delete from History from History is in Cohort Explorer and allows the user to remove an item from the History section J Delete from History Deleted Items Deleted Items is the Recycle Bin for BIS a Deleted Items Detail View is allowing the user to view the results or artifacts in table format showing Detail View more detailed information about each artifact The D
233. sed to create the New Cohort will be used to create the Data Definition Note BIS will transition any Cohort Filter to the Highest Entity type before launching Cohort Reporter In the Example below the user created a Cohort Filter green area which in turn created a New Cohort yellow area then clicked the Create Repot button red area Flee Cohort Explorer Ch All hl Create Cohort P7 Create Report 23 Clinical Pattern F Cohort Filter History ic09 DI List Cancer View BE Icon View Current Cohort Count 630 100 Once Cohort Reporter is open the user will see the New Cohort yellow area below displayed as the starting Cohort and the Cohort Filter translated to a Data Definition green area below TransMed Systems Inc 143 BIS USER S MANUAL ys A Report Setup Hater Faoert f Collapse All J Clear Data Definition Cohort Reporter and its functions are displayed in detail below v For more Conversion Examples please refer to the Cohort Explorer Section in the BIS User s Example Document Integration with Reference Entities If the Cohort Filter ends with a Reference Entity BIS is unable to launch Cohort Reporter from Cohort Explorer The user will be prompted with a message letting them know why the Filter cannot be converted in to Cohort Reporter Report Generation Error BIS is unable to launch Cohort Reporter since
234. ser can create a query in BIS that is Find all Samples in BIS that are linked to a Diagnosis In this case the user is interested in querying for Samples and NOT Diagnoses Without the Transition Trait the user TransMed Systems Inc ps BIS USER S MANUAL as would have to transition from Sample to Diagnosis filter on Diagnosis Exists then transition back to Sample While Transition Traits make the above query simpler and faster the user can still perform the query using transitions and get the same result What a user cannot do without Transition Traits however is filter on the absence of a relationship Take the example above but change the parameters Find all Samples in BIS that are NOT linked to a Diagnosis In this case running a query using a transition will not work because there is nothing to transition to We are looking for the absence of Diagnoses so by definition transitioning to these diagnoses would remove all members of the current cohort from Cohort Explorer Any filter after that point would simply return zero values TransMed Systems Inc pa BIS USER S MANUAL BIS Logical Model BIS Logical Model sample Subject Entity Values Sample Entity Values Experiment Entity Values i a Experiment gt RNA Amplification Ls cDNA Microarray QC C Entity O Module Record C Subject CJ Sample L Experiment o Physician Reference Entity Entity Entity Relationship
235. space New Project button allows the user to create a new project from a Patient Cohort that is saved within the Workspace New Time Window allows the user to adda New Time Window to a Clinical Pattern within the Clinical Pattern Editor New Gene List from all n New Gene List from selected feal New Item List from all fe New Item List from selected na New Time Window BIS USER S MANUAL ys New Workspace Numeric Traits Observation View Ontologies New Workspace button allows the user to create a new Workspace within the Project Notes allows the user to add a note on Workspace artifacts Report artifacts Workspaces and projects Workspace and project notes will be displayed on the properties tabs and all artifacts notes will be displayed as the user requests them All users are able to view and edit notes Numeric Traits are used to module purely numeric data things like height weight white blood cell count etc The values recorded by Numeric Traits can be integer or decimal values Alters view of data results in Cohort Explorer to show the user Patient by row and one column per filter detail 3 Observation Details The Ontologies is one of the information panels inside of the Gene Viewer This will give the user information about that gene s Ontologies relationships TransMed Systems Inc 245 BIS USER S MANUAL a Open Cohort Open Cohort Filter Open Cohort
236. st Members The General Information panel has the general information about the Choice List and its creation information The user has the option to edit information or notes about the Choice List while on this panel gt Jal ICD9 List ii Tools Em Breast Ox Ea Edit Info B 10D9 List List Name Description List Type Item Count Created By Last Updated Lst Members Notes a _ Edit Notes Breast Dx All ICDS codes that include breast tissue related diagnoses ICO List 36 jmutz 08 Aug 2013 04 07 45 PM The List Members panel will display a sortable table of all choices saved to the list TransMed Systems Inc CE BIS USER S MANUAL ee Po ICD9 List Breast Dx Breast Dx ICDS List 174 3 Paget s disease of breast lower inner quadrant 174 8 Neoplasm malignant of breast other specified sites 174 5 Neoplasm malignant of breast lower outer quadrant 175 9 Malignant neoplasm of breast male 174 0 Neoplasm malignant of breast nipple and areola 174 0 Malignant neoplasm of breast nipple and areola 175 9 Breast cancer male 175 0 Malignant neoplasm of nipple and areola of male breast 174 9 Breast cancer female 174 1 Malignant neoplasm of breast central portion TransMed Systems Inc 820 BIS USER S MANUAL a Gene List Gene List Viewer How to Create a Gene List Create an Analysis tool that has gene referen
237. stages Choice Traits are not typically used directly in BIS analytical features but are used in querying and reporting Text Traits Text Traits are used to capture Observations that simply hold chunks of free form text entered by the user in some way BIS has no way of knowing the contents of this text data and does not attempt to analyze or parse it to determine if it contains numeric or date values As such text fields cannot be used directly in analysis Text fields can be searched on so they are useful for things like MRN name etc Transition Traits Transition Traits are a special kind of Trait that can be somewhat confusing to use at first To understand the need for and the purpose of Transition Traits we must first discuss Entities TransMed Systems Inc ao o BIS USER S MANUAL as Modules and Relationships in BIS The following section discusses these concepts in detail Transition Traits are explained at the end of the Relationships section Traits and Data Containers To make Traits useful in BIS they must be used to collect identify and analyze information While we could just associate the data that is collected with individual Traits this would make BIS very difficult to use A typical BIS installation will have 2 000 or more Traits if all of these were off on their own they would be difficult to find quickly and associate with one another The solution to this is to group sets of Traits together wh
238. t Patient Details Entity Details will display all the Entities in the current Cohort as a Table While in this lid sane bce view the user can double click on any Entity and the Single Entity Viewer will open Entity Details View T Expenment Details amei Patient Details View Non Matching is one Patient Details View of the result viewing options in Clinical Non Matching Pattern Matcher This view displays the Patients that did not match the pattern a Patient Details Not Matching Patient Details View Matching is one of the Patient Details View result viewing options in Clinical Pattern Matching Matcher This view displays the Patients that matched the pattern amp Patient Details Matching TransMed Systems Inc 247 BIS USER S MANUAL a A pivot table is a visual data summarization Data within the pivot table can be sorted counted averaged or totaled into a collapsible table In BIS the pivot table will take the data generated from the defined definition and organize it in a usable format Once data is Pivot Table generated a pivot table can be created The icon with the exclamation flag denotes that one or more of the variables within the chart needs to be defined or that the data needs to be regenerated The gear icon overlay is showing that the tool is in process A project is the main platform that Project Workspaces are established Projects can limit users and security Proj
239. t Cohort Clinical Data Admin Access Explorer Reporter Analyzer Patterns Export BisAdministrators Project Administrators OATestGroupl BisUsers _ 2 BisPowerUsers a BisTestProjectGroupl The Users tab allows for users to be individually assigned privileges regardless of Group access e When checkbox is checked next to User Name checkboxes to the right become active BIS Admin sets privileges per User e For more information on Permissions see the Project Permissions Dialog section above Edit Project Permissions Groups Users Effective Permissions All users shown below are part of the master group defined in your enterprise security management tool If there is a user missing from this list please make sure they are configured correctly in your security setup eerie Project Identified Cohort Cohort Cohort Clinical Data caiman Admin Access Explorer Reporter Analyzer Patterns Export avilner bberns beardgill bistestuser cfong clieberman cmazzanti cmecreless cwebb The Effective Permissions tab allows for administrators to view the overall privilege assigned per user regardless of Group access TransMed Systems Inc 48 BIS USER S MANUAL as Edit Project Permissions Groups Users Effective Permissions Effective Permissions All users shown below are part of the master group defined in your enterprise secunty management tool If there i
240. t Explorer Open in Cohort Reporter Open in Clinical Pattern Matcher e Open in Cohort Explorer This will open Cohort Explorer with a new source Cohort that contains the merge of Cohorts selected in Venn This will be a New Cohort that will not be saved to the Workspace e Open in Cohort Reporter This will open Cohort Reporter with the selected Cohort s merged together as the starting Cohort for the Report e Open in Clinical Pattern Matcher This will open Clinical Pattern Matcher with the selected Cohort s merged together as the starting Cohort Open e lf the user has one of the Entity Identifiers highlighted this button will be active and launch the Single Entity Viewer for the selected Entity e f the user has one of the Gene Identifiers highlighted this button will be active and launch the Gene Viewer for the selected Gene e f the user has one of the Choice Identifiers highlighted this button will be active and launch the Choice Viewer for the selected Entity Special Choice Traits only Create Cohort The Create Cohort button dropdown in the toolbar will change with the Cohort Entity type For example if the Cohorts being compared in the diagram are Patient Cohorts the button will display from Patients TransMed Systems Inc aoo BIS USER S MANUAL as By using this button the user can save the selected and merged Cohort s to the current Workspace Export Data This will allow the user to expo
241. t Filter panel will instead display the following Tal Patient Cohort A Radiation Open Source Cohort i Save Cohort Filter 2 Open Cohort Filter V This Cohort Filter is Protected This Cohort Filter contains one or more protected Traits and therefore cannot be viewed in de identified mode The commands Open Source Cohort Save Filter List and Open Filter List in Cohort Explorer in the RHS toolbar are disabled for De Identified users with the exception of the Open Source Cohort If the Source Cohort DOES NOT contain a protected Trait this button is enabled for all users with access to the Workspace No Source Cohort and Filter List information is displayed in the RHS panel TransMed Systems Inc a BIS USER S MANUAL as Source Cohort amp Cohort Filter Toolbar e Open Source Cohort Opens the source Entity Cohort in its own Cohort Viewer If there is no Source Cohort this command is disabled e Save Cohort Filter Saves a copy of the associated filter list as an item in the user s Workspace This is disabled if there is no associated Filter List e Open Cohort Filter in Cohort Explorer Opens Cohort Explorer with the Source Cohort as the root Cohort and the Filter List as the filter list for the Cohort Explorer session This will bring the Cohort Explorer back to the state it was in when the user originally saved the Entity Cohort Y For more Cohort Viewer Examples please refer to the General Section in the BIS
242. t Tile red area below Choose Filter on Specific Vales green area below Add a Low Value High Value or both to filter boxes black area below Set relational operator and inclusive check purple area below Click OK yellow area below TransMed Systems Inc a58 BIS USER S MANUAL ae Numeric Range Currency Constraint 0 All Observations O Filter on all values Repeat 1 Greater T Equal to Currency All Observations Less Than Between Relational Operators e Greater Than Inclusive 2Y e Greater Than Exclusive un checked gt Y e Equal to Y e Less Than Inclusive lt Y e Less Than Exclusive un checked lt Y e Between Inclusive Y and Exclusive X Between Y and X e Between Inclusive X and Exclusive Y Between Y and X e Between Inclusive Both Between Y and X e Between Exclusive Both un checked Between Y and X Repeat Count of Variables All Events Entities Modules and Traits can have a Repeat associated The Repeat will look in the Patient history for the number of times a variable met the match before the next event is found Repeat Options Once 1 variable value appears only Once in the patient s history Zero or More Times 0 N variable value does or does not appear in the history optional variable One or More Times 1 N variable value appears One or More times in the history Two or More
243. t is important that BIS knows what type of data is recorded in the Observations for the Traits in the logical model so that it knows what operations are valid to perform on that data To do this BIS requires that a data type is specified when defining a Trait There are seven different Trait data types in BIS as follows Numeric Traits aia Numeric Traits are used to record purely numeric data things like height weight white a blood cell count etc The values recorded by Numeric Traits can be integer or real values The Trait optionally can be defined as having a Unit of Measure UoM as well For example the UoM for the Weight Trait could be kilograms and for the Height Trait it could be centimeters If a VoM is defined for a Trait it is assumed that all observations made for that Trait are done for that UoM Numeric Traits are the primary analytical Trait type in BIS Almost all calculations and statistical analysis done in BIS is done on observations for Numeric Traits Currency Traits Currency Traits are used to record purely numeric data in currency format things like fees deductibles cost etc The values recorded by Currency Traits are real number values and have a higher level of precision than regular numeric traits Currency traits can optionally be defined as having a Unit of Measure UoM as well For example the UoM for the Deductible Trait could be a value like USD or S If a UoM is defined for a Tr
244. t to save or print the table e Drill Down orange Takes the selected cell s and displays the correlating Report Data e Show Chart blue Opens a visualization area which will convert the data grid into a chart format e Show Totals green Displays the sum totals of the columns Pivot Display The Pivot Display is where all of the calculated data will display based on the rows and columns chosen e Item An element that appears as a row or header column e Group A collection of items treated as a single item The user can group items manually or automatically e Grand Totals Appear below the rows in a Pivot Table or to the right of the columns and display totals for all the rows or columns in the table The user can choose to display the totals by checking the toolbar box above e Subtotals Display subtotal amounts for rows or columns in the table Filtering Fields Variables The user can filter the Column Labels blue arrow or Row Labels areas purple arrows Once the user hovers over the Field the Filter Icon will display yellow circle below By clicking on the triangle green triangle the user can sort the fields by low to high or high to low Tumor Size DA Pathology Grade P 0 4 Grand Total The Filter icon will populate a box specific to that variable type and allow the user to omit add variables from to the Pivot Display TransMed Systems Inc o BIS USER S MANUAL ee wi Moderate Chec
245. tches against it e Search The Search button green arrow allows the user to browse the current Clinical Patterns saved to the Workspace to find a Clinical Pattern to use in calculating matches It will launch the standard BIS item browser pop up window to allow the user to find the appropriate Clinical Pattern in their Workspace e Remove The Remove button yellow arrow allows the user to remove the currently selected Clinical Pattern BIS will remove the Clinical Pattern from Clinical Pattern Matcher tool and replace it with a new unsaved Clinical Pattern The user will then have to edit this Clinical Pattern and save it before they can run a Pattern Match Choosing a Clinical Pattern Depending on how the Clinical Pattern Matcher was opened the user may want to choose a different Clinical Pattern To do this the user should click the Search icon above the Clinical Pattern section to select a saved Clinical Pattern from the current Workspace The user can then find the Clinical Pattern in the Workspace list highlight and click OK The selected Clinical Pattern will now be the Clinical Pattern in the Clinical Pattern section Clinical Pattern i Fai B gt DX gt M gt D T n e oe a leme eres Deleting a Clinical Pattern Depending on how the Clinical Pattern Matcher was opened the user may want to delete the current Clinical Pattern The user can remove the currently selected Clinical Pattern by clicking the d
246. te The items marked favorite will show by default when BIS is opened Properties Opens the Workspace Properties for the highlighted selected Workspace TransMed Systems Inc a BIS USER S MANUAL ae Notes Allow the user to add a note on Workspaces Workspace notes will be displayed on the properties tabs All users are able to view and edit notes Project Properties Opens the Project Properties for the Project associated with the highlighted selected Workspace Refresh Refreshes the current tab View Allows the user to choose from a dropdown how the Workspace will display Icon View or Detail View Desktop Search Allows the user to search for Workspaces as well as Artifacts within Workspaces The user has the option to open the Artifact or Workspace from within the Search window E BIS Desktop Fo pea fg Favorite Properties f kater Z Refresh i iton View y O PA Desktop Search Close Search Results Search Results Context Menu Most of the toolbar functions are also available in the right click context menu The user can highlight and then right click on a Workspace to see menu options The context menu is also available while in search mode ii Tools Y aa BIS Desktop Te iy New Workspace Popen k i Favorite id Properties EI Notes Us Project Properties Refresh we Favorite Workspaces Bugs _ Mutz A Open t Open Workspace Identified Test Project Test Pr Pr ee
247. ter l Back o Up a Group Species Patient Link pal Same Patient Constraint iiil All Observations T Apply Filter 4 Search Choices Name W Homo sapiens Macaca mulatta W Mus musculus _ C Elegans 3 of 19 choices selected Y For more Filter Panel Examples please refer to the Cohort Explorer Section in the BIS User s Example Document Grouping Panel The Grouping Panel is displayed in the Data Explorer area of the Cohort Explorer tab The Grouping Panel allows the user to statistically Group on variables before the selected results are applied to the Cohort Filter TransMed Systems Inc EE BIS USER S MANUAL ys The advanced grouping options displayed in the Grouping Panel will vary based on the selected variable Entities and Modules have similar Grouping Panels which include e Back Up and Filter navigation buttons o Back allows the user to move back to the previous panel displayed o Up allows user to move up to Owner Module o Filter allows the user to switch to the Filter Panel e Entity Module Icon e Entity Module Name displayed in bold e Owner Module displayed below the Entity Module name e Link Options o Link options allow the user to define the relationship of the Entity to the previous item breadcrumb in the Cohort Filter e Constraint Options o Constraint options allow the user
248. ter on specific dates Enter date Relational Operators After Inclusive gt Y After Exclusive un checked gt Y Equal to Y Before Inclusive lt Y Before Exclusive un checked lt Y Between Inclusive Y and Exclusive X Between Y and X Between Inclusive X and Exclusive Y Between Y and X Between Inclusive Both Between Y and X Between Exclusive Both un checked Between Y and X Choice Trait When using the Advanced Filter options on a Choice Trait the user must first click the button next to Filter on Specific Choices This will enable the Filter options so the user can add Filter values and apply the Trait to the Cohort Filter Steps for using Advanced Filter Options 1 2 3 TransMed Systems Inc a Choose Filter on Specific Choices green area below Optional Add a saved Choice List from the Workspace yellow area below This will then show only the Choices on that list in the Filter Area Check the Choices to be filtered on red area below BIS USER S MANUAL as a a e The user can re sort the checked items by clicking on the button This will make all checked Choices move to the top of the list for easy viewing e The user can save the currently checked Choices as a new Choice List by clicking the button e The count at the bottom of the choice area will update as Choices are checked and un checked 4 Click Apply Fil
249. the end of the current Cohort Filter o Save Cohort Filter Saves the current Cohort Filter to the Workspace at the Cohort Level assigned in the Cohort Type dropdown menu F Cohort Filter PA Open Cohort Filter g Append Cohort Filter a Save Cohort Filter e Export Data Export Data allows the user to export data grids from Cohort Explorer For the user to export from within Cohort Explorer the user must have the results displayed in Entity Details View Group Details View or Observation Details View Based on the current View the user may have the option to Export All Data or Export Selected Data o Current Export Formats CSV XML XLSX R SAS and SPSS Ea Export Selected Data TransMed Systems Inc a36 BIS USER S MANUAL ae e History The history can be viewed at the bottom of the Cohort Explorer data results this will show the history of filters used during the current Cohort Explorer session To turn off on the History view the user can click on the History button Cohort Filter Results The Cohort Filter Results are displayed on the right hand side of the Cohort Explorer tab There are four sections within the area Cohort Filter Breadcrumbs Results Toolbar Results Viewing Area and Cohort Filter History ah ohart Explorer H TO awl nl Creve Cohort Create Hipo Pt Cietetal Polti F Cohet Filter GE Hiaba 9 Ji Tiisemot Wd Experiment Cohort Filt
250. the selected TransMed Systems Inc 140 BIS USER S MANUAL ys ICDs hnes 173 9 Cancer of breast male Cohort Type ij Sample gt Count Patient ID Sample ID gt MRN1050 7ifa3idi MRN1030 9b61ba01 mn1050 b0Se2666 MREN10E Ofealsef MRN108 15e2b 8e 324 Rows 2 Selected 2 Columns Observation Details View Observation Details will display all details about the current Entity relative to the current Cohort Filter and display the Start and End Timestamp for the filter in the breadcrumb if a timestamp exists While in Observation Details View the user can select an entity to open the Single Entity Viewer Multi Select one or more Entitles from the list and create a Cohort from the selected or Export the selected ae ICDS agnosis gt 175 9 Can fb cor of breast Cohort Type pal Patient E Count J Patent ID MAN3338 MRNS385 MRNS35 MRNAT2S MAN1648 History Diagnosis Diagnosis Diagnosis Diagnosis Diagnosis Diagnosis ICS Diagnosis Date End Date E 175 9 Cancer of breast male 8 19 9908 12 00 00 AM 175 9 Cancer of breast male 12 18 2004 12 00 00 AM 175 9 Cancer of breast male 10 17 2004 12 00 00 AM 175 9 Cancer of breast male 5 3 2004 12 00 00 AM 175 9 Cancer of breast male 12 4 2003 12 00 00 AM m F 108 Observations 6 Columns The History section of Cohort Explorer allows the user to see the steps taken to get
251. tient to child Samples to child This Linking relationship is showing that the current Cohort Filter ends in an Entity green box from there the user added another Entity red box To get to the newly added Entity the Cohort Filter had to transition through 1 Entity yellow box Steps of Linking Relationship 1 Patient Entity Transition One to Many to Child Entity Type Sample 2 Sample Entity Transition One to Many to the Child Entity Type Experiment Some potential Linking Relationships are shown below e Entity gt Entity Linking Relationship pat lt J Patient Sample From parent Patient to child Samples Patient Sample Experiment Q lt s lt E From parent Patient to child Samples to child Expenments J gt Q Sample Patient From child Samples to parent Patient e Entity gt Module Linking Relationship Q 2 Is Same Patient to 06 Chemistry pie m Same Sample p a to Tumor Stage sample Sample Experiment Jus D From parent Sample to child Experiments to Molecular Observation TransMed Systems Inc a2 BIS USER S MANUAL as e Module gt Entity Linking Relationship Patient Sample B S lt ii ne Se From parent Patient to child Samples Patient Sample Experiment a i Io Q lt s lt From parent Patient to child Samples to i child Experiments e Entity gt Trait Linking Relationship gt Same Patient to S BUN
252. tion below for more details BISGroups This is a containment item that serves as the root item for all BIS related groups In the Security amp Permissions section of the Project Properties tab all groups displayed must be a child of BISGroups BISGroups can be either another group or if the customer is using Active Directory an Organizations Unit The main purpose of the BISGroups group is to limit the number of customer defined groups that appear in the security pop up windows in the application A customer s security infrastructure can contain hundreds of different groups within their organization 99 of which are not related to BIS and thus should not appear in the security interface for BIS To eliminate the need for BIS Users to scroll through 1 Refer to the document BIS Installation Instructions for more information TransMed Systems Inc a BIS USER S MANUAL as these hundreds of unrelated groups BIS only displays those groups that are defined as being BIS relevant A group is BlS relevant if it is a subgroup of the BISGroups group Groups of Groups Some of the different group configurations for BIS can become quite confusing A lot of this has to do with how security providers work Almost all enterprise security systems contain two important items users and groups Users represent user accounts created to validate user access to various systems in the enterprise Groups exist simply as a means to collect
253. tion process is complete the user can double click and download the file 123 My Large Subject File pa File cgi se 1 1 2012 10 09 33 PM IMPORTANT NOTE Some browsers implement very strict pop up blocking functions that may prevent you from downloading files from BIS If you are having trouble downloading files from BIS please check that pop up windows are enabled for the application TransMed Systems Inc paa BIS USER S MANUAL as Cohort Explorer Integration with Cohort Reporter Cohort Explorer has the ability to launch the Cohort Reporter tool without closing the Cohort Explorer tab Cohort Report is a full featured report generator that allows the user to easily create complex reports and perform analysis on the data in BIS Unlike Cohort Explorer which returns Entity counts Cohort Reporter returns a list of values and observations based on the report Definition Entity counts can be achieved by changing the results viewing level Create Report The Create Report button launches a new Cohort Reporter session with the current Cohort as the starting Cohort BIS will attempt to translate the current filter set in Cohort Explorer to a Report Data Definition for Cohort Reporter With just the click of a button the user can open Cohort Reporter from Cohort Explorer after defining a Cohort The Cohort created in Cohort Explorer will load as a New Cohort unsaved into Cohort Reporter and the Cohort Filter u
254. to define the set of results returned More on Constraint options in the Constraint Options in the Filter amp Grouping Panel section e Group Button e Advanced Grouping Options o Grouping options allow the user to select how they would like to group the results Navigation Buttons Entity Name Entity Icon Link Options Constraint Options ae Group z Group Button Advanced Grouping Group by all values no values Traits have a different set of Grouping Panels A Trait Grouping Panel is defined by the Trait type which includes e Back Up and Filter navigation buttons o Back allows the user to move Back to the previous panel displayed o Up allows user to move up to Owner Module o Filter allows the user to switch to the Filter Panel e Trait Icon o Note the page color behind the Trait icon denotes the Owner Entity type e Trait Name displayed in bold TransMed Systems Inc p BIS USER S MANUAL as e Owner Module displayed below the Trait name e Link Options o Link options allow the user to define the relationship of the Trait to the previous item breadcrumb in the Cohort Filter e Constraint Options o Constraint options allow the user to define the set of results returned More on Constraint options in the Constraint Options in the Filter amp Grouping Panel section e Group Button e Advance Grouping Options o Grouping options allow the user to select how they would lik
255. to the current Cohort Filter The entries in the History section can be opened as a Cohort removed or selected for a Venn diagram comparison TransMed Systems Inc pa BIS USER S MANUAL ys A Open Cohort Fas Delete from History Venn Filters Type Member Count Timestamp All gt ICD9 175 9 Cancer of breast male Patient 108 8 30 2013 2 36 05 PM All gt Cancer True Expenment 3895 8 30 2013 1 58 47 PM All gt Breast Dx True gt Skin True Expenment 1266 8 30 2013 1 54 20 PM Export in Workspace Explorer Users can export the Cohort Explorer data in Entity Details View Group Details View or Observation Details View The user may have more than one export option based on the selected view and Entities selected Users can export data from any of these views even if the data cannot be displayed The export button prompts the user for a file name Save New File File Name Grid export for EntityDetails on 20 Sep 2012 Workspace Location a A smut gt M Dr Smith s Cohorts Exports Failed Invaild Reports Deleted Items a Grid export for GroupDetails on 20 Sep 2012 Because Cohort Explorer files can contain hundreds of thousands of rows of data creating the export file may take a couple minutes This file generation process is completely asynchronous The file in the Workspace will be displayed with a gear over its icon until the background process of creating the file is complete Once the file crea
256. tory of filters used during the current Cohort Explorer session The Icon Details denotes that the current view is the default view based on the number of selections This is found in Data Explorer and the Selector tools BIS USER S MANUAL Sy Icon View Identified User Interactions Invert Selection TransMed Systems Inc a Icon view is the default view in BIS Desktop Workspace Explorer and Cohort Explorer This view shows all workspaces artifacts or data results as an icon with minimal information An Identified User has an all access pass to the project or Workspace they are defined as an Identified User for This means that the user can see all protected Traits without observation changes The Interactions is one of the information panels inside of the Gene Viewer This will give the user information about that gene s Interactions Invert Selection is one of the options in Multi Select Mode It inverts the selected rows with the unselected rows The Level refers to the Level of generated Report Data The levels are determined by the Data Definition one level per parent and child node will be created for different viewing and summary options Links in BIS are a direct relationship between an Entity and a Module or Trait BIS USER S MANUAL ys Match View Module Move to Initial New Folder TransMed Systems Inc 243 When a user Logs Out of BIS it will disconnect their user
257. trators Sophia user Group user David Avery user user In this case all users added to the secondary BISAdministrators group will all have access to BIS because that group is a member of the BISUsers group In this case the users will have the following access e Brian standard user access to BIS e David administrator access to BIS e Avery administrator access to BIS e Sophia standard user access to BIS Data De Identification The data De Identification features of BIS sit at a layer below the Project Entitlement functionality As such Projects cannot define their own set of protected Traits The same data De Identification scheme will apply uniformly to a single installation of BIS and is not configurable on a Project by Project basis In BIS Project capability the desire is to control a user s access to identified data on a Project by Project basis As an example a user logging into BIS might only have De dentified access to the Project A but could have Identified access to Project B which they could then administer and control The user s access to all Workspaces in both Project A and B is determined by their Data Access permissions to the Project itself In the BIS Desktop tab a user can see both Identified and De Identified Projects and Workspaces that they have access to in the same location De Identification Scheme Applicability There will be only one De Identification schema for a
258. tween a Project that contains identified data and one that contains de identified data All Projects and Workspaces point to the same set of data it is the view of the data that the system allows the user to see that is changed If a user opens a Workspace in Identified mode they will see all of the same items that another user would see if they opened the Workspace in De Identified mode Functional Entitlement Project Permissions Functional Entitlement gives BIS Administrators the ability to define specific roles or limit functions per BIS user or BIS Group BIS will allow Group or user specific permissions on the Project level The ultimate permissions for a user are determined by combining the user s assigned permissions and the permissions of any groups in which the user is a member Project Permissions Dialog BIS Admins can choose to Edit Permissions on the Security amp Permissions Panel of Project Properties Within the Edit Permissions window there are three permission tabs Groups Users and Effective Permissions The Group tab allows for all users in the Group to be assigned the same privileges at once e When the checkbox next to Group name is checked checkboxes to the right become active BIS Admin sets privileges per Group TransMed Systems Inc 300 BIS USER S MANUAL ae Edit Project Permissions Groups Users Effective Permissions All groups shown below are part of the master group defined
259. urrent Cohorts or Clinical Pattern has been changed requires a re calculate Clinical Pattern Matcher Toolbar ee View Icon View ie Create Cohort ES Open Cohort Venn e Venn diagram Will open the Venn diagram tool and display the current matched Cohort along with the original Cohorts selected by the user es Clinical Pattern Matcher View ga Icon View Cohorts 7 DDI Females 7 ee 29 Patients DDI Males d Patients Sets In Venn Grouping List Name Set Count I 8 0x2M gt D Matches 330 D Females E lt 0 males TransMed Systems Inc a65 BIS USER S MANUAL as Create Cohort Gives the user the option to both create and save either the Matching or Non Matching Cohort to the Workspace by clicking on the Create Cohort dropdown The user will then be prompted with the Save New Patient Cohort pop up window io Create Cohort Ke Matching Patients Gl Non Matching Patients Open Cohort The Open Cohort button gives the user the option to open Matching or Non Matching Cohorts in Cohort Explorer and Cohort Reporter By clicking the Open button the user will have several choices Aopen Cohort Ry Matching Patients in Cohort Explorer x Non Matching Patients in Cohort Explorer Wy Matching Patients in Cohort Reporter ka Non Matching Patients in Cohort Reporter e Matching Patients in Cohort Explorer This will launch Cohort Explorer with the Matching
260. vel is found in the Data Edit Level Definition This allows the user to Edit the highlighted Level of the Definition Edit Notes allows the user to add or edit notes on Workspace artifacts Workspaces and Projects Workspace and Project notes Edit Notes will be displayed on the properties tabs and all artifact notes will be displayed as the user requests them All users are able to view and edit notes TransMed Systems Inc 2350 BIS USER S MANUAL ys Edit Permissions Edit Trait Filter Edit Transforms Enable Auditing ETL Refresh TransMed Systems Inc 2360 Edit Permissions allows the admin user to create or edit the security permissions and define which Users have access to the a Project or Workspace Within those users choose who has Identified or De Identified EA Edit Germissions access The Edit Trait Filter is found in the Data Definition This allows the user to Edit the highlighted Trait EA Edit Trait Filter Edit Transforms allows the user to add or edit a pre defined Transform to the Report Data ao Edit Transforms Disable Auditing is found in Project Properties It allows Admin users to turn On P Enable Auditing the Auditing process for the Project Entities are the primary component of the logical model in BIS and exist by themselves All analysis and reporting in BIS is based around the various Entities that have been configured in the system Typical Entities defined i
261. vot Field Field Name Pathology Grade Group Interval Edit Pivot Field Group Interval Default Cancel Column Labels Edit Pivot Field Field Name Summary Type Summary Display Type Group Interval Numeric Interval Range aooo Pivot Results S Pivot Table LS DDIPivot 2 Refresh CE Collapse All rs Save Print Data 4 Drill Down jul Show Chart Show Totals Show Grand Totals Pathology Grade 4 9 3 E Grand Total Female Total Moderately Differentiated Well Differentiated O Male Total Moderately Differentiated Poorly Differentiated Grand Total TransMed Systems Inc o BIS USER S MANUAL Sy Pivot Chart Selected Rows Female Moderately Differentiated amp Male Moderately Differentiated i l i m Bar Side By Side Series 2D Use Cell Selection Show Points Labels Display Legend Invert Axes Female Moderately Differentiated Male Moderately Differentiated Drill Down Option The user is allowed to select one or more cells from the Pivot Table to view the full report information about the Patients associated with the cell s and or create a Cohort from the Patient s associated with those cell s Refresh _ Collapse All Gender a Pathology Grade Female Total Moderately Differentiated Well Differentiated Male Total Moderately Differentiated Poorly Differentiated Grand Total Highlight cell s then click the
262. wo observations for Date Time Traits Timestamp Traits Timestamp traits are special Date Time traits used in BIS to indicate when observations were recorded There are two types of timestamps Start shown on the left with the green arrow and End shown with the red square Timestamps when recorded apply to all related observations made for a module at a given time Most often for observations recorded at a single point in time only the Timestamp Start trait will be used An example of this would be Time of administration for medications like pills or injections If a set of observations need to refer to a period instead of a single point in time then both the Timestamp start and end traits will be used This is more common for traits like Surgery or Hospital Stay which can spans from several hours up to several weeks or months Timestamps are important in BIS because they are the traits that allow for longitudinal ordering of observations in the various tools The ability to pose queries like Show me all patients whose first administered medication was Ibuprofen requires the presence of the Timestamp traits Choice Trait Choice Traits are used to record observations from a defined list of choices All values for Choice Trait observations must be one of the choices defined for that Trait Choice Traits are useful for recording observations from multiple choice lists like ICD 9 codes ethnicity or cancer
263. xample in the previous paragraph illustrates the problem with allowing full deletion The other side of the coin however is the fact that most items the user wants to delete in BIS are NOT involved in highly inter dependent relationships Usually it is just that the user created an item by mistake and wants to get rid of it To balance the need to avoid invalidating research due to item deletion but still allowing the user to unclutter their Workspace by getting rid of unwanted Workspace items BIS has Soft Delete capability TransMed Systems Inc 67 BIS USER S MANUAL ys How Soft Delete Works The delete feature in BIS is properly called a soft delete this means that deleting an item from the Workspace removes it from its containing folder but the item is never purged from BIS Instead the item is moved to a new special location called the Deleted Items folder 1 a Workspace Explorer ij Tools P Mute Pea New Folder A Open Edit Info Deleted Items Folder Deleted Items Folder anova results Patient Cohort 7 Patients All Workspaces in BIS now come with a special folder called Deleted Items by default This folder is created when the Workspace is created It cannot be deleted renamed or moved by the user The Deleted Items folder is always displayed as the first folder of the Workspace in the Display area of Workspace Explorer Deleting Items The user can select multiple items
264. xt Informatio Area vassnnsiasensaverancmnaieneaansnaabansntangerakeaanmmsansonnna KAERRA TANAAN ATEENA RENREN AAEREN RAEE RAER 20 P DESK O e E E OE TEI E E TE E 20 AUINENS 25 VS N US E eara E se cin EE E EE E at ange O E 25 Project Level AuUditiNE crussir iaa 25 Auditing Configuration wavecpcneseasnsecnnaescseewaucsnenpenssuenscescasnecuessventnicd quvuiecacosnmattenennaeupsstenaeae ann seganearedssannneese yannatcsuemvegesente 25 BIS AUGIE L g Viewer TOOl sczcissassncvaveaceateediavaniedeysaevaeesasnnedewarsaeeasdervaceaweedsed iaiee aversentavedunvate Qevauadendsaaetaceuusasecsidevunderiareas 25 SO CUNY AE NEA E A E T TA E OOA E E O 27 EDAP IDEE ON aae E E E E E E EE E AES 27 B USO OTON anar E E EE A EAO TTE T EEA EN E A EO 27 D ts Dedden ficat OU stings gars aaestccuser ata rE ER EREE E E EEEE toe sanailta ash alieasndaeaiaqaann eur bmantiacmmnakeaanmmmnveqeaunteneyanes 29 Functional Entitlement Project Permissions cccccssssecccccesssecccceeececcsaeseececssueccessueasccessuensceeesaaueeeessaaaeseessagasess 30 Project Permissions Dialog scacescsetin eres sacetes cece avs nE cadena scan oem nonce arse eee 30 Project ACMINIStratOr soiseid a n E EE E A E ES E E i 32 G6 aie gig EAO r EE EEE EE EE ee eee ee TEE 32 CONE REDO E ie E T E E NE A T E EEE E 32 CONANA ZET arr E AE EEA EE EAN EEEE EE EEEREN 33 TransMed Systems Inc un BIS USER S MANUAL as Clinical Pattern Matcher iseseisana N EE E E T 33 PDO a A E EA A EA A E E AA
265. xt value Numeric Trait When using the Advanced Grouping options for a Numeric Trait Real or Integer the user must select Group by specific numeric range Steps to using Advanced Grouping Options 1 Select Group by specific numeric range green area below 2 Select the method the Observation values should be grouped by using the dropdown red area below e Quintile Will group Observations into 6 groupings Quintile 1 5 and No Data Values e Quartile Will group Observations into 5 groupings Quartile 1 4 and No Data Values e Custom Will group Observations into as many custom groupings as defined and No Data Values 3 Click Group TransMed Systems Inc ao BIS USER S MANUAL as o Up T Filter 13 URINE_PH 08 Urinalysis Link pal g Same Patient Constraint tH All Observations Quintile Quartile Custom Currency Trait When using the Advanced Grouping options for a Currency Trait the user must select Group by specific numeric range Steps to using Advanced Grouping Options 1 Select Group by specific numeric range green area below 2 Select the method the Observation values should be grouped by using dropdown red area below Quintile Will group Observations into 6 groupings Quintile 1 5 and No Data Values e Quartile Will group Observations into 5 groupings Quartile 1 4
266. y all values no values C Group by specific numeric range Quartile Trait Advanced Grouping Options Each Trait type has its own Advanced Grouping options This filter once again limits the data Entities returned Text Trait When using the Advanced Grouping options for a Text Trait the user must select Group by specific text values Steps to using Advanced Grouping Options 1 Select Group by specific text values green area below 2 Add a text value to group by red area below 3 Select the method the Observation values should be Grouped by using the dropdown yellow area below e Starts With Will group results as Observations that Start With the value entered and No Data Values e Ends With Will group results as Observations that End With the value entered and No Data Values e Contains Will group results as Observations that Contain the value entered and No Data Values e Exact Match Will group results as Observations that are an Exact Match to the values entered default and No Data Values 4 Click Group 5 Results will display two groups Observations that ___ _ the value entered and No Data Values TransMed Systems Inc 119 BIS USER S MANUAL as eC Back o Up T Filter Last Name Patient Link S Same Patient Constraint iiil All Observations iJ Group by all values no values Group by specific te
267. yellow area below 3 Click Group TransMed Systems Inc az BIS USER S MANUAL as T Filter Patient Link S Same Patent Constraint iiil All Observations For more Grouping Panel Examples please refer to the Cohort Explorer Section in the BIS User s Example Document Linking Relationships in the Filter amp Grouping Panel The Linking options in Cohort Explorer are the same for the Filter Panel and the Grouping Panel Possible Linking Options and Relationships that are available in Cohort Explorer are described below Note that based on the current Cohort Filter the user may get different Linking Options and the most specific Linking Option is always the first displayed in the Link dropdown menu Entity Linking Options When adding an Entity to the Cohort Filter the user may have multiple Linking options based on the current Cohort Filter Linking Options display the Linking relationship in bold with the Linking description below it The arrows displayed in the Linking options also show the Relationships between variables One to Many gt Many to One Direct of the Same The Entities and Modules are displayed as Icons e Entities e Modules Traits TransMed Systems Inc 125 BIS USER S MANUAL ee The Link options dropdown shows the user the entire Linking relationship using the Icons and Arrows Example Patient Sample Experiment From parent Pa
268. ysis so BIS offsets the patient s DOB by a random amount The keep all of the measurements for a patient valid all other dates for that patient including dates in its child entities now have to be offset by the same amount The result is that the same date offset is not just used for all date values for a specific Entity but for all Entities that are its direct descendants in a hierarchy So for our example above if a date offset for a patient is generated to be 10 days all dates that are related to that patient will be offset 10 days for De Identified access Likewise all dates for samples that belong to that patient will also be offset 10 days and all experiments that belong to those samples will be offset by 10 days Entities and Traits There are two fundamental relationships that exist between Traits and Entities ownership and containment All Traits in BIS are owned by a specific type of Entity Traits that are owned by an Entity can only be added to data containers also owned by that Entity either the Entity itself or Modules that the Entity owns The same Trait cannot be added to any data container owned by a different Entity However just because an Entity owns a Trait does not mean that the Trait has to be contained within the Entity data container A Trait that is owned by an Entity can either be contained within the Entity or any Module also owned by that Entity Consider the following Patient Diagnosis E

BIS User`s Manual - TransMed Systems

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